diff options
Diffstat (limited to 'academic')
983 files changed, 21469 insertions, 5128 deletions
diff --git a/academic/3D-ICE/3D-ICE.SlackBuild b/academic/3D-ICE/3D-ICE.SlackBuild new file mode 100644 index 0000000000..05c6d82380 --- /dev/null +++ b/academic/3D-ICE/3D-ICE.SlackBuild @@ -0,0 +1,165 @@ +#!/bin/bash + +# Slackware build script for 3D-ICE + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=3D-ICE +VERSION=${VERSION:-3.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=${PRGNAM,,} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# unpack requirements +tar xvf $CWD/superlu_4.3.tar.gz + +if [ "${SYSTEMC:-no}" == "yes" ]; then + sed -i '/^SYSTEMC_MAIN/ s/$(HOME).*/\/usr/' makefile.def + sed -i '/^SYSTEMC_LIB/ s/-$(SYSTEMC_ARCH)/'${LIBDIRSUFFIX}'/' makefile.def + # it has to use the same standard which was used to compile SystemC + sed -i '/^CXXFLAGS/ s/c++11/c++17/' makefile.def + OPT_BUILD="SYSTEMC_WRAPPER=y" +fi + +# do not test the plugin +sed -i '59s/plugin//' Makefile +sed -i '66s/plugintest//' test/Makefile +sed -i '166,184d' test/Makefile + + +cd SuperLU_4.3 +cp MAKE_INC/make.linux make.inc +sed -i -e '/^SuperLUroot/ s/$(HOME)\/Codes\/SuperLU_4.3/../' make.inc +sed -i -e '/^BLASLIB/ s/-L\/usr\/lib/-L\/usr\/lib\/x86_64-linux-gnu/' make.inc +# doesn't compile with two threads +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make -j1 +cd .. + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make $OPT_BUILD +make test +make doc + +# install +install -d $PKG/usr/bin +install -m 0755 bin/3D-ICE-Client $PKG/usr/bin +install -m 0755 bin/3D-ICE-Emulator $PKG/usr/bin +install -m 0755 bin/3D-ICE-Server $PKG/usr/bin + +if [ "${SYSTEMC:-no}" == "yes" ]; then + install -m 0755 bin/3D-ICE-SystemC-Client $PKG/usr/bin +fi + +mkdir -p $PKG/usr/include/3d-ice +cp -av include/* $PKG/usr/include/3d-ice + +mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} +cp -av lib/libthreed-ice-3.1.0.a $PKG/usr/lib${LIBDIRSUFFIX} + +mkdir -p $PKG/usr/libexec/$PRGNAM-$VERSION +cp -av utils/{draw_temp_map.py,draw_temp_map_ani.py} $PKG/usr/libexec/$PRGNAM-$VERSION + +# before copy other document files, let's install the doc folder +# and fix the permissions +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a doc $PKG/usr/doc/$PRGNAM-$VERSION +# fix doc permissions +find -L $PKG/usr/doc/$PRGNAM-$VERSION -type f \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 755 \ + -o -perm 511 \) -exec chmod 644 {} \; + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a CHANGELOG COPYING TODO \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/3D-ICE/3D-ICE.info b/academic/3D-ICE/3D-ICE.info new file mode 100644 index 0000000000..f39dc43916 --- /dev/null +++ b/academic/3D-ICE/3D-ICE.info @@ -0,0 +1,10 @@ +PRGNAM="3D-ICE" +VERSION="3.1" +HOMEPAGE="https://www.epfl.ch/labs/esl/research/open-source-software-projects/3d-ice" +DOWNLOAD="https://github.com/esl-epfl/3d-ice/archive/3.1/3d-ice-3.1.tar.gz https://portal.nersc.gov/project/sparse/superlu/superlu_4.3.tar.gz" +MD5SUM="36da449c813c6ec7fcd04fb35f8a1679 b72c6309f25e9660133007b82621ba7c" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="blas" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/3D-ICE/README b/academic/3D-ICE/README new file mode 100644 index 0000000000..414cf1cf4d --- /dev/null +++ b/academic/3D-ICE/README @@ -0,0 +1,10 @@ + 3D-ICE stands for 3D Interlayer Cooling Emulator. It is a +Linux-based Thermal Emulator Library written in C, which can perform +transient thermal analyses of vertically stacked 3D integrated +circuits with inter-tier Microchannel Liquid Cooling. The latest +version, namely 3D-ICE 3.1, supports fully customized non-uniform +thermal modeling and different heat sink models. + + + If you want to enable the SystemC wrapper, set the environment +variable SYSTEMC=yes. diff --git a/academic/3D-ICE/slack-desc b/academic/3D-ICE/slack-desc new file mode 100644 index 0000000000..85ddec2742 --- /dev/null +++ b/academic/3D-ICE/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +3D-ICE: 3D-ICE (Thermal Emulator Library written in C) +3D-ICE: +3D-ICE: +3D-ICE: 3D-ICE stands for 3D Interlayer Cooling Emulator. It is a Linux-based +3D-ICE: Thermal Emulator Library written in C, which can perform transient +3D-ICE: thermal analyses of vertically stacked 3D integrated circuits with +3D-ICE: inter-tier Microchannel Liquid Cooling. The latest version, namely +3D-ICE: 3D-ICE 3.1, supports fully customized non-uniform thermal modeling +3D-ICE: and different heat sink models. +3D-ICE: +3D-ICE: diff --git a/academic/Mnemosyne/Mnemosyne.SlackBuild b/academic/AlphaPlot/AlphaPlot.SlackBuild index d8a1562ceb..5b597e923f 100644 --- a/academic/Mnemosyne/Mnemosyne.SlackBuild +++ b/academic/AlphaPlot/AlphaPlot.SlackBuild @@ -1,8 +1,8 @@ #!/bin/bash -# Slackware build script for Mnemosyne - -# Copyright 2014 R. S. Ananda Murthy, Mysore, India +# Slackware build script for AlphaPlot +# +# Copyright 2022, Fellype do Nascimento, Guaratingueta - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,8 +24,8 @@ cd $(dirname $0) ; CWD=$(pwd) -PRGNAM=Mnemosyne -VERSION=${VERSION:-2.6.1} +PRGNAM=AlphaPlot +VERSION=${VERSION:-1.02} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -77,21 +77,20 @@ find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -python3 setup.py build -python3 setup.py install --prefix=/usr --root=$PKG + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Now I will remove this icon which is not of 48x48 pixels size -rm $PKG/usr/share/icons/mnemosyne.png +qmake-qt5 +make +make install INSTALL_ROOT=$PKG -mkdir -p $PKG/usr/share/icons/hicolor/48x48/apps -install -m0644 $CWD/mnemosyne.png $PKG/usr/share/icons/hicolor/48x48/apps/mnemosyne.png -#chmod -x $PKG/usr/share/icons/hicolor/48x48/apps/mnemosyne.png +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a README $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README.md COPYING Changelog $PKG/usr/doc/$PRGNAM-$VERSION +cp -a $PKG/usr/share/doc/alphaplot/*.* $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -rf $PKG/usr/share/doc mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/AlphaPlot/AlphaPlot.info b/academic/AlphaPlot/AlphaPlot.info new file mode 100644 index 0000000000..8108426b35 --- /dev/null +++ b/academic/AlphaPlot/AlphaPlot.info @@ -0,0 +1,10 @@ +PRGNAM="AlphaPlot" +VERSION="1.02" +HOMEPAGE="https://alphaplot.sourceforge.io/" +DOWNLOAD="https://github.com/narunlifescience/AlphaPlot/archive/1.02/AlphaPlot-1.02.tar.gz" +MD5SUM="c4a0d0b4ff78d4b7a75d13128df534be" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Fellype do Nascimento" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/AlphaPlot/README b/academic/AlphaPlot/README new file mode 100644 index 0000000000..c66e461dc1 --- /dev/null +++ b/academic/AlphaPlot/README @@ -0,0 +1,4 @@ +Alpha Plot is a free application for Scientific Data Analysis and +Visualization for Windows, Linux and Mac OS X (probably BSD also). +It can generate different types of publication quality 2D and 3D +plots with extensive visual customization. diff --git a/academic/AlphaPlot/doinst.sh b/academic/AlphaPlot/doinst.sh new file mode 100644 index 0000000000..d4daff51d1 --- /dev/null +++ b/academic/AlphaPlot/doinst.sh @@ -0,0 +1,19 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi + +if [ -e usr/share/icons/locolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/locolor >/dev/null 2>&1 + fi +fi diff --git a/academic/flashqard/slack-desc b/academic/AlphaPlot/slack-desc index d03f1ed5cc..a03106331a 100644 --- a/academic/flashqard/slack-desc +++ b/academic/AlphaPlot/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -flashqard: flashqard (educational software to improve your learning process) -flashqard: -flashqard: This aim is achieved by using the widely used method, called -flashqard: Leitner System, and the idea of "different card types for -flashqard: different purposes". -flashqard: -flashqard: http://www.flashqard-project.org/ -flashqard: -flashqard: -flashqard: -flashqard: +AlphaPlot: AlphaPlot (data analysis and visualization) +AlphaPlot: +AlphaPlot: Application for statistical analysis and data visualization which can +AlphaPlot: generate different types of publication quality 2D and 3D plots with +AlphaPlot: extensive visual customization. +AlphaPlot: +AlphaPlot: +AlphaPlot: +AlphaPlot: +AlphaPlot: +AlphaPlot: diff --git a/academic/AstroImageJ/AstroImageJ.SlackBuild b/academic/AstroImageJ/AstroImageJ.SlackBuild new file mode 100644 index 0000000000..21d1234e00 --- /dev/null +++ b/academic/AstroImageJ/AstroImageJ.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/bash + +# Slackware build script for astroimagej + +# Copyright 2023 Christopher Duston (christopher.duston@protonmail.com) +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=AstroImageJ +VERSION=${VERSION:-v5.3.2.00} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +#### These lines are to ensure the build can happen on multilib systems. +if [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + LIBDIRSUFFIX="64" +else + LIBDIRSUFFIX="" +fi +#### + +set -e + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +rm -rf $PKG +mkdir -p $TMP $PKG +rm -rf $TMP/$PRGNAM-$VERSION +cd $TMP || exit 1 + +tar xvf $CWD/${PRGNAM}-${VERSION}-linux-x86_64Bit.tar.gz || exit 1 + +cd ${PRGNAM} + +chown -R root:root . +chmod -R u+w,go+r-w,a-s . + +# Putting these here so they are correctly removed by removepkg. +mkdir -p $PKG/usr/lib64 $PKG/usr/bin +cp -r $TMP/$PRGNAM $PKG/usr/lib64 +cp $CWD/astroimagej $PKG/usr/bin + +# Documentation +PKGDOC=$PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKGDOC +cp -a LICENSE MANIFEST.MF README.txt $PKG/usr/doc/$PRGNAM-$VERSION +find $PKG/usr/doc/$PRGNAM-$VERSION -type f -exec chmod 644 {} \; +cat $CWD/$PRGNAM.SlackBuild > $PKGDOC/$PRGNAM.SlackBuild + +# Create the ./install directory and copy the slack-desc into it +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +# Strip objects from a bunch of files sbopkglint complains about: +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/*.so +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/jexec +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/server/*.so +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/jspawnhelper +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/simengine +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/criu +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/pauseengine +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/criuengine +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/bin/* +# Make these files executable, for the same reason... +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/*.so +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/jexec +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/server/*.so +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/jspawnhelper +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/simengine +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/criu +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/pauseengine +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/criuengine +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/bin/* +chmod a+x $PKG/usr/bin/astroimagej + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.tgz diff --git a/academic/AstroImageJ/AstroImageJ.info b/academic/AstroImageJ/AstroImageJ.info new file mode 100644 index 0000000000..d8e30979fe --- /dev/null +++ b/academic/AstroImageJ/AstroImageJ.info @@ -0,0 +1,10 @@ +PRGNAM="AstroImageJ" +VERSION="v5.3.2.00" +HOMEPAGE="https://www.astro.louisville.edu/software/astroimagej/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://www.astro.louisville.edu/software/astroimagej/installation_packages/AstroImageJ-v5.3.2.00-linux-x86_64Bit.tar.gz" +MD5SUM_x86_64="0c34050d12a4427ba710c44339af2c61" +REQUIRES="" +MAINTAINER="Christopher L Duston" +EMAIL="christopher.duston@protonmail.com" diff --git a/academic/AstroImageJ/README b/academic/AstroImageJ/README new file mode 100644 index 0000000000..e6d8ec3199 --- /dev/null +++ b/academic/AstroImageJ/README @@ -0,0 +1,32 @@ +ImageJ is a graphical user interface (GUI) driven, public domain, +Java-based, software package for general image processing +traditionally used mainly in life sciences fields. The image processing +capabilities of ImageJ are useful and extendable to other scientific +fields. Here we present AstroImageJ (AIJ), which provides an astronomy +specific image display environment and tools for astronomy specific +image calibration and data reduction. Although AIJ maintains the +general purpose image processing capabilities of ImageJ, AIJ is +streamlined for time-series differential photometry, light curve +detrending and fitting, and light curve plotting, especially for +applications requiring ultra-precise light curves (e.g., exoplanet +transits). AIJ reads and +writes standard FITS files, as well as other common image formats, +provides FITS header viewing and editing, and is World Coordinate +System (WCS) aware, including an automated interface to the +astrometry.net web portal for plate solving images. AIJ provides +research grade image calibration and analysis tools with a GUI driven +approach, and easily installed cross-platform compatibility. It +enables new users, even at the level of undergraduate student, high +school student, or amateur astronomer, to quickly start processing, +modeling, and plotting astronomical image data with one tightly +integrated software package. + +Rather than building from source, this package just copies a binary +into the system. It is recommended that post-installation, the user +changes the permissions of the install directory so that the user can +update the software: + +# chown -R myname.users /usr/lib64/AstroImageJ + +It is further recommend to update to the latest daily build - in +particular, the WCS-finding routine is broken on earlier versions. diff --git a/academic/AstroImageJ/astroimagej b/academic/AstroImageJ/astroimagej new file mode 100644 index 0000000000..1096bd8524 --- /dev/null +++ b/academic/AstroImageJ/astroimagej @@ -0,0 +1,4 @@ +#!/bin/sh +cd /usr/lib64/AstroImageJ/ +./AstroImageJ +exit diff --git a/academic/AstroImageJ/slack-desc b/academic/AstroImageJ/slack-desc new file mode 100644 index 0000000000..dc2aa0aa28 --- /dev/null +++ b/academic/AstroImageJ/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +AstroImageJ: AstroImageJ (Astronomical Image Processing) +AstroImageJ: +AstroImageJ: AstroImageJ is a graphical user interface (GUI) driven, public +AstroImageJ: domain, Java-based, software package for astronomical image +AstroImageJ: processing. +AstroImageJ: +AstroImageJ: It is recommended to change the permissions of the install +AstroImageJ: directory so that the user can update the software: +AstroImageJ: # chown -R myname.users /usr/lib64/AstroImageJ +AstroImageJ: +AstroImageJ: Homepage: https://www.astro.louisville.edu/software/astroimagej/ diff --git a/academic/CAFS_divergence/CAFS_divergence.SlackBuild b/academic/CAFS_divergence/CAFS_divergence.SlackBuild index e69a064cab..0afc945503 100644 --- a/academic/CAFS_divergence/CAFS_divergence.SlackBuild +++ b/academic/CAFS_divergence/CAFS_divergence.SlackBuild @@ -33,11 +33,13 @@ TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac + ARCH=$( uname -m ) +fi + +# 2023-05-16 DW: 64bit only +if [ "$ARCH" != "x86_64" ]; then + printf "\n$ARCH is not supported... \n" + exit 1 fi # If the variable PRINT_PACKAGE_NAME is set, then this script will report what @@ -54,11 +56,6 @@ OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP diff --git a/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild b/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild index e18c9f2b26..fe93e4dc6e 100644 --- a/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild +++ b/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild @@ -30,14 +30,19 @@ BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +# 2023-05-16 DW: add a real test if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi +if [[ $ARCH != i?86 ]] && [ "$ARCH" != "x86_64" ]; then + printf "\n$ARCH is not supported... \n" + exit 1 +fi + # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information # could be useful to other scripts. @@ -52,11 +57,6 @@ OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - # The zipped names of the 32bit and 64bit versions differ too much, so # let's set them here. BINNAM=caps diff --git a/academic/DRAMPower/DRAMPower.SlackBuild b/academic/DRAMPower/DRAMPower.SlackBuild new file mode 100644 index 0000000000..0d8b89966a --- /dev/null +++ b/academic/DRAMPower/DRAMPower.SlackBuild @@ -0,0 +1,148 @@ +#!/bin/bash + +# Slackware build script for DRAMPower + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=DRAMPower +VERSION=${VERSION:-4.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +TRACES_COMMIT=e640d3f7ff3766cdf4a799943f81e6ffe0946fb4 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# correct the path for xerces-c library +sed -i '89s#lib#&'${LIBDIRSUFFIX}'#' Makefile + +# disable downloading traces file +sed -i '127,128s/^/#/' Makefile + +# fix for unpacking traces +sed -i '131s/^/#/' Makefile +sed -i '131a\\tmkdir -p traces && unzip -j -d traces traces.zip' Makefile + +# fix example makefile +sed -i 's#DRAMPOWER_PATH ?=.*#DRAMPOWER_PATH ?= /usr/share/'$PRGNAM-$VERSION'#' test/libdrampowertest/Makefile +sed -i 's/MYPATH :=.*/MYPATH := ./' test/libdrampowertest/Makefile +sed -i '72,73s#-iquote ${DRAMPOWER_PATH}/src ##' test/libdrampowertest/Makefile +sed -i '72,73s#-L${DRAMPOWER_PATH}/src/ ##' test/libdrampowertest/Makefile +sed -i '72,73s#$# -I/usr/include/libdrampower#' test/libdrampowertest/Makefile + +sed -i -e 's/test: all/test: $(BINARY) $(BINARY2)/' \ + -e 's/all:/all: $(BINARY) $(BINARY2)\n/' \ + -e '72i $(BINARY):' -e '73i\\n$(BINARY2):' test/libdrampowertest/Makefile +sed -i '34a # Modified for slackbuilds.org at 29 Oct 2022 by William PC - Seattle (USA)' test/libdrampowertest/Makefile + +cp -av $CWD/DRAMPowerTraces-$TRACES_COMMIT.zip traces.zip + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make + +# installing +install -d $PKG/usr/bin +install -m 755 drampower $PKG/usr/bin +install -d $PKG/usr/include/libdrampower +install -m 644 src/libdrampower/*.h $PKG/usr/include/libdrampower +install -m 644 src/*.h $PKG/usr/include/libdrampower +install -d $PKG/usr/include/libdrampower/xmlparser +install -m 644 src/xmlparser/*.h $PKG/usr/include/libdrampower/xmlparser +install -d $PKG/usr/lib${LIBDIRSUFFIX} +install -m 644 src/{libdrampower.a,libdrampowerxml.a} $PKG/usr/lib${LIBDIRSUFFIX} + +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -av memspecs traces $PKG/usr/share/$PRGNAM-$VERSION + +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/examples +cp -av test/libdrampowertest $PKG/usr/share/$PRGNAM-$VERSION/examples + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + ChangeLog README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/DRAMPower/DRAMPower.info b/academic/DRAMPower/DRAMPower.info new file mode 100644 index 0000000000..16fb158264 --- /dev/null +++ b/academic/DRAMPower/DRAMPower.info @@ -0,0 +1,12 @@ +PRGNAM="DRAMPower" +VERSION="4.1" +HOMEPAGE="https://www.uni-kl.de/en/3d-dram/tools/drampower" +DOWNLOAD="https://github.com/tukl-msd/DRAMPower/archive/v4.1/DRAMPower-4.1.tar.gz \ + https://github.com/Sv3n/DRAMPowerTraces/archive/e640d3f7ff3766cdf4a799943f81e6ffe0946fb4/DRAMPowerTraces-e640d3f7ff3766cdf4a799943f81e6ffe0946fb4.zip" +MD5SUM="9f93091c13c01d32f7cc22e609a8f1c3 \ + 8c3bbf7d031f531f5630e0058e22d8e3" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="xerces-c" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/DRAMPower/README b/academic/DRAMPower/README new file mode 100644 index 0000000000..be3cb3f5fa --- /dev/null +++ b/academic/DRAMPower/README @@ -0,0 +1,29 @@ + DRAMPower is an open source tool for fast and accurate DRAM power +and energy estimation for DRAM memories. The latest version of +the tool is v4.0 and features many important improvements, such as +significantly improved analysis speed (at least 10x), enabling +analysis of much larger traces, as well as support for DDR2/DDR3, +LPDDR/LPDDR2, DDR4 and Wide I/O memories. The tool is based on the +DRAM power model developed jointly by the Computer Engineering +Research Group at TU Delft and the Electronic Systems Group at +TU Eindhoven and has been verified by the Microelectronic System +Design Research Group at TU Kaiserslautern with equivalent +circuit-level simulations, which established that the error of +the tool to be < 2% for all memory operations of any granularity +for all memories supported by DRAMPower. DRAMPower is also part +of the computer architecture simulator gem5. + + + Invocation example: + # drampower -m /usr/share/DRAMPower-4.1/memspecs/MICRON_1Gb_DDR3-\ +1066_8bit_G.xml -c /usr/share/DRAMPower-4.1/traces/commands.trace + + Examples of using the library are located at: + # /usr/share/DRAMPower-4.1/examples/libdrampowertest + + You can copy them to a working dir and then run "make test" for +testing, as following: + # cp -av /usr/share/DRAMPower-4.1/examples/libdrampowertest . + # cd libdrampowertest + # make test + diff --git a/academic/DRAMPower/slack-desc b/academic/DRAMPower/slack-desc new file mode 100644 index 0000000000..c7c49f03c4 --- /dev/null +++ b/academic/DRAMPower/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +DRAMPower: DRAMPower (DRAM Power and Energy Estimation for DRAM) +DRAMPower: +DRAMPower: +DRAMPower: DRAMPower is an open source tool for fast and accurate DRAM power +DRAMPower: and energy estimation for DRAM memories. The latest version of +DRAMPower: the tool is v4.0 and features many important improvements, such as +DRAMPower: significantly improved analysis speed (at least 10x), enabling +DRAMPower: analysis of much larger traces, as well as support for DDR2/DDR3, +DRAMPower: LPDDR/LPDDR2, DDR4 and Wide I/O memories. +DRAMPower: +DRAMPower: diff --git a/academic/DRAMSim2/DRAMSim2.SlackBuild b/academic/DRAMSim2/DRAMSim2.SlackBuild new file mode 100644 index 0000000000..e7fa8e329d --- /dev/null +++ b/academic/DRAMSim2/DRAMSim2.SlackBuild @@ -0,0 +1,123 @@ +#!/bin/bash + +# Slackware build script for DRAMSim2 + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=DRAMSim2 +VERSION=${VERSION:-2.2.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +if [ "${DEBUG:-no}" == "yes" ]; then + OPT_BUILD="DEBUG=1" +fi + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make $OPT_BUILD +make libdramsim.so + +# installing +mkdir -p $PKG/usr/bin +mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} +mkdir -p $PKG/usr/share/$PRGNAM + +cp -a DRAMSim $PKG/usr/bin +cp -a libdramsim.so $PKG/usr/lib${LIBDIRSUFFIX} +cp -a example_app $PKG/usr/share/$PRGNAM +cp -a ini $PKG/usr/share/$PRGNAM +cp -a traces $PKG/usr/share/$PRGNAM +cp -a system.ini.example $PKG/usr/share/$PRGNAM + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README README.pdf README.tex \ + $PKG/usr/doc/$PRGNAM-$VERSION + +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/DRAMSim2/DRAMSim2.info b/academic/DRAMSim2/DRAMSim2.info new file mode 100644 index 0000000000..7b876bb68c --- /dev/null +++ b/academic/DRAMSim2/DRAMSim2.info @@ -0,0 +1,10 @@ +PRGNAM="DRAMSim2" +VERSION="2.2.2" +HOMEPAGE="https://github.com/umd-memsys/DRAMSim2" +DOWNLOAD="https://github.com/umd-memsys/DRAMSim2/archive/v2.2.2/DRAMSim2-2.2.2.tar.gz" +MD5SUM="c8bf7b58fd67a93f091dcf13bf191602" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini@hotmail.com" diff --git a/academic/DRAMSim2/README b/academic/DRAMSim2/README new file mode 100644 index 0000000000..583bc1a5a1 --- /dev/null +++ b/academic/DRAMSim2/README @@ -0,0 +1,7 @@ + DRAMSim2 is a cycle accurate model of a DRAM memory controller, the +DRAM modules which comprise system storage, and the bus by which they +communicate. All major components in a modern memory system are +modeled as their own respective objects within the source, including: +ranks, banks, command queue, the memory controller, etc. + +For setting the DEBUG mode use the enviroment variable DEBUG=1 diff --git a/academic/DRAMSim2/slack-desc b/academic/DRAMSim2/slack-desc new file mode 100644 index 0000000000..311a47785d --- /dev/null +++ b/academic/DRAMSim2/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +DRAMSim2: DRAMSim2 (A cycle accurate DRAM simulator) +DRAMSim2: +DRAMSim2: +DRAMSim2: DRAMSim2 is a cycle accurate model of a DRAM memory controller, the +DRAMSim2: DRAM modules which comprise system storage, and the bus by which they +DRAMSim2: communicate. All major components in a modern memory system are +DRAMSim2: modeled as their own respective objects within the source, including: +DRAMSim2: ranks, banks, command queue, the memory controller, etc. +DRAMSim2: +DRAMSim2: +DRAMSim2: diff --git a/academic/Xyce/Xyce.SlackBuild b/academic/DRAMSys/DRAMSys.SlackBuild index 2b4a5c743c..bf56134fd2 100644 --- a/academic/Xyce/Xyce.SlackBuild +++ b/academic/DRAMSys/DRAMSys.SlackBuild @@ -1,8 +1,8 @@ #!/bin/bash -# Slackware build script for Xyce +# Slackware build script for DRAMSys -# Copyright 2015 William PC (Slack-it) - Seattle (USA) +# Copyright 2022 William PC - Seattle, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,17 +24,17 @@ cd $(dirname $0) ; CWD=$(pwd) -PRGNAM=Xyce -VERSION=${VERSION:-6.5} +PRGNAM=DRAMSys +VERSION=${VERSION:-20220830} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -SRCNAM="$PRGNAM" +COMMIT=09f6dcbb91351e6ee7cadfc7bc8b29d97625db8f if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -52,8 +52,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -71,49 +71,60 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM-$VERSION -tar xvf $CWD/$SRCNAM-$VERSION.tar.gz -tar xvf $CWD/$SRCNAM\_Docs-$VERSION.tar.gz -tar xvf $CWD/$SRCNAM\_Regression-$VERSION.tar.gz -for d in $SRCNAM-$VERSION $SRCNAM\_Docs-$VERSION $SRCNAM\_Regression-$VERSION ; do - chown -R root:root $d - find -L $d \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -done -cd $SRCNAM-$VERSION - -if [ "${NONFREE:-no}" == yes ]; then - COPT_DEPS="-DXyce_NONFREE_MODEL=ON" +rm -rf $PRGNAM-$COMMIT +tar xvf $CWD/$PRGNAM-$COMMIT.tar.gz +cd $PRGNAM-$COMMIT + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# unpack requirements +tar xvf $CWD/json-efcc826ecb9b55893397f749e5514316ba8629bb.tar.gz --strip-component 1 -C DRAMSys/library/src/common/third_party/nlohmann +tar xvf $CWD/sqlite-amalgamation-9be05e13408dd8cf8dafe8f11b1700a28194e07e.tar.gz --strip-component 1 -C DRAMSys/library/src/common/third_party/sqlite-amalgamation + +if [ "${POWER:-no}" == "yes" ]; then + # fix for using system installed DRAMPower + sed -i '48,50s/^/#/' DRAMSys/library/CMakeLists.txt + sed -i '247s#PRIVATE.*#PRIVATE /usr/include/libdrampower#' DRAMSys/library/CMakeLists.txt + sed -i '263s/^/#/' DRAMSys/library/CMakeLists.txt + sed -i '266s/DRAMPower/drampower/' DRAMSys/library/CMakeLists.txt + OPT="-DDRAMSYS_WITH_DRAMPOWER:BOOL=ON" else - COPT_DEPS="-DXyce_NONFREE_MODEL=OFF" -fi - -if [ "${PARALLEL:-no}" == yes ]; then - COPT_DEPS="$COPTS_DEPS -DXyce_PARALLEL_MPI=ON \ - -DLIB_MPI=/usr/lib${LIBDIRSUFFIX} -DINC_MPI=/usr/include" -else - COPT_DEPS="$COPTS_DEPS -DXyce_PARALLEL_MPI=OFF" + OPT="-DDRAMSYS_WITH_DRAMPOWER:BOOL=OFF" fi mkdir -p build cd build + SYSTEMC_HOME=/usr \ cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS -std=c++11 -DXyce_NOX_SIZETYPE" \ - -DCMAKE_INSTALL_PREFIX=/opt/$PRGNAM \ - $COPT_DEPS \ - -DXyce_ENABLE_SHARED=yes \ - -DCMAKE_BUILD_TYPE=Release .. + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_CXX_STANDARD=17 \ + $OPT \ + -DCMAKE_BUILD_TYPE=Release ../DRAMSys make - make install DESTDIR=$PKG +# make install/strip DESTDIR=$PKG cd .. -# Install the test suite manually -mv $TMP/$PRGNAM\_Regression-$VERSION \ - $PKG/opt/$PRGNAM +# installing +install -d $PKG/usr/bin +install -m 0755 build/simulator/DRAMSys $PKG/usr/bin +install -d $PKG/usr/lib${LIBDIRSUFFIX} +install -m 0644 build/library/libDRAMSysLibrary.so $PKG/usr/lib${LIBDIRSUFFIX} + +mkdir -p $PKG/usr/share/DRAMSys/ +cp -av DRAMSys/library/resources/* $PKG/usr/share/$PRGNAM + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -121,7 +132,8 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr find $PKG -depth -type d -empty -delete || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING $TMP/${PRGNAM}_Docs-$VERSION/*.pdf $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE.txt README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/DRAMSys/DRAMSys.info b/academic/DRAMSys/DRAMSys.info new file mode 100644 index 0000000000..e6cfe22eb2 --- /dev/null +++ b/academic/DRAMSys/DRAMSys.info @@ -0,0 +1,14 @@ +PRGNAM="DRAMSys" +VERSION="20220830" +HOMEPAGE="https://github.com/tukl-msd/DRAMSys" +DOWNLOAD="https://github.com/tukl-msd/DRAMSys/archive/09f6dcbb91351e6ee7cadfc7bc8b29d97625db8f/DRAMSys-09f6dcbb91351e6ee7cadfc7bc8b29d97625db8f.tar.gz \ + https://github.com/nlohmann/json/archive/efcc826ecb9b55893397f749e5514316ba8629bb/json-efcc826ecb9b55893397f749e5514316ba8629bb.tar.gz \ + https://github.com/azadkuh/sqlite-amalgamation/archive/9be05e13408dd8cf8dafe8f11b1700a28194e07e/sqlite-amalgamation-9be05e13408dd8cf8dafe8f11b1700a28194e07e.tar.gz" +MD5SUM="812ef08562d99038669c5eb881e85c63 \ + 14999edd13ec7697cce179e344615c2a \ + d557d04aa385876917d7d63977b94931" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="SystemC" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/DRAMSys/README b/academic/DRAMSys/README new file mode 100644 index 0000000000..c294454387 --- /dev/null +++ b/academic/DRAMSys/README @@ -0,0 +1,13 @@ + DRAMSys4.0 is a flexible DRAM subsystem design space exploration +framework based on SystemC TLM-2.0. It was developed at the +Microelectronic Systems Design Research Group and Fraunhofer IESE. + + + If you want to enable power simulation set the environment variable +POWER=yes, this requires the package DRAMPower. + If you want to run thermal simulations install 3D-ICE with SystemC +wrapper enabled. + +# invocation example +# DRAMSys /usr/share/DRAMSys/simulations/ddr3-example.json \ + /usr/share/DRAMSys diff --git a/academic/QtiPlot/slack-desc b/academic/DRAMSys/slack-desc index c6e9172090..b1fe79727d 100644 --- a/academic/QtiPlot/slack-desc +++ b/academic/DRAMSys/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -QtiPlot: QtiPlot (Data Analysis and Visualisation) -QtiPlot: -QtiPlot: QtiPlot is a program for two- and three-dimensional graphical -QtiPlot: presentation of data sets and for data analysis. Plots can be -QtiPlot: produced from data sets stored in tables or from analytical -QtiPlot: functions. -QtiPlot: -QtiPlot: Home: https://www.qtiplot.com/ -QtiPlot: -QtiPlot: -QtiPlot: +DRAMSys: DRAMSys (DRAM subsystem design space exploration framework) +DRAMSys: +DRAMSys: +DRAMSys: +DRAMSys: DRAMSys4.0 is a flexible DRAM subsystem design space exploration +DRAMSys: framework based on SystemC TLM-2.0. It was developed at the +DRAMSys: Microelectronic Systems Design Research Group and Fraunhofer IESE. +DRAMSys: +DRAMSys: +DRAMSys: +DRAMSys: diff --git a/academic/DRAMsim3/DRAMsim3.SlackBuild b/academic/DRAMsim3/DRAMsim3.SlackBuild new file mode 100644 index 0000000000..25d92d313a --- /dev/null +++ b/academic/DRAMsim3/DRAMsim3.SlackBuild @@ -0,0 +1,127 @@ +#!/bin/bash + +# Slackware build script for DRAMsim3 + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=DRAMsim3 +VERSION=${VERSION:-1.0.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# NOTE: Not working right now, it requires atlas +# which is unavailable to 15.0 yet. +# enable THERMAL +#if [ "${THERMAL:-no}" == "yes" ];then +# OPTS="-DTHERMAL=ON" +# sed -i 's#../ext/SuperLU_MT_3.1/SRC/##' src/sp_ienv.c +# sed -i 's#../ext/SuperLU_MT_3.1/SRC/##' src/thermal_solver.c +#fi + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + $OPTS \ + -DCMAKE_BUILD_TYPE=Release .. + make +# doesn't have install rule +# make install/strip DESTDIR=$PKG +cd .. + +# Manual installation +mkdir -p $PKG/usr/{bin,lib${LIBDIRSUFFIX}} +cp -a build/dramsim3main $PKG/usr/bin +cp -a libdramsim3.so $PKG/usr/lib${LIBDIRSUFFIX} + +# additional stuff +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a configs scripts tests $PKG/usr/share/$PRGNAM-$VERSION + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/DRAMsim3/DRAMsim3.info b/academic/DRAMsim3/DRAMsim3.info new file mode 100644 index 0000000000..513affc87a --- /dev/null +++ b/academic/DRAMsim3/DRAMsim3.info @@ -0,0 +1,10 @@ +PRGNAM="DRAMsim3" +VERSION="1.0.0" +HOMEPAGE="https://github.com/umd-memsys/DRAMsim3" +DOWNLOAD="https://github.com/umd-memsys/DRAMsim3/archive/1.0.0/DRAMsim3-1.0.0.tar.gz" +MD5SUM="ae5079649cac0987236939b13c28e51e" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini@hotmail.com" diff --git a/academic/DRAMsim3/README b/academic/DRAMsim3/README new file mode 100644 index 0000000000..93e5ce9b8d --- /dev/null +++ b/academic/DRAMsim3/README @@ -0,0 +1,7 @@ + DRAMsim3 models the timing paramaters and memory controller behavior +for several DRAM protocols such as DDR3, DDR4, LPDDR3, LPDDR4, GDDR5, +GDDR6, HBM, HMC, STT-MRAM. It is implemented in C++ as an objected +oriented model that includes a parameterized DRAM bank model, DRAM +controllers, command queues and system-level interfaces to interact +with a CPU simulator (GEM5, ZSim) or trace workloads. It is designed +to be accurate, portable and parallel. diff --git a/academic/DRAMsim3/slack-desc b/academic/DRAMsim3/slack-desc new file mode 100644 index 0000000000..1e16441727 --- /dev/null +++ b/academic/DRAMsim3/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +DRAMsim3: DRAMsim3 (DRAM simulator) +DRAMsim3: +DRAMsim3: DRAMsim3 models the timing paramaters and memory controller behavior +DRAMsim3: for several DRAM protocols such as DDR3, DDR4, LPDDR3, LPDDR4, GDDR5, +DRAMsim3: GDDR6, HBM, HMC, STT-MRAM. It is implemented in C++ as an objected +DRAMsim3: oriented model that includes a parameterized DRAM bank model, DRAM +DRAMsim3: controllers, command queues and system-level interfaces to interact +DRAMsim3: with a CPU simulator (GEM5, ZSim) or trace workloads. It is designed +DRAMsim3: to be accurate, portable and parallel. +DRAMsim3: +DRAMsim3: diff --git a/academic/Data2FCS/Data2FCS.SlackBuild b/academic/Data2FCS/Data2FCS.SlackBuild index 46937a2e26..eb366a5fb8 100644 --- a/academic/Data2FCS/Data2FCS.SlackBuild +++ b/academic/Data2FCS/Data2FCS.SlackBuild @@ -57,7 +57,7 @@ cd $PRGNAM-$VERSION # This is Data2FCS mkdir $PRGNAM cd $PRGNAM -unzip $CWD/${PRGNAM}\ ${VERSION}.zip +unzip $CWD/${PRGNAM}\ ${VERSION}.zip || unzip $CWD/${PRGNAM}%20${VERSION}.zip install -D -m755 $PRGNAM.jar $PKG/usr/bin/$PRGNAM.jar # Rename these, so we include them as documentation @@ -68,7 +68,7 @@ cd .. # This is FCS2Data mkdir $PRGADD cd $PRGADD -unzip $CWD/${PRGADD}\ ${VERSION}.zip +unzip $CWD/${PRGADD}\ ${VERSION}.zip || unzip $CWD/${PRGADD}%20${VERSION}.zip install -D -m755 $PRGADD.jar $PKG/usr/bin/$PRGADD.jar # Rename these, so we include them as documentation, too diff --git a/academic/Data2FCS/Data2FCS.info b/academic/Data2FCS/Data2FCS.info index 4f36916b72..f24c6cfcc4 100644 --- a/academic/Data2FCS/Data2FCS.info +++ b/academic/Data2FCS/Data2FCS.info @@ -7,6 +7,6 @@ MD5SUM="59b89861defa64a34ede2ea97e1194b5 \ aa327e522bfc9b18e72f20ae1dbcdace" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/DendroPy/DendroPy.SlackBuild b/academic/DendroPy/DendroPy.SlackBuild index 274424b4fd..6beba20b5f 100644 --- a/academic/DendroPy/DendroPy.SlackBuild +++ b/academic/DendroPy/DendroPy.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for DendroPy -# Copyright 2019-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2019-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=DendroPy -VERSION=${VERSION:-4.4.0} +VERSION=${VERSION:-4.5.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/DendroPy/DendroPy.info b/academic/DendroPy/DendroPy.info index 9fd1030ffa..d0ded1b95c 100644 --- a/academic/DendroPy/DendroPy.info +++ b/academic/DendroPy/DendroPy.info @@ -1,8 +1,8 @@ PRGNAM="DendroPy" -VERSION="4.4.0" +VERSION="4.5.1" HOMEPAGE="https://dendropy.org/" -DOWNLOAD="https://github.com/jeetsukumaran/DendroPy/archive/v4.4.0/DendroPy-4.4.0.tar.gz" -MD5SUM="171d9f435bc990778a0460a8224b3d76" +DOWNLOAD="https://github.com/jeetsukumaran/DendroPy/archive/v4.5.1/DendroPy-4.5.1.tar.gz" +MD5SUM="c00c554c26c4a3136c835bb37ecafae7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/EMBASSY/EMBASSY.SlackBuild b/academic/EMBASSY/EMBASSY.SlackBuild index 4003914686..337de5f778 100644 --- a/academic/EMBASSY/EMBASSY.SlackBuild +++ b/academic/EMBASSY/EMBASSY.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for EMBASSY -# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=EMBASSY VERSION=${VERSION:-6.6.0} # Keep this the same version as EMBOSS -BUILD=${BUILD:-2} +BUILD=${BUILD:-4} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -64,6 +64,9 @@ else LIBDIRSUFFIX="" fi +# where to look for libraries +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/EMBOSS" + # EMBASSY components and their versions CBSTOOLS=CBSTOOLS-1.0.0.650 CLUSTALOMEGA=CLUSTALOMEGA-1.1.0 @@ -122,11 +125,13 @@ find -L . \ # Build CBSTOOLS cd $TMP/$PRGNAM-$VERSION/$CBSTOOLS -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ @@ -137,240 +142,272 @@ make install DESTDIR=$PKG # Build CLUSTALOMEGA cd $TMP/$PRGNAM-$VERSION/$CLUSTALOMEGA -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/CLUSTALOMEGA \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build DOMAINATRIX cd $TMP/$PRGNAM-$VERSION/$DOMAINATRIX -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/DOMAINATRIX \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build DOMALIGN cd $TMP/$PRGNAM-$VERSION/$DOMALIGN -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/DOMALIGN \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build DOMSEARCH cd $TMP/$PRGNAM-$VERSION/$DOMSEARCH -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/DOMSEARCH \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build EMNU cd $TMP/$PRGNAM-$VERSION/$EMNU -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/EMNU \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build ESIM4 cd $TMP/$PRGNAM-$VERSION/$ESIM4 -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/ESIM4 \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build HMMER cd $TMP/$PRGNAM-$VERSION/$HMMER -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/HMMER \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build IPRSCAN cd $TMP/$PRGNAM-$VERSION/$IPRSCAN -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/IPRSCAN \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build MEME cd $TMP/$PRGNAM-$VERSION/$MEME -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/MEME \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build MSE cd $TMP/$PRGNAM-$VERSION/$MSE -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/MSE \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build MYEMBOSS cd $TMP/$PRGNAM-$VERSION/$MYEMBOSS -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSS \ - --build=$ARCH-slackware-linux + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ + --build=$ARCH-slackware-linuxx make make install DESTDIR=$PKG # Build MYEMBOSSDEMO cd $TMP/$PRGNAM-$VERSION/$MYEMBOSSDEMO -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSSDEMO \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build PHYLIPNEW cd $TMP/$PRGNAM-$VERSION/$PHYLIPNEW -CFLAGS="$SLKCFLAGS -fcommon" \ -CXXFLAGS="$SLKCFLAGS -fcommon" \ +CFLAGS="$SLKCFLAGS -fcommon $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS -fcommon $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/PHYLIPNEW \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build SIGNATURE cd $TMP/$PRGNAM-$VERSION/$SIGNATURE -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/SIGNATURE \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build STRUCTURE cd $TMP/$PRGNAM-$VERSION/$STRUCTURE -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/STRUCTURE \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build TOPO cd $TMP/$PRGNAM-$VERSION/$TOPO -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/TOPO \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG @@ -378,19 +415,23 @@ make install DESTDIR=$PKG # Build VIENNA cd $TMP/$PRGNAM-$VERSION/$VIENNA # -std=gnu89 fixes build with gcc-5.2 (inline functions HairpinE and LoopEnergy) -CFLAGS="$SLKCFLAGS -std=gnu89" \ -CXXFLAGS="$SLKCFLAGS -std=gnu89" \ +CFLAGS="$SLKCFLAGS -std=gnu89 $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS -std=gnu89 $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/VIENNA \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG +mv $PKG/usr/share/PHYLIPNEW $PKG/usr/share/EMBOSS + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -398,6 +439,8 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/CONTENTS > $PKG/usr/doc/$PRGNAM-$VERSION/CONTENTS +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/EMBOSS/EMBOSS.SlackBuild b/academic/EMBOSS/EMBOSS.SlackBuild index fab49fe818..bc69dbfcb6 100644 --- a/academic/EMBOSS/EMBOSS.SlackBuild +++ b/academic/EMBOSS/EMBOSS.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for EMBOSS -# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=EMBOSS VERSION=${VERSION:-6.6.0} -BUILD=${BUILD:-2} +BUILD=${BUILD:-4} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -86,7 +83,8 @@ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/$PRGNAM \ + --bindir=/usr/lib${LIBDIRSUFFIX}/$PRGNAM/bin \ --with-x \ --sysconfdir=/etc \ --localstatedir=/var \ @@ -96,6 +94,15 @@ CXXFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG +# Make jEmboss find the binaries +sed -i "s|/usr/bin/|/usr/lib${LIBDIRSUFFIX}/$PRGNAM/bin/|g" $PKG/usr/share/EMBOSS/jemboss/resources/jemboss.properties +sed -i "s|/usr/bin:|/usr/lib${LIBDIRSUFFIX}/$PRGNAM:/usr/bin:|g" $PKG/usr/share/EMBOSS/jemboss/resources/jemboss.properties + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/bin/runJemboss.sh . +cd - + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -106,10 +113,16 @@ cp -a \ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +cd $PKG/usr/doc/$PRGNAM-$VERSION +ln -s ../../share/$PRGNAM/doc . +cd - + mkdir -p $PKG/usr/share/{applications,pixmaps} cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh diff --git a/academic/EMBOSS/EMBOSS.info b/academic/EMBOSS/EMBOSS.info index 2fef385af0..fa59d8b420 100644 --- a/academic/EMBOSS/EMBOSS.info +++ b/academic/EMBOSS/EMBOSS.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/sboppetrov/files/EMBOSS/EMBOSS-6.6.0. MD5SUM="cc3fca80cb0618deb10fa0d29fe90e4b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/FCSalyzer/FCSalyzer.SlackBuild b/academic/FCSalyzer/FCSalyzer.SlackBuild index de48dcbf08..fd95771eb2 100644 --- a/academic/FCSalyzer/FCSalyzer.SlackBuild +++ b/academic/FCSalyzer/FCSalyzer.SlackBuild @@ -53,7 +53,7 @@ cd $TMP rm -rf $TMP/$PRGNAM-$VERSION mkdir -p $TMP/$PRGNAM-$VERSION cd $TMP/$PRGNAM-$VERSION -unzip $CWD/${PRGNAM}\ ${SRCVER}.zip +unzip $CWD/${PRGNAM}\ ${SRCVER}.zip || unzip $CWD/${PRGNAM}%20${SRCVER}.zip chown -R root:root . find -L . \ diff --git a/academic/FCSalyzer/FCSalyzer.info b/academic/FCSalyzer/FCSalyzer.info index fea6661e19..bd781e3a7d 100644 --- a/academic/FCSalyzer/FCSalyzer.info +++ b/academic/FCSalyzer/FCSalyzer.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/fcsalyzer/files/Version%200.9.22-alph MD5SUM="5a100f3fb10acfcc3935d847c2a386a1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/FastTree/FastTree.SlackBuild b/academic/FastTree/FastTree.SlackBuild new file mode 100644 index 0000000000..6c954faf8d --- /dev/null +++ b/academic/FastTree/FastTree.SlackBuild @@ -0,0 +1,85 @@ +#!/bin/bash + +# Slackware build script for FastTree + +# Copyright 2023 Petar Petrov, slackalaxy at gmail dot com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=FastTree +VERSION=${VERSION:-2.1.11} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir -p $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +cp $CWD/$PRGNAM.c . +gcc $SLKCFLAGS -o FastTree FastTree.c -lm +install -D -m755 FastTree $PKG/usr/bin/FastTree + +cd $PKG/usr/bin +ln -s FastTree fasttree + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/FastTree/FastTree.info b/academic/FastTree/FastTree.info new file mode 100644 index 0000000000..006113cf06 --- /dev/null +++ b/academic/FastTree/FastTree.info @@ -0,0 +1,10 @@ +PRGNAM="FastTree" +VERSION="2.1.11" +HOMEPAGE="http://www.microbesonline.org/fasttree/" +DOWNLOAD="http://www.microbesonline.org/fasttree/FastTree.c" +MD5SUM="83bf082910e1d704e1b1b35f5e263ece" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/FastTree/README b/academic/FastTree/README new file mode 100644 index 0000000000..4398c4f343 --- /dev/null +++ b/academic/FastTree/README @@ -0,0 +1,17 @@ +FastTree infers approximately-maximum-likelihood phylogenetic trees from +alignments of nucleotide or protein sequences. FastTree can handle +alignments with up to a million of sequences in a reasonable amount of +time and memory. For large alignments, FastTree is 100-1,000 times +faster than PhyML 3.0 or RAxML 7. FastTree is open-source software. + +FastTree is more accurate than PhyML 3 with default settings, and much +more accurate than the distance-matrix methods that are traditionally +used for large alignments. FastTree uses the Jukes-Cantor or generalized +time-reversible (GTR) models of nucleotide evolution and the JTT +(Jones-Taylor-Thornton 1992), WAG (Whelan & Goldman 2001), or LG (Le and +Gascuel 2008) models of amino acid evolution. To account for the varying +rates of evolution across sites, FastTree uses a single rate for each +site (the "CAT" approximation). To quickly estimate the reliability of +each split in the tree, FastTree computes local support values with the +Shimodaira-Hasegawa test (these are the same as PhyML 3's "SH-like local +supports"). diff --git a/academic/FastTree/References b/academic/FastTree/References new file mode 100644 index 0000000000..01aef49abf --- /dev/null +++ b/academic/FastTree/References @@ -0,0 +1,14 @@ +These papers describe FastTree: the first paper describes FastTree 1.0, +and the second paper describes heuristic minimum-evolution SPR moves, +maximum-likelihood NNIs, and SH-like local supports. We have also +eliminated the O(N2) steps in the neighbor-joining phase, and +implemented maximum-likelihood NNI moves and SH-like supports (see the +ChangeLog). + +Price, M.N., Dehal, P.S., and Arkin, A.P. (2009) FastTree: Computing +Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix. +Molecular Biology and Evolution 26:1641-1650, doi:10.1093/molbev/msp077. + +Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 -- +Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, +5(3):e9490. doi:10.1371/journal.pone.0009490. diff --git a/academic/FastTree/slack-desc b/academic/FastTree/slack-desc new file mode 100644 index 0000000000..e74540e239 --- /dev/null +++ b/academic/FastTree/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +FastTree: FastTree (Infers approximately-ML phylogenetic trees) +FastTree: +FastTree: FastTree infers approximately-maximum-likelihood phylogenetic trees +FastTree: from alignments of nucleotide or protein sequences. FastTree can +FastTree: handle alignments with up to a million of sequences in a reasonable +FastTree: amount of time and memory. +FastTree: +FastTree: http://www.microbesonline.org/fasttree/ +FastTree: +FastTree: +FastTree: diff --git a/academic/FigTree/FigTree.SlackBuild b/academic/FigTree/FigTree.SlackBuild new file mode 100644 index 0000000000..f70e42ca9a --- /dev/null +++ b/academic/FigTree/FigTree.SlackBuild @@ -0,0 +1,75 @@ +#!/bin/bash + +# Slackware build script for FigTree + +# Copyright 2023 Petar Petrov, slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=FigTree +VERSION=${VERSION:-1.4.4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +ARCH=noarch + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${PRGNAM}_v${VERSION} +tar xvf $CWD/${PRGNAM}_v${VERSION}.tgz +cd ${PRGNAM}_v${VERSION} +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +install -D -m 755 bin/figtree $PKG/usr/bin/figtree +install -D -m 644 lib/figtree.jar $PKG/usr/share/$PRGNAM/figtree.jar +install -D -m 644 images/figtree.png $PKG/usr/share/pixmaps/figtree.png +install -D -m 644 $CWD/FigTree.desktop $PKG/usr/share/applications/FigTree.desktop + +sed -i "s:-Xmx512m:-Xmx1024m:" $PKG/usr/bin/figtree +sed -i "s:lib:/usr/share/$PRGNAM:" $PKG/usr/bin/figtree + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/FigTree/FigTree.desktop b/academic/FigTree/FigTree.desktop new file mode 100644 index 0000000000..1b20f2067f --- /dev/null +++ b/academic/FigTree/FigTree.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Name=FigTree +Comment=Phylogenetic Viewer +Exec=figtree +Icon=figtree +StartupNotify=false +Type=Application +Categories=Education diff --git a/academic/FigTree/FigTree.info b/academic/FigTree/FigTree.info new file mode 100644 index 0000000000..eb72999634 --- /dev/null +++ b/academic/FigTree/FigTree.info @@ -0,0 +1,10 @@ +PRGNAM="FigTree" +VERSION="1.4.4" +HOMEPAGE="http://tree.bio.ed.ac.uk/software/figtree/" +DOWNLOAD="https://github.com/rambaut/figtree/releases/download/v1.4.4/FigTree_v1.4.4.tgz" +MD5SUM="7039dbb6109c66512599a1ae7b972be6" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="zulu-openjdk8" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/FigTree/README b/academic/FigTree/README new file mode 100644 index 0000000000..f80a4534f3 --- /dev/null +++ b/academic/FigTree/README @@ -0,0 +1,3 @@ +FigTree is designed as a graphical viewer of phylogenetic trees and as a +program for producing publication-ready figures. It can display +summarized and annotated trees produced by BEAST. diff --git a/academic/FigTree/doinst.sh b/academic/FigTree/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/FigTree/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/FigTree/slack-desc b/academic/FigTree/slack-desc new file mode 100644 index 0000000000..27bc500ce7 --- /dev/null +++ b/academic/FigTree/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +FigTree: FigTree (A graphical viewer of phylogenetic trees) +FigTree: +FigTree: FigTree is designed as a graphical viewer of phylogenetic trees +FigTree: and as a program for producing publication-ready figures. +FigTree: +FigTree: http://tree.bio.ed.ac.uk/software/figtree/ +FigTree: +FigTree: +FigTree: +FigTree: +FigTree: diff --git a/academic/FreeFem/FreeFem.SlackBuild b/academic/FreeFem/FreeFem.SlackBuild index 30ca0bf8dd..982341fdae 100644 --- a/academic/FreeFem/FreeFem.SlackBuild +++ b/academic/FreeFem/FreeFem.SlackBuild @@ -1,9 +1,9 @@ #!/bin/bash # Slackware build script for FreeFem -# Based on the Slackware 14.2 SlackBuild and on PKGBUILD script for freefem from AUR +# Based on the Slackware 15.0 SlackBuild and on PKGBUILD script for freefem from AUR # -# Copyright 2019-2020, Fellype do Nascimento, Campinas - Brazil +# Copyright 2019-2023, Fellype do Nascimento, Guaratinguetá - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,11 +26,11 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=FreeFem -VERSION=${VERSION:-4.5} +VERSION=${VERSION:-4.14} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -SRCVER=${SRCVER:-4.5} # Variable used in some versions that are numbered as x.y-z +SRCVER=${SRCVER:-4.14} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -40,9 +40,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -55,12 +52,15 @@ OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" SPEC="" + LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" SPEC="" + LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" SPEC="-spec linux-g++-64" + LIBDIRSUFFIX="64" fi @@ -84,6 +84,7 @@ cp $CWD/tetgen1.5.1-beta1.tar.gz 3rdparty/pkg autoreconf -i ./configure \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ --prefix=/usr \ --sysconfdir=/etc \ --disable-mumps \ @@ -93,19 +94,20 @@ autoreconf -i find . -name Makefile -exec sed -i 's+^gcc+gcc =+' {} \; find . -name Makefile -exec sed -i 's+^dir+dir =+' {} \; +find . -name Makefile -exec sed -i "s:/usr/lib/ff++/:/usr/lib${LIBDIRSUFFIX}/ff++/:" {} \; -## TODO: Enable mumps - FreeFem fails to compile with this option enabled up to now +## TODO: Enable mumps make make install DESTDIR=$PKG -find "$PKG"/usr/lib/ff++/ -name "*.h" -exec chmod o+r {} \; +find "$PKG"/usr/lib${LIBDIRSUFFIX}/ff++/ -name "*.h" -exec chmod o+r {} \; find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS CHANGELOG.md README.md $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS CHANGELOG.md LICENSE.md README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/FreeFem/FreeFem.info b/academic/FreeFem/FreeFem.info index c61fc4c006..d936d143c5 100644 --- a/academic/FreeFem/FreeFem.info +++ b/academic/FreeFem/FreeFem.info @@ -1,14 +1,14 @@ PRGNAM="FreeFem" -VERSION="4.5" +VERSION="4.14" HOMEPAGE="https://freefem.org/" -DOWNLOAD="https://github.com/FreeFem/FreeFem-sources/archive/v4.5/FreeFem-sources-4.5.tar.gz \ - http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz \ +DOWNLOAD="https://github.com/FreeFem/FreeFem-sources/archive/v4.14/FreeFem-sources-4.14.tar.gz \ + https://master.dl.sourceforge.net/project/openfoam-extend/foam-extend-3.0/ThirdParty/metis-5.1.0.tar.gz \ http://www.tetgen.org/1.5/src/tetgen1.5.1-beta1.tar.gz" -MD5SUM="4df8fe1c1bc2c042df1f74371e846748 \ +MD5SUM="ca73e2353138e6c6cebdd9cc8df60b7f \ 5465e67079419a69e0116de24fce58fe \ 3d55c197bcbfc611b7ced6f343643756" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="arpack-ng hdf5 openmpi suitesparse" +REQUIRES="arpack-ng camd hdf5 suitesparse" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/Gabedit/Gabedit.SlackBuild b/academic/Gabedit/Gabedit.SlackBuild new file mode 100644 index 0000000000..1ee40ab8ca --- /dev/null +++ b/academic/Gabedit/Gabedit.SlackBuild @@ -0,0 +1,123 @@ +#!/bin/bash + +# Slackware build script for Gabedit + +# Copyright 2022 Giancarlo Dessì, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=Gabedit +VERSION=${VERSION:-2.5.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +SRCNAM=GabeditSrc +SRCVER=$( echo ${VERSION} | tr -d . ) + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM$SRCVER +tar xvf $CWD/$SRCNAM$SRCVER.tar.gz +cd $SRCNAM$SRCVER +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +make + +# The source has not an installing process: the build creates only an executable +# binary file in the current directory, so we have todo manually a minimal install +# process + +#Install the executable file +mkdir -p $PKG/usr/bin +cp -av ./gabedit $PKG/usr/bin + +#Create and install desktop entry +mkdir -p $PKG/usr/share/applications +cat <<EOF > $PKG/usr/share/applications/Gabedit.desktop +[Desktop Entry] +Name=Gabedit +Comment=Molecular editor +Exec=gabedit %f +Icon=Gabedit +Terminal=false +Type=Application +Categories=Education;GTK; +StartupNotify=true +MimeType= +EOF + +#Install icons +mkdir -p $PKG/usr/share/pixmaps +cp -a pixmaps/Gabedit.xpm $PKG/usr/share/pixmaps +cp -a icons/Gabedit*.png $PKG/usr/share/pixmaps + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a ChangeLog License $CWD/References $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/Gabedit/Gabedit.info b/academic/Gabedit/Gabedit.info new file mode 100644 index 0000000000..b38c531b20 --- /dev/null +++ b/academic/Gabedit/Gabedit.info @@ -0,0 +1,10 @@ +PRGNAM="Gabedit" +VERSION="2.5.1" +HOMEPAGE="http://gabedit.sourceforge.net/" +DOWNLOAD="https://sourceforge.net/projects/gabedit/files/gabedit/Gabedit251/GabeditSrc251.tar.gz/download" +MD5SUM="8edd3911908ed70c7efbfdd8ec1dea21" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="gtkglext" +MAINTAINER="Giancarlo Dessì" +EMAIL="slack@giand.it" diff --git a/academic/Gabedit/README b/academic/Gabedit/README new file mode 100644 index 0000000000..289199d0b7 --- /dev/null +++ b/academic/Gabedit/README @@ -0,0 +1,8 @@ +Gabedit is a graphical user interface to computational chemistry +packages like deMon2k, Gamess-US, Gaussian, Molcas, Molpro, MPQC, +MOPAC, Orca, PCGamess and Q-Chem. + +It can display a variety of calculation results including support for +most major molecular file formats. The advanced "Molecule Builder" +allows to rapidly sketch in molecules and examine them in 3D. Graphics +can be exported to various formats, including animations. diff --git a/academic/Gabedit/References b/academic/Gabedit/References new file mode 100644 index 0000000000..9114484ed3 --- /dev/null +++ b/academic/Gabedit/References @@ -0,0 +1,7 @@ +Please use the following citations in any report or publication: + +Gabedit: +A graphical user interface for computational chemistry softwares. +Allouche, A.-R., +Journal of Computational Chemistry, 32 (2011) 174–182. +doi: 10.1002/jcc.21600 diff --git a/academic/Gabedit/doinst.sh b/academic/Gabedit/doinst.sh new file mode 100644 index 0000000000..f25bed6fb6 --- /dev/null +++ b/academic/Gabedit/doinst.sh @@ -0,0 +1,19 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi + +if [ -e usr/share/glib-2.0/schemas ]; then + if [ -x /usr/bin/glib-compile-schemas ]; then + /usr/bin/glib-compile-schemas usr/share/glib-2.0/schemas >/dev/null 2>&1 + fi +fi diff --git a/academic/Gabedit/slack-desc b/academic/Gabedit/slack-desc new file mode 100644 index 0000000000..3c60c50686 --- /dev/null +++ b/academic/Gabedit/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +Gabedit: Gabedit (Graphical User Interface to computational chemistry) +Gabedit: +Gabedit: Gabedit can display a variety of calculation results including +Gabedit: support for most major molecular file formats. +Gabedit: +Gabedit: +Gabedit: +Gabedit: +Gabedit: Home page: http://gabedit.sourceforge.net/ +Gabedit: +Gabedit: diff --git a/academic/Gblocks/Gblocks.SlackBuild b/academic/Gblocks/Gblocks.SlackBuild index 168de23746..aebb925d1f 100644 --- a/academic/Gblocks/Gblocks.SlackBuild +++ b/academic/Gblocks/Gblocks.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for Gblocks -# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,18 +26,22 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=Gblocks VERSION=${VERSION:-0.91b} -BUILD=${BUILD:-2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi +if [[ $ARCH != i?86 ]] && [ "$ARCH" != "x86_64" ]; then + printf "\n$ARCH is not supported... \n" + exit 1 +fi + # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information # could be useful to other scripts. @@ -52,11 +56,6 @@ OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - # Determine the source arch if [ "$ARCH" = "x86_64" ]; then SRCARCH="64" @@ -84,6 +83,7 @@ install -D -m755 Gblocks $PKG/usr/bin/$PRGNAM mkdir -p $PKG/usr/share/$PRGNAM cp -a more_alignments nad3.pir paths $PKG/usr/share/$PRGNAM +chmod 0755 $PKG/usr/share/$PRGNAM/more_alignments find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/Gblocks/Gblocks.info b/academic/Gblocks/Gblocks.info index 0f414d6a29..6e8312a598 100644 --- a/academic/Gblocks/Gblocks.info +++ b/academic/Gblocks/Gblocks.info @@ -3,7 +3,7 @@ VERSION="0.91b" HOMEPAGE="http://molevol.cmima.csic.es/castresana/Gblocks.html" DOWNLOAD="http://ponce.cc/slackware/sources/repo/Gblocks_Linux_0.91b.tar.Z" MD5SUM="8b62e8447eaea37a86c35e1bf5996580" -DOWNLOAD_x86_64="http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z" +DOWNLOAD_x86_64="https://ponce.cc/slackware/sources/repo/Gblocks_Linux64_0.91b.tar.Z" MD5SUM_x86_64="c2c752ae4cbfda0b8bf09e6662585252" REQUIRES="" MAINTAINER="Petar Petrov" diff --git a/academic/GeoGebra/GeoGebra.info b/academic/GeoGebra/GeoGebra.info index 60db5293eb..85644a1b45 100644 --- a/academic/GeoGebra/GeoGebra.info +++ b/academic/GeoGebra/GeoGebra.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/slackbuildsdirectlinks/files/GeoGebra MD5SUM="55e025c1671d074428a0adb66e1fa3d8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="openjdk7" +REQUIRES="zulu-openjdk7" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild b/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild index b311b81328..9a04eb6fc4 100644 --- a/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild +++ b/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild @@ -25,11 +25,10 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=Gridcoin-Research -VERSION=${VERSION:-5.3.2.0} +VERSION=${VERSION:-5.4.7.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -NUMJOBS=${NUMJOBS:-1} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -108,7 +107,7 @@ CXXFLAGS="$SLKCFLAGS" \ $usepnp \ --build=$ARCH-slackware-linux -make -j${NUMJOBS} +make make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ diff --git a/academic/Gridcoin-Research/Gridcoin-Research.info b/academic/Gridcoin-Research/Gridcoin-Research.info index 973eb55d22..a28295c32f 100644 --- a/academic/Gridcoin-Research/Gridcoin-Research.info +++ b/academic/Gridcoin-Research/Gridcoin-Research.info @@ -1,8 +1,8 @@ PRGNAM="Gridcoin-Research" -VERSION="5.3.2.0" +VERSION="5.4.7.0" HOMEPAGE="https://gridcoin.us/" -DOWNLOAD="https://github.com/gridcoin-community/Gridcoin-Research/archive/5.3.2.0/Gridcoin-Research-5.3.2.0.tar.gz" -MD5SUM="b9a445955960d9af7a54bd26df6904e1" +DOWNLOAD="https://github.com/gridcoin-community/Gridcoin-Research/archive/5.4.7.0/Gridcoin-Research-5.4.7.0.tar.gz" +MD5SUM="8c42dfd8deaa754d78aa248785e724b0" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/Gridcoin-Research/README b/academic/Gridcoin-Research/README index c5d43b5115..2fc9a1a4f5 100644 --- a/academic/Gridcoin-Research/README +++ b/academic/Gridcoin-Research/README @@ -16,8 +16,24 @@ and any other configurations that you require. For details, see https://wiki.gridcoin.us/Gridcoinresearch_config_file and in /usr/share/Gridcoin-Research-$VERSION/doc/ -Note: New gridcoinsettings.json file +Notes: +1. New gridcoinsettings.json file This file contains settings changed by the node while running and settings stored in this file override the read-only settings in the gridcoinresearch.conf file (see changelog and documentation). + +2. Berkeley DB update + +Previous versions built against Slackware's Berkeley DB version 4.8. +Since [5.4.2.0] 2023-03-26, leisure, "LaVerne", upstream source +includes Berkeley DB version 5.3 in tree and will standardize all +wallet.dat files to the bdb 5.3 format. THIS IS VERY IMPORTANT! +This ugrade will be completely transparent. Please review the +release notes on +https://github.com/gridcoin-community/Gridcoin-Research/releases + +** NOTE: ** +This is a MANDATORY upgrade for versions 5.4.5 and below to fix an +inadvertent fork as a result of an inadvertent protocol change. +If you are already on 5.4.6 this upgrade is "leisure." diff --git a/academic/HMMER/HMMER.SlackBuild b/academic/HMMER/HMMER.SlackBuild index 31412857ed..923c84093c 100644 --- a/academic/HMMER/HMMER.SlackBuild +++ b/academic/HMMER/HMMER.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for HMMER -# Copyright 2016-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=HMMER -VERSION=${VERSION:-3.3.2} +VERSION=${VERSION:-3.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -102,6 +102,8 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +chmod 0644 $PKG/usr/man/man1/* + # Include some tutorial examples mkdir -p $PKG/usr/share/$PRGNAM cp -a testsuite tutorial $PKG/usr/share/$PRGNAM diff --git a/academic/HMMER/HMMER.info b/academic/HMMER/HMMER.info index 3d8efe947b..6e938301df 100644 --- a/academic/HMMER/HMMER.info +++ b/academic/HMMER/HMMER.info @@ -1,8 +1,8 @@ PRGNAM="HMMER" -VERSION="3.3.2" +VERSION="3.4" HOMEPAGE="http://hmmer.org/" -DOWNLOAD="http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz" -MD5SUM="ea03d88b4e8228a1dc6d84d56af27195" +DOWNLOAD="http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz" +MD5SUM="b1ed21ceea33930222c84f8c4d9f4240" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/IGV/IGV.SlackBuild b/academic/IGV/IGV.SlackBuild index 8b3532ebcb..38a9d08e7e 100644 --- a/academic/IGV/IGV.SlackBuild +++ b/academic/IGV/IGV.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for IGV -# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=IGV -VERSION=${VERSION:-2.9.4} +VERSION=${VERSION:-2.16.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -71,9 +71,14 @@ find -L . \ # Place it in /opt and make a symlink later mkdir -p $PKG/opt/$PRGNAM cp -a $JDK lib igv.args igv.sh igv_hidpi.sh $PKG/opt/$PRGNAM +chmod 0755 $PKG/opt/IGV/jdk-11/lib/{jli,server}/*.so +chmod 0755 $PKG/opt/IGV/jdk-11/lib/*.so + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/share/{applications,pixmaps} -cp IGV_64.png $PKG/usr/share/pixmaps/$PRGNAM.png +cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/IGV/IGV.info b/academic/IGV/IGV.info index cbfc74e093..23341260cc 100644 --- a/academic/IGV/IGV.info +++ b/academic/IGV/IGV.info @@ -1,10 +1,10 @@ PRGNAM="IGV" -VERSION="2.9.4" +VERSION="2.16.2" HOMEPAGE="http://software.broadinstitute.org/software/igv/home" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://data.broadinstitute.org/igv/projects/downloads/2.9/IGV_Linux_2.9.4_WithJava.zip" -MD5SUM_x86_64="bf510e5f868daf5772ce51a4ce3213ab" +DOWNLOAD_x86_64="https://data.broadinstitute.org/igv/projects/downloads/2.16/IGV_Linux_2.16.2_WithJava.zip" +MD5SUM_x86_64="19adb2bac44d46373fc021fbad3cce10" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/IGV/IGV.png b/academic/IGV/IGV.png Binary files differnew file mode 100644 index 0000000000..3d618f23a6 --- /dev/null +++ b/academic/IGV/IGV.png diff --git a/academic/ITK/ITK.SlackBuild b/academic/ITK/ITK.SlackBuild index bc13af67ce..4ecf6cb456 100644 --- a/academic/ITK/ITK.SlackBuild +++ b/academic/ITK/ITK.SlackBuild @@ -29,7 +29,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ITK SRCNAM=InsightToolkit VERSION=${VERSION:-4.13.2} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -41,9 +41,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -82,50 +79,10 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -patch -p1 <<'endpatch' ---- InsightToolkit-4.13.2/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h.cp -+++ InsightToolkit-4.13.2/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h -@@ -96,6 +96,39 @@ - # define VCL_GCC_81 - # else - # define VCL_GCC_80 -+# endif -+# elif (__GNUC__==9) -+# define VCL_GCC_9 -+# if (__GNUC_MINOR__ > 2 ) -+# define VCL_GCC_93 -+# elif (__GNUC_MINOR__ > 1 ) -+# define VCL_GCC_92 -+# elif (__GNUC_MINOR__ > 0 ) -+# define VCL_GCC_91 -+# else -+# define VCL_GCC_90 -+# endif -+# elif (__GNUC__==10) -+# define VCL_GCC_10 -+# if (__GNUC_MINOR__ > 2 ) -+# define VCL_GCC_103 -+# elif (__GNUC_MINOR__ > 1 ) -+# define VCL_GCC_102 -+# elif (__GNUC_MINOR__ > 0 ) -+# define VCL_GCC_101 -+# else -+# define VCL_GCC_100 -+# endif -+# elif (__GNUC__==11) -+# define VCL_GCC_11 -+# if (__GNUC_MINOR__ > 2 ) -+# define VCL_GCC_113 -+# elif (__GNUC_MINOR__ > 1 ) -+# define VCL_GCC_112 -+# elif (__GNUC_MINOR__ > 0 ) -+# define VCL_GCC_111 -+# else -+# define VCL_GCC_110 - # endif - # else - # error "Dunno about this gcc" -endpatch +# Do not fail on more recent versions of gcc + sed -i 's,# error "Dunno about this gcc",# define VCL_GCC_80,' \ + "Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h" + sed -i "s/lib\b/lib${LIBDIRSUFFIX}/" CMakeLists.txt sed -i "s|/opj_config.h|& \$\{CMAKE_CURRENT_BINARY_DIR\}/openjpeg_mangle.h|" \ @@ -135,12 +92,13 @@ mkdir -p build cd build cmake \ -DCMAKE_C_FLAGS="$SLKCFLAGS" \ - -DCMAKE_CXX_FLAGS="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS="$SLKCFLAGS -std=c++11" \ -DCMAKE_INSTALL_PREFIX=/usr \ -DITK_FORBID_DOWNLOADS=ON \ -DITK_WRAP_PYTHON=OFF \ -DBUILD_SHARED_LIBS=ON \ -DBUILD_EXAMPLES=OFF \ + -DBUILD_TESTING=OFF \ -DITK_USE_SYSTEM_LIBRARIES=ON \ -DITK_USE_SYSTEM_DCMTK=ON \ -DITK_USE_SYSTEM_DOUBLECONVERSION=ON \ @@ -151,6 +109,8 @@ cd build -DITK_USE_SYSTEM_PNG=ON \ -DITK_USE_SYSTEM_TIFF=ON \ -DITK_USE_SYSTEM_ZLIB=ON \ + -DModule_ITKIOMINC=ON \ + -DModule_ITKIOTransformMINC=ON \ -DCMAKE_BUILD_TYPE=Release .. make install DESTDIR=$PKG cd .. diff --git a/academic/ITK/ITK.info b/academic/ITK/ITK.info index d72260cfa6..86da5fa2d4 100644 --- a/academic/ITK/ITK.info +++ b/academic/ITK/ITK.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/InsightSoftwareConsortium/ITK/releases/download/v4. MD5SUM="d140ddabe22428e86bc5053e0d268872" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="double-conversion gtest hdf5" +REQUIRES="double-conversion antlr4 hdf5" MAINTAINER="Benjamin Trigona-Harany" EMAIL="slackbuilds@jaxartes.net" diff --git a/academic/Isabelle/Isabelle b/academic/Isabelle/Isabelle new file mode 100644 index 0000000000..24f157255a --- /dev/null +++ b/academic/Isabelle/Isabelle @@ -0,0 +1,3 @@ +#!/bin/sh + +exec /opt/Isabelle/MY_TEMPLATE $@ diff --git a/academic/Isabelle/Isabelle.SlackBuild b/academic/Isabelle/Isabelle.SlackBuild new file mode 100644 index 0000000000..eb9721e53d --- /dev/null +++ b/academic/Isabelle/Isabelle.SlackBuild @@ -0,0 +1,82 @@ +#!/bin/bash + +# Slackware build script for Isabelle + +# Copyright 2023, Lockywolf +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=Isabelle +VERSION=${VERSION:-2022} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM$VERSION +tar xvf $CWD/$PRGNAM${VERSION}_linux.tar.gz +cd $PRGNAM$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +install -Dm755 $CWD/Isabelle $PKG/usr/bin/Isabelle +install -d -m 755 $PKG/opt/$PRGNAM +cp -r . $PKG/opt/$PRGNAM +sed -i "s/MY_TEMPLATE/$PRGNAM$VERSION/g" $PKG/usr/bin/Isabelle + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ +ANNOUNCE COPYRIGHT doc README ROOTS \ +CONTRIBUTORS Isabelle.options NEWS ROOT \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/Isabelle/Isabelle.info b/academic/Isabelle/Isabelle.info new file mode 100644 index 0000000000..effbc710fb --- /dev/null +++ b/academic/Isabelle/Isabelle.info @@ -0,0 +1,10 @@ +PRGNAM="Isabelle" +VERSION="2022" +HOMEPAGE="https://isabelle.in.tum.de/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://isabelle.in.tum.de/dist/Isabelle2022_linux.tar.gz" +MD5SUM_x86_64="52340538b76b0493beae0a444d623fe6" +REQUIRES="" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.Isabelle_2023-07-17@lockywolf.net" diff --git a/academic/Isabelle/README b/academic/Isabelle/README new file mode 100644 index 0000000000..133899ddbe --- /dev/null +++ b/academic/Isabelle/README @@ -0,0 +1,17 @@ +Isabelle is a generic proof assistant. It allows mathematical formulas +to be expressed in a formal language and provides tools for proving +those formulas in a logical calculus. Isabelle was originally +developed at the University of Cambridge and Technische Universität +München, but now includes numerous contributions from institutions and +individuals worldwide. + +Isabelle is written in polyML, Java, and Scala, but does not require +them to be installed from SBo. + +This build is bundling: jEdit, vscodium, jdk-17, so be careful about +its interference with other packages. + +A lot of proofs certified with Isabelle can be found on +https://www.isa-afp.org/ + +This build repackages the binary build. diff --git a/academic/Isabelle/slack-desc b/academic/Isabelle/slack-desc new file mode 100644 index 0000000000..72e6651a95 --- /dev/null +++ b/academic/Isabelle/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +Isabelle: Isabelle (generic proof assistant) +Isabelle: +Isabelle: Isabelle is a generic proof assistant. It allows mathematical +Isabelle: formulas to be expressed in a formal language and provides tools for +Isabelle: proving those formulas in a logical calculus. Isabelle was +Isabelle: originally developed at the University of Cambridge and Technische +Isabelle: Universitat Munchen, but now includes numerous contributions from +Isabelle: institutions and individuals worldwide. +Isabelle: +Isabelle: +Isabelle: diff --git a/academic/Kst/Kst.SlackBuild b/academic/Kst/Kst.SlackBuild index ebb7cca8f8..44e4fea74b 100644 --- a/academic/Kst/Kst.SlackBuild +++ b/academic/Kst/Kst.SlackBuild @@ -1,13 +1,32 @@ #!/bin/bash + # Slackware build script for Kst -# Based on Slackware 14.1 SlackBuild and AUR PKGBUILD for Kst -# Written by Fellype do Nascimento <fellype(at)gmail.com> -# last modification of this build script: 2014/12/10 +# Copyright 2014-2023 Fellype do Nascimento, Guaratingueta, Brazil +# SBo team have contributed to the maintenance of this build script :) +# +# Based on Slackware 15.0 SlackBuild and AUR PKGBUILD for Kst +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. cd $(dirname $0) ; CWD=$(pwd) PRGNAM=Kst -VERSION=${VERSION:-2.0.8} +VERSION=${VERSION:-20221025_5fdd819} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -32,10 +51,10 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX=""; CHOST=i486 +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX=""; CHOST=i486 + SLKCFLAGS="-O2 -march=i686 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC"; SLKLDFLAGS="-L/usr/lib64"; LIBDIRSUFFIX="64" fi @@ -46,7 +65,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar -zxvf $CWD/$PRGNAM-$VERSION.tar.gz +tar -xvf $CWD/$PRGNAM-$VERSION.tar.?z cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -55,19 +74,24 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Fix build failure with gsl-2.1 (gsl API change) -patch -p1 < $CWD/Kst_gsl2.patch +# Fix the path for H5Cpp.h +patch -p1 < $CWD/fix_hdf5_path.patch src/datasources/hdf5/hdf5.h + +# Fix an issue with the newer cmake +sed -i "s|else(GCC|elseif(GCC|" CMakeLists.txt || exit 1 sed -i "s/find_package\(PythonLibs REQUIRED\)/SET \(PythonLibs \"\/usr\/lib${LIBDIRSUFFIX}\/libpython2.7.so\"\)/" \ -./cmake/pyKst/CMakeLists.txt -sed -i "s/\${NUMPY_VERSION_PATCH}/0/" ./cmake/modules/FindNumPy.cmake +./cmake/pyKst/CMakeLists.txt || exit 1 +sed -i "s/\${NUMPY_VERSION_PATCH}/0/" ./cmake/modules/FindNumPy.cmake || exit 1 cp -r ./cmake/pyKst/* ./pyKst/ cmake ./ \ --Dkst_release=1 \ --Dkst_version_string=1 \ +-Dkst_release=2 \ +-Dkst_version_string=$VERSION \ -Dkst_svnversion=0 \ -Dkst_python=1 \ --DPYTHON_EXECUTABLE=/usr/bin/python2.7 \ +-Dkst_qt4=OFF \ +-Dkst_qt5=ON \ +-DPYTHON_EXECUTABLE=/usr/bin/python2 \ -Dkst_python_prefix=/usr/lib$LIBDIRSUFFIX/python2.7 \ -Dkst_install_prefix=/usr/ \ -Dkst_install_libdir=/usr/lib$LIBDIRSUFFIX diff --git a/academic/Kst/Kst.info b/academic/Kst/Kst.info index 8912bc7380..adff979071 100644 --- a/academic/Kst/Kst.info +++ b/academic/Kst/Kst.info @@ -1,10 +1,10 @@ PRGNAM="Kst" -VERSION="2.0.8" -HOMEPAGE="https://kst-plot.kde.org/" -DOWNLOAD="http://netcologne.dl.sourceforge.net/project/kst/Kst%202.0.8/Kst-2.0.8.tar.gz" -MD5SUM="6f52c16edb63e8980520bfdaebed3eae" +VERSION="20221025_5fdd819" +HOMEPAGE="https://apps.kde.org/kst/" +DOWNLOAD="https://sourceforge.net/projects/slackbuildsdirectlinks/files/Kst/Kst-20221025_5fdd819.tar.xz" +MD5SUM="402fac69d4701cd7f223159e70b73439" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="scipy" +REQUIRES="python2-scipy" MAINTAINER="Fellype do Nascimento" -EMAIL="fellype(at)gmail.com" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/Kst/Kst_gsl2.patch b/academic/Kst/Kst_gsl2.patch deleted file mode 100644 index 1a7db24321..0000000000 --- a/academic/Kst/Kst_gsl2.patch +++ /dev/null @@ -1,53 +0,0 @@ -diff -u -r Kst-2.0.8/src/plugins/fits/non_linear.h Kst-2.0.8-patched/src/plugins/fits/non_linear.h ---- Kst-2.0.8/src/plugins/fits/non_linear.h 2014-02-13 09:41:44.000000000 +0000 -+++ Kst-2.0.8-patched/src/plugins/fits/non_linear.h 2015-11-18 22:28:40.761417846 +0000 -@@ -18,6 +18,7 @@ - #include <gsl/gsl_blas.h> - #include <gsl/gsl_multifit_nlin.h> - #include <gsl/gsl_statistics.h> -+#include <gsl/gsl_version.h> - #include "common.h" - - struct data { -@@ -177,7 +178,15 @@ - } - iIterations++; - } while( iStatus == GSL_CONTINUE && iIterations < MAX_NUM_ITERATIONS ); -+ -+#if GSL_MAJOR_VERSION >=2 -+ gsl_matrix *J=gsl_matrix_alloc(pSolver->fdf->n, pSolver->fdf->p); -+ gsl_multifit_fdfsolver_jac (pSolver, J); -+ gsl_multifit_covar( J, 0.0, pMatrixCovariance ); -+ gsl_matrix_free(J); -+#else - gsl_multifit_covar( pSolver->J, 0.0, pMatrixCovariance ); -+#endif - - // - // determine the fitted values... -diff -u -r Kst-2.0.8/src/plugins/fits/non_linear_weighted.h Kst-2.0.8-patched/src/plugins/fits/non_linear_weighted.h ---- Kst-2.0.8/src/plugins/fits/non_linear_weighted.h 2014-02-13 09:41:44.000000000 +0000 -+++ Kst-2.0.8-patched/src/plugins/fits/non_linear_weighted.h 2015-11-18 22:28:44.004399807 +0000 -@@ -18,6 +18,7 @@ - #include <gsl/gsl_blas.h> - #include <gsl/gsl_multifit_nlin.h> - #include <gsl/gsl_statistics.h> -+#include <gsl/gsl_version.h> - #include "common.h" - - struct data { -@@ -193,7 +194,14 @@ - } - while( iStatus == GSL_CONTINUE && iIterations < MAX_NUM_ITERATIONS ); - -+#if GSL_MAJOR_VERSION >=2 -+ gsl_matrix *J=gsl_matrix_alloc(pSolver->fdf->n, pSolver->fdf->p); -+ gsl_multifit_fdfsolver_jac (pSolver, J); -+ gsl_multifit_covar( J, 0.0, pMatrixCovariance ); -+ gsl_matrix_free(J); -+#else - gsl_multifit_covar( pSolver->J, 0.0, pMatrixCovariance ); -+#endif - - // - // determine the fitted values... diff --git a/academic/Kst/README b/academic/Kst/README index 87d0adcf94..314ac53aab 100644 --- a/academic/Kst/README +++ b/academic/Kst/README @@ -16,6 +16,7 @@ without KDE, but you get additional features when running on a platform with KDE). Optional dependencies are: +- hdf5 (provides support for the HDF5 file formats) - netcdf (which provides support for files in the netCDF format) - muParser (which is used in the general non-linear fitting plugin) - GetData (which provides support for files in the Dirfile format) diff --git a/academic/Kst/fix_hdf5_path.patch b/academic/Kst/fix_hdf5_path.patch new file mode 100644 index 0000000000..bcdc1403ae --- /dev/null +++ b/academic/Kst/fix_hdf5_path.patch @@ -0,0 +1,11 @@ +--- Kst-20220116_2b8e03e/src/datasources/hdf5/hdf5.h 2022-01-15 22:42:17.000000000 -0300 ++++ Kst-20220116_2b8e03e/src/datasources/hdf5/hdf5.h.new 2022-03-01 09:50:10.407808017 -0300 +@@ -18,7 +18,7 @@ + #include <dataplugin.h> + + #include <QFileInfo> +-#include <hdf5/serial/H5Cpp.h> ++#include <H5Cpp.h> + #include <exception> + + #include "debug.h" diff --git a/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild b/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild index a64fe00125..99d17512b7 100644 --- a/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild +++ b/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild @@ -31,14 +31,8 @@ TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} COMMIT=4e4416321c75828ac8ea55d36f5a65ebd39058c5 +ARCH=noarch -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information # could be useful to other scripts. @@ -51,8 +45,6 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -ARCH=noarch - set -e # Construct the source tarball name. diff --git a/academic/MetaPhlAn2/MetaPhlAn2.info b/academic/MetaPhlAn2/MetaPhlAn2.info index af4e05652d..72744ccf5a 100644 --- a/academic/MetaPhlAn2/MetaPhlAn2.info +++ b/academic/MetaPhlAn2/MetaPhlAn2.info @@ -1,10 +1,10 @@ PRGNAM="MetaPhlAn2" VERSION="20201202_git4e4416" HOMEPAGE="http://huttenhower.sph.harvard.edu/metaphlan2" -DOWNLOAD="https://github.com/biobakery/MetaPhlAn2/archive/4e4416/4e4416321c75828ac8ea55d36f5a65ebd39058c5.tar.gz" +DOWNLOAD="https://github.com/biobakery/MetaPhlAn2/archive/4e4416/MetaPhlAn2-4e4416321c75828ac8ea55d36f5a65ebd39058c5.tar.gz" MD5SUM="7f07d766a84b0da247a404c05e6f9eb6" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="pysam biopython msgpack-python pandas scipy DendroPy bowtie2 muscle samtools-legacy bcftools ncbi-blast+ RAxML" +REQUIRES="pysam biopython msgpack-python pandas python2-scipy DendroPy bowtie2 muscle samtools-legacy bcftools ncbi-blast+ RAxML" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/Mnemosyne/Mnemosyne.info b/academic/Mnemosyne/Mnemosyne.info deleted file mode 100644 index 1379980bc3..0000000000 --- a/academic/Mnemosyne/Mnemosyne.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="Mnemosyne" -VERSION="2.6.1" -HOMEPAGE="https://mnemosyne-proj.org/" -DOWNLOAD="https://downloads.sourceforge.net/project/mnemosyne-proj/mnemosyne/mnemosyne-2.6.1/Mnemosyne-2.6.1.tar.gz" -MD5SUM="2b2f8fd019370af4d107f696f29ee3a2" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="PyOpenGL CherryPy matplotlib WebOb" -MAINTAINER="R. S. Ananda Murthy" -EMAIL="rsamurti@gmail.com" diff --git a/academic/Mnemosyne/README b/academic/Mnemosyne/README deleted file mode 100644 index b3e2d1449f..0000000000 --- a/academic/Mnemosyne/README +++ /dev/null @@ -1,7 +0,0 @@ -Mnemosyne aims to be a user-friendly flash card program, -with a clean, deceptively simple interface that does not -require you to wrap your head around complicated concepts -before you can start using it. At the same time, under the hood -it is very powerful, and its architecture allows infinite -extensibility and customisibility through plugins and a -scripting API, for the benefit of power users. diff --git a/academic/Mnemosyne/mnemosyne.png b/academic/Mnemosyne/mnemosyne.png Binary files differdeleted file mode 100644 index 6dbd6120b7..0000000000 --- a/academic/Mnemosyne/mnemosyne.png +++ /dev/null diff --git a/academic/NWChem/NWChem.SlackBuild b/academic/NWChem/NWChem.SlackBuild new file mode 100644 index 0000000000..ac62916771 --- /dev/null +++ b/academic/NWChem/NWChem.SlackBuild @@ -0,0 +1,170 @@ +#!/bin/bash + +# Slackware build script for NWChem + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=NWChem +VERSION=${VERSION:-7.0.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM="nwchem-$VERSION-release.revision-b9985dfa-srconly.2020-10-12" + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf nwchem-$VERSION +tar xvf $CWD/$SRCNAM.tar.bz2 +cd nwchem-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +case "$ARCH" in + i?86) NWCHEM_ARCH=LINUX ;; + armv7l) NWCHEM_ARCH=LINUX ;; + aarch64) NWCHEM_ARCH=LINUX64 ;; + *) NWCHEM_ARCH=LINUX64 ;; +esac + +if [ "${BLAS:-no}" == "yes" ]; then + BLASOPT="-lblas" + LAPACK_LIB="/usr/lib${LIBDIRSUFFIX}/liblapack.so" + INTBLAS=n +else + INTBLAS=y +fi + +# whatever set always try to build with MPI, +# actually it checks if the BUILD_MPI is defined or not +# the version 7.0.2 doesn't support buildings without MPI +if [ "${MPI:-no}" == "yes" ]; then + BUILD_MPI="y" +else + BUILD_MPI="n" +fi + +if [ "${PYTHON:-no}" == "yes" ]; then + OPT_MODULE="python" +fi + +# fix for "integer expression expected" +sed -i 's/ $(GNUMAJOR) / "$(GNUMAJOR)" /g' src/config/makefile.h +sed -i 's/ $(GNUMINOR) / "$(GNUMINOR)" /g' src/config/makefile.h +sed -i 's/\(-eq\|-gt\|-ge\) \([0-9]*\)/\1 "\2"/g' src/config/makefile.h + +cd src +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +NWCHEM_TOP=$(pwd)/.. \ +NWCHEM_TARGET=$NWCHEM_ARCH \ +NWCHEM_MODULES="all $OPT_MODULE" \ +USE_MPI=$BUILD_MPI \ +USE_INTERNALBLAS=$INTBLAS \ +BLASOPT=$BLASOPT \ +LAPACK_LIB="$LAPACK_LIB" \ +make +cd .. + +# perform installation +install -d $PKG/usr/bin +install -m 0755 bin/$NWCHEM_ARCH/nwchem $PKG/usr/bin + +mkdir -p $PKG/usr/share/$PKGNAM-$VERSION +cp -ar src/basis/libraries $PKG/usr/share/$PRGNAM-$VERSION +cp -ar src/data $PKG/usr/share/$PRGNAM-$VERSION +cp -ar src/nwpw/libraryps $PKG/usr/share/$PRGNAM-$VERSION + +cat <<EOF >> $PKG/usr/share/$PRGNAM-$VERSION/nwchemrc.default +nwchem_basis_library /usr/share/$PRGNAM-$VERSION/data/libraries/ +nwchem_nwpw_library /usr/share/$PRGNAM-$VERSION/data/libraryps/ +ffield amber +amber_1 /usr/share/$PRGNAM-$VERSION/data/amber_s/ +amber_2 /usr/share/$PRGNAM-$VERSION/data/amber_q/ +amber_3 /usr/share/$PRGNAM-$VERSION/data/amber_x/ +amber_4 /usr/share/$PRGNAM-$VERSION/data/amber_u/ +spce /usr/share/$PRGNAM-$VERSION/data/solvents/spce.rst +charmm_s /usr/share/$PRGNAM-$VERSION/data/charmm_s/ +charmm_x /usr/share/$PRGNAM-$VERSION/data/charmm_x/ +EOF + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/NWChem/NWChem.info b/academic/NWChem/NWChem.info new file mode 100644 index 0000000000..4f2effb9d9 --- /dev/null +++ b/academic/NWChem/NWChem.info @@ -0,0 +1,10 @@ +PRGNAM="NWChem" +VERSION="7.0.2" +HOMEPAGE="https://www.nwchem-sw.org" +DOWNLOAD="https://github.com/nwchemgit/nwchem/releases/download/v7.0.2-release/nwchem-7.0.2-release.revision-b9985dfa-srconly.2020-10-12.tar.bz2" +MD5SUM="b39f42eeacd7e984eee8b7ebc3dfe9f8" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="mpich" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/NWChem/README b/academic/NWChem/README new file mode 100644 index 0000000000..59b0933021 --- /dev/null +++ b/academic/NWChem/README @@ -0,0 +1,15 @@ + NWChem aims to provide its users with computational chemistry tools +that are scalable both in their ability to treat large scientific +computational chemistry problems efficiently, and in their use of +available parallel computing resources from high-performance parallel +supercomputers to conventional workstation clusters. + + + The default configuration file is at: + /usr/share/NWChem-VERSION/nwchemrc.default copy it to your working +directory. + + If you want to install the Python module set the environment +variable PYTHON=yes. + By default it uses a internal blas library, if you want to use +another blas library please set BLAS=yes and install blas and lapack. diff --git a/academic/NWChem/slack-desc b/academic/NWChem/slack-desc new file mode 100644 index 0000000000..b1b7a375b8 --- /dev/null +++ b/academic/NWChem/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +NWChem: NWChem (Open Source High-Performance Computational Chemistry) +NWChem: +NWChem: +NWChem: NWChem aims to provide its users with computational chemistry tools +NWChem: that are scalable both in their ability to treat large scientific +NWChem: computational chemistry problems efficiently, and in their use of +NWChem: available parallel computing resources from high-performance parallel +NWChem: supercomputers to conventional workstation clusters. +NWChem: +NWChem: +NWChem: diff --git a/academic/OpenFOAM/OpenFOAM.SlackBuild b/academic/OpenFOAM/OpenFOAM.SlackBuild index 5e3a5a4c9c..3e98f9b8d5 100644 --- a/academic/OpenFOAM/OpenFOAM.SlackBuild +++ b/academic/OpenFOAM/OpenFOAM.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for OpenFOAM -# Copyright 2017, 2018, 2019, 2020 Lorenzo Trevisan, Caorle, Venice, Italy +# Copyright 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024 Lorenzo Trevisan, Caorle, Venice, Italy # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=OpenFOAM -VERSION=${VERSION:-8} +VERSION=${VERSION:-11} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/OpenFOAM/OpenFOAM.info b/academic/OpenFOAM/OpenFOAM.info index df75c6f7c1..52786f5932 100644 --- a/academic/OpenFOAM/OpenFOAM.info +++ b/academic/OpenFOAM/OpenFOAM.info @@ -1,10 +1,10 @@ PRGNAM="OpenFOAM" -VERSION="8" +VERSION="11" HOMEPAGE="https://openfoam.org/" -DOWNLOAD="https://github.com/OpenFOAM/OpenFOAM-8/archive/version-8/OpenFOAM-8-version-8.tar.gz \ - https://github.com/OpenFOAM/ThirdParty-8/archive/version-8/ThirdParty-8-version-8.tar.gz" -MD5SUM="261dc0d01c4417b737487a60ab4784aa \ - a1beb9f9ce9ca547cd458ec6c1472bcd" +DOWNLOAD="https://github.com/OpenFOAM/OpenFOAM-11/archive/version-11/OpenFOAM-11-version-11.tar.gz \ + https://github.com/OpenFOAM/ThirdParty-11/archive/version-11/ThirdParty-11-version-11.tar.gz" +MD5SUM="81862ded202dc13eb285d399e2ce1741 \ + fcd80fb7fa8d011d1a055cd30323ae58" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi CGAL" diff --git a/academic/OpenFOAM/OpenFOAM.sh b/academic/OpenFOAM/OpenFOAM.sh index a4e69f6d1e..02c71aa6ed 100644 --- a/academic/OpenFOAM/OpenFOAM.sh +++ b/academic/OpenFOAM/OpenFOAM.sh @@ -1 +1 @@ -. /opt/OpenFOAM/OpenFOAM-8/etc/bashrc +. /opt/OpenFOAM/OpenFOAM-11/etc/bashrc diff --git a/academic/OpenFOAM/README b/academic/OpenFOAM/README index d91ec421c8..a72cf10568 100644 --- a/academic/OpenFOAM/README +++ b/academic/OpenFOAM/README @@ -10,4 +10,4 @@ multi-core processors and multi-processor computers. Optional dependency: graphviz (for documentation with graphs) You can build with multiple jobs by setting the MAKEFLAGS environment -variable. +variable (e.g. export MAKEFLAGS="-j$(nproc)" at bash prompt). diff --git a/academic/OpenMM/OpenMM.SlackBuild b/academic/OpenMM/OpenMM.SlackBuild new file mode 100644 index 0000000000..2696983b1f --- /dev/null +++ b/academic/OpenMM/OpenMM.SlackBuild @@ -0,0 +1,165 @@ +#!/bin/bash + +# Slackware build script for OpenMM + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=OpenMM +VERSION=${VERSION:-7.7.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=${PRGNAM,,} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# fix library installation path +# note: the other solution requires less lines, +# but it was after cmake +sed -i \ + -e 's#/lib RUNTIME_DIRECTORY /lib#/lib'${LIBDIRSUFFIX}' RUNTIME_DIRECTORY /lib'${LIBDIRSUFFIX}'#' \ + -e 's#/lib/plugins RUNTIME_DIRECTORY /lib/plugins#/lib'${LIBDIRSUFFIX}'/plugins RUNTIME_DIRECTORY /lib'${LIBDIRSUFFIX}'/plugins#' \ + platforms/*/*/CMakeLists.txt \ + plugins/*/CMakeLists.txt \ + plugins/*/platforms/*/CMakeLists.txt + +sed -i 's#${CMAKE_INSTALL_PREFIX}/lib#&'${LIBDIRSUFFIX}'#' \ + plugins/*/CMakeLists.txt \ + plugins/*/platforms/*/CMakeLists.txt \ + platforms/*/CMakeLists.txt \ + platforms/*/*/CMakeLists.txt + +# fix installation path for examples and licenses +sed -i 's#\(DESTINATION\) \(examples\)#\1 share/'$PRGNAM'/\2#' \ + examples/CMakeLists.txt +sed -i 's#\(DESTINATION\) \(licenses\)#\1 doc/'$PRGNAM-$VERSION'/\2#' \ + docs-source/CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DBUILD_SHARED_LIBS=ON \ + -DPYTHON_EXECUTABLE=/usr/bin/python3 \ + $OPT_BUILD \ + -DCMAKE_BUILD_TYPE=Release .. + + # fix installation path of library "libOpenMM.so" + sed -i 's#${CMAKE_INSTALL_PREFIX}/lib#&'${LIBDIRSUFFIX}'#' \ + cmake_install.cmake + + make + make install/strip DESTDIR=$PKG + + if [ ${PYTHON:-no} == yes ]; then + cd python + # require the CFLAGS for linking with the OpenMM libraries + CFLAGS="-L$PKG/usr/lib${LIBDIRSUFFIX}" \ + OPENMM_INCLUDE_PATH="/usr/include;$PKG/usr/include" \ + OPENMM_LIB_PATH="/usr/lib${LIBDIRSUFFIX};$PKG/usr/lib${LIBDIRSUFFIX}" \ + python3 setup.py install --root=$PKG + # remove temporary folder from python module library path + PYVER=$( python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])' ) + sed -i 's#;'$PKG'/usr/lib'${LIBDIRSUFFIX}'##' $PKG/usr/lib${LIBDIRSUFFIX}/python$PYVER/site-packages/openmm/version.py + cd .. + fi +cd .. + +# update example's makefile +sed -i \ + -e '21s#/usr/local/openmm#/usr#' \ + -e '31s#/lib#&'${LIBDIRSUFFIX}'#' \ + $PKG/usr/share/$PRGNAM/examples/Makefile + +# prune empty dirc "usr/docs" +rm -fr $PKG/usr/docs + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + {CODE_OF_CONDUCT,CONTRIBUTING,SUPPORT}.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/OpenMM/OpenMM.info b/academic/OpenMM/OpenMM.info new file mode 100644 index 0000000000..816a633fb0 --- /dev/null +++ b/academic/OpenMM/OpenMM.info @@ -0,0 +1,10 @@ +PRGNAM="OpenMM" +VERSION="7.7.0" +HOMEPAGE="https://openmm.org" +DOWNLOAD="https://github.com/openmm/openmm/archive/7.7.0/openmm-7.7.0.tar.gz" +MD5SUM="659712580bffde569f0c1663f7df7e68" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/OpenMM/README b/academic/OpenMM/README new file mode 100644 index 0000000000..3bd6b80eb9 --- /dev/null +++ b/academic/OpenMM/README @@ -0,0 +1,10 @@ + A high-performance toolkit for molecular simulation. Use it as an +application, a library, or a flexible programming environment. We +include extensive language bindings for Python, C, C++, and even +Fortran. + + If you want to build the Python package set the environment +variable PYTHON=yes (this requires numpy3). + +NOTE: if you want to use the python module with OpenCL you shall, +install a OpenCL runtime, such as pocl, or other vendor specific. diff --git a/academic/pyfits/slack-desc b/academic/OpenMM/slack-desc index 5ff2aaec0b..70197f20a3 100644 --- a/academic/pyfits/slack-desc +++ b/academic/OpenMM/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -pyfits: pyfits (a Python extension for working with FITS files) -pyfits: -pyfits: PyFITS provides an interface to FITS formatted files in the Python -pyfits: scripting language. PyFITS was a development project of the Science -pyfits: Software Branch at the Space Telescope Science Institute. -pyfits: -pyfits: Homepage: https://github.com/spacetelescope/PyFITS -pyfits: -pyfits: -pyfits: -pyfits: +OpenMM: OpenMM (high-performance toolkit for molecular simulation) +OpenMM: +OpenMM: +OpenMM: +OpenMM: A high-performance toolkit for molecular simulation. Use it as an +OpenMM: application, a library, or a flexible programming environment. We +OpenMM: include extensive language bindings for Python, C, C++, and even +OpenMM: Fortran. +OpenMM: +OpenMM: +OpenMM: diff --git a/academic/OpenVSP/OpenVSP.SlackBuild b/academic/OpenVSP/OpenVSP.SlackBuild new file mode 100644 index 0000000000..9cade4a39e --- /dev/null +++ b/academic/OpenVSP/OpenVSP.SlackBuild @@ -0,0 +1,137 @@ +#!/bin/bash + +# Slackware build script for OpenVSP + +# Copyright 2022 Lenard Spencer, Orlando, Florida, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=OpenVSP +VERSION=${VERSION:-3.31.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${PRGNAM}-${PRGNAM}_$VERSION +tar -xvf $CWD/${PRGNAM}_$VERSION.tar.gz || tar -xvf $CWD/${PRGNAM}-${PRGNAM}_$VERSION.tar.gz +cd $PRGNAM-${PRGNAM}_$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p build buildlibs + +cd buildlibs + cmake \ + -DVSP_USE_SYSTEM_LIBXML2=true \ + -DVSP_USE_SYSTEM_FLTK=true \ + -DVSP_USE_SYSTEM_GLM=false \ + -DVSP_USE_SYSTEM_GLEW=true \ + -DVSP_USE_SYSTEM_CMINPACK=false \ + -DVSP_USE_SYSTEM_LIBIGES=false \ + -DVSP_USE_SYSTEM_EIGEN=true \ + -DVSP_USE_SYSTEM_CODEELI=false \ + -DVSP_USE_SYSTEM_CPPTEST=false \ + -DCMAKE_BUILD_TYPE=Release \ + -Wno-dev \ + ../Libraries + make + +cd ../build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DVSP_LIBRARY_PATH=$TMP/${PRGNAM}-${PRGNAM}_$VERSION/buildlibs \ + -DCMAKE_INSTALL_PREFIX=/opt/$PRGNAM \ + -DCMAKE_BUILD_TYPE=Release \ + -Wno-dev .. + make + make install DESTDIR=$PKG +cd .. + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +for i in 16 32 64 128; do + convert vspIcon.png -resize ${i}x${i}! $PRGNAM-${i}.png + install -D -m 0644 $PRGNAM-${i}.png \ + $PKG/usr/share/icons/hicolor/${i}x${i}/apps/$PRGNAM.png +done +install -D -m0644 $CWD/OpenVSP.desktop \ + $PKG/usr/share/applications/OpenVSP.desktop + +# Create symlink to executable: +(mkdir -p $PKG/usr/bin ; cd $PKG/usr/bin ; ln -sf ../../opt/OpenVSP/vsp ) + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/OpenVSP/OpenVSP.desktop b/academic/OpenVSP/OpenVSP.desktop new file mode 100644 index 0000000000..b9c345e7fc --- /dev/null +++ b/academic/OpenVSP/OpenVSP.desktop @@ -0,0 +1,9 @@ +[Desktop Entry] +Name=OpenVSP +GenericName=OpenVSP +Comment=3D Aircraft Modeler +Exec=vsp +Icon=OpenVSP +Terminal=false +Type=Application +Categories=Graphics; diff --git a/academic/OpenVSP/OpenVSP.info b/academic/OpenVSP/OpenVSP.info new file mode 100644 index 0000000000..a366bf2c19 --- /dev/null +++ b/academic/OpenVSP/OpenVSP.info @@ -0,0 +1,10 @@ +PRGNAM="OpenVSP" +VERSION="3.31.1" +HOMEPAGE="http://openvsp.org" +DOWNLOAD="https://github.com/OpenVSP/OpenVSP/archive/OpenVSP_3.31.1/OpenVSP-OpenVSP_3.31.1.tar.gz" +MD5SUM="5267cdc9d1c6050fd0b8bc963e179b87" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="fltk" +MAINTAINER="Lenard Spencer" +EMAIL="lenardrspencer@gmail.com" diff --git a/academic/OpenVSP/README b/academic/OpenVSP/README new file mode 100644 index 0000000000..79c0c29acd --- /dev/null +++ b/academic/OpenVSP/README @@ -0,0 +1,13 @@ +OpenVSP is a parametric aircraft geometry tool. OpenVSP allows the +user to create a 3D model of an aircraft defined by common engineering +parameters. This model can be processed into formats suitable for +engineering analysis. + +The predecessors to OpenVSP have been developed by J.R. Gloudemans and +others for NASA since the early 1990's. On January 10 2012, OpenVSP +was released as an open source project under the NASA Open Source +Agreement (NOSA) version 1.3. + +You can download sample aircraft at http://hangar.openvsp.org. + +Requires fltk from Slackware's /extra folder. diff --git a/academic/Mnemosyne/doinst.sh b/academic/OpenVSP/doinst.sh index aea0f894eb..aea0f894eb 100644 --- a/academic/Mnemosyne/doinst.sh +++ b/academic/OpenVSP/doinst.sh diff --git a/academic/OpenVSP/slack-desc b/academic/OpenVSP/slack-desc new file mode 100644 index 0000000000..2aed2df60f --- /dev/null +++ b/academic/OpenVSP/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +OpenVSP: OpenVSP (3D aircraft modeling tool) +OpenVSP: +OpenVSP: OpenVSP is a parametric aircraft geometry tool that allows the user +OpenVSP: to create a 3D model of an aircraft defined by common engineering +OpenVSP: parameters. This model can be processed into formats suitable for +OpenVSP: engineering analysis. OpenVSP was released as an open source project +OpenVSP: under the NASA Open Source Agreement (NOSA) version 1.3. +OpenVSP: +OpenVSP: +OpenVSP: homepage: http://openvsp.org +OpenVSP: diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild index 41e235cda0..351fde6f1f 100644 --- a/academic/PhyML/PhyML.SlackBuild +++ b/academic/PhyML/PhyML.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for PhyML -# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -27,7 +27,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=PhyML -VERSION=${VERSION:-3.3.20200621} +VERSION=${VERSION:-3.3.20220408} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -123,45 +123,49 @@ sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG -# This is Phyrex -./autogen.sh -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --mandir=/usr/man \ - --enable-phyrex \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux - -# Use our CFLAGS +# This is Phyrex but it breaks at the moment + ./autogen.sh + ./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --enable-phyrex \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + + # Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG -# This is PhyTime -./autogen.sh -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --mandir=/usr/man \ - --enable-phytime \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux - -# Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile - -CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make -make install DESTDIR=$PKG +# # This is PhyTime +# ./autogen.sh +# ./configure \ +# --prefix=/usr \ +# --libdir=/usr/lib${LIBDIRSUFFIX} \ +# --sysconfdir=/etc \ +# --localstatedir=/var \ +# --mandir=/usr/man \ +# --enable-phytime \ +# --docdir=/usr/doc/$PRGNAM-$VERSION \ +# --build=$ARCH-slackware-linux +# +# # Use our CFLAGS +# sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile +# +# CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make +# make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +# fix permissions for docs +chmod 0644 doc/*.{pdf,tex,bib} +chmod 0644 doc/fig/*.pdf + # Include some examples mkdir -p $PKG/usr/share/$PRGNAM cp -a examples $PKG/usr/share/$PRGNAM diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info index ec04310e99..9b34384c9f 100644 --- a/academic/PhyML/PhyML.info +++ b/academic/PhyML/PhyML.info @@ -1,8 +1,8 @@ PRGNAM="PhyML" -VERSION="3.3.20200621" +VERSION="3.3.20220408" HOMEPAGE="https://github.com/stephaneguindon/phyml/" -DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20200621/phyml-3.3.20200621.tar.gz" -MD5SUM="12622e111c388bcb16696660033143b5" +DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20220408/phyml-3.3.20220408.tar.gz" +MD5SUM="b35e641af77d7f058cf1ddc73be5e0b7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi" diff --git a/academic/PyAMG/PyAMG.SlackBuild b/academic/PyAMG/PyAMG.SlackBuild index 6b17681db1..3b16dca8b5 100644 --- a/academic/PyAMG/PyAMG.SlackBuild +++ b/academic/PyAMG/PyAMG.SlackBuild @@ -32,7 +32,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -50,8 +50,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/PyAMG/PyAMG.info b/academic/PyAMG/PyAMG.info index 3b3933387b..f2fa54b086 100644 --- a/academic/PyAMG/PyAMG.info +++ b/academic/PyAMG/PyAMG.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/pyamg/pyamg/releases/download/v2.1.0/official_pyamg MD5SUM="b04419a4e751d5333bc97fb1786e9e09" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="nose numpy scipy" +REQUIRES="nose python2-scipy" MAINTAINER="Alexander Bruy" EMAIL="alexander dot bruy at gmail dot com" diff --git a/academic/QtiPlot/QtiPlot.SlackBuild b/academic/QtiPlot/QtiPlot.SlackBuild deleted file mode 100644 index 9457c38d8e..0000000000 --- a/academic/QtiPlot/QtiPlot.SlackBuild +++ /dev/null @@ -1,229 +0,0 @@ -#!/bin/bash - -# Slackware build script for QtiPlot - -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com -# All rights reserved. -# -# Redistribution and use of this script, with or without modification, is -# permitted provided that the following conditions are met: -# -# 1. Redistributions of this script must retain the above copyright -# notice, this list of conditions and the following disclaimer. -# -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -cd $(dirname $0) ; CWD=$(pwd) - -PRGNAM=QtiPlot -VERSION=${VERSION:-0.9.8.9} -BUILD=${BUILD:-2} -TAG=${TAG:-_SBo} -PKGTYPE=${PKGTYPE:-tgz} - -SRCNAM=$(echo $PRGNAM | tr A-Z a-z) - -QTEXENGINE=QTeXEngine-0.3-opensource -UNOFPLUGIN=importOPJ-20111106 - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) export ARCH=i486 ;; - arm*) export ARCH=arm ;; - *) export ARCH=$( uname -m ) ;; - esac -fi - -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. -if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then - echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" - exit 0 -fi - -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" - QMAKESPEC="linux-g++" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" - QMAKESPEC="linux-g++" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" - QMAKESPEC="linux-g++-64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" - QMAKESPEC="linux-g++" -fi - -# Define these here, as numbers change between Slackware releases. The -# folder names are used for some documentation path fixes, needed to -# generate the html manual later on. -DOCBOOK=dsssl-stylesheets-1.79 -CHUNK=xsl-stylesheets-1.78.1 -DOCBOOKX=xml-dtd-4.5 - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -mkdir $PRGNAM-$VERSION -cd $PRGNAM-$VERSION -tar xvf $CWD/$SRCNAM-$VERSION.tar.bz2 -unzip $CWD/$QTEXENGINE.zip -tar xvf $CWD/$UNOFPLUGIN.tar.gz -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -# Copy QTeXEngine and importOPJ to their locations to be built later -cp -a QTeXEngine $SRCNAM-$VERSION/3rdparty -cp -a $UNOFPLUGIN/qtiplot/src/plugins $SRCNAM-$VERSION/qtiplot/src -cp -a $UNOFPLUGIN/qtiplot/importOPJ.pro $SRCNAM-$VERSION/qtiplot -cd $SRCNAM-$VERSION - -# Patches for recent libpng, sip, gsl, etc -# thanks to slack_jack, Raveriux, ponce, Arch and Gentoo -patch -p0 -d 3rdparty/qwtplot3d < $CWD/qwtplot3d-libpng15.patch -patch -p1 < $CWD/sip-4.15.patch -patch -p1 < $CWD/qtiplot-0.9.8.9-private.patch -patch -p1 < $CWD/pyqt-4.11.patch -patch -p1 < $CWD/qtiplot-0.9.8.9_gsl-2.patch - -# Use the custom build.conf -cp $CWD/build.conf.slack build.conf - -# Make qtiplot.pro aware of the unofficial importOPJ plugin. Thanks to -# the author of the plugin, Stephan Zevenhuizen. For more info visit -# this site: http://www.staff.science.uu.nl/~zeven101/qtiplot.html -patch -p1 -i $CWD/importOPJ.patch -sed -i "143 a Q_IMPORT_PLUGIN(FreeSoftwareQtiPlotImportOPJ);" qtiplot/src/core/main.cpp - -# Fix qwtplot3d -sed -i "10 a #include <GL/glu.h>" 3rdparty/qwtplot3d/include/qwt3d_openglhelper.h - -# Make a few path fixes to qtiplot.pro -sed -i "s:/usr/local:/usr/share:" qtiplot/qtiplot.pro -sed -i "s:/share/man:/man:" qtiplot/qtiplot.pro -sed -i "s:/share/doc/qtiplot:/doc/$PRGNAM-$VERSION:" qtiplot/qtiplot.pro - -# Point to the right places of qt-assistant-compat, libreoffice (when -# installed), latex, java, the QtiPlot html manual and fitPlugins -sed -i "s:<QAssistantClient>:<QtAssistant/qassistantclient.h>:" qtiplot/src/core/ApplicationWindow.cpp -sed -i "s:/usr/bin/soffice:/usr/bin/libreoffice:" qtiplot/src/core/ApplicationWindow.cpp -sed -i "s:/usr/bin/latex:/usr/share/texmf/bin/latex:" qtiplot/src/core/ApplicationWindow.cpp -sed -i "s:/usr/bin/java:/usr/lib${LIBDIRSUFFIX}/java/bin/java:" qtiplot/src/core/ApplicationWindow.cpp -sed -i "s:/index.html:/html/index.html:" qtiplot/src/core/ApplicationWindow.cpp -sed -i "s:/local/qtiplot/fitPlugins:/lib${LIBDIRSUFFIX}/qtiplot/plugins:" qtiplot/src/core/ApplicationWindow.cpp - -# Path fixes, needed to generate the html manual -sed -i "s:stylesheet/dsssl/modular:${DOCBOOK}:" manual/qtiplot.dsl -sed -i "s:stylesheet/nwalsh:${CHUNK}:" manual/qtiplot_html.xsl -sed -i "s:schema/dtd/4.4:${DOCBOOKX}:" manual/docbook-en/index.docbook - -# Build QtiPlot's qwt -cd 3rdparty/qwt -qmake -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 - -# Build QtiPlot's qwtplot3d -cd ../qwtplot3d -qmake -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 - -# Build QTeXEngine -cd ../QTeXEngine -qmake -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 - -# Build importOPJ -cd ../../qtiplot -qmake importOPJ.pro -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 - -# Make the html manual. If you want to generate the handbook as a PDF, -# change "web" to "en" below and make sure you have installed dblatex. -cd ../manual -make -j1 web - -# Build QtiPlot -cd ../qtiplot -qmake qtiplot.pro "QMAKESPEC=$QMAKESPEC" -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 "QMAKESPEC=$QMAKESPEC" -make -j1 install INSTALL_ROOT=$PKG - -# Generate translations and copy them to their proper place -lrelease qtiplot.pro -mkdir -p $PKG/usr/share/qtiplot/translations -cp translations/*.qm $PKG/usr/share/qtiplot/translations - -# Copy some python examples -mkdir -p $PKG/usr/share/qtiplot/python-examples -cp examples/python/* $PKG/usr/share/qtiplot/python-examples - -# Build fitPlugins -cd ../fitPlugins -qmake "QMAKESPEC=$QMAKESPEC" -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 "QMAKESPEC=$QMAKESPEC" -make -j1 install INSTALL_ROOT=$PKG -cd .. - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done - -# Menu item, icon and mime types. The .xml is from Arch -mkdir -p $PKG/usr/share/{pixmaps,applications,mime/packages} -cp qtiplot_logo.png $PKG/usr/share/pixmaps/qtiplot.png -cp $CWD/qtiplot.desktop $PKG/usr/share/applications -cp $CWD/qtiplot.xml $PKG/usr/share/mime/packages - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - README.html gpl_licence.txt qtiplot.css qtiplot_logo.png \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -cat $CWD/build.conf.slack > $PKG/usr/doc/$PRGNAM-$VERSION/build.conf.slack - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/QtiPlot/QtiPlot.info b/academic/QtiPlot/QtiPlot.info deleted file mode 100644 index dcbffe5315..0000000000 --- a/academic/QtiPlot/QtiPlot.info +++ /dev/null @@ -1,14 +0,0 @@ -PRGNAM="QtiPlot" -VERSION="0.9.8.9" -HOMEPAGE="https://www.qtiplot.com/" -DOWNLOAD="http://sourceforge.net/projects/qtiplot.berlios/files/qtiplot-0.9.8.9.tar.bz2 \ - http://sourceforge.net/projects/qtiplot.berlios/files/QTeXEngine-0.3-opensource.zip \ - http://sourceforge.net/projects/sboppetrov/files/QtiPlot/importOPJ-20111106.tar.gz" -MD5SUM="652096a365851da3b5f6fefdcbe2aaec \ - d1b234623770ec6209b14d1b5137f2f1 \ - 6f6925beb9e27f2ea0fbd01f23da548a" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="alglib muParser qt-assistant-compat tamu_anova" -MAINTAINER="Petar Petrov" -EMAIL="slackalaxy@gmail.com" diff --git a/academic/QtiPlot/README b/academic/QtiPlot/README deleted file mode 100644 index 950c7a7f05..0000000000 --- a/academic/QtiPlot/README +++ /dev/null @@ -1,32 +0,0 @@ -QtiPlot is a program for two- and three-dimensional graphical -presentation of data sets and for data analysis. Plots can be produced -from data sets stored in tables or from analytical functions. QtiPlot -offers a complete alternative solution to software like Origin, -SigmaPlot, SPSS, Regressi or Igor Pro. QtiPlot is used for teaching as -well as for complex data analysis and visualisation in companies, high -schools, universities and reseach institutes all over the world. - -Features: - -- Fully Python scriptable -- OpenGL based 3D plotting -- Publication quality plots and easy export to various image formats - (EMF, EPS, PS, PDF, SVG, BMP, JPG, PNG, TIFF, etc ...) -- Easy integration with LaTeX typesetting system -- Powerful and versatile spreadsheets with column-logic calculations - and easy import/export of multiple files -- One-click access to extensive built-in data analysis routines -- Advanced statistical analysis: Student's t-Test, ANOVA, chi-square - test for variance, normality test (Shapiro-Wilk) -- Linear and nonlinear curve fitting with weighting and estimation of - statistical errors of the fit-parameters -- Multi-peak fitting -- Image analysis tools -- Templates support: all settings for plots, tables and matrices can - be saved and restored later on for a fast editing process -- Project files based on folders, a powerful project explorer with - built-in drag and drop and searching facilities - -QtiPlot comes with its own, slightly modified versions of qwt and -qwtplot3d, while the script additionally builds in QTeXEngine and the -unofficial importOPJ plugin. diff --git a/academic/QtiPlot/build.conf.slack b/academic/QtiPlot/build.conf.slack deleted file mode 100644 index 22ac622871..0000000000 --- a/academic/QtiPlot/build.conf.slack +++ /dev/null @@ -1,75 +0,0 @@ -isEmpty( QTI_ROOT ) { - message( "each file including this config needs to set QTI_ROOT to the dir containing this file!" ) -} - -# System specific configuration -SYS_INCLUDEPATH = /usr/include -SYS_LIBS = -L/usr/lib${LIBDIRSUFFIX} -lz -lGLU - -# zlib (http://www.zlib.net/) -#ZLIB_INCLUDEPATH = $$QTI_ROOT/3rdparty/zlib/ -ZLIB_INCLUDEPATH = - - -# muParser (http://muparser.sourceforge.net/) -MUPARSER_INCLUDEPATH = -MUPARSER_LIBS = -lmuparser - -# GNU Sientific Library (http://www.gnu.org/software/gsl/) -GSL_INCLUDEPATH = -GSL_LIBS = -lgsl -lgslcblas - -# QWT - use local copy till upstream catches up -# (http://qwt.sourceforge.net/index.html) -QWT_INCLUDEPATH = $$QTI_ROOT/3rdparty/qwt/src -QWT_LIBS = $$QTI_ROOT/3rdparty/qwt/lib/libqwt.a - -# QwtPlot3D - use local copy till upstream catches up -# (http://qwtplot3d.sourceforge.net/) -QWT3D_INCLUDEPATH = $$QTI_ROOT/3rdparty/qwtplot3d/include -QWT3D_LIBS = $$QTI_ROOT/3rdparty/qwtplot3d/lib/libqwtplot3d.a - -# libpng -LIBPNG_LIBS = -lpng - -# QTeXEngine (http://soft.proindependent.com/qtexengine/) -TEX_ENGINE_INCLUDEPATH = $$QTI_ROOT/3rdparty/QTeXEngine/src -TEX_ENGINE_LIBS = $$QTI_ROOT/3rdparty/QTeXEngine/libQTeXEngine.a - -# ALGLIB (http://www.alglib.net/) -ALGLIB_INCLUDEPATH = /usr/include/libalglib -ALGLIB_LIBS = -lalglib - -# TAMUANOVA (http://www.stat.tamu.edu/~aredd/tamuanova/) -TAMUANOVA_INCLUDEPATH = /usr/include/tamu_anova -TAMUANOVA_LIBS = -ltamuanova - -# the python interpreter to use -PYTHON = python - -# Qt tools - allows to use specific versions -LUPDATE = lupdate -LRELEASE = lrelease - -# Target specific configuration: configure Qtiplot itself -contains( TARGET, qtiplot ) { -# building without muParser doesn't work yet -SCRIPTING_LANGS += muParser -SCRIPTING_LANGS += Python - -# a console displaying output of scripts -DEFINES += SCRIPTING_CONSOLE - -# Uncomment the following line if you want to perform a custom -# installation using the *.path variables defined in ./qtiplot.pro. -CONFIG += CustomInstall - -# Uncomment the following line if you want to build QtiPlot as a browser plugin (not working on Internet Explorer). -#CONFIG += BrowserPlugin - -#CONFIG += release -#CONFIG += debug - -# Uncomment the following line if you want to link statically against Qt. -#CONFIG += StaticBuild -} diff --git a/academic/QtiPlot/importOPJ.patch b/academic/QtiPlot/importOPJ.patch deleted file mode 100644 index 12a0d2073b..0000000000 --- a/academic/QtiPlot/importOPJ.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff -pruN qtiplot-0.9.8.9.orig/qtiplot/qtiplot.pro qtiplot-0.9.8.9/qtiplot/qtiplot.pro ---- qtiplot-0.9.8.9.orig/qtiplot/qtiplot.pro 2011-11-02 18:55:25.000000000 +0200 -+++ qtiplot-0.9.8.9/qtiplot/qtiplot.pro 2012-08-03 01:27:29.649544418 +0300 -@@ -232,3 +232,14 @@ contains(CONFIG, BrowserPlugin){ - RC_FILE = qtiplot.rc - include(../3rdparty/QtSolutions/qtbrowserplugin/src/qtbrowserplugin.pri) - } -+ -+############################################################### -+##################### OriginPlugin ############################ -+############################################################### -+ -+TARGET = qtiplot -+DESTDIR = -+LIBS += ../tmp/qtiplot/libFreeSoftwareQtiPlotImportOPJ.a -+ -+ -+include(src/plugins/OriginPlugin/OriginPlugin.pri) diff --git a/academic/QtiPlot/pyqt-4.11.patch b/academic/QtiPlot/pyqt-4.11.patch deleted file mode 100644 index dc7d56f3e3..0000000000 --- a/academic/QtiPlot/pyqt-4.11.patch +++ /dev/null @@ -1,33 +0,0 @@ - qtiplot/python-sipcmd.py | 21 ++++++++++++++++++--- - 1 file changed, 18 insertions(+), 3 deletions(-) - -diff --git a/qtiplot/python-sipcmd.py b/qtiplot/python-sipcmd.py -index f643194..d8d1ef2 100755 ---- a/qtiplot/python-sipcmd.py -+++ b/qtiplot/python-sipcmd.py -@@ -27,6 +27,21 @@ - # # - ############################################################################ - --from PyQt4 import pyqtconfig --config = pyqtconfig.Configuration() --print " ".join([config.sip_bin, "-I", config.pyqt_sip_dir, config.pyqt_sip_flags]) -+from __future__ import print_function -+ -+import os -+import sipconfig -+import PyQt4.QtCore -+ -+try: -+ # >= 4.10 -+ SIP_FLAGS = PyQt4.QtCore.PYQT_CONFIGURATION['sip_flags'] -+except: -+ import PyQt4.pyqtconfig -+ SIP_FLAGS = PyQt4.pyqtconfig.Configuration().pyqt_sip_flags -+ -+PYQT_SIP_DIR = os.path.join(sipconfig.Configuration().default_sip_dir, 'PyQt4') -+SIP_BIN = sipconfig.Configuration().sip_bin -+SIP_INC_DIR = sipconfig.Configuration().sip_inc_dir -+ -+print(" ".join([SIP_BIN, "-I", PYQT_SIP_DIR, SIP_FLAGS])) - diff --git a/academic/QtiPlot/qtiplot-0.9.8.9-private.patch b/academic/QtiPlot/qtiplot-0.9.8.9-private.patch deleted file mode 100644 index 1dd92fd1a3..0000000000 --- a/academic/QtiPlot/qtiplot-0.9.8.9-private.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff -ruN qtiplot-0.9.8.9.orig/qtiplot/src/plot2D/ImageWidget.h qtiplot-0.9.8.9/qtiplot/src/plot2D/ImageWidget.h ---- qtiplot-0.9.8.9.orig/qtiplot/src/plot2D/ImageWidget.h 2010-10-17 09:04:05.000000000 +0200 -+++ qtiplot-0.9.8.9/qtiplot/src/plot2D/ImageWidget.h 2013-11-01 12:11:36.559973891 +0100 -@@ -67,10 +67,10 @@ - void setWindowName(const QString& name){d_window_name = name;}; - - static QPixmap windowPixmap(ApplicationWindow *mw, const QString& name, const QSize& size); -+ void paintEvent(QPaintEvent *e); - - private: - void draw(QPainter *painter, const QRect& r); -- void paintEvent(QPaintEvent *e); - QPixmap d_pix; - //! The file from which the image was loaded. - QString d_file_name; - diff --git a/academic/QtiPlot/qtiplot-0.9.8.9_gsl-2.patch b/academic/QtiPlot/qtiplot-0.9.8.9_gsl-2.patch deleted file mode 100644 index d6ff7d00b0..0000000000 --- a/academic/QtiPlot/qtiplot-0.9.8.9_gsl-2.patch +++ /dev/null @@ -1,52 +0,0 @@ -diff -u -r qtiplot-0.9.8.9/qtiplot/src/analysis/Fit.cpp qtiplot-0.9.8.9-patched/qtiplot/src/analysis/Fit.cpp ---- qtiplot-0.9.8.9/qtiplot/src/analysis/Fit.cpp 2011-10-17 11:06:00.000000000 +0100 -+++ qtiplot-0.9.8.9-patched/qtiplot/src/analysis/Fit.cpp 2015-11-18 22:26:22.535193469 +0000 -@@ -39,6 +39,7 @@ - #include <gsl/gsl_statistics.h> - #include <gsl/gsl_blas.h> - #include <gsl/gsl_cdf.h> -+#include <gsl/gsl_version.h> - - #include <QApplication> - #include <QMessageBox> -@@ -106,6 +107,10 @@ - gsl_multifit_fdfsolver * Fit::fitGSL(gsl_multifit_function_fdf f, int &iterations, int &status) - { - const gsl_multifit_fdfsolver_type *T; -+#if GSL_MAJOR_VERSION >=2 -+ gsl_matrix *J=0; -+#endif -+ - if (d_solver) - T = gsl_multifit_fdfsolver_lmder; - else -@@ -128,7 +133,14 @@ - } - - if (status){ -+#if GSL_MAJOR_VERSION >=2 -+ J=gsl_matrix_alloc(s->fdf->n, s->fdf->p); -+ gsl_multifit_fdfsolver_jac (s, J); -+ gsl_multifit_covar (J, 0.0, covar); -+ gsl_matrix_free(J); -+#else - gsl_multifit_covar (s->J, 0.0, covar); -+#endif - iterations = 0; - return s; - } -@@ -155,7 +167,14 @@ - status = gsl_multifit_test_delta (s->dx, s->x, d_tolerance, d_tolerance); - } while (inRange && status == GSL_CONTINUE && (int)iter < d_max_iterations); - -+#if GSL_MAJOR_VERSION >=2 -+ J=gsl_matrix_alloc(s->fdf->n, s->fdf->p); -+ gsl_multifit_fdfsolver_jac (s, J); -+ gsl_multifit_covar (J, 0.0, covar); -+ gsl_matrix_free(J); -+#else - gsl_multifit_covar (s->J, 0.0, covar); -+#endif - - iterations = iter; - return s; diff --git a/academic/QtiPlot/qtiplot.desktop b/academic/QtiPlot/qtiplot.desktop deleted file mode 100644 index cf93e4911a..0000000000 --- a/academic/QtiPlot/qtiplot.desktop +++ /dev/null @@ -1,7 +0,0 @@ -[Desktop Entry] -Type=Application -Exec=qtiplot -Terminal=false -Name=QtiPlot -Icon=qtiplot -Categories=Office; diff --git a/academic/QtiPlot/qtiplot.xml b/academic/QtiPlot/qtiplot.xml deleted file mode 100644 index 7ad4c4aa02..0000000000 --- a/academic/QtiPlot/qtiplot.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info"> - <mime-type type="application/x-qtiplot-project"> - <sub-class-of type="text/plain"/> - <comment>QtiPlot project file</comment> - <glob pattern="*.qti" /> - </mime-type> - <mime-type type="application/x-qtiplot-project-compressed"> - <comment>Compressed QtiPlot project file</comment> - <glob pattern="*.qti.gz" /> - </mime-type> - <mime-type type="application/x-qtiplot-project-backup"> - <sub-class-of type="text/plain"/> - <comment>QtiPlot project file backup</comment> - <glob pattern="*.qti~" /> - </mime-type> -</mime-info> diff --git a/academic/QtiPlot/qwtplot3d-libpng15.patch b/academic/QtiPlot/qwtplot3d-libpng15.patch deleted file mode 100644 index 828f0c6d84..0000000000 --- a/academic/QtiPlot/qwtplot3d-libpng15.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- 3rdparty/gl2ps/gl2ps.c.orig 2012-01-29 18:15:34.000000000 -0500 -+++ 3rdparty/gl2ps/gl2ps.c 2012-01-29 18:16:08.000000000 -0500 -@@ -47,6 +47,7 @@ - #endif - - #if defined(GL2PS_HAVE_LIBPNG) -+#include <zlib.h> - #include <png.h> - #endif - diff --git a/academic/QtiPlot/sip-4.15.patch b/academic/QtiPlot/sip-4.15.patch deleted file mode 100644 index 504223190a..0000000000 --- a/academic/QtiPlot/sip-4.15.patch +++ /dev/null @@ -1,32 +0,0 @@ ---- ./qtiplot/src/analysis/FFT.cpp.orig 2011-07-06 11:51:08.000000000 +0000 -+++ ./qtiplot/src/analysis/FFT.cpp 2013-10-23 23:07:45.674925476 +0000 -@@ -353,7 +353,7 @@ - ml->arrangeLayers(false, false); - } - --bool FFT::setDataFromTable(Table *t, const QString& realColName, const QString& imagColName, int from, int to) -+bool FFT::setDataFromTable(Table *t, const QString& realColName, const QString& imagColName, int from, int to, bool unused) - { - d_init_err = true; - ---- ./qtiplot/src/analysis/FFT.h.orig 2011-07-05 22:05:03.000000000 +0000 -+++ ./qtiplot/src/analysis/FFT.h 2013-10-23 23:11:34.277924367 +0000 -@@ -52,6 +52,8 @@ - Matrix *realOutputMatrix(){return d_re_out_matrix;} - Matrix *imaginaryOutputMatrix(){return d_im_out_matrix;} - -+ bool setDataFromTable(Table *t, const QString& realColName, const QString& imagColName = QString(), int from = 0, int to = -1, bool unused = false); -+ - private: - void init(); - void output(); -@@ -60,8 +62,6 @@ - void fftTable(); - void fftMatrix(); - -- bool setDataFromTable(Table *t, const QString& realColName, const QString& imagColName = QString(), int from = 0, int to = -1); -- - double d_sampling; - //! Flag telling if an inverse FFT must be performed. - bool d_inverse; - diff --git a/academic/R/R.SlackBuild b/academic/R/R.SlackBuild index a7c14b12ae..3ee98369fc 100644 --- a/academic/R/R.SlackBuild +++ b/academic/R/R.SlackBuild @@ -2,7 +2,7 @@ # SlackBuild script for R -# Copyright 2019-2020 Andrew Payne <phalange@komputermatrix.com> +# Copyright 2019-2022 Andrew Payne <phalange@komputermatrix.com> # Copyright 2014-2017 melikamp, Andrew Rowland # This program is free software: you can redistribute it and/or modify @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=R -VERSION=${VERSION:-4.0.0} +VERSION=${VERSION:-4.3.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -82,7 +82,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +tar xvf $CWD/$PRGNAM-$VERSION.tar.xz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -115,6 +115,8 @@ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a {COPYING,INSTALL,README,SVN-REVISION,VERSION,VERSION-NICK} \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/R/R.info b/academic/R/R.info index e06bdf1195..45cf892f94 100644 --- a/academic/R/R.info +++ b/academic/R/R.info @@ -1,8 +1,8 @@ PRGNAM="R" -VERSION="4.0.0" -HOMEPAGE="http://www.r-project.org/" -DOWNLOAD="https://cran.r-project.org/src/base/R-4/R-4.0.0.tar.gz" -MD5SUM="48c487c68112cb3191f3015c6277a50b" +VERSION="4.3.3" +HOMEPAGE="https://www.r-project.org/" +DOWNLOAD="https://cran.r-project.org/src/base/R-4/R-4.3.3.tar.xz" +MD5SUM="5602f5996107c346dba12a16e866d2e2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/R/README b/academic/R/README index cdd9f7dbd6..0ebd1faa48 100644 --- a/academic/R/README +++ b/academic/R/README @@ -1,20 +1,10 @@ -R is an integrated suite of software facilities for data manipulation, -calculation and graphical display. It includes - -* an effective data handling and storage facility, - -* a suite of operators for calculations on arrays, in particular -matrices, - -* a large, coherent, integrated collection of intermediate tools for -data analysis, - -* graphical facilities for data analysis and display either on-screen -or on hardcopy, and - -* a well-developed, simple and effective programming language which -includes conditionals, loops, user-defined recursive functions and -input and output facilities. +R is a language and environment for statistical computing and +graphics. It is a GNU project which is similar to the S language and +environment which was developed at Bell Laboratories (formerly AT&T, +now Lucent Technologies) by John Chambers and colleagues. R can be +considered as a different implementation of S. There are some +important differences, but much code written for S runs unaltered +under R. Notes: diff --git a/academic/R/slack-desc b/academic/R/slack-desc index f6e2acfb82..bbc419bba3 100644 --- a/academic/R/slack-desc +++ b/academic/R/slack-desc @@ -9,11 +9,11 @@ R: R (language and environment for statistical computing) R: R: R is a language and environment for statistical computing and -R: graphics. It is a GNU project which is similar to the S language -R: and environment which was developed at Bell Laboratories -R: by John Chambers and colleagues. R can be considered as a -R: different implementation of S. There are some important -R: differences, but much code written for S runs unaltered under R. +R: graphics. It is a GNU project which is similar to the S language and +R: environment which was developed at Bell Laboratories (formerly AT&T, +R: now Lucent Technologies) by John Chambers and colleagues. +R: +R: R: R: Homepage: https://www.r-project.org/ R: diff --git a/academic/RepeatMasker/README.SLACKWARE b/academic/RepeatMasker/README.SLACKWARE index dd3313fd62..0e92803b9e 100644 --- a/academic/RepeatMasker/README.SLACKWARE +++ b/academic/RepeatMasker/README.SLACKWARE @@ -1,31 +1,22 @@ -After install go fo /opt/RepeatMasker and run the RepeatMasker -Configuration Program: +After install go to /opt/RepeatMasker and run the Configuration Program: # perl ./configure -Paths are as follows: - -**PERL PROGRAM** -/usr/bin/perl - -**REPEATMASKER INSTALLATION DIRECTORY** -/opt/RepeatMasker - -**TRF PROGRAM** -/usr/bin/trf +* The full path including the name for the TRF program. +TRF_PRGM: /usr/bin/trf Add a Search Engine: 1. CrossMatch: you should obtain this yourself, with the proper license, following the instructions here http://www.phrap.org/ 2. RMBlast - NCBI Blast with RepeatMasker extensions: this is available from SBo. -3. WUBlast/ABBlast (required by DupMasker): you should obtain this +3. HMMER3.1 & DFAM: this is available from SBo. +4. ABBlast/WUBlast (required by DupMasker): you should obtain this yourself, with the proper license, following the instructions here https://blast.advbiocomp.com/licensing/ -4. HMMER3.1 & DFAM: this is available from SBo. -**RMBlast (rmblastn) INSTALLATION PATH** +* RMBlast (rmblastn) INSTALLATION PATH /usr/bin -**HMMER INSTALLATION PATH** +* HMMER INSTALLATION PATH /usr/bin diff --git a/academic/RepeatMasker/RepeatMasker.SlackBuild b/academic/RepeatMasker/RepeatMasker.SlackBuild index 33c83c436d..5d15586aeb 100644 --- a/academic/RepeatMasker/RepeatMasker.SlackBuild +++ b/academic/RepeatMasker/RepeatMasker.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for RepeatMasker -# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,13 +25,12 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=RepeatMasker -VERSION=${VERSION:-4.1.2_p1} +VERSION=${VERSION:-4.1.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -SRCVER=4.1.2-p1 # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information @@ -52,7 +51,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM -tar xvf $CWD/$PRGNAM-$SRCVER.tar.gz +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM chown -R root:root . find -L . \ @@ -65,6 +64,8 @@ find -L . \ mkdir -p $PKG/opt/$PRGNAM cp -a * $PKG/opt/$PRGNAM +rm $PKG/opt/$PRGNAM/{bluegrad.jpg,HTMLAnnotHeader.html,INSTALL,LICENSE,README.md,ReleaseNotes} + # Make a symlink mkdir -p $PKG/usr/bin cd $PKG/usr/bin @@ -74,10 +75,9 @@ cd - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# Better just copy these and not move them from their original dir mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - bluegrad.jpg daterepeats.help HTMLAnnotHeader.html INSTALL LICENSE README.md repeatmasker.help ReleaseNotes \ + bluegrad.jpg daterepeats.help HTMLAnnotHeader.html LICENSE README.md repeatmasker.help ReleaseNotes \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/README.SLACKWARE > $PKG/usr/doc/$PRGNAM-$VERSION/README.SLACKWARE diff --git a/academic/RepeatMasker/RepeatMasker.info b/academic/RepeatMasker/RepeatMasker.info index e36cdaf964..3731dbe0f3 100644 --- a/academic/RepeatMasker/RepeatMasker.info +++ b/academic/RepeatMasker/RepeatMasker.info @@ -1,10 +1,10 @@ PRGNAM="RepeatMasker" -VERSION="4.1.2_p1" +VERSION="4.1.5" HOMEPAGE="http://www.repeatmasker.org/" -DOWNLOAD="http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz" -MD5SUM="fbab50d0c467a9beca316020efc20ee4" +DOWNLOAD="http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.5.tar.gz" +MD5SUM="cc9c7ea4303ef11c3d2ca56af5207609" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="perl-Text-Soundex trfind HMMER ncbi-rmblastn" +REQUIRES="python3-h5py perl-Text-Soundex trfind HMMER ncbi-rmblastn" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/STAR/README b/academic/STAR/README index 7d410d628f..ae22618ac8 100644 --- a/academic/STAR/README +++ b/academic/STAR/README @@ -2,9 +2,20 @@ STAR aligns short and long RNA-seq reads to a reference genome using uncompressed suffix arrays, resulting in fast, accurate mapping. STAR is capable of unbiased de novo detection of canonical splice junctions, can discover non-canonical splices and chimeric (fusion) -transcripts and can map full-length RNA sequences. Comes with -STARsolo for: mapping, demultiplexing and gene quantification for +transcripts and can map full-length RNA sequences. Comes with +STARsolo for: mapping, demultiplexing and gene quantification for single cell RNA-seq (See STARmanual). +The make command for building the program assumes that the cpu is +supporting AVX extensions, included in intel processors since Sandy +Bridge (2008) and in AMD cpus since Bulldozer (2011). See the +Slackbuild if other processors can be supported. Reference: https://www.ncbi.nlm.nih.gov/pubmed/23104886 + + +LIMITATIONS +This release was tested with the default parameters for human and +mouse genomes. Mammal genomes require at least 16GB of RAM, ideally +32GB. Please contact the author for a list of recommended parameters +for much larger or much smaller genomes. diff --git a/academic/STAR/STAR.SlackBuild b/academic/STAR/STAR.SlackBuild index f5abdc97dd..bc4913730e 100644 --- a/academic/STAR/STAR.SlackBuild +++ b/academic/STAR/STAR.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for STAR -# Copyright 2018-2021 Rob van Nues <sborg63@disroot.org> +# Copyright 2018-2023 Rob van Nues <sborg63@disroot.org> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,11 +25,20 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=STAR -VERSION=${VERSION:-2.7.9a} +VERSION=${VERSION:-2.7.11b} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +# This script is set for processors that support "Advanced Vector Extensions", +# (AVX), included since 2008 in Intel processors (Sandy Bridge) and since 2011 +# in AMD cpus (Bulldozer). AVX is an implementation of "Single Instruction +# stream-Multiple Data streams" (SIMD) to process vector type data. +# If no AVX (`cat /proc/cpuinfo | grep 'avx'`) is present, specify the +# available SIMD architecture (https://en.wikichip.org/wiki/x86/extensions), +# e.g. with "Streaming SIMD Extensions" use 'sse', and uncomment the next line. +#SIMD=${SIMD:-sse}; echo "Using ${SIMD} as SIMD" + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -38,9 +47,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -55,7 +61,7 @@ if [ "$ARCH" = "x86_64" ]; then LIBDIRSUFFIX="64" else echo "Sorry, this program does not run/compile on your architecture ($ARCH)" - exit 1 + exit 0 fi set -e @@ -83,9 +89,16 @@ find -L . \ # https://github.com/alexdobin/STAR/issues/447 #so let's forget about this for now +#For processors that do not support AVX extensions, specify the target SIMD architecture +#make STAR CXXFLAGS_SIMD=sse cd source - - make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" + if [ ! -z "${SIMD}" ]; then + echo "make with CXXFLAG_SIMD=${SIMD}" + make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" CXXFLAGS_SIMD="$SIMD" + else + echo "default make" + make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" + fi mkdir -p $PKG/usr/bin install -Dm755 $PRGNAM "$PKG/usr/bin/${PRGNAM}" @@ -104,6 +117,7 @@ cp -a \ source/parametersDefault doc/${PRGNAM}manual.pdf CHANGES.md LICENSE README.md RELEASEnotes.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +chmod 644 $PKG/usr/doc/$PRGNAM-$VERSION/parametersDefault mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/STAR/STAR.info b/academic/STAR/STAR.info index 4c3a22024f..6c9a4bff5e 100644 --- a/academic/STAR/STAR.info +++ b/academic/STAR/STAR.info @@ -1,10 +1,10 @@ PRGNAM="STAR" -VERSION="2.7.9a" +VERSION="2.7.11b" HOMEPAGE="https://github.com/alexdobin/STAR" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.7.9a/STAR-2.7.9a.tar.gz" -MD5SUM_x86_64="432c55d7ee7223c9099206a697bd9c30" +DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.7.11b/STAR-2.7.11b.tar.gz" +MD5SUM_x86_64="9e21d9930989b1be3ffc50b818489d55" REQUIRES="" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/SU2/README b/academic/SU2/README index fd4519ee57..b70ea47277 100644 --- a/academic/SU2/README +++ b/academic/SU2/README @@ -8,12 +8,26 @@ flow, elasticity, electrodynamics, chemically-reacting flows, and many others. Under active development by individuals all around the world on GitHub and is released under an open-source license. -Builds parallel version by default. -For serial version, delete the following configuration lines from -su2.Slackbuild script: +Optional dependencies: mpich or openmpi; OpenBLAS ---enable-mpi ---with-cxx=/usr/bin/mpicxx ---with-cc=/usr/bin/mpicc +Build options can be controlled by passing MESONOPTS to the SlackBuild +script. -and then no need for mpich / openmpi. +Builds parallel version by default if mpich or openmpi installed. If +mpich, use: + +MESONOPTS="-Dcustom-mpi=true -Dextra-deps=mpich" + +For OpenBlas, add "-Denable-openblas=true" + +See the docs for a complete list of options. + +Following installation, add these to your ~/.bashrc: + +export SU2_RUN=/usr/bin +export PATH=$PATH:$SU2_RUN +export PYTHONPATH=$PYTHONPATH:$SU2_RUN + +Warning: This SlackBuild requires network access when it runs, meaning +it downloads files from the Internet with root access. You should +decide for yourself whether or not you think this is a good idea. diff --git a/academic/SU2/SU2.SlackBuild b/academic/SU2/SU2.SlackBuild index ec10bbbfb3..60fe3cd784 100644 --- a/academic/SU2/SU2.SlackBuild +++ b/academic/SU2/SU2.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for SU2 # -# Copyright 2019 Judah Milgram, Washington DC USA +# Copyright 2019-2023 Judah Milgram, Washington DC USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,10 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - cd $(dirname $0) ; CWD=$(pwd) PRGNAM=SU2 -VERSION=${VERSION:-6.2.0} +VERSION=${VERSION:-7.5.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -39,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -80,33 +76,22 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -./bootstrap - -# For serial version, delete --enable-mpi, --with-cxx, and --with-cc +CXXFLAGS="-march=native -funroll-loops -O2" \ + ./meson.py build --prefix=/usr ${MESONOPTS} -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux \ - --enable-mpi \ - --with-cxx=/usr/bin/mpicxx \ - --with-cc=/usr/bin/mpicc +# This fix build on current +sed -i '/#pragma once/a #include <cstdint>' SU2_CFD/include/output/filewriter/CParaviewXMLFileWriter.hpp -make -make install-strip DESTDIR=$PKG +DESTDIR=$PKG ./ninja -C build install -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +find $PKG -print0 | xargs -0 file | \ + grep -e "executable" -e "shared object" | \ + grep ELF | cut -f 1 -d : | \ + xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ -COPYING INSTALL README.md \ +AUTHORS.md COPYING LICENSE.md README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/SU2/SU2.info b/academic/SU2/SU2.info index a7fb802ad1..6350ae105f 100644 --- a/academic/SU2/SU2.info +++ b/academic/SU2/SU2.info @@ -1,10 +1,10 @@ PRGNAM="SU2" -VERSION="6.2.0" +VERSION="7.5.1" HOMEPAGE="https://su2code.github.io/docs/home/" -DOWNLOAD="https://github.com/su2code/SU2/archive/v6.2.0/SU2-6.2.0.tar.gz" -MD5SUM="c74d1dbe52d6239c4f9c75cbd3102a90" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="mpich" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/su2code/SU2/archive/v7.5.1/SU2-7.5.1.tar.gz" +MD5SUM_x86_64="7a9696af3496079dd5df501620e477cb" +REQUIRES="" MAINTAINER="Judah Milgram" -EMAIL="milgram@cgpp.com" +EMAIL="milgram / cgpp / com" diff --git a/academic/SU2/slack-desc b/academic/SU2/slack-desc index 67f9c3b830..cbc26417e8 100644 --- a/academic/SU2/slack-desc +++ b/academic/SU2/slack-desc @@ -16,4 +16,4 @@ SU2: flow, elasticity, electrodynamics, chemically-reacting flows, and many SU2: others. Under active development by individuals all around the world SU2: on GitHub and is released under an open-source license. SU2: -SU2: Home page: https://su2code.github.io/docs/home/ +SU2: Home page: https://su2code.github.io diff --git a/academic/SeqMonk/SeqMonk.SlackBuild b/academic/SeqMonk/SeqMonk.SlackBuild index 10fa8efaef..b60bcfaf2e 100644 --- a/academic/SeqMonk/SeqMonk.SlackBuild +++ b/academic/SeqMonk/SeqMonk.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for SeqMonk -# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=SeqMonk -VERSION=${VERSION:-1.47.1} +VERSION=${VERSION:-1.48.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -93,15 +93,19 @@ sed -i 's:java -version:$RealBin/jre/bin/java -version:' seqmonk # Change icon path and category in the desktop file sed -i "s:/usr/local/SeqMonk/uk/ac/bbsrc/babraham/SeqMonk/Resources/monk.svg:$EXENAM:" $EXENAM.desktop sed -i "s:Categories=Application:Categories=Education:" $EXENAM.desktop +sed -i '/Encoding=UTF-8/d' $EXENAM.desktop mkdir -p $PKG/opt/$PRGNAM cp -a \ com edu Help jre net Scripts Templates uk *.jar seqmonk seqmonk_import \ $PKG/opt/$PRGNAM +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - INSTALL.txt LICENSE LICENSE.txt NOTICE_FOR_COMMONS_MATH_CODE.txt README.md README.txt RELEASE_NOTES.txt \ + LICENSE LICENSE.txt NOTICE_FOR_COMMONS_MATH_CODE.txt README.md README.txt RELEASE_NOTES.txt \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/SeqMonk/SeqMonk.info b/academic/SeqMonk/SeqMonk.info index af8b37178c..96c43dcda5 100644 --- a/academic/SeqMonk/SeqMonk.info +++ b/academic/SeqMonk/SeqMonk.info @@ -1,10 +1,10 @@ PRGNAM="SeqMonk" -VERSION="1.47.1" +VERSION="1.48.1" HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/seqmonk_v1.47.1_linux64.tar.gz" -MD5SUM_x86_64="e7c80b113e4c80d26e7eca468a636134" +DOWNLOAD_x86_64="https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/seqmonk_v1.48.1_linux64.tar.gz" +MD5SUM_x86_64="6f2e51bf589682e35fedfcf0fdb2667b" REQUIRES="R" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/SimEng/README b/academic/SimEng/README new file mode 100644 index 0000000000..acc2230a48 --- /dev/null +++ b/academic/SimEng/README @@ -0,0 +1,28 @@ + SimEng is a framework for building modern, cycle-accurate processor +simulators. Its goals are to be: + + - Fast, typically 4-5X faster than gem5 + - Easy to use and modify to model desired microarchitecture + configurations. New cores can be configured in just a few hours + - Scalable, from simple scalar microarchitectures up to the most + sophisticated, superscalar, out-of-order designs + - Capable of supporting a wide range of instruction set + architectures (ISAs), starting with Armv8 but eventually including + RISC-V, x86, POWER, etc. + - Accurate, aiming for simulated cycle times being within 5-10% of + real hardware + - Open source, with a permissive license to enable collaboration + across academia and industry + + SimEng places an emphasis on performance and ease of use, whilst +maintaining a clean, modern, simple and well-documented code base. +For example, the current out-of-order (OoO) model is implemented +in around 10,000 lines of simple C++, with another 9,000 lines or +so implementing the specifics of the Armv8 ISA, and around 13,000 +lines of code in the accompanying test suite. SimEng should be +simple to read and understand, making it ideal to modify to your +requirements and include it in your projects. + + + Invocation example: + # simeng /usr/share/SimEng-0.9.4/configs/a64fx.yaml diff --git a/academic/SimEng/SimEng.SlackBuild b/academic/SimEng/SimEng.SlackBuild new file mode 100644 index 0000000000..fc7a9d8832 --- /dev/null +++ b/academic/SimEng/SimEng.SlackBuild @@ -0,0 +1,142 @@ +#!/bin/bash + +# Slackware build script for SimEng + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=SimEng +VERSION=${VERSION:-0.9.4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +YAMLCPP_VERSION=yaml-cpp-0.7.0 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# fix library installation path +sed -i '55s#DESTINATION lib#&'${LIBDIRSUFFIX}'/'$PRGNAM'#' src/lib/CMakeLists.txt +sed -i '72s#lib#&'${LIBDIRSUFFIX}'/'$PRGNAM'#' CMakeLists.txt + + +mkdir -p build +cd build + +# unpack dependences +mkdir -p _deps/{capstone-lib,yaml-cpp}-src +tar xvf $CWD/capstone-Armv9.2-update.tar.gz -C _deps/capstone-lib-src --strip-components 1 +tar xvf $CWD/yaml-cpp-$YAMLCPP_VERSION.tar.gz -C _deps/yaml-cpp-src --strip-components 1 + + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_INSTALL_LIBDIR=lib${LIBDIRSUFFIX} \ + -DCMAKE_INSTALL_MANDIR=/usr/man \ + -DCMAKE_INSTALL_DOCDIR=/usr/doc/$PRGNAM-$VERSION \ + -DCMAKE_INSTALL_DATAROOTDIR=/usr \ + -DBUILD_SHARED_LIBS=ON \ + -DFETCHCONTENT_FULLY_DISCONNECTED=ON \ + $OPTS \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +# install libraries used by SimEng +cp -av build/_deps/yaml-cpp-build/libyaml-cpp.so* \ + build/_deps/capstone-lib-build/libcapstone.so* \ + $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM + +# install additional files +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a configs $PKG/usr/share/$PRGNAM-$VERSION + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + {CONTRIBUTORS,LICENSE,RELEASE-NOTES}.txt docs \ + LICENSE_{CAPSTONE,GTEST,LLVM,YAML-CPP}.txt \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/SimEng/SimEng.info b/academic/SimEng/SimEng.info new file mode 100644 index 0000000000..6b132fdca2 --- /dev/null +++ b/academic/SimEng/SimEng.info @@ -0,0 +1,14 @@ +PRGNAM="SimEng" +VERSION="0.9.4" +HOMEPAGE="https://uob-hpc.github.io/SimEng" +DOWNLOAD="https://github.com/UoB-HPC/SimEng/archive/0.9.4/SimEng-0.9.4.tar.gz \ + https://github.com/UoB-HPC/capstone/archive/Armv9.2-update/capstone-Armv9.2-update.tar.gz \ + https://github.com/jbeder/yaml-cpp/archive/yaml-cpp-0.7.0/yaml-cpp-yaml-cpp-0.7.0.tar.gz" +MD5SUM="2f249f7b38cc716cb13f1a5b41555b92 \ + c837da9aad754299d9ee62007f428e76 \ + 74d646a3cc1b5d519829441db96744f0" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/SimEng/slack-desc b/academic/SimEng/slack-desc new file mode 100644 index 0000000000..0c74a32504 --- /dev/null +++ b/academic/SimEng/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +SimEng: SimEng (framework for cycle-accurate processor simulator) +SimEng: +SimEng: The Simulation Engine (SimEng) is a framework for building modern +SimEng: cycle-accurate processor simulators. It aims to be: +SimEng: - Fast +SimEng: - Easy to use and modify to desired configurations +SimEng: - Scalable, supporting simulation of simple scalar cores, up to +SimEng: superscalar out-of-order designs +SimEng: - Capable of supporting a wide range of ISAs. +SimEng: - Open source, with a permissive license to enable collaboration +SimEng: across academia and industry diff --git a/academic/TreeGraph/TreeGraph.info b/academic/TreeGraph/TreeGraph.info index f1b09a32c3..9adcb3a231 100644 --- a/academic/TreeGraph/TreeGraph.info +++ b/academic/TreeGraph/TreeGraph.info @@ -5,6 +5,6 @@ DOWNLOAD="http://treegraph.bioinfweb.info/Download/Complete/TreeGraph_2.15.0-887 MD5SUM="4ca90fbb7cb7aae9a37d99ac742bd22f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README index a82c7160b2..4807f340a8 100644 --- a/academic/ViennaRNA/README +++ b/academic/ViennaRNA/README @@ -3,6 +3,15 @@ A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. +A recent addition, RNAxplorer, requires lapacke (which requires +lapack that depends on a version of blas). During configuration the +step for RNAxplorer stalls (on missing lapack) because it does not +find the version of blas that has been used for compiling lapack +(see https://github.com/ViennaRNA/ViennaRNA/issues/206). +An extra variable ($BLAS) in the SlackBuild sets openblas as the +version of blas used for lapack(e). Please, adjust $BLAS to the blas +used on your system. + A tutorial (see /usr/doc/$PRGNAM-$VERSION/RNA-tutorial-$VERSION.pdf) and examples can be found in /usr/share/$PRGNAM/tutorial and /usr/share/$PRGNAM/examples @@ -27,28 +36,13 @@ Amongst other things, the ViennRNA implementations allow you to: alignment - predict melting curves - search for sequences folding into a given structure -- compare two secondary structures +- compare two secondary structures - predict hybridization structures of two RNA molecules -The package includes `Perl 5` and `Python 3` modules that give access +The package includes `Perl` and `Python 3` modules that give access to almost all functions of the C library from within the respective -scripting languages. For this reason, python3 is a dependency - -The `Python 2` module can be built as well, or instead of the one -for `Python 3`; just edit the SlackBuild or run it by setting build -options PYTHON=yes PYTHON3=no. (e.g. in sbopkg or run it from -the commandline -within the directory containing the SlackBuild -script and downloaded source archive- as: `PYTHON=yes PYTHON3=no -./ViennaRNA.SlackBuild`) - -There is also a set of programs for analyzing sequence and distance -data using split decomposition, statistical geometry, and cluster -methods. They are not maintained any more and not built by default. - -The code very rarely uses static arrays, and all programs should work -for sequences up to a length of 32,700 (if you have huge amounts of -memory that is). +scripting languages. -For further info see: +For further/most recent info see: https://www.tbi.univie.ac.at/RNA/documentation.html diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild index 68465ebbaa..42ae76bbd7 100644 --- a/academic/ViennaRNA/ViennaRNA.SlackBuild +++ b/academic/ViennaRNA/ViennaRNA.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for ViennaRNA -# Copyright 2018-2021 Rob van Nues +# Copyright 2018-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,11 +25,17 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ViennaRNA -VERSION=${VERSION:-2.5.0} +VERSION=${VERSION:-2.6.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +# RNAxplorer requires lapacke (which requires lapack that requires blas) +# but cannot see what blas is used for compiling lapack +# please adjust $BLAS to the blas installed on your system +BLAS=${BLAS:-openblas} + + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -38,9 +44,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -92,8 +95,7 @@ find -L . \ # - RNAlocmin # - Swig (all scripting interfaces) # - Perl interface -# - Python interface -# - Python 3 interface +# - Python 3 interface (= Python interface) # - Streaming SIMD Extension support # in the case of run time/ make/ or configure problems try turning off: # - Link Time Optimization (LTO) @@ -104,12 +106,12 @@ find -L . \ # for Z-score filtering via statically linked libsvm: # - SVM Z-score filter in RNALfold # - GNU Scientific Library for RNApvmin - +# everything is enabled here cluster="" ; [ "${CLUSTER:-yes}" != "no" ] && cluster="--with-cluster" kinwalker="" ; [ "${KINWALKER:-yes}" != "no" ] && kinwalker="--with-kinwalker" # Default enabled features: forester="" ; [ "${FORESTER:-yes}" != "no" ] && forester="--with-forester" -kinfold="" ; [ "${KINFOLD:-yes}" != "no" ] && kinwalk="--with-kinfold" +kinfold="" ; [ "${KINFOLD:-yes}" != "no" ] && kinfold="--with-kinfold" rnalocmin="" ; [ "${RNALOCMIN:-yes}" != "no" ] && rnalocmin="--with-rnalocmin" perl="" ; [ "${PERL:-yes}" != "no" ] && perl="--with-perl" # python = python3 @@ -131,14 +133,12 @@ CXXFLAGS="$SLKCFLAGS" \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux \ + --with-blas=$BLAS \ --with-python2=no \ --with-doc=no \ $cluster \ $kinwalker \ $forester \ - $cluster \ - $kinwalker \ - $forester \ $kinfold \ $rnalocmin \ $perl \ @@ -170,11 +170,13 @@ for perlscript in $PKG/usr/share/ViennaRNA/bin/*.pl ; do done rm -r $PKG/usr/share/ViennaRNA/bin -# no need for that file it is outdated anyway +# re-organise info files the Slackware/SBo way +mkdir $PKG/usr/info/ rm $PKG/usr/share/info/dir - -#gzip info file -gzip -9 $PKG/usr/share/info/*.info +#gzip and move info file +gzip -9 $PKG/usr/share/info/*.info* +mv $PKG/usr/share/info/*.info* $PKG/usr/info/ +rmdir $PKG/usr/share/info find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done @@ -196,12 +198,16 @@ if [[ -e $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf ]]; then fi cp -a \ - NEWS README.md AUTHORS COPYING THANKS INSTALL CHANGELOG.md license.txt \ + NEWS README.md AUTHORS COPYING THANKS CHANGELOG.md license.txt \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/douninst.sh > $PKG/install/douninst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ViennaRNA/ViennaRNA.info b/academic/ViennaRNA/ViennaRNA.info index f4a91c9d7e..b871a31ccc 100644 --- a/academic/ViennaRNA/ViennaRNA.info +++ b/academic/ViennaRNA/ViennaRNA.info @@ -1,10 +1,10 @@ PRGNAM="ViennaRNA" -VERSION="2.5.0" +VERSION="2.6.4" HOMEPAGE="https://www.tbi.univie.ac.at/RNA" -DOWNLOAD="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_5_x/ViennaRNA-2.5.0.tar.gz" -MD5SUM="48be55f33d08d01b4778ab78eec51a69" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/ViennaRNA-2.6.4.tar.gz" +MD5SUM_x86_64="6d8fd8ffe44d70399bff220f709a2b55" +REQUIRES="lapacke" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/ViennaRNA/doinst.sh b/academic/ViennaRNA/doinst.sh new file mode 100644 index 0000000000..fe39c0a9d2 --- /dev/null +++ b/academic/ViennaRNA/doinst.sh @@ -0,0 +1,4 @@ +if [ -x /usr/bin/install-info ]; then + /usr/bin/install-info --info-dir=usr/info usr/info/RNAlib.info.gz 1> /dev/null 2>&1 +fi + diff --git a/academic/ViennaRNA/douninst.sh b/academic/ViennaRNA/douninst.sh new file mode 100644 index 0000000000..1bef502028 --- /dev/null +++ b/academic/ViennaRNA/douninst.sh @@ -0,0 +1,6 @@ +if [ -x /usr/bin/install-info -a -d usr/info ]; then + ( cd usr/info + rm -f dir + for i in *.info*; do /usr/bin/install-info $i dir 2>/dev/null; done + ) +fi diff --git a/academic/WolframEngine/README b/academic/WolframEngine/README new file mode 100644 index 0000000000..d3830009fb --- /dev/null +++ b/academic/WolframEngine/README @@ -0,0 +1,10 @@ +The free Wolfram Engine implements the Wolfram Language with interfaces +suitable for use in software projects. The Wolfram Engine is the heart +of Wolfram products such as Mathematica, Wolfram|One and Wolfram|Alpha. +It is licensed for non-production use. + +The Wolfram Engine and Mathematica are the same core engine, but with a +different interface and different licensing. + +The Wolfram Engine contains a program WolframScript for running the +Wolfram Engine from a command line or script. diff --git a/academic/WolframEngine/WolframEngine.SlackBuild b/academic/WolframEngine/WolframEngine.SlackBuild new file mode 100644 index 0000000000..36198ffaa4 --- /dev/null +++ b/academic/WolframEngine/WolframEngine.SlackBuild @@ -0,0 +1,136 @@ +#!/bin/bash + +# Slackware build script for WolframEngine + +# Copyright 2023-2024, Alexander Verbovetsky, Moscow, Russia +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=WolframEngine +VERSION=${VERSION:-14.0.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + ARCH="$( uname -m )" +fi + +if [ "$ARCH" != "x86_64" ]; then + echo "Only x86_64 is supported." + exit 1 +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION + +SCRIPT=$(find -L $CWD -maxdepth 1 -type f -exec grep -al \ +"label=\"Wolfram Engine ${VERSION} for LINUX Installer Archive\"" {} \;) +eval $(grep -a "^filesizes=" -m 1 $SCRIPT) +eval $(grep -a "^MD5=" $SCRIPT) +ssize=$(grep -a offset -m 1 $SCRIPT | sed 's/^.* \([0-9]\+\) .*$/\1/') +((ssize++)) +tail +$ssize $SCRIPT | head -c $filesizes | tee >(tar x) \ + | md5sum | grep $MD5 > /dev/null +MDIR="/opt/$PRGNAM" +mkdir -p $PKG$MDIR +find -L Unix/Files -maxdepth 2 -type f -name "contents.tar.?z" \ + -exec tar xvf '{}' -C $PKG$MDIR \; + +chown -R root:root $PKG$MDIR +find -L $PKG$MDIR \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p $PKG/usr/bin +for i in $(find -L $PKG$MDIR/Executables \ + -maxdepth 1 -type f -printf "%f\n"); do + ln -s $MDIR/Executables/${i} $PKG/usr/bin +done +ln -s $MDIR/SystemFiles/Kernel/Binaries/Linux-x86-64/wolframscript \ + $PKG/usr/bin + +mkdir -p $PKG/usr/share/mime/application +cp -a $PKG$MDIR/SystemFiles/Installation/*.xml \ + $PKG/usr/share/mime/application + +mkdir -p $PKG/usr/share/icons/hicolor/{32x32,64x64,128x128}/{apps,mimetypes} +for i in 32 64 128; do +cp -a $PKG$MDIR/SystemFiles/FrontEnd/SystemResources/X/App-$i.png \ + $PKG/usr/share/icons/hicolor/${i}x${i}/apps/wolfram-wolframlanguage.png +for m in $(basename -a \ + $(ls $PKG$MDIR/SystemFiles/FrontEnd/SystemResources/X/vnd.wolfram.*${i}.png) \ + | cut -d- -f1); do +cp -a $PKG$MDIR/SystemFiles/FrontEnd/SystemResources/X/${m}-${i}.png \ + $PKG/usr/share/icons/hicolor/${i}x${i}/mimetypes/application-${m}.png +done +done + +find -L $PKG/opt/WolframEngine/SystemFiles -type f \ + \( -name "*.so" -o -name '*.so.*' \) -exec chmod 755 {} \; + +mkdir -p $PKG/usr/man/man1 +for i in $(find -L $PKG$MDIR/SystemFiles/SystemDocumentation/Unix \ + -maxdepth 1 -type f -name "*.1" -printf "%f\n"); do +gzip -9 -c $PKG$MDIR/SystemFiles/SystemDocumentation/Unix/${i} \ + > $PKG/usr/man/man1/${i}.gz +done + +INFO=$(find -L Unix/Files -maxdepth 2 -type f -name "info" -exec cat '{}' \+ \ + | sort -u) +CreationID=$(echo "$INFO" | grep "^CreationID" | awk '{print $2}') +VersionNumber=$(echo "$INFO" | grep "^VersionNumber" | awk '{print $2}') +ReleaseNumber=$(echo "$INFO" | grep "^ReleaseNumber" | awk '{print $2}') +MinorReleaseNumber=$(echo "$INFO" | grep "^MinorReleaseNumber" \ + | awk '{print $2}') +FullVersionNumber="${VersionNumber}.${ReleaseNumber}.${MinorReleaseNumber}" + +echo "${CreationID}" > $PKG$MDIR/.CreationID +echo "FullVersionNumber: ${FullVersionNumber}" > $PKG$MDIR/.Revision +echo "CreationID: ${CreationID}" >> $PKG$MDIR/.Revision +echo "${FullVersionNumber}" > $PKG$MDIR/.VersionID + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/WolframEngine/WolframEngine.info b/academic/WolframEngine/WolframEngine.info new file mode 100644 index 0000000000..53c9e9da08 --- /dev/null +++ b/academic/WolframEngine/WolframEngine.info @@ -0,0 +1,10 @@ +PRGNAM="WolframEngine" +VERSION="14.0.0" +HOMEPAGE="https://www.wolfram.com/engine/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://account.wolfram.com/dl/WolframEngine?platform=Linux&version=14.0" +MD5SUM_x86_64="42c9f852a1f6505429e5941e6c699d23" +REQUIRES="" +MAINTAINER="Alexander Verbovetsky" +EMAIL="alik@ejik.org" diff --git a/academic/WolframEngine/doinst.sh b/academic/WolframEngine/doinst.sh new file mode 100644 index 0000000000..1b37a9827f --- /dev/null +++ b/academic/WolframEngine/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/WolframEngine/slack-desc b/academic/WolframEngine/slack-desc new file mode 100644 index 0000000000..f064200dd5 --- /dev/null +++ b/academic/WolframEngine/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +WolframEngine: WolframEngine (Wolfram Language Engine) +WolframEngine: +WolframEngine: The free Wolfram Engine implements the Wolfram Language with +WolframEngine: interfaces suitable for use in software projects. The Wolfram Engine +WolframEngine: is the heart of Wolfram products such as Mathematica, Wolfram|One +WolframEngine: and Wolfram|Alpha. It is licensed for non-production use. +WolframEngine: +WolframEngine: The Wolfram Engine contains a program WolframScript for running the +WolframEngine: Wolfram Engine from a command line or script. +WolframEngine: +WolframEngine: Homepage: https://www.wolfram.com/engine/ diff --git a/academic/WordNet/WordNet.SlackBuild b/academic/WordNet/WordNet.SlackBuild index a33e6cff3d..049ef6008c 100644 --- a/academic/WordNet/WordNet.SlackBuild +++ b/academic/WordNet/WordNet.SlackBuild @@ -15,7 +15,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -33,8 +33,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/Xyce/README b/academic/Xyce/README deleted file mode 100644 index 14d894e3e0..0000000000 --- a/academic/Xyce/README +++ /dev/null @@ -1,43 +0,0 @@ -Xyce is an open source, SPICE-compatible, high-performance analog -circuit simulator, capable of solving extremely large circuit -problems by supporting large-scale parallel computing platforms. It -also supports serial execution on all common desktop platforms, and -small-scale parallel runs on Unix-like systems. In addition to analog -electronic simulation, Xyce has also been used to investigate more -general network systems, such as neural networks and power grids. - -The Xyce Parallel Electronic Simulator is a SPICE-compatible circuit -simulator, developed internally at Sandia National Laboratories -and funded by the National Nuclear Security Administration's -Advanced Simulation and Computing (ASC) Campaign. In continuous -development since 1999, Xyce is designed to run on large-scale -parallel computing platforms, though it also executes efficiently on a -variety of architectures, including single processor workstations. As -a mature platform for large-scale parallel circuit simulation, Xyce -supports standard capabilities available from commercial simulators, -in addition to a variety of devices and models specific to Sandia's -needs. - -The package is intalled at: /opt/Xyce -Remember to set the library and path: - -PATH=$PATH:/opt/Xyce/bin - -For 32-bit: -LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/Xyce/lib - -For 64-bit: -LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/Xyce/lib64 - -To run the suite test: -# cd /opt/Xyce/Xyce_Regression-6.3/TestScripts -# ./run_xyce_regression - -For parallel simulation trilinos must be compiled with MPI. - -Additonal requirements: - - MPI (openmpi/mpich) - - parMETIS - -NOTE: Sources are not downloadable via wget. Please download manually -via browser. diff --git a/academic/Xyce/Xyce.info b/academic/Xyce/Xyce.info deleted file mode 100644 index 79667ceed8..0000000000 --- a/academic/Xyce/Xyce.info +++ /dev/null @@ -1,14 +0,0 @@ -PRGNAM="Xyce" -VERSION="6.5" -HOMEPAGE="https://xyce.sandia.gov/index.html" -DOWNLOAD="https://xyce.sandia.gov/downloads/_assets/documents/Xyce-6.5.tar.gz \ - https://xyce.sandia.gov/downloads/_assets/documents/Xyce_Docs-6.5.tar.gz \ - https://xyce.sandia.gov/downloads/_assets/documents/Xyce_Regression-6.5.tar.gz" -MD5SUM="916c70f4c387b14197d85178c5791ad5 \ - 5bd0f1696e7d6ad9a60cd4868e84fe37 \ - 1346f1fe6b273b8954df43ac0945b329" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="trilinos" -MAINTAINER="William PC" -EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/Xyce/slack-desc b/academic/Xyce/slack-desc deleted file mode 100644 index 56b4252044..0000000000 --- a/academic/Xyce/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -Xyce: Xyce (Xyce Parallel Electronic Simulator) -Xyce: -Xyce: The Xyce Parallel Electronic Simulator is a SPICE-compatible circuit -Xyce: simulator, developed internally at Sandia National Laboratories and -Xyce: funded by the National Nuclear Security Administration's Advanced -Xyce: Simulation and Computing (ASC) Campaign. In continuous development -Xyce: since 1999, Xyce is designed to run on large-scale parallel computing -Xyce: platforms, though it also executes efficiently on a variety of xyce: -Xyce: architectures, including single processor workstations. -Xyce: -Xyce: diff --git a/academic/abella/README b/academic/abella/README deleted file mode 100644 index 7954d1e751..0000000000 --- a/academic/abella/README +++ /dev/null @@ -1,33 +0,0 @@ -Abella is an interactive theorem prover based on lambda-tree syntax. - -This means that Abella is well-suited for reasoning about the -meta-theory of programming languages and other logical systems -which manipulate objects with binding. For example, the following -applications are included in the distribution of Abella. - -* Various results on the lambda calculus involving big-step - evaluation, small-step evaluation, and typing judgments -* Cut-admissibility for a sequent calculus -* Part 1a and Part 2a of the POPLmark challenge -* Takahashi's proof of the Church-Rosser theorem -* Tait's logical relations argument for weak normalization of the - simply-typed lambda calculus -* Girard's proof of strong normalization of the simply-typed lambda - calculus -* Some ?-calculus meta-theory -* Relation between ?-reduction and paths in A-calculus - -For Full List: -http://abella-prover.org/examples/index.html - -Abella uses a two-level logic approach to reasoning. Specifications -are made in the logic of second-order hereditary Harrop formulas using -lambda-tree syntax. This logic is executable and is a subset of the -AProlog language (see the Teyjus system for an implementation of this -language). - -The reasoning logic of Abella is the culmination of a series -of extensions to proof theory for the treatment of definitions, -lambda-tree syntax, and generic judgments. The reasoning logic of -Abella is able to encode the semantics of our specification logic as a -definition and thereby reason over specifications in that logic. diff --git a/academic/abella/abella.info b/academic/abella/abella.info deleted file mode 100644 index 88abb3f04c..0000000000 --- a/academic/abella/abella.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="abella" -VERSION="2.0.6" -HOMEPAGE="http://abella-prover.org/" -DOWNLOAD="http://abella-prover.org/distributions/abella-2.0.6.tar.gz" -MD5SUM="077cb3fbbdf35159e4b8860faf431c6a" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="ocamlbuild ocaml-findlib" -MAINTAINER="Jefferson Rocha" -EMAIL="root@slackjeff.com.br" diff --git a/academic/abella/slack-desc b/academic/abella/slack-desc deleted file mode 100644 index 15174390e7..0000000000 --- a/academic/abella/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. Line -# up the first '|' above the ':' following the base package name, and the '|' on -# the right side marks the last column you can put a character in. You must make -# exactly 11 lines for the formatting to be correct. It's also customary to -# leave one space after the ':'. - - |-----handy-ruler------------------------------------------------------| -abella: abella (interactive theorem prover based on lambda-tree syntax) -abella: -abella: Abella is an interactive theorem prover based on lambda-tree syntax. -abella: This means that Abella is well-suited for reasoning about the meta -abella: theory of programming languages and other logical systems which -abella: manipulate objects with binding. -abella: For example, the following applications are included in the -abella: distribution of Abella. -abella: -abella: http://abella-prover.org/ -abella: diff --git a/academic/abntex/abntex.SlackBuild b/academic/abntex/abntex.SlackBuild index ec4940e05f..6728604dc1 100644 --- a/academic/abntex/abntex.SlackBuild +++ b/academic/abntex/abntex.SlackBuild @@ -27,15 +27,12 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=abntex -VERSION=${VERSION:-0.9_beta2} +VERSION=${VERSION:-20200715_f0a4d3c} ARCH=noarch BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -MAJOR=$(echo $VERSION | cut -d _ -f 1) -MINOR=$(echo $VERSION | cut -d _ -f 2) - # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information # could be useful to other scripts. @@ -48,17 +45,14 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -FORCE_LYX=${FORCE_LYX:-NO} -LYX_PATH=${LYX_PATH:-/usr/share/lyx} - set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$MAJOR -tar xvf $CWD/$PRGNAM-$MAJOR-$MINOR.tar.gz -cd $PRGNAM-$MAJOR +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.?z +cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ @@ -66,23 +60,15 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; -patch < $CWD/Makefile.diff - -find texmf/ lyx/ -type f -exec chmod 644 {} \; - -echo quit | make doc -make install DESTDIR=$PKG - -# Lyx may not have been installed -if [ "$FORCE_LYX" != "NO" ]; then - mkdir -p $PKG/usr/share/lyx - cp -rf lyx/layouts/ $PKG/$LYX_PATH -fi - +find . -name ".gitignore" -exec rm {} \; +make install PREFIX=/usr DESTDIR=$PKG +sh build.sh +cd target +for i in *.zip ; do unzip $i ; done +rm *.zip *.tar.gz mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - LEIAME LEIAME.administracao LEIAME.linux compiled.docs/* lyx/ \ - $PKG/usr/doc/$PRGNAM-$VERSION +find . -name "*.pdf" -exec cp -a {} $PKG/usr/doc/$PRGNAM-$VERSION/ \; +cp ../*.md ../LICENSE $PKG/usr/doc/$PRGNAM-$VERSION find $PKG/usr/doc/$PRGNAM-$VERSION -type f -exec chmod 644 {} \; cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/abntex/abntex.info b/academic/abntex/abntex.info index 9ced2dab26..a57b0537a5 100644 --- a/academic/abntex/abntex.info +++ b/academic/abntex/abntex.info @@ -1,8 +1,8 @@ PRGNAM="abntex" -VERSION="0.9_beta2" +VERSION="20200715_f0a4d3c" HOMEPAGE="http://www.abntex.net.br/" -DOWNLOAD="http://downloads.sourceforge.net/abntex/abntex-0.9-beta2.tar.gz" -MD5SUM="4c5bc2d5388ddf03df754072116ab1f8" +DOWNLOAD="https://ponce.cc/slackware/sources/repo/abntex-20200715_f0a4d3c.tar.xz" +MD5SUM="f2cc9267ae71b14f9d9780fa824e8878" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/acl2/README b/academic/acl2/README new file mode 100644 index 0000000000..ac87fba1ef --- /dev/null +++ b/academic/acl2/README @@ -0,0 +1,7 @@ +ACL2 is a logic and programming language in which you can model +computer systems, together with a tool to help you prove properties of +those models. "ACL2" denotes "A Computational Logic for Applicative +Common Lisp". ACL2 is part of the Boyer-Moore family of provers, for +which its authors have received the 2005 ACM Software System Award + +There is some support for Emacs >24 in /opt/acl2/books/emacs/ diff --git a/academic/acl2/acl2 b/academic/acl2/acl2 new file mode 100755 index 0000000000..65892c9f9e --- /dev/null +++ b/academic/acl2/acl2 @@ -0,0 +1,4 @@ +#!/bin/sh + +export ACL2_SYSTEM_BOOKS=/opt/acl2/books/ +/opt/acl2/saved_acl2 $@ diff --git a/academic/acl2/acl2.SlackBuild b/academic/acl2/acl2.SlackBuild new file mode 100644 index 0000000000..027caca8ba --- /dev/null +++ b/academic/acl2/acl2.SlackBuild @@ -0,0 +1,98 @@ +#!/bin/bash + +# Slackware build script for acl2 + +# Copyright 2023, Lockywolf +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=acl2 +VERSION=${VERSION:-8.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} + -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + + +export SBCL_HOME=/usr/lib${LIBDIRSUFFIX}/sbcl +gmake LISP='sbcl --no-sysinit --no-userinit --disable-debugger' +install -Dm755 $CWD/acl2 $PKG/usr/bin/acl2 +install -d -m755 $PKG/opt/acl2 +cp -r . $PKG/opt/acl2/ + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE doc workshops.html \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/acl2/acl2.info b/academic/acl2/acl2.info new file mode 100644 index 0000000000..bda4fa3394 --- /dev/null +++ b/academic/acl2/acl2.info @@ -0,0 +1,10 @@ +PRGNAM="acl2" +VERSION="8.5" +HOMEPAGE="https://www.cs.utexas.edu/users/moore/acl2/v8-5/" +DOWNLOAD="https://github.com/acl2-devel/acl2-devel/releases/download/8.5/acl2-8.5.tar.gz" +MD5SUM="ec2c62dbdffdc345252bc5a68ad830fc" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="sbcl" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.acl2_2023-07-16@lockywolf.net" diff --git a/academic/acl2/slack-desc b/academic/acl2/slack-desc new file mode 100644 index 0000000000..1d7f0f6b1b --- /dev/null +++ b/academic/acl2/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +acl2: acl2 (Computational Logic for Applicative Common Lisp) +acl2: +acl2: ACL2 is a logic and programming language in which you can model +acl2: computer systems, together with a tool to help you prove properties +acl2: of those models. "ACL2" denotes "A Computational Logic for +acl2: Applicative Common Lisp". ACL2 is part of the Boyer-Moore family of +acl2: provers, for which its authors have received the 2005 ACM Software +acl2: System Award +acl2: +acl2: +acl2: diff --git a/academic/aeskulap/README b/academic/aeskulap/README new file mode 100644 index 0000000000..5e074de1a0 --- /dev/null +++ b/academic/aeskulap/README @@ -0,0 +1,8 @@ +aeskulap (medical image viewer) + +aeskulap is able to load a series of special images stored in the DICOM +format for review. Additionally Aeskulap is able to query and fetch +DICOM images from archive nodes (also called PACS) over the network. +The goal of this project is to create a full open source replacement +for commercially available DICOM viewers. + diff --git a/academic/aeskulap/aeskulap.SlackBuild b/academic/aeskulap/aeskulap.SlackBuild new file mode 100644 index 0000000000..a9088f66c1 --- /dev/null +++ b/academic/aeskulap/aeskulap.SlackBuild @@ -0,0 +1,122 @@ +#!/bin/bash + +# Slackware build script for aeskulap + +# Copyright 2011 Federico Lupi, flupi@mclink.it, http://www.mclink.it/personal/MG2508 +# Modified by Matt Dinslage (daedra1980@gmail.com) +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=aeskulap +VERSION=${VERSION:-0.2.2_e710562d} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +patch -p1 < $CWD/newDicomElement.patch + +# point to the correct lib version depending on the arch +sed -i 's/lib -ldcmjpeg/%{_lib} -ldcmjpeg/' configure.ac +libtoolize --force --copy --install +autoreconf --force --install +intltoolize --force --copy --automake + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --disable-static \ + --with-gsettings \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + ABOUT-NLS COPYING NEWS COPYING.DOC COPYING.LIB ChangeLog INSTALL README \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/aeskulap/aeskulap.info b/academic/aeskulap/aeskulap.info new file mode 100644 index 0000000000..4078803b08 --- /dev/null +++ b/academic/aeskulap/aeskulap.info @@ -0,0 +1,10 @@ +PRGNAM="aeskulap" +VERSION="0.2.2_e710562d" +HOMEPAGE="https://gitlab.com/stefanhusmann/aeskulap" +DOWNLOAD="https://www.dropbox.com/s/84xpkwtgj0r2bd8/aeskulap-0.2.2_e710562d.tar.gz" +MD5SUM="6be6239b2bec4744db7e3b203e29d77f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="dcmtk" +MAINTAINER="M.Dinslage" +EMAIL="daedra1980@gmail.com" diff --git a/academic/aeskulap/doinst.sh b/academic/aeskulap/doinst.sh new file mode 100644 index 0000000000..09b892d002 --- /dev/null +++ b/academic/aeskulap/doinst.sh @@ -0,0 +1,15 @@ +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi + +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/glib-2.0/schemas ]; then + if [ -x /usr/bin/glib-compile-schemas ]; then + /usr/bin/glib-compile-schemas usr/share/glib-2.0/schemas >/dev/null 2>&1 + fi +fi diff --git a/academic/aeskulap/newDicomElement.patch b/academic/aeskulap/newDicomElement.patch new file mode 100644 index 0000000000..4ffc76015b --- /dev/null +++ b/academic/aeskulap/newDicomElement.patch @@ -0,0 +1,269 @@ +Author: Gert Wollny <gewo@debian.org> +Description: correct code for newDicomElement now being a member of DcmItem +Bug: https://bugs.debian.org/865591 + +--- a/imagepool/netloader.cpp ++++ b/imagepool/netloader.cpp +@@ -102,29 +102,29 @@ bool NetLoader::run() { + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("STUDY"); + query.insert(e); + +- e = newDicomElement(DCM_PatientName); ++ e = DcmItem::newDicomElement(DCM_PatientName); + query.insert(e); + +- e = newDicomElement(DCM_PatientID); ++ e = DcmItem::newDicomElement(DCM_PatientID); + query.insert(e); + +- e = newDicomElement(DCM_StudyDate); ++ e = DcmItem::newDicomElement(DCM_StudyDate); + query.insert(e); + +- e = newDicomElement(DCM_StudyTime); ++ e = DcmItem::newDicomElement(DCM_StudyTime); + query.insert(e); + +- e = newDicomElement(DCM_AccessionNumber); ++ e = DcmItem::newDicomElement(DCM_AccessionNumber); + query.insert(e); + +- e = newDicomElement(DCM_StudyID); ++ e = DcmItem::newDicomElement(DCM_StudyID); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + e->putString(studyinstanceuid.c_str()); + query.insert(e); + +@@ -150,22 +150,22 @@ bool NetLoader::run() { + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("SERIES"); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + e->putString(studyinstanceuid.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SeriesInstanceUID); ++ e = DcmItem::newDicomElement(DCM_SeriesInstanceUID); + e->putString(i->c_str()); + query.insert(e); + +- e = newDicomElement(DCM_Modality); ++ e = DcmItem::newDicomElement(DCM_Modality); + query.insert(e); + +- e = newDicomElement(DCM_SeriesNumber); ++ e = DcmItem::newDicomElement(DCM_SeriesNumber); + query.insert(e); + + std::cout << "C-Move request:" << std::endl; +--- a/imagepool/netquery.cpp ++++ b/imagepool/netquery.cpp +@@ -196,64 +196,64 @@ void query_from_net( + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("STUDY"); + query.insert(e); + +- e = newDicomElement(DCM_SpecificCharacterSet); ++ e = DcmItem::newDicomElement(DCM_SpecificCharacterSet); + e->putString(dicom_enc.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_PatientName); ++ e = DcmItem::newDicomElement(DCM_PatientName); + e->putString(patientsname.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_PatientID); ++ e = DcmItem::newDicomElement(DCM_PatientID); + e->putString(convert_string_to(patientid.c_str(), system_enc).c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SOPClassesInStudy); ++ e = DcmItem::newDicomElement(DCM_SOPClassesInStudy); + query.insert(e); + +- e = newDicomElement(DCM_ModalitiesInStudy); ++ e = DcmItem::newDicomElement(DCM_ModalitiesInStudy); + e->putString(modality.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_PatientBirthDate); ++ e = DcmItem::newDicomElement(DCM_PatientBirthDate); + query.insert(e); + +- e = newDicomElement(DCM_PatientSex); ++ e = DcmItem::newDicomElement(DCM_PatientSex); + query.insert(e); + +- e = newDicomElement(DCM_StudyDate); ++ e = DcmItem::newDicomElement(DCM_StudyDate); + e->putString(date.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_StudyTime); ++ e = DcmItem::newDicomElement(DCM_StudyTime); + query.insert(e); + +- e = newDicomElement(DCM_NumberOfStudyRelatedSeries); ++ e = DcmItem::newDicomElement(DCM_NumberOfStudyRelatedSeries); + query.insert(e); + +- e = newDicomElement(DCM_NumberOfStudyRelatedInstances); ++ e = DcmItem::newDicomElement(DCM_NumberOfStudyRelatedInstances); + query.insert(e); + +- e = newDicomElement(DCM_AccessionNumber); ++ e = DcmItem::newDicomElement(DCM_AccessionNumber); + e->putString(accessionnumber.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_StudyID); ++ e = DcmItem::newDicomElement(DCM_StudyID); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + query.insert(e); + +- e = newDicomElement(DCM_StudyDescription); ++ e = DcmItem::newDicomElement(DCM_StudyDescription); + e->putString(description.c_str()); + query.insert(e); + + // StationName not allowed in StudyRoot +- /*e = newDicomElement(DCM_StationName); ++ /*e = DcmItem::newDicomElement(DCM_StationName); + e->putString(station.c_str()); + query.insert(e);*/ + +@@ -284,36 +284,36 @@ void query_series_from_net(const std::st + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("SERIES"); + query.insert(e); + +- e = newDicomElement(DCM_SpecificCharacterSet); ++ e = DcmItem::newDicomElement(DCM_SpecificCharacterSet); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + e->putString(studyinstanceuid.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SeriesInstanceUID); ++ e = DcmItem::newDicomElement(DCM_SeriesInstanceUID); + query.insert(e); + +- e = newDicomElement(DCM_SeriesNumber); ++ e = DcmItem::newDicomElement(DCM_SeriesNumber); + query.insert(e); + +- e = newDicomElement(DCM_Modality); ++ e = DcmItem::newDicomElement(DCM_Modality); + query.insert(e); + +- e = newDicomElement(DCM_SeriesDescription); ++ e = DcmItem::newDicomElement(DCM_SeriesDescription); + query.insert(e); + +- e = newDicomElement(DCM_SeriesTime); ++ e = DcmItem::newDicomElement(DCM_SeriesTime); + query.insert(e); + +- e = newDicomElement(DCM_StationName); ++ e = DcmItem::newDicomElement(DCM_StationName); + query.insert(e); + +- e = newDicomElement(DCM_NumberOfSeriesRelatedInstances); ++ e = DcmItem::newDicomElement(DCM_NumberOfSeriesRelatedInstances); + query.insert(e); + + +@@ -357,22 +357,22 @@ int query_series_instances(const std::st + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("IMAGE"); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + e->putString(studyinstanceuid.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SeriesInstanceUID); ++ e = DcmItem::newDicomElement(DCM_SeriesInstanceUID); + e->putString(seriesinstanceuid.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SOPInstanceUID); ++ e = DcmItem::newDicomElement(DCM_SOPInstanceUID); + query.insert(e); + +- e = newDicomElement(DCM_InstanceNumber); ++ e = DcmItem::newDicomElement(DCM_InstanceNumber); + query.insert(e); + + std::cout << "NEW QUERY:" << std::endl; +@@ -394,21 +394,21 @@ int query_study_series(const std::string + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("SERIES"); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + e->putString(studyinstanceuid.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SeriesInstanceUID); ++ e = DcmItem::newDicomElement(DCM_SeriesInstanceUID); + query.insert(e); + +- e = newDicomElement(DCM_SeriesNumber); ++ e = DcmItem::newDicomElement(DCM_SeriesNumber); + query.insert(e); + +- e = newDicomElement(DCM_Modality); ++ e = DcmItem::newDicomElement(DCM_Modality); + query.insert(e); + + std::cout << "NEW QUERY:" << std::endl; +--- a/imagepool/poolassociation.h ++++ b/imagepool/poolassociation.h +@@ -101,7 +101,7 @@ public: + return false; + } + +- DcmElement *elem = newDicomElement(tag); ++ DcmElement *elem = DcmItem::newDicomElement(tag); + if (elem == NULL) { + printf("cannot create element for tag: (%04x,%04x)", g, e); + return false; diff --git a/academic/aeskulap/slack-desc b/academic/aeskulap/slack-desc new file mode 100644 index 0000000000..5a3a8776e8 --- /dev/null +++ b/academic/aeskulap/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +aeskulap: aeskulap (medical image viewer) +aeskulap: +aeskulap: It is able to load a series of special images stored in the DICOM +aeskulap: format for review. Additionally Aeskulap is able to query and fetch +aeskulap: DICOM images from archive nodes (also called PACS) over the network. +aeskulap: The goal of this project is to create a full open source replacement +aeskulap: for commercially available DICOM viewers. +aeskulap: +aeskulap: http://aeskulap.nongnu.org/ +aeskulap: +aeskulap: diff --git a/academic/aline/aline.info b/academic/aline/aline.info index 63f7ee3446..177b2fff14 100644 --- a/academic/aline/aline.info +++ b/academic/aline/aline.info @@ -1,7 +1,7 @@ PRGNAM="aline" VERSION="1.0.025" HOMEPAGE="http://crystal.scb.uwa.edu.au/charlie/software/aline/" -DOWNLOAD="http://crystal.scb.uwa.edu.au/charlie/software/aline/aline_011208.tar.gz" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/aline/aline_011208.tar.gz" MD5SUM="6e462b37bb016de731a3352cc9503cd9" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/aliview/aliview.SlackBuild b/academic/aliview/aliview.SlackBuild index f3e5e9d0b7..22c0580eac 100644 --- a/academic/aliview/aliview.SlackBuild +++ b/academic/aliview/aliview.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for aliview -# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,11 +25,13 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=aliview -VERSION=${VERSION:-1.27} +VERSION=${VERSION:-1.28} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +ARCH=noarch + # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information # could be useful to other scripts. @@ -42,8 +44,6 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -ARCH=noarch - set -e rm -rf $PKG diff --git a/academic/aliview/aliview.info b/academic/aliview/aliview.info index d02ba7f9b8..41abed4471 100644 --- a/academic/aliview/aliview.info +++ b/academic/aliview/aliview.info @@ -1,10 +1,10 @@ PRGNAM="aliview" -VERSION="1.27" +VERSION="1.28" HOMEPAGE="http://www.ormbunkar.se/aliview/" -DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-versions-all/linux-version-1.27/aliview.tgz" -MD5SUM="5e16b3ce0a9680972f5a271e5d4ac6b9" +DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-versions-all/linux-version-1.28/aliview.tgz" +MD5SUM="1eac87a0f88f3815707df27d3a9970dc" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/amd/amd.SlackBuild b/academic/amd/amd.SlackBuild index b8c3a202cb..4cca1d563e 100644 --- a/academic/amd/amd.SlackBuild +++ b/academic/amd/amd.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/amplifx/amplifx.SlackBuild b/academic/amplifx/amplifx.SlackBuild index 5c0887e412..72ed55d7e4 100644 --- a/academic/amplifx/amplifx.SlackBuild +++ b/academic/amplifx/amplifx.SlackBuild @@ -31,7 +31,18 @@ BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -ARCH=i386 +# 2023-05-16 DW: do a proper test for ARCH +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [[ $ARCH != i?86 ]]; then + printf "\n$ARCH is not supported... \n" >/dev/stderr + exit 1 +fi # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information diff --git a/academic/amplifx/amplifx.info b/academic/amplifx/amplifx.info index a1406f86c0..22c69f2e7b 100644 --- a/academic/amplifx/amplifx.info +++ b/academic/amplifx/amplifx.info @@ -1,7 +1,7 @@ PRGNAM="amplifx" VERSION="1.7.0" HOMEPAGE="https://inp.univ-amu.fr/en/amplifx-manage-test-and-design-your-primers-for-pcr" -DOWNLOAD="https://jim.inp.univ-amu.fr/IMG/zip/AmplifX_Lin_Latest.zip" +DOWNLOAD="https://slackware.uk/~urchlay/src/AmplifX_Lin_Latest.zip" MD5SUM="ff84d1c4a800dcb651beaa877ff7b1ca" DOWNLOAD_x86_64="UNSUPPORTED" MD5SUM_x86_64="" diff --git a/academic/antiprism/antiprism.SlackBuild b/academic/antiprism/antiprism.SlackBuild index e17e282c7a..a294efedfd 100644 --- a/academic/antiprism/antiprism.SlackBuild +++ b/academic/antiprism/antiprism.SlackBuild @@ -8,13 +8,13 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=antiprism VERSION=${VERSION:-0.23} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -32,8 +32,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -83,6 +83,8 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/archaeopteryx/archaeopteryx.info b/academic/archaeopteryx/archaeopteryx.info index 798daf28ed..94a8958bb5 100644 --- a/academic/archaeopteryx/archaeopteryx.info +++ b/academic/archaeopteryx/archaeopteryx.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.phyloxml.org/download/forester/forester_1050.jar" MD5SUM="023de2f0a48cbd236c5054fe839b1d72" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/aris/aris.SlackBuild b/academic/aris/aris.SlackBuild index 05aee51aaa..6230b1e7d5 100644 --- a/academic/aris/aris.SlackBuild +++ b/academic/aris/aris.SlackBuild @@ -2,9 +2,11 @@ # Slackware build script for GNU aris -# Originally written by Juan M. Lasca <juanmlasca at gmail dot com> -# Currently maintained by Philip Lacroix <slackph at posteo dot de> - +# Copyright 2013-2020 Juan M. Lasca <juanmlasca@gmail.com> +# Copyright 2020-2022 Philip Lacroix <slackph at posteo dot de> +# Copyright 2022 Juan M. Lasca <juanmlasca@gmail.com> +# All rights reserved. +# # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: # @@ -26,7 +28,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=aris VERSION=${VERSION:-2.2} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,9 +40,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -79,11 +78,10 @@ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ - --disable-static \ --build=$ARCH-slackware-linux -# Fix path for local manual -patch src/aris.c < $CWD/help_path.diff +# Fix path for local manual and multiple symbol definitions +cat $CWD/docs_and_build.patch | patch -p1 || exit make make install DESTDIR=$PKG @@ -91,7 +89,6 @@ make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# Install documentation mkdir -p $PKG/usr/info $PKG/usr/doc/$PRGNAM-$VERSION cp -a doc/$PRGNAM.info $PKG/usr/info/ gzip -9 $PKG/usr/info/$PRGNAM.info diff --git a/academic/aris/aris.info b/academic/aris/aris.info index 484ce06315..f22ad0f438 100644 --- a/academic/aris/aris.info +++ b/academic/aris/aris.info @@ -6,5 +6,5 @@ MD5SUM="523e2c40f17e6e857b533c22a26ff4e1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Philip Lacroix" -EMAIL="slackph at posteo dot de" +MAINTAINER="Juan M. Lasca" +EMAIL="juanmlasca@gmail.com" diff --git a/academic/aris/docs_and_build.patch b/academic/aris/docs_and_build.patch new file mode 100644 index 0000000000..e1335922c7 --- /dev/null +++ b/academic/aris/docs_and_build.patch @@ -0,0 +1,66 @@ +# * Change documentation location +# * Instead of allowing multiple definitions (allocations in header files), +# declare global variables in headers, and allocate them in their +# corresponding .c files, with a reasonable initial value. + +diff -u3 aris-2.2/src/app.c aris-2.2-patched/src/app.c +--- aris-2.2/src/app.c 2014-02-28 10:17:24.000000000 -0300 ++++ aris-2.2-patched/src/app.c 2022-08-11 15:28:59.318566050 -0300 +@@ -46,6 +46,9 @@ + #include "elm-conn.xpm" + #include "nil-conn.xpm" + ++ ++aris_app * the_app = 0; ++ + // Macro to get the length of a file. + + #ifndef WIN32 +diff -u3 aris-2.2/src/app.h aris-2.2-patched/src/app.h +--- aris-2.2/src/app.h 2014-02-27 22:32:07.000000000 -0300 ++++ aris-2.2-patched/src/app.h 2022-08-11 13:01:06.315136621 -0300 +@@ -106,6 +106,6 @@ + + int app_set_color (aris_app * app, int index, int red, int green, int blue); + /* The main application */ +-aris_app * the_app; ++extern aris_app * the_app; + + #endif /* ARIS_APP_H */ +diff -u3 aris-2.2/src/aris.c aris-2.2-patched/src/aris.c +--- aris-2.2/src/aris.c 2014-02-28 10:29:10.000000000 -0300 ++++ aris-2.2-patched/src/aris.c 2022-08-11 15:38:22.990593330 -0300 +@@ -844,8 +844,7 @@ + + if (the_app->working_dir) + { +- parent = g_file_get_parent (parent); +- sprintf (the_app->help_file, "file://%s/doc/aris/index.html", g_file_get_path (parent)); ++ sprintf (the_app->help_file, "file:///usr/doc/aris-" PACKAGE_VERSION "/html/index.html"); + } + + int ret; +diff -u3 aris-2.2/src/process.c aris-2.2-patched/src/process.c +--- aris-2.2/src/process.c 2014-03-06 17:53:32.000000000 -0300 ++++ aris-2.2-patched/src/process.c 2022-08-11 15:27:56.582563013 -0300 +@@ -26,6 +26,8 @@ + #include <ctype.h> + #include <math.h> + ++struct connectives_list main_conns = { 0 }; ++ + /* Eliminates a negation from a string. + * input: + * not_str - the string from which to eliminate the negation. +diff -u3 aris-2.2/src/process.h aris-2.2-patched/src/process.h +--- aris-2.2/src/process.h 2014-03-02 16:30:39.000000000 -0300 ++++ aris-2.2-patched/src/process.h 2022-08-11 13:04:45.004147205 -0300 +@@ -170,7 +170,7 @@ + + // The main connectives. + +-struct connectives_list main_conns; ++extern struct connectives_list main_conns; + + // Definitions. + diff --git a/academic/aris/help_path.diff b/academic/aris/help_path.diff deleted file mode 100644 index 0d2853fcbe..0000000000 --- a/academic/aris/help_path.diff +++ /dev/null @@ -1,11 +0,0 @@ ---- a/aris.c 2021-02-10 17:51:33.532759576 +0400 -+++ b/aris.c 2021-02-10 17:52:15.210759108 +0400 -@@ -845,7 +845,7 @@ - if (the_app->working_dir) - { - parent = g_file_get_parent (parent); -- sprintf (the_app->help_file, "file://%s/doc/aris/index.html", g_file_get_path (parent)); -+ sprintf (the_app->help_file, "file:///usr/doc/aris-2.2/html/index.html", g_file_get_path (parent)); - } - - int ret; diff --git a/academic/armadillo/armadillo.SlackBuild b/academic/armadillo/armadillo.SlackBuild index bd5f66da65..dbe7598f03 100644 --- a/academic/armadillo/armadillo.SlackBuild +++ b/academic/armadillo/armadillo.SlackBuild @@ -22,11 +22,15 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220402 bkw: Modified by SlackBuilds.org, BUILD=2: +# - fix download URL. +# - add SlackBuild to doc dir. + cd $(dirname $0) ; CWD=$(pwd) PRGNAM=armadillo VERSION=${VERSION:-8.100.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -40,9 +44,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -77,9 +78,9 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ mkdir -p build cd build @@ -88,14 +89,12 @@ cd build -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Release .. make - make install DESTDIR=$PKG + make install/strip DESTDIR=$PKG cd .. -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a $DOCS $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/armadillo/armadillo.info b/academic/armadillo/armadillo.info index 9d8c336afc..5a883d954f 100644 --- a/academic/armadillo/armadillo.info +++ b/academic/armadillo/armadillo.info @@ -1,7 +1,7 @@ PRGNAM="armadillo" VERSION="8.100.0" HOMEPAGE="http://arma.sourceforge.net/" -DOWNLOAD="http://sourceforge.net/projects/arma/files/armadillo-8.100.0.tar.xz" +DOWNLOAD="https://slackware.uk/~urchlay/src/armadillo-8.100.0.tar.xz" MD5SUM="5f4aa46d15d9d364874fa4bde1a7add0" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/arpack-ng/arpack-ng.SlackBuild b/academic/arpack-ng/arpack-ng.SlackBuild index 5e2a88456a..7893fe9968 100644 --- a/academic/arpack-ng/arpack-ng.SlackBuild +++ b/academic/arpack-ng/arpack-ng.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for arpack-ng -# Copyright 2014-2021 Kyle Guinn <elyk03@gmail.com> +# Copyright 2014-2024 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=arpack-ng -VERSION=${VERSION:-3.8.0} +VERSION=${VERSION:-3.9.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,24 +38,18 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="CHANGES COPYING README.md TODO" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i586" ]; then +if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then @@ -80,17 +74,18 @@ cd $PRGNAM-$VERSION chown -R root:root . chmod -R u+w,go-w,a+rX-st . +patch -p1 < $CWD/patches/pkgconfig.diff patch -p1 < $CWD/patches/atlas-lib-rename.diff ./bootstrap ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=\${exec_prefix}/lib${LIBDIRSUFFIX} \ --sysconfdir=/etc \ --localstatedir=/var \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ + --mandir=\${prefix}/man \ + --infodir=\${prefix}/info \ + --docdir=\${prefix}/doc/$PRGNAM-$VERSION \ --disable-dependency-tracking \ --enable-icb \ --build=$ARCH-slackware-linux \ diff --git a/academic/arpack-ng/arpack-ng.info b/academic/arpack-ng/arpack-ng.info index 10dc19bd10..6f6426c4bf 100644 --- a/academic/arpack-ng/arpack-ng.info +++ b/academic/arpack-ng/arpack-ng.info @@ -1,10 +1,10 @@ PRGNAM="arpack-ng" -VERSION="3.8.0" +VERSION="3.9.1" HOMEPAGE="https://github.com/opencollab/arpack-ng" -DOWNLOAD="https://github.com/opencollab/arpack-ng/archive/3.8.0/arpack-ng-3.8.0.tar.gz" -MD5SUM="bb4cf448f2480a0ffe5517d579f980c3" +DOWNLOAD="https://github.com/opencollab/arpack-ng/archive/3.9.1/arpack-ng-3.9.1.tar.gz" +MD5SUM="8f66485ae9d7e676b42aeead2bf5757e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas lapack" +REQUIRES="lapack" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/arpack-ng/patches/pkgconfig.diff b/academic/arpack-ng/patches/pkgconfig.diff new file mode 100644 index 0000000000..73a00eb23d --- /dev/null +++ b/academic/arpack-ng/patches/pkgconfig.diff @@ -0,0 +1,142 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -807,7 +807,7 @@ + set(prefix ${CMAKE_INSTALL_PREFIX}) + set(exec_prefix \${prefix}) + set(libdir ${CMAKE_INSTALL_FULL_LIBDIR}) +-set(includedir ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}) ++set(includedir ${CMAKE_INSTALL_FULL_INCLUDEDIR}) + set(PACKAGE_NAME ${PROJECT_NAME}) + set(PACKAGE_VERSION ${arpack_ng_VERSION}) + set(PACKAGE_URL "https://github.com/opencollab/arpack-ng/") +@@ -830,15 +830,15 @@ + endforeach() + string(REPLACE ";" " " PARPACK_PC_LIBS_PRIVATE "${PARPACK_PC_LIBS_PRIVATE}") + +-configure_file(pkg-config/arpack.pc.in "${PROJECT_BINARY_DIR}/arpack${LIBSUFFIX}${ITF64SUFFIX}.pc" @ONLY) +-configure_file(pkg-config/parpack.pc.in "${PROJECT_BINARY_DIR}/parpack${LIBSUFFIX}${ITF64SUFFIX}.pc" @ONLY) ++configure_file(SRC/arpack.pc.in "${PROJECT_BINARY_DIR}/SRC/arpack${LIBSUFFIX}${ITF64SUFFIX}.pc" @ONLY) ++configure_file(PARPACK/SRC/MPI/parpack.pc.in "${PROJECT_BINARY_DIR}/PARPACK/SRC/MPI/parpack${LIBSUFFIX}${ITF64SUFFIX}.pc" @ONLY) + + install(TARGETS arpack + EXPORT arpackngTargets + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) +-install(FILES "${PROJECT_BINARY_DIR}/arpack${LIBSUFFIX}${ITF64SUFFIX}.pc" ++install(FILES "${PROJECT_BINARY_DIR}/SRC/arpack${LIBSUFFIX}${ITF64SUFFIX}.pc" + DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + + if (MPI) +@@ -847,7 +847,7 @@ + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) +- install(FILES "${PROJECT_BINARY_DIR}/parpack${LIBSUFFIX}${ITF64SUFFIX}.pc" ++ install(FILES "${PROJECT_BINARY_DIR}/PARPACK/SRC/MPI/parpack${LIBSUFFIX}${ITF64SUFFIX}.pc" + DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + endif () + +diff --git a/Makefile.am b/Makefile.am +--- a/Makefile.am ++++ b/Makefile.am +@@ -26,8 +26,3 @@ + + EXTRA_DIST = README.md PARPACK_CHANGES CHANGES DOCUMENTS VISUAL_STUDIO \ + detect_arpack_bug.m4 CMakeLists.txt +- +-pkgconfig_DATA = arpack@LIBSUFFIX@@ITF64SUFFIX@.pc parpack@LIBSUFFIX@@ITF64SUFFIX@.pc +- +-# Due to the LIBSUFFIX/ITF64SUFFIX, configure doesn't automatically clean this file: +-DISTCLEANFILES = arpack@LIBSUFFIX@@ITF64SUFFIX@.pc parpack@LIBSUFFIX@@ITF64SUFFIX@.pc +diff --git a/PARPACK/SRC/MPI/Makefile.am b/PARPACK/SRC/MPI/Makefile.am +--- a/PARPACK/SRC/MPI/Makefile.am ++++ b/PARPACK/SRC/MPI/Makefile.am +@@ -46,3 +46,8 @@ + libparpack@LIBSUFFIX@@ITF64SUFFIX@_la_LIBADD += $(top_builddir)/ICB/libdbgicb.la $(top_builddir)/ICB/libstaicb.la + libparpack@LIBSUFFIX@@ITF64SUFFIX@_la_CPPFLAGS = $(AM_CPPFLAGS) -I$(top_builddir) + endif ++ ++pkgconfig_DATA = parpack@LIBSUFFIX@@ITF64SUFFIX@.pc ++ ++# Due to the LIBSUFFIX/ITF64SUFFIX, configure doesn't automatically clean this file: ++DISTCLEANFILES = parpack@LIBSUFFIX@@ITF64SUFFIX@.pc +diff --git a/pkg-config/parpack.pc.in b/PARPACK/SRC/MPI/parpack.pc.in +rename from pkg-config/parpack.pc.in +rename to PARPACK/SRC/MPI/parpack.pc.in +--- a/pkg-config/parpack.pc.in ++++ b/PARPACK/SRC/MPI/parpack.pc.in +@@ -1,7 +1,7 @@ + prefix=@prefix@ + exec_prefix=@exec_prefix@ + libdir=@libdir@ +-includedir=@includedir@/arpack@ITF64SUFFIX@ ++includedir=@includedir@ + + Name: @PACKAGE_NAME@ + Description: Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems +@@ -10,4 +10,4 @@ + Requires.private: arpack@LIBSUFFIX@@ITF64SUFFIX@ + Libs: -L${libdir} -lparpack@LIBSUFFIX@@ITF64SUFFIX@ + Libs.private: @PARPACK_PC_LIBS_PRIVATE@ +-Cflags: -I${includedir} ++Cflags: -I${includedir}/arpack@ITF64SUFFIX@ +diff --git a/SRC/Makefile.am b/SRC/Makefile.am +--- a/SRC/Makefile.am ++++ b/SRC/Makefile.am +@@ -33,3 +33,8 @@ + libarpack@LIBSUFFIX@@ITF64SUFFIX@_la_LIBADD += $(top_builddir)/ICB/libdbgicb.la $(top_builddir)/ICB/libstaicb.la + libarpack@LIBSUFFIX@@ITF64SUFFIX@_la_CPPFLAGS = $(AM_CPPFLAGS) -I$(top_builddir) + endif ++ ++pkgconfig_DATA = arpack@LIBSUFFIX@@ITF64SUFFIX@.pc ++ ++# Due to the LIBSUFFIX/ITF64SUFFIX, configure doesn't automatically clean this file: ++DISTCLEANFILES = arpack@LIBSUFFIX@@ITF64SUFFIX@.pc +diff --git a/pkg-config/arpack.pc.in b/SRC/arpack.pc.in +rename from pkg-config/arpack.pc.in +rename to SRC/arpack.pc.in +--- a/pkg-config/arpack.pc.in ++++ b/SRC/arpack.pc.in +@@ -1,7 +1,7 @@ + prefix=@prefix@ + exec_prefix=@exec_prefix@ + libdir=@libdir@ +-includedir=@includedir@/arpack@ITF64SUFFIX@ ++includedir=@includedir@ + + Name: @PACKAGE_NAME@ + Description: Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems +@@ -9,4 +9,4 @@ + URL: @PACKAGE_URL@ + Libs: -L${libdir} -larpack@LIBSUFFIX@@ITF64SUFFIX@ + Libs.private: @ARPACK_PC_LIBS_PRIVATE@ +-Cflags: -I${includedir} ++Cflags: -I${includedir}/arpack@ITF64SUFFIX@ +diff --git a/configure.ac b/configure.ac +--- a/configure.ac ++++ b/configure.ac +@@ -347,14 +347,12 @@ + AC_SUBST([PARPACK_PC_LIBS_PRIVATE], ["$LAPACK_LIBS $BLAS_LIBS $MPI_Fortran_LIBS"]) + + AC_CONFIG_FILES([ +- arpack$LIBSUFFIX$ITF64SUFFIX.pc:pkg-config/arpack.pc.in +- parpack$LIBSUFFIX$ITF64SUFFIX.pc:pkg-config/parpack.pc.in ++ SRC/arpack$LIBSUFFIX$ITF64SUFFIX.pc:SRC/arpack.pc.in ++ PARPACK/SRC/MPI/parpack$LIBSUFFIX$ITF64SUFFIX.pc:PARPACK/SRC/MPI/parpack.pc.in + ], [], [LIBSUFFIX="$LIBSUFFIX"; ITF64SUFFIX="$ITF64SUFFIX"]) + + dnl We do NOT want arpackng*.cmake files to be created: @MPI@ can not be replaced. +-AC_CONFIG_FILES([ +- tstAutotoolsInstall.sh:pkg-config/tstAutotoolsInstall.sh.in +-], [], [abs_top_builddir="$abs_top_builddir"]) ++AC_CONFIG_FILES([tstAutotoolsInstall.sh], [chmod +x tstAutotoolsInstall.sh], [abs_top_builddir="$abs_top_builddir"]) + + AC_CONFIG_FILES([ + arpackdef.h +diff --git a/pkg-config/tstAutotoolsInstall.sh.in b/tstAutotoolsInstall.sh.in +old mode 100755 +new mode 100644 +rename from pkg-config/tstAutotoolsInstall.sh.in +rename to tstAutotoolsInstall.sh.in diff --git a/academic/arpack/arpack.SlackBuild b/academic/arpack/arpack.SlackBuild index 3c4efe07e2..cc21abf76f 100644 --- a/academic/arpack/arpack.SlackBuild +++ b/academic/arpack/arpack.SlackBuild @@ -33,7 +33,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -51,8 +51,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -88,6 +88,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +# Disable parallel building otherwise build fails +MAKEFLAGS=-j1 + mkdir static shared cd shared for dir in ../SRC ../UTIL; do diff --git a/academic/avogadro/README b/academic/avogadro/README deleted file mode 100644 index ef97a2fae0..0000000000 --- a/academic/avogadro/README +++ /dev/null @@ -1,6 +0,0 @@ -Avogadro is a molecular graphics and modelling system targeted at -molecules and biomolecules. It can visualize properties like molecular -orbitals or electrostatic potentials and features an intuitive -molecular builder. - -Optionally numpy can be installed for python support. diff --git a/academic/avogadro/avogadro-1.1.1-python_openbabel.patch b/academic/avogadro/avogadro-1.1.1-python_openbabel.patch deleted file mode 100644 index c819b08502..0000000000 --- a/academic/avogadro/avogadro-1.1.1-python_openbabel.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff -up avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt.openbabel avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt ---- avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt.openbabel 2013-12-06 09:50:04.000000000 -0600 -+++ avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt 2016-01-25 13:50:10.469758655 -0600 -@@ -20,8 +20,8 @@ if (WIN32) - set_target_properties(python-module PROPERTIES SUFFIX ".pyd") - target_link_libraries(python-module avogadro ${PYTHON_LIBRARIES}) - else() -- target_link_libraries(python-module stdc++ avogadro -- ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES}) -+ target_link_libraries(python-module stdc++ avogadro -+ ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${OPENBABEL2_LIBRARIES} ${Boost_LIBRARIES}) - endif() - - # Let's try to use this instead: diff --git a/academic/avogadro/avogadro-1.2.0-libmsym.patch b/academic/avogadro/avogadro-1.2.0-libmsym.patch deleted file mode 100644 index 818b2e434b..0000000000 --- a/academic/avogadro/avogadro-1.2.0-libmsym.patch +++ /dev/null @@ -1,29 +0,0 @@ -diff -Naur avogadro-1.2.0.orig/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt avogadro-1.2.0/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt ---- avogadro-1.2.0.orig/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt 2016-06-08 14:19:45.000000000 +0000 -+++ avogadro-1.2.0/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt 2016-08-01 04:18:55.910888721 +0000 -@@ -7,13 +7,13 @@ - set(LIBMSYM_PATCH_VERSION 0) - set(LIBMSYM_VERSION ${LIBMSYM_MAJOR_VERSION}.${LIBMSYM_MINOR_VERSION}.${LIBMSYM_PATCH_VERSION}) - --set(INSTALL_LIB_DIR lib CACHE PATH "Installation directory for msym library") -+set(INSTALL_LIB_DIR lib${LIB_SUFFIX} CACHE PATH "Installation directory for msym library") - set(INSTALL_INCLUDE_DIR include CACHE PATH "Installation directory for header files") - - if(WIN32 AND NOT CYGWIN) - set(DEF_INSTALL_CMAKE_DIR CMake) - else() -- set(DEF_INSTALL_CMAKE_DIR lib/cmake/libmsym) -+ set(DEF_INSTALL_CMAKE_DIR lib${LIB_SUFFIX}/cmake/libmsym) - endif() - set(INSTALL_CMAKE_DIR ${DEF_INSTALL_CMAKE_DIR} CACHE PATH "Installation directory for CMake files") - -@@ -29,6 +29,9 @@ - file (GLOB source src/*.c) - add_library (msym ${source}) - if (BUILD_SHARED_LIBS) -+ if(CMAKE_SYSTEM_NAME MATCHES Linux) -+ target_link_libraries(msym m) -+ endif() - set_target_properties (msym PROPERTIES - POSITION_INDEPENDENT_CODE "TRUE") - endif () diff --git a/academic/avogadro/avogadro.info b/academic/avogadro/avogadro.info deleted file mode 100644 index 68813ecc75..0000000000 --- a/academic/avogadro/avogadro.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="avogadro" -VERSION="1.2.0" -HOMEPAGE="http://avogadro.cc/" -DOWNLOAD="http://ponce.cc/slackware/sources/repo/avogadro-1.2.0.tar.gz" -MD5SUM="3206068fc27bd3b717c568ee72f1e5ec" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="openbabel" -MAINTAINER="Larry Hajali" -EMAIL="larryhaja[at]gmail[dot]com" diff --git a/academic/avogadroapp/README b/academic/avogadroapp/README new file mode 100644 index 0000000000..692ec7f1c2 --- /dev/null +++ b/academic/avogadroapp/README @@ -0,0 +1,23 @@ +Avogadro Application is the graphic user interface of Avogadro 2. + +Avogadro is an advanced molecular editor designed for cross-platform +use in computational chemistry, molecular modeling, bioinformatics, +materials science, and related areas. It offers flexible rendering and +a powerful plugin architecture. + +Managed by OpenChemistry, Avogadro 2 it is based on QT5 libraries and +it is a rewrite of the old Avogadro 1.x. + +By default the script builds avogadroapp with shared libraries. If you +want to enable the building with static libraries, pass the variable +SHARED=no to the script: + + SHARED=no ./avogadroapp.SlackBuild (hdf5 required) + +Warning: the computational settings made through the Input Generator +require the MoleQueue server running to submit jobs to local +applications or remote HPC clusters. + +Since Avogadro 2 version 1.98.0, the build requires cmake at version +3.24 or greater. This version is the latest compatible with Slackware +15.0 that has cmake remained at the version 3.21. diff --git a/academic/avogadroapp/avogadroapp.SlackBuild b/academic/avogadroapp/avogadroapp.SlackBuild new file mode 100644 index 0000000000..e8b6905bd1 --- /dev/null +++ b/academic/avogadroapp/avogadroapp.SlackBuild @@ -0,0 +1,118 @@ +#!/bin/bash + +# Slackware build script for avogadroapp + +# Copyright 2020-2022 Giancarlo Dessì, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=avogadroapp +VERSION=${VERSION:-1.97.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +SHAREDLIBS="" ; [ "${SHARED:-yes}" = "yes" ] && SHAREDLIBS="-DBUILD_SHARED_LIBS=ON" + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION avogadro-i18n* +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +# Following archive must be unpacked in /tmp since the build process +# searches it as parallel directory and tries to connect to github if +# not found +tar xvf $CWD/avogadro-i18n-$VERSION.tar.gz +mv avogadro-i18n-$VERSION avogadro-i18n + +# Now we can change directory to $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + $SHAREDLIBS \ + .. + make + make install DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a *.md LICENSE $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# Remove doc files installed by make install in /usr/share/doc/AvogadroApp that is redundant +rm -rf $PKG/usr/share/doc + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/avogadroapp/avogadroapp.info b/academic/avogadroapp/avogadroapp.info new file mode 100644 index 0000000000..e98567822d --- /dev/null +++ b/academic/avogadroapp/avogadroapp.info @@ -0,0 +1,12 @@ +PRGNAM="avogadroapp" +VERSION="1.97.0" +HOMEPAGE="https://github.com/OpenChemistry/avogadroapp" +DOWNLOAD="https://github.com/OpenChemistry/avogadroapp/archive/1.97.0/avogadroapp-1.97.0.tar.gz \ + https://github.com/OpenChemistry/avogadro-i18n/archive/1.97.0/avogadro-i18n-1.97.0.tar.gz" +MD5SUM="748afd9c2af5d7e193fbbb7c939223a3 \ + 58b31e2047e4467befb2e63eff59672b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="avogadrolibs" +MAINTAINER="Giancarlo Dessì" +EMAIL="slack@giand.it" diff --git a/academic/drawtiming/doinst.sh b/academic/avogadroapp/doinst.sh index 65c7e2eeb9..65c7e2eeb9 100644 --- a/academic/drawtiming/doinst.sh +++ b/academic/avogadroapp/doinst.sh diff --git a/academic/avogadroapp/slack-desc b/academic/avogadroapp/slack-desc new file mode 100644 index 0000000000..030caebdb3 --- /dev/null +++ b/academic/avogadroapp/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +avogadroapp: avogadroapp (graphic user interface of Avogadro 2) +avogadroapp: +avogadroapp: Avogadro Application is the graphic interface of Avogadro 2, an +avogadroapp: advanced molecular editor designed for cross-platform use in +avogadroapp: computational chemistry, molecular modeling, bioinformatics, +avogadroapp: materials science, and related areas. It offers flexible rendering +avogadroapp: and a powerful application on one plugin architecture. +avogadroapp: +avogadroapp: Homepage: https://github.com/OpenChemistry/avogadroapp +avogadroapp: +avogadroapp: diff --git a/academic/avogadrolibs/README b/academic/avogadrolibs/README new file mode 100644 index 0000000000..4990e7bf74 --- /dev/null +++ b/academic/avogadrolibs/README @@ -0,0 +1,37 @@ +Avogadro Libraries is a subproject of Avogadro 2 as implementation of +Avogadro 1.x mantained by OpenChemistry. It provides 3D rendering, +visualization, analysis and data processing useful in computational +chemistry, molecular modeling, bioinformatics, materials science, and +related areas. +Avogadro Libraries is a dependency required by the graphic interface +user Avogadro Application (avogadroapp). + +This slackbuild requires as needed some dependencies (autodetected) +that improve Avogadro Libraries. You can enable or disable them by +passing variables to the script +(e.g. VAR=yes|no ./avogadrolibs.SlackBuild): + +LIBMSYM=yes|no (default: yes, libmsym required) +SPGLIB=yes|no (default: yes, spglib required) +MMTF=yes|no (default: yes, mmtf-cpp required) +HDF5=yes|no (default: no, hdf5 required) +VTK=yes|no (default: no, VTK required) + +The extension Avogadro Generators (disabled by default) installs +Python input generators that can be run by the Avogadro 2 application +(avogadroapp) to generate input for various codes (Dalton, Q-Chem, +Orca, NWChem, ecc.): these scripts will be installed in a location +where the Avogadro 2 application can find them if the Plugin +Downloader is executed from the graphic interface user. +To enable the extension the dependency pybind11 is required and you +have to pass the variable PYTHON=yes to the slackbuild script: + +PYTHON=yes ./avogadrolibs.SlackBuild + +WARNING: the build enabling the support of VTK libraries works only +with VTK < 9.0 or VTK >= 9.2.6. The build against VTK 9.0.x fails. +Other versions of VTK 9.x earlier than 9.2.6 are not tested. + +Since Avogadro 2 version 1.98.0, the build requires cmake at version +3.24 or greater. This version is the latest compatible with Slackware +15.0 that has cmake remained at the version 3.21. diff --git a/academic/avogadrolibs/avogadrolibs.SlackBuild b/academic/avogadrolibs/avogadrolibs.SlackBuild new file mode 100644 index 0000000000..825baf7b68 --- /dev/null +++ b/academic/avogadrolibs/avogadrolibs.SlackBuild @@ -0,0 +1,157 @@ +#!/bin/bash + +# Slackware build script for avogadrolibs + +# Copyright 2020-2022 Giancarlo Dessì, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=avogadrolibs +VERSION=${VERSION:-1.97.0} +BUILD=${BUILD:-3} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +MVERSION=${MVERSION:-1.0.0} +CVERSION=${CVERSION:-1.0.1} +AVERSION=${AVERSION:-1.97.0} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +#These are features which are disabled by default +USEHDF5="" ; [ "${HDF5:-no}" = "yes" ] && USEHDF5="-DUSE_HDF5=ON" +USEPYTHON="" ; [ "${PYTHON:-no}" = "yes" ] && USEPYTHON="-DUSE_PYTHON=ON" +USEVTK="" ; [ "${VTK:-no}" = "yes" ] && USEVTK="-DUSE_VTK=ON" + +#These are features which are enabled by default +USELIBMSYM="" ; [ "${LIBMSYM:-yes}" = "no" ] && USELIBMSYM="-DUSE_LIBMSYM=OFF" +USESPGLIB="-DSPGLIB_INCLUDE_DIR=/usr/include/spglib" ; [ "${SPGLIB:-yes}" = "no" ] && \ + USESPGLIB="-DUSE_SPGLIB=OFF" +USEMMTF="" ; [ "${MMTF:-yes}" = "no" ] && USEMMTF="-DUSE_MMTF=OFF" + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} +GENXRDPATH=$TMP/$PRGNAM-$VERSION/build/avogadro/qtplugins/plotxrd/bin + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION molecules crystals avogadrogenerators +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +# Following archives must be unpacked in /tmp since the build process +# searches them as parallel directories and tries to connect to github +# if not found +tar xvf $CWD/molecules-$MVERSION.tar.gz +tar xvf $CWD/crystals-$CVERSION.tar.gz +mv molecules-$MVERSION molecules +mv crystals-$CVERSION crystals +if [ "${PYTHON}" = "yes" ]; then + tar xvf $CWD/avogenerators-$AVERSION.tar.gz + mv avogenerators-$AVERSION avogadrogenerators +fi + +# Now we can change directory to $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# fix issues that generate cmake warnings +patch -p1 < $CWD/fix_cmake-find-package.diff +# fix build error cause ambiguous definition in source code +# (thanks to StefanBruens from OpenChemistry in GitHub) +patch -p1 < $CWD/fix_mmtfformat_cpp.diff + +mkdir -p build +# Following steps prevent the download of the executable genXrdPattern +# needed by the build process and include it in the source tree +mkdir -p $GENXRDPATH +cp $CWD/linux64-genXrdPattern $GENXRDPATH +mv $GENXRDPATH/linux64-genXrdPattern $GENXRDPATH/genXrdPattern +chmod 755 $GENXRDPATH/genXrdPattern + +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_POLICY_DEFAULT_CMP0072=NEW \ + -DENABLE_TESTING=OFF \ + -DENABLE_TRANSLATIONS=ON \ + $USEHDF5 \ + $USEPYTHON \ + $USELIBMSYM \ + $USESPGLIB \ + $USEMMTF \ + $USEVTK \ + .. + make + make install DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a *.md LICENSE CITATION.cff $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# Remove doc files installed by make install in /usr/share/doc/AvogadroLibs that are redundant +rm -rf $PKG/usr/share/doc + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/avogadrolibs/avogadrolibs.info b/academic/avogadrolibs/avogadrolibs.info new file mode 100644 index 0000000000..50472adccb --- /dev/null +++ b/academic/avogadrolibs/avogadrolibs.info @@ -0,0 +1,18 @@ +PRGNAM="avogadrolibs" +VERSION="1.97.0" +HOMEPAGE="https://github.com/OpenChemistry/avogadrolibs" +DOWNLOAD="https://github.com/OpenChemistry/avogadrolibs/archive/1.97.0/avogadrolibs-1.97.0.tar.gz \ + https://github.com/OpenChemistry/molecules/archive/1.0.0/molecules-1.0.0.tar.gz \ + https://github.com/OpenChemistry/crystals/archive/1.0.1/crystals-1.0.1.tar.gz \ + https://github.com/OpenChemistry/avogenerators/archive/1.97.0/avogenerators-1.97.0.tar.gz \ + https://github.com/psavery/genXrdPattern/releases/download/1.0-static/linux64-genXrdPattern" +MD5SUM="a7cc488fb0ab65516117304df62fb2e9 \ + bad118f80a942fe0f082b2a9075ae3b9 \ + b05b526928b89fd27a5784b24c419613 \ + d115ab0f5f4dbf10d2ba2d1191c80a59 \ + e1b3c1d6b951ed83a037567490d75f1d" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="molequeue mmtf-cpp libmsym spglib" +MAINTAINER="Giancarlo Dessì" +EMAIL="slack@giand.it" diff --git a/academic/avogadrolibs/fix_cmake-find-package.diff b/academic/avogadrolibs/fix_cmake-find-package.diff new file mode 100644 index 0000000000..542919c2cc --- /dev/null +++ b/academic/avogadrolibs/fix_cmake-find-package.diff @@ -0,0 +1,42 @@ +--- avogadrolibs-1.95.1/cmake/FindSpglib.cmake 2022-17-04 15:40:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/cmake/FindSpglib.cmake 2022-17-04 15:40:01.000000000 +0200 +@@ -12,7 +12,7 @@ + set(SPGLIB_INCLUDE_DIRS "${SPGLIB_INCLUDE_DIR}") + + include(FindPackageHandleStandardArgs) +-find_package_handle_standard_args(SPGLIB DEFAULT_MSG SPGLIB_INCLUDE_DIR ++find_package_handle_standard_args(Spglib DEFAULT_MSG SPGLIB_INCLUDE_DIR + SPGLIB_LIBRARY) + + mark_as_advanced(SPGLIB_INCLUDE_DIR SPGLIB_LIBRARY) +--- avogadrolibs-1.95.1/cmake/FindLibArchive.cmake 2022-17-04 15:50:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/cmake/FindLibArchive.cmake 2022-17-04 15:50:01.000000000 +0200 +@@ -14,7 +14,7 @@ + set(LIBARCHIVE_LIBRARIES "${LIBARCHIVE_LIBRARY}") + + include(FindPackageHandleStandardArgs) +-find_package_handle_standard_args(LIBARCHIVE DEFAULT_MSG LIBARCHIVE_INCLUDE_DIR ++find_package_handle_standard_args(LibArchive DEFAULT_MSG LIBARCHIVE_INCLUDE_DIR + LIBARCHIVE_LIBRARY) + + mark_as_advanced(LIBARCHIVE_INCLUDE_DIR LIBARCHIVE_LIBRARY) +--- avogadrolibs-1.95.1/python/CMakeLists.txt 2022-17-04 16:00:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/python/CMakeLists.txt 2022-17-04 16:00:01.000000000 +0200 +@@ -1,7 +1,7 @@ + find_package(PythonInterp 3 REQUIRED) + find_package(PythonLibs 3 REQUIRED) + set(PYBIND11_PYTHON_VERSION "3" CACHE STRING "") +-set(PYBIND11_CPP_STANDARD "-std=c++11" CACHE STRING "") ++set(CMAKE_CXX_STANDARD 14 CACHE STRING "") + find_package(pybind11 REQUIRED) + + find_package(Eigen3 REQUIRED) +--- avogadrolibs-1.95.1/avogadro/qtplugins/quantuminput/CMakeLists.txt 2022-18-04 19:00:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/avogadro/qtplugins/quantuminput/CMakeLists.txt 2022-18-04 19:00:01.000000000 +0200 +@@ -41,3 +41,5 @@ + else() ++ if(USE_PYTHON) +- message("Avogadro Generators not found at ${_prefix}!") ++ message("Avogadro Generators not found at ${_prefix}!") ++ endif() + endif() diff --git a/academic/avogadrolibs/fix_mmtfformat_cpp.diff b/academic/avogadrolibs/fix_mmtfformat_cpp.diff new file mode 100644 index 0000000000..03b3994b29 --- /dev/null +++ b/academic/avogadrolibs/fix_mmtfformat_cpp.diff @@ -0,0 +1,31 @@ +Ref: https://github.com/OpenChemistry/avogadrolibs/commit/0db79eb15b2f1dda1dd07a807b98086698cfee7a +Thanks to StefanBruens from OpenChemistry project + +--- avogadrolibs-1.97.0/avogadro/io/mmtfformat.cpp 2023-20-03 18:50:00.000000000 +0200 ++++ avogadrolibs-1.97.0-fixed/avogadro/io/mmtfformat.cpp 2023-20-03 18:50:01.000000000 +0200 +@@ -33,21 +33,25 @@ + + MMTFFormat::~MMTFFormat() = default; + ++namespace { + // from latest MMTF code, under the MIT license + // https://github.com/rcsb/mmtf-cpp/blob/master/include/mmtf/structure_data.hpp ++#if MMTF_SPEC_VERSION_MAJOR <= 1 && MMTF_SPEC_VERSION_MINOR < 1 + bool is_polymer(const unsigned int chain_index, + const std::vector<mmtf::Entity>& entity_list) + { + for (const auto & i : entity_list) { + if (std::find(i.chainIndexList.begin(), + i.chainIndexList.end(), + chain_index) != i.chainIndexList.end()) { + return (i.type == "polymer" || + i.type == "POLYMER"); + } + } + return false; + } ++#endif ++} // namespace + + bool MMTFFormat::read(std::istream& file, Molecule& molecule) + { diff --git a/academic/avogadrolibs/slack-desc b/academic/avogadrolibs/slack-desc new file mode 100644 index 0000000000..a04b7ca223 --- /dev/null +++ b/academic/avogadrolibs/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +avogadrolibs: avogadrolibs (Libraries for Avogadro 2) +avogadrolibs: +avogadrolibs: Avogadro libraries provide 3D rendering, visualization, analysis and +avogadrolibs: data processing useful in computational chemistry, molecular +avogadrolibs: modeling, bioinformatics, materials science, and related areas. +avogadrolibs: Avogadro 2 is being developed as part of the Open Chemistry project +avogadrolibs: at Kitware, along with companion tools and libraries to support. +avogadrolibs: +avogadrolibs: Homepage: https://github.com/OpenChemistry/avogadrolibs +avogadrolibs: +avogadrolibs: diff --git a/academic/bcftools/bcftools.SlackBuild b/academic/bcftools/bcftools.SlackBuild index 0f378d90b8..b7a8433557 100644 --- a/academic/bcftools/bcftools.SlackBuild +++ b/academic/bcftools/bcftools.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bcftools -# Copyright 2017-2021 Rob van Nues # All rights reserved. +# Copyright 2017-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -24,7 +24,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=bcftools -VERSION=${VERSION:-1.14} +VERSION=${VERSION:-1.19} +HTSLIBV=${HTSLIBV:-1.19} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -77,7 +78,7 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Force linking to installed htslib -rm -r htslib-$VERSION +rm -r htslib-$HTSLIBV CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -107,7 +108,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS README LICENSE INSTALL NEWS \ + AUTHORS README LICENSE NEWS \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/bcftools/bcftools.info b/academic/bcftools/bcftools.info index 08c8e8b949..1998ed001c 100644 --- a/academic/bcftools/bcftools.info +++ b/academic/bcftools/bcftools.info @@ -1,8 +1,8 @@ PRGNAM="bcftools" -VERSION="1.14" +VERSION="1.19" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.14/bcftools-1.14.tar.bz2" -MD5SUM="9822006ff0f6a268ea4effafa39c84ac" +DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.19.tar.bz2" +MD5SUM="9b4e8be279024d19f36bbaad1d2bdb41" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="htslib" diff --git a/academic/bcftools/slack-desc b/academic/bcftools/slack-desc index 2f85ffb7dd..f4c0b9871b 100644 --- a/academic/bcftools/slack-desc +++ b/academic/bcftools/slack-desc @@ -10,9 +10,9 @@ bcftools: bcftools (BCF calling tools) bcftools: bcftools: bcftools contains all the "vcf..." commands which previously lived in bcftools: the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and -bcftools: the samtools BCF calling from bcftools subdirectory of the previous +bcftools: the samtools BCF calling from bcftools subdirectory of the 'legacy' bcftools: samtools. BCFtools are meant as a faster replacement for most of the -bcftools: perl VCFtools commands. Bcftools comes with its own hstlib sources. +bcftools: perl VCFtools commands. bcftools: bcftools: Homepage: http://www.htslib.org bcftools: diff --git a/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild b/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild index a360f96262..0c04857e46 100644 --- a/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild +++ b/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild @@ -22,11 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220404 bkw: Modified by SlackBuilds.org, BUILD=2: +# - strip binary. + cd $(dirname $0) ; CWD=$(pwd) PRGNAM=bedGraphToBigWig VERSION=${VERSION:-4} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,9 +41,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -64,7 +64,7 @@ rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION -install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -s -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/bedtools/bedtools.SlackBuild b/academic/bedtools/bedtools.SlackBuild index e514a8370f..78b678111f 100644 --- a/academic/bedtools/bedtools.SlackBuild +++ b/academic/bedtools/bedtools.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bedtools -# Copyright 2014-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2014-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=bedtools DIRNAM=bedtools2 -VERSION=${VERSION:-2.30.0} +VERSION=${VERSION:-2.31.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -39,9 +39,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 diff --git a/academic/bedtools/bedtools.info b/academic/bedtools/bedtools.info index e1d978e114..31f2e1b4da 100644 --- a/academic/bedtools/bedtools.info +++ b/academic/bedtools/bedtools.info @@ -1,8 +1,8 @@ PRGNAM="bedtools" -VERSION="2.30.0" +VERSION="2.31.0" HOMEPAGE="http://bedtools.readthedocs.org/" -DOWNLOAD="https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools-2.30.0.tar.gz" -MD5SUM="6d89611900bceacb9883e51103e18ab8" +DOWNLOAD="https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools-2.31.0.tar.gz" +MD5SUM="d840193968e345947b076eaa322a9420" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/bibletime/README b/academic/bibletime/README index 7a44c6d012..3a862cfa06 100644 --- a/academic/bibletime/README +++ b/academic/bibletime/README @@ -2,3 +2,8 @@ BibleTime is a Bible study application for Linux. It is based on the K Desktop Environment and uses the Sword programming library to work with Bible texts, commentaries, dictionaries, and books provided by the Crosswire Bible Society. + +You will need bible text as well as the dependencies listed. +sword-data-KJV available on slackbuilds.org provides a basic +King James Version with strongs. bibletime includes bookshelf manager +which allows you to download other versions over the internet. diff --git a/academic/bibletime/bibletime.SlackBuild b/academic/bibletime/bibletime.SlackBuild index c8e60c594f..a25bde4b12 100644 --- a/academic/bibletime/bibletime.SlackBuild +++ b/academic/bibletime/bibletime.SlackBuild @@ -27,13 +27,15 @@ # Modified by Robert Delahunt [twinreverb[at]puresimplicity.net # Modified 2018/19/20 by Tim Dickson (dickson.tim@googlemail.com) -# Modified 20200918 by B. Watson <yalhcru@gmail.com> +# Modified 20200918 by B. Watson <urchlay@slackware.uk> +# Modified 20220412 by Tim Dickson (dickson.tim@googlemail.com) +# updated for v3.0.3 and fix doc location by Tim Dickson (dickson.tim@googlemail.com) cd $(dirname $0) ; CWD=$(pwd) PRGNAM=bibletime -VERSION=${VERSION:-3.0} -BUILD=${BUILD:-2} +VERSION=${VERSION:-3.0.3} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -80,14 +82,8 @@ rm -rf $PRGNAM-$VERSION tar -xJvf $CWD/$PRGNAM-$VERSION.tar.xz cd $PRGNAM-$VERSION -#we need to patch the cmake file to skip tests as they fail at the moment -#hopefully they will be fixed in 3.0.1 - -sed -i "/BTTests/s/^/#/" cmake/BTApplication.cmake - mkdir -p build cd build - export "PATH=/opt/cmake-202x/bin:$PATH" cmake \ -Wno-dev \ -DCMAKE_BUILD_TYPE=Release \ @@ -95,6 +91,7 @@ cd build -DCMAKE_SKIP_RPATH:BOOL=ON \ -DCMAKE_C_FLAGS="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS="$SLKCFLAGS" \ + -DBT_DOCDIR="doc/$PRGNAM-$VERSION" \ -DLIB_SUFFIX=$LIBDIRSUFFIX .. make make install DESTDIR=$PKG diff --git a/academic/bibletime/bibletime.info b/academic/bibletime/bibletime.info index 1cc0826cea..dc3f8b1300 100644 --- a/academic/bibletime/bibletime.info +++ b/academic/bibletime/bibletime.info @@ -1,8 +1,8 @@ PRGNAM="bibletime" -VERSION="3.0" +VERSION="3.0.3" HOMEPAGE="http://www.bibletime.info/" -DOWNLOAD="https://github.com/bibletime/bibletime/releases/download/v3.0/bibletime-3.0.tar.xz" -MD5SUM="c90bcafa7938ff0257a8599c3d9cb024" +DOWNLOAD="https://github.com/bibletime/bibletime/releases/download/v3.0.3/bibletime-3.0.3.tar.xz" +MD5SUM="07c4f717f15be1418c0e3f434ee2983c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="sword po4a fop" diff --git a/academic/biopython/biopython.SlackBuild b/academic/biopython/biopython.SlackBuild index 4fadf0ddd1..d21249dac8 100644 --- a/academic/biopython/biopython.SlackBuild +++ b/academic/biopython/biopython.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for biopython -# Copyright 2019-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2019-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=biopython -VERSION=${VERSION:-1.78} +VERSION=${VERSION:-1.81} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -79,9 +79,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -if $(python3 -c 'import sys' 2>/dev/null); then - python3 setup.py install --root=$PKG -fi +python3 setup.py install --root=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/biopython/biopython.info b/academic/biopython/biopython.info index 065965da62..db278d6620 100644 --- a/academic/biopython/biopython.info +++ b/academic/biopython/biopython.info @@ -1,10 +1,10 @@ PRGNAM="biopython" -VERSION="1.78" +VERSION="1.81" HOMEPAGE="https://biopython.org/" -DOWNLOAD="http://biopython.org/DIST/biopython-1.78.tar.gz" -MD5SUM="acb2e70be7a002108659f1856c60b123" +DOWNLOAD="http://biopython.org/DIST/biopython-1.81.tar.gz" +MD5SUM="06cabd14f55d624db366ff75efb60ed2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="numpy" +REQUIRES="python2-numpy" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/boinc/README b/academic/boinc/README index 35ab04a75a..f63d0e2e4c 100644 --- a/academic/boinc/README +++ b/academic/boinc/README @@ -14,21 +14,19 @@ types of scientific research. It's safe, secure, and easy. Building -(1) BOINC needs a static library for wxGTK3, compile with - - STATIC=yes ./wxGTK3.SlackBuild - -(2) Edit DATADIR in the script or run +(1) Edit DATADIR in the script or run DATADIR="/home/<user>/.boinc_data" ./boinc.SlackBuild -to set the data directory in your user's home and build the package. +to set the data directory in your user's home, or prefered data path, +and build the package. The default data path is /var/lib/boinc_data. -(3) If you do not wish to build the boincmgr GUI, +(2) If you do not wish to build the boincmgr GUI, BOINCMGR=no ./boinc.SlackBuild -then you do not need to install the dependencies (wxGTK3). +then you do not need to install the dependencies (wxWidgets). See +README.Slackware for details on headless configuration. After installation you need to join a BOINC project: http://boinc.berkeley.edu/projects.php diff --git a/academic/boinc/README.Slackware b/academic/boinc/README.Slackware new file mode 100644 index 0000000000..c0f1ceb4e3 --- /dev/null +++ b/academic/boinc/README.Slackware @@ -0,0 +1,34 @@ +For headless operation, a start up script is included. The script will +execute as root with the data directory as '/var/lib/boinc_data'. +Modify as needed: + +BOINC_DIR=/var/lib/boinc_data # directory of boinc data files +BOINC_USER=root # user that will run boinc process +BOINC_OPTIONS="--dir $BOINC_DIR --redirectio" + +Refer to the boinc manpage for parameters you can add to +BOINC_OPTIONS. + +To run boinc on boot, add the following code to /etc/rc.d/rc.local: + +if [ -x /etc/rc.d/rc.boinc ]; then + /etc/rc.d/rc.boinc start +fi + +and to /etc/rc.d/rc.local_shutdown + +if [ -x /etc/rc.d/rc.boinc ]; then + /etc/rc.d/rc.boinc stop +fi + +Note 1: +The default configuration enables boinc control on the running +host via boinccmg or boincmgr on the same running host. To truly run +headless, you will need to configure boinc to allow RPC access from +another host. + +Note 2: +If you use the default data path of /var/lib/boinc_data as a non-root +user, before first use, you will need to create that path and set the +appropriate user permissions. + diff --git a/academic/boinc/boinc.SlackBuild b/academic/boinc/boinc.SlackBuild index 83ffac3f80..8f8330ac87 100644 --- a/academic/boinc/boinc.SlackBuild +++ b/academic/boinc/boinc.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for boinc -# Copyright 2013-2018 Edward Koenig, Vancouver, WA, USA <kingbeowulf@gmail.com> +# Copyright 2013-2022 Edward Koenig, Vancouver, WA, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,17 +22,19 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # -# TODO: add rc.boinc. +# 08DEC2022: +# Version update +# switched to wxWidgets-3.2 +# Bypass wxconfig symlink for compatibility. cd $(dirname $0) ; CWD=$(pwd) PRGNAM=boinc -VERSION=${VERSION:-7.16.16} -BRANCH=${BRANCH:-7.16} +VERSION=${VERSION:-7.24.1} +BRANCH=${BRANCH:-7.24} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -NUMJOBS=${NUMJOBS:-1} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -42,9 +44,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -71,7 +70,7 @@ fi set -e # Your default working directory location. Pass with DATADIR=<dir> Boinc.SlackBuild -DATADIR=${DATADIR:-'$HOME/.boinc_data'} +DATADIR=${DATADIR:-'/var/lib/boinc_data'} BOINCMGR=${BOINCMGR:-yes} if [ "$BOINCMGR" = "yes" ]; then @@ -108,9 +107,10 @@ CXXFLAGS="$SLKCFLAGS" \ --disable-shared \ $do_mgr \ --with-x \ + --with-wx-config=/usr/lib$LIBDIRSUFFIX/wx/config/gtk3-unicode-3.2 \ --build=$ARCH-slackware-linux -make -j${NUMJOBS} +make make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ @@ -122,15 +122,25 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r cat $CWD/boincgui.sh > $PKG/usr/bin/boincgui.sh sed -i "s|WORKDIR|$DATADIR|g" $PKG/usr/bin/boincgui.sh chmod +x $PKG/usr/bin/boincgui.sh +mkdir -p $PKG/etc/rc.d +cat $CWD/rc.boinc.txt > $PKG/etc/rc.d/rc.boinc.new mkdir -p $PKG/usr/share/{applications,pixmaps} cp $CWD/boinc.desktop $PKG/usr/share/applications cp $CWD/boinc.png $PKG/usr/share/pixmaps mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING COPYING.LESSER COPYRIGHT INSTALL todo notes $PKG/usr/doc/$PRGNAM-$VERSION +cp -a COPYING COPYING.LESSER COPYRIGHT INSTALL notes $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + +# remove unneeded init script, systemd service +rm -rf $PKG/etc/default +rm -rf $PKG/etc/init.d +rm -rf $PKG/usr/lib +rm -f $PKG/usr/bin/boinc_client + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh diff --git a/academic/boinc/boinc.info b/academic/boinc/boinc.info index f8f8fc215e..4d1bb74cdd 100644 --- a/academic/boinc/boinc.info +++ b/academic/boinc/boinc.info @@ -1,10 +1,10 @@ PRGNAM="boinc" -VERSION="7.16.16" +VERSION="7.24.1" HOMEPAGE="https://boinc.berkeley.edu/" -DOWNLOAD="https://github.com/BOINC/boinc/archive/client_release/7.16/7.16.16/boinc-client_release-7.16-7.16.16.tar.gz" -MD5SUM="debf658ed8748c1c434c12f8a8a932a1" +DOWNLOAD="https://github.com/BOINC/boinc/archive/client_release/7.24/7.24.1/boinc-client_release-7.24-7.24.1.tar.gz" +MD5SUM="1844352e5b2ef9c9cf2325e1f991a5cc" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="wxGTK3" +REQUIRES="wxWidgets" MAINTAINER="Edward W. Koenig" EMAIL="kingbeowulf@linuxgalaxy.org" diff --git a/academic/boinc/boincgui.sh b/academic/boinc/boincgui.sh index 435bb29e63..5251e68d78 100644 --- a/academic/boinc/boincgui.sh +++ b/academic/boinc/boincgui.sh @@ -1,6 +1,6 @@ #!/bin/bash # -# Copyright 2013-2014 Edward Koenig, Vancouver, WA, USA <kingbeowulf@gmail.com> +# Copyright 2013-2014 Edward W. Koenig, Vancouver, WA, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is diff --git a/academic/boinc/doinst.sh b/academic/boinc/doinst.sh index 5fb28930db..9634ecf6f7 100644 --- a/academic/boinc/doinst.sh +++ b/academic/boinc/doinst.sh @@ -1,3 +1,29 @@ +config() { + NEW="$1" + OLD="$(dirname $NEW)/$(basename $NEW .new)" + # If there's no config file by that name, mv it over: + if [ ! -r $OLD ]; then + mv $NEW $OLD + elif [ "$(cat $OLD | md5sum)" = "$(cat $NEW | md5sum)" ]; then + # toss the redundant copy + rm $NEW + fi + # Otherwise, we leave the .new copy for the admin to consider... +} + +preserve_perms() { + NEW="$1" + OLD="$(dirname $NEW)/$(basename $NEW .new)" + if [ -e $OLD ]; then + cp -a $OLD ${NEW}.incoming + cat $NEW > ${NEW}.incoming + mv ${NEW}.incoming $NEW + fi + config $NEW +} + +preserve_perms etc/rc.d/rc.boinc.new + if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi diff --git a/academic/boinc/rc.boinc.txt b/academic/boinc/rc.boinc.txt new file mode 100644 index 0000000000..e84583ed0b --- /dev/null +++ b/academic/boinc/rc.boinc.txt @@ -0,0 +1,105 @@ +#!/bin/bash + +# rc.boinc - BOINC startup/control script for Slackware Linux +# +# Copyright 2022 Edward Koenig, Vancouver, WA, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +BOINC_DIR=//var/lib/boinc_data # directory of boinc files +BOINC_BIN=/usr/bin/boinc # name of the boinc binary +BOINC_USER=root # user that will run boinc process +BOINC_OPTIONS="--dir $BOINC_DIR --redirectio" +# "--dir $BOINC_DIR --daemon" will send logs syslog instead of +# stdoutdae.txt and stderrdae.txt + +boinc_status() { + if ( ps -ef | grep "$BOINC_BIN$" > /dev/null 2>&1 ); then + return 0 + else + return 3 +fi +} + +boinc_start() { + boinc_status + if [ $? = 0 ]; then + echo "BOINC is already running" + exit 1 + fi + + if [ ! -d $BOINC_DIR ]; then + echo "ERROR: $BOINC_DIR does not exist" + exit 1 + elif [ ! -x $BOINC_BIN ]; then + echo "ERROR: $BOINC_BIN does not exist or not executable" + exit 1 + fi + + echo "Starting BOINC client" + su - $BOINC_USER -c "cd $BOINC_DIR; exec $BOINC_BIN $BOINC_OPTIONS" & + +} + +boinc_stop() { + echo "Stopping BOINC client" + killall $BOINC_BIN +} + +boinc_restart() { + echo "Restarting BOINC client" + + boinc_status + if [ $? = 0 ]; then + boinc_stop + sleep 3 + boinc_start + else + boinc_start +fi +} + + +case "$1" in + start) + boinc_start + exit 0 + ;; + stop) + boinc_stop + exit 0 + ;; + restart) + boinc_restart + exit 0 + ;; + status) + boinc_status + if [ $? = 0 ]; then + echo "BOINC is running" + else + echo "BOINC is not running" + fi + ;; + *) + echo "Usage: $0 start|stop|restart|status" + exit 1 + ;; + +esac diff --git a/academic/bowtie/bowtie.SlackBuild b/academic/bowtie/bowtie.SlackBuild index f9ba26ee43..ad3c81770e 100644 --- a/academic/bowtie/bowtie.SlackBuild +++ b/academic/bowtie/bowtie.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bowtie -# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=bowtie -VERSION=${VERSION:-1.3.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-1.3.1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -50,18 +50,12 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then +if [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" + printf "\n$ARCH is unsupported by bowtie\n" + exit 1 fi set -e @@ -70,8 +64,8 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION-src -unzip $CWD/${PRGNAM}-${VERSION}-src.zip -cd $PRGNAM-$VERSION-src +tar xvf $CWD/${PRGNAM}-${VERSION}.tar.gz +cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -79,14 +73,14 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +sed -i "s|-O3|$SLKCFLAGS -O3|" Makefile make install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM -install -D -m755 $PRGNAM-build $PKG/usr/bin/$PRGNAM-build -install -D -m755 $PRGNAM-build-s $PKG/usr/bin/$PRGNAM-build-s -install -D -m755 $PRGNAM-inspect $PKG/usr/bin/$PRGNAM-inspect +executables=$( ls bowtie-* ) +for b in ${executables[@]}; do + install -D -m755 $b $PKG/usr/bin/$b +done # Copy genomic data, scripts and more mkdir -p $PKG/usr/share/$PRGNAM diff --git a/academic/bowtie/bowtie.info b/academic/bowtie/bowtie.info index d3da6c5093..4713d9bae4 100644 --- a/academic/bowtie/bowtie.info +++ b/academic/bowtie/bowtie.info @@ -1,10 +1,10 @@ PRGNAM="bowtie" -VERSION="1.3.0" +VERSION="1.3.1" HOMEPAGE="http://bowtie-bio.sourceforge.net/index.shtml" -DOWNLOAD="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.0/bowtie-1.3.0-src.zip" -MD5SUM="2055d1ab066a8f3f015bdffa26509335" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/BenLangmead/bowtie/archive/v1.3.1/bowtie-1.3.1.tar.gz" +MD5SUM_x86_64="06b0377e967501ce73bca087e6c5fcb0" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild b/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild index 6055ae5246..262e05cab7 100644 --- a/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild +++ b/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=bowtie2-legacy VERSION=${VERSION:-2.1.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -81,6 +81,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +sed -i "s,flag > 0,flag != 0," aligner_result.cpp # Use our FLAGS sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile diff --git a/academic/bowtie2/bowtie2.SlackBuild b/academic/bowtie2/bowtie2.SlackBuild index f659668de5..37f440626e 100644 --- a/academic/bowtie2/bowtie2.SlackBuild +++ b/academic/bowtie2/bowtie2.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for bowtie2 # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com -# Copyright 2018-2021 Rob van Nues sborg63@disroot.org +# Copyright 2018-2024 Rob van Nues sborg63@disroot.org # # All rights reserved. # @@ -27,7 +27,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=bowtie2 -VERSION=${VERSION:-2.4.4} +VERSION=${VERSION:-2.5.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -40,9 +40,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -52,18 +49,12 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then +if [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" + printf "\n$ARCH is unsupported by $PRGNAM\n" + exit 1 fi set -e diff --git a/academic/bowtie2/bowtie2.info b/academic/bowtie2/bowtie2.info index 1fd73195b3..6942bdcfcd 100644 --- a/academic/bowtie2/bowtie2.info +++ b/academic/bowtie2/bowtie2.info @@ -1,10 +1,10 @@ PRGNAM="bowtie2" -VERSION="2.4.4" +VERSION="2.5.3" HOMEPAGE="https://github.com/BenLangmead/bowtie2/releases" -DOWNLOAD="https://github.com/BenLangmead/bowtie2/archive/v2.4.4/bowtie2-2.4.4.tar.gz" -MD5SUM="b9da62b01d904149ffc6f5caad7fd1b1" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/BenLangmead/bowtie2/archive/v2.5.3/bowtie2-2.5.3.tar.gz" +MD5SUM_x86_64="c9bb6edaf47c4487efd4b2a055912182" REQUIRES="tbb" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/bpp-core/bpp-core.SlackBuild b/academic/bpp-core/bpp-core.SlackBuild index 7199ab6ef5..ea5ae35b52 100644 --- a/academic/bpp-core/bpp-core.SlackBuild +++ b/academic/bpp-core/bpp-core.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bpp-core -# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -79,6 +76,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# thanks Debian +patch -p1 -i $CWD/gcc11.patch + sed -i "s|cmake-package-location lib/cmake|cmake-package-location lib${LIBDIRSUFFIX}/cmake|" CMakeLists.txt mkdir -p build @@ -96,7 +96,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/bpp-core/gcc11.patch b/academic/bpp-core/gcc11.patch new file mode 100644 index 0000000000..d4db303a25 --- /dev/null +++ b/academic/bpp-core/gcc11.patch @@ -0,0 +1,13 @@ +Description: Including limits lib to fix gcc-11 FTBFS +Author: Nilesh Patra <nilesh@debian.org> +Last-Update: 2021-04-15 +--- a/src/Bpp/Graph/GlobalGraph.cpp ++++ b/src/Bpp/Graph/GlobalGraph.cpp +@@ -42,6 +42,7 @@ + #include <sstream> + #include <string> + #include <vector> ++#include <limits> + + #include "../Exceptions.h" + #include "../Text/TextTools.h" diff --git a/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild b/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild index ab590a6ff9..31a4b60cc8 100644 --- a/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild +++ b/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bpp-phyl-omics -# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -96,7 +93,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/bpp-phyl/bpp-phyl.SlackBuild b/academic/bpp-phyl/bpp-phyl.SlackBuild index 5cae5d3670..d1de4c4a79 100644 --- a/academic/bpp-phyl/bpp-phyl.SlackBuild +++ b/academic/bpp-phyl/bpp-phyl.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bpp-phyl -# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -96,7 +93,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/bpp-popgen/bpp-popgen.SlackBuild b/academic/bpp-popgen/bpp-popgen.SlackBuild index da35866122..11e65b03be 100644 --- a/academic/bpp-popgen/bpp-popgen.SlackBuild +++ b/academic/bpp-popgen/bpp-popgen.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bpp-popgen -# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -96,7 +93,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild b/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild index 0c91a9548b..c81730ea5a 100644 --- a/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild +++ b/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bpp-seq-omics -# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -96,7 +93,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/bpp-seq/bpp-seq.SlackBuild b/academic/bpp-seq/bpp-seq.SlackBuild index 50f0a19f7c..298386625e 100644 --- a/academic/bpp-seq/bpp-seq.SlackBuild +++ b/academic/bpp-seq/bpp-seq.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bpp-seq -# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -38,14 +38,12 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -96,7 +94,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild b/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild index 220aed50d2..ea548edbdf 100644 --- a/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild +++ b/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bpp1.9-utils -# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -39,9 +39,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -65,7 +62,6 @@ else LIBDIRSUFFIX="" fi -# This is needed for vCAPS to find its libraries at runtime. Thanks Urchlay! LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" set -e @@ -87,6 +83,8 @@ find -L . \ export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH" sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" NumCalc.spec +source /etc/profile.d/gcc5.sh + mkdir -p build cd build cmake \ @@ -101,14 +99,13 @@ sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" NumCalc/cmake_install.cmake make DESTDIR=$PKG install cd .. -rm -f $PKG/usr/lib$LIBDIRSUFFIX/Bpp1.9/libbpp-numcalc.a - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +chmod 0644 AUTHORS ChangeLog COPYING cp -a \ - AUTHORS ChangeLog COPYING INSTALL \ + AUTHORS ChangeLog COPYING \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/bpp1.9-numcalc/bpp1.9-numcalc.info b/academic/bpp1.9-numcalc/bpp1.9-numcalc.info index 0a1c619ed1..026698cbb2 100644 --- a/academic/bpp1.9-numcalc/bpp1.9-numcalc.info +++ b/academic/bpp1.9-numcalc/bpp1.9-numcalc.info @@ -1,7 +1,7 @@ PRGNAM="bpp1.9-numcalc" VERSION="1.8.0" HOMEPAGE="http://biopp.univ-montp2.fr/" -DOWNLOAD="http://biopp.univ-montp2.fr/repos/sources/bpp-numcalc-1.8.0.tar.gz" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-numcalc-1.8.0.tar.gz" MD5SUM="0d6d51aaefcb4f89816704feae010bc9" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild b/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild index 94f338cef3..fa951d6f2e 100644 --- a/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild +++ b/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bpp1.9-phyl -# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -39,9 +39,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -65,7 +62,6 @@ else LIBDIRSUFFIX="" fi -# This is needed for vCAPS to find its libraries at runtime. Thanks Urachlay! LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" set -e @@ -90,6 +86,8 @@ patch -p1 -i $CWD/caps_TreeTemplateTools.patch export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH" sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Phyl.spec +source /etc/profile.d/gcc5.sh + mkdir -p build cd build cmake \ @@ -104,15 +102,13 @@ cd build make DESTDIR=$PKG install cd .. -# Remove static library -rm -f $PKG/usr/lib64/Bpp1.9/libbpp-phyl.a - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +chmod 0644 AUTHORS ChangeLog COPYING cp -a \ - AUTHORS ChangeLog COPYING INSTALL \ + AUTHORS ChangeLog COPYING \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/bpp1.9-phyl/bpp1.9-phyl.info b/academic/bpp1.9-phyl/bpp1.9-phyl.info index 26d984b0c4..ae873c0a59 100644 --- a/academic/bpp1.9-phyl/bpp1.9-phyl.info +++ b/academic/bpp1.9-phyl/bpp1.9-phyl.info @@ -1,7 +1,7 @@ PRGNAM="bpp1.9-phyl" VERSION="1.9.0" HOMEPAGE="http://biopp.univ-montp2.fr/" -DOWNLOAD="http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-1.9.0.tar.gz" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-phyl-1.9.0.tar.gz" MD5SUM="1b100b688faca52419e9f782798b8add" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild b/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild index 4d076f1a69..fcea3aef1d 100644 --- a/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild +++ b/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bpp1.9-seq -# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -39,9 +39,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -65,7 +62,6 @@ else LIBDIRSUFFIX="" fi -# This is needed for vCAPS to find its libraries at runtime. Thanks Urchlay! LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" set -e @@ -87,6 +83,8 @@ find -L . \ export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH" sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Seq.spec +source /etc/profile.d/gcc5.sh + mkdir -p build cd build cmake \ @@ -101,15 +99,13 @@ cd build make DESTDIR=$PKG install cd .. -# Remove static lib -rm -f $PKG/usr/lib64/Bpp1.9/libbpp-seq.a - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +chmod 0644 AUTHORS ChangeLog COPYING cp -a \ - AUTHORS ChangeLog COPYING INSTALL \ + AUTHORS ChangeLog COPYING \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/bpp1.9-seq/bpp1.9-seq.info b/academic/bpp1.9-seq/bpp1.9-seq.info index 35b6d40f95..0d6d9f38df 100644 --- a/academic/bpp1.9-seq/bpp1.9-seq.info +++ b/academic/bpp1.9-seq/bpp1.9-seq.info @@ -1,7 +1,7 @@ PRGNAM="bpp1.9-seq" VERSION="1.7.0" HOMEPAGE="http://biopp.univ-montp2.fr/" -DOWNLOAD="http://biopp.univ-montp2.fr/repos/sources/bpp-seq-1.7.0.tar.gz" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-seq-1.7.0.tar.gz" MD5SUM="4256293637ac4131c0d030f5265b8b8b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild index f38058baff..6840376b84 100644 --- a/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild +++ b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bpp1.9-utils -# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -39,9 +39,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -84,11 +81,13 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # This is needed on newer systems (-current) -sed -i "s:file;:file.good();:g" Utils/FileTools.cpp +#sed -i "s:file;:file.good();:g" Utils/FileTools.cpp # Use custom install place, so libs can coexist with latest Bio++ sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Utils.spec +source /etc/profile.d/gcc5.sh + mkdir -p build cd build cmake \ @@ -105,15 +104,12 @@ sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Utils/cmake_install.cmake make DESTDIR=$PKG install cd .. -# static library not needed -rm -f $PKG/usr/lib$LIBDIRSUFFIX/Bpp1.9/libbpp-utils.a - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS ChangeLog COPYING INSTALL \ + AUTHORS ChangeLog COPYING \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/bpp1.9-utils/bpp1.9-utils.info b/academic/bpp1.9-utils/bpp1.9-utils.info index 8e7863e9f1..8ee8062200 100644 --- a/academic/bpp1.9-utils/bpp1.9-utils.info +++ b/academic/bpp1.9-utils/bpp1.9-utils.info @@ -1,10 +1,10 @@ PRGNAM="bpp1.9-utils" VERSION="1.5.0" HOMEPAGE="http://biopp.univ-montp2.fr/" -DOWNLOAD="http://biopp.univ-montp2.fr/repos/sources/bpp-utils-1.5.0.tar.gz" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-utils-1.5.0.tar.gz" MD5SUM="4625b7f2146caa1815ed7dc433d5eb78" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="gcc5" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.copm" diff --git a/academic/bppsuite/bppsuite.SlackBuild b/academic/bppsuite/bppsuite.SlackBuild index e8804980e6..4e4bc8c2d2 100644 --- a/academic/bppsuite/bppsuite.SlackBuild +++ b/academic/bppsuite/bppsuite.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bppsuite -# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -106,7 +103,7 @@ rm -f $PKG/usr/info/dir gzip -9 $PKG/usr/info/*.info* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt README.md $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/bppsuite/bppsuite.info b/academic/bppsuite/bppsuite.info index 97626a2bff..ccd92962fe 100644 --- a/academic/bppsuite/bppsuite.info +++ b/academic/bppsuite/bppsuite.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/BioPP/bppsuite/archive/v2.4.1/bppsuite-2.4.1.tar.gz MD5SUM="d254ffd9e121b408aed36f49e62920d1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="bpp-seq-omics bpp-phyl-omics bpp-popgen" +REQUIRES="bpp-phyl-omics bpp-popgen" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/btf/btf.SlackBuild b/academic/btf/btf.SlackBuild index 820d913277..453b49631f 100644 --- a/academic/btf/btf.SlackBuild +++ b/academic/btf/btf.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/cadabra2/README b/academic/cadabra2/README index 0533ffcdd3..e26c444234 100644 --- a/academic/cadabra2/README +++ b/academic/cadabra2/README @@ -1,11 +1,12 @@ Cadabra is a symbolic computer algebra system (CAS) designed specifically for the solution of problems encountered in field theory. It has extensive functionality for tensor computer algebra, tensor -polynomial simplification including multi-term symmetries, fermions and -anti-commuting variables, Clifford algebras and Fierz transformations, -component computations, implicit coordinate dependence, multiple index -types and many more. The input format is a subset of TeX. Both a -command-line and a graphical interface are available. +polynomial simplification including multi-term symmetries, fermions +and anti-commuting variables, Clifford algebras and Fierz +transformations, component computations, implicit coordinate +dependence, multiple index types and many more. The input format is a +subset of TeX. Both a command-line and a graphical interface are +available. * Designed for field-theory problems, with handling of anti-commuting and non-commuting objects without special notations for their @@ -21,13 +22,14 @@ command-line and a graphical interface are available. * Allows for both abstract and component computations. -* A standalone graphical notebook interface which can also be used as a - front-end for SymPy. +* A standalone graphical notebook interface which can also be used as + a front-end for SymPy. * Input and output using a subset of LaTeX notation. * Programmable using Python. -If this SlackBuild run on a system which has Mathematica (not on SBo) -installed, the support of Mathematica can be enabled by setting the -environment variable MMA=ON (default: MMA=OFF). +If this SlackBuild is running on a system which has WolframEngine +(available on SBo) or Mathematica (not on SBo) installed, its support +in Cadabra can be enabled by setting the environment variable MMA=ON +(default: MMA=OFF). diff --git a/academic/cadabra2/cadabra2.SlackBuild b/academic/cadabra2/cadabra2.SlackBuild index 9a4d96a6dd..dff731aad7 100644 --- a/academic/cadabra2/cadabra2.SlackBuild +++ b/academic/cadabra2/cadabra2.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cadabra2 -# Copyright 2017-2021, Alexander Verbovetsky, Moscow, Russia +# Copyright 2017-2024, Alexander Verbovetsky, Moscow, Russia # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=cadabra2 -VERSION=${VERSION:-2.3.6.3} +VERSION=${VERSION:-2.4.5.6} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -39,9 +39,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -81,34 +78,23 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; sed --in-place \ - -e "s/\(DESTINATION lib\)/\1${LIBDIRSUFFIX}/" \ - client_server/CMakeLists.txt - -sed --in-place \ - -e "s/\(CMAKE_INSTALL_PREFIX}\/lib\)/\1${LIBDIRSUFFIX}/" \ - CMakeLists.txt + -e "s|/lib/python|/lib${LIBDIRSUFFIX}/python|" \ + CMakeLists.txt core/cadabra2-cli.cc client_server/Server.cc sed --in-place \ -e '/^execute_process(COMMAND texhash)$/d' \ frontend/latex/install.cmake -sed --in-place \ - -e '/^install(CODE\s\+"execute_process(COMMAND \(touch\|gtk-update-icon-cache.*\|chmod go+r\) ${ICON_PREFIX}\/share\/icons\/hicolor\(\|\/icon-theme\.cache\))")$/d' \ - frontend/gtkmm/CMakeLists.txt - find ./ -type f -name '*.py' -exec \ - sed -i -e 's|#!/usr/bin/python\>|#!/usr/bin/python3|' \ - -e 's|#!/usr/bin/env python\>|#!/usr/bin/env python3|' {} \; + sed -i -e 's|#!/usr/bin/env python\>|#!/usr/bin/env python3|' {} \; mkdir -p build cd build - export "PATH=/opt/cmake-202x/bin:$PATH" cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ -DSQLITE3_INCLUDE_DIR=/usr/include \ - -DENABLE_SYSTEM_JSONCPP=ON \ -DENABLE_MATHEMATICA=${MMA^^} \ -DCMAKE_BUILD_TYPE=Release .. make diff --git a/academic/cadabra2/cadabra2.info b/academic/cadabra2/cadabra2.info index 99e6eff0c1..54385565de 100644 --- a/academic/cadabra2/cadabra2.info +++ b/academic/cadabra2/cadabra2.info @@ -1,10 +1,10 @@ PRGNAM="cadabra2" -VERSION="2.3.6.3" +VERSION="2.4.5.6" HOMEPAGE="https://cadabra.science" -DOWNLOAD="https://downloads.sourceforge.net/slackbuildsdirectlinks/cadabra2/cadabra2-2.3.6.3.tar.gz" -MD5SUM="9e792260d2b6dea2bb7c5d8a0a627662" +DOWNLOAD="https://github.com/kpeeters/cadabra2/archive/2.4.5.6/cadabra2-2.4.5.6.tar.gz" +MD5SUM="769833ed91bb6999cdf86bd3f26710a7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="python3-matplotlib python3-gmpy2 python3-sympy jsoncpp" +REQUIRES="python3-matplotlib python3-gmpy2 python3-sympy" MAINTAINER="Alexander Verbovetsky" EMAIL="alik@ejik.org" diff --git a/academic/calc/calc.SlackBuild b/academic/calc/calc.SlackBuild index b53906a3be..8b51ed982c 100644 --- a/academic/calc/calc.SlackBuild +++ b/academic/calc/calc.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=calc -VERSION=${VERSION:-2.12.9.1} +VERSION=${VERSION:-2.14.1.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/calc/calc.info b/academic/calc/calc.info index 7aa20d8a72..9ba6856746 100644 --- a/academic/calc/calc.info +++ b/academic/calc/calc.info @@ -1,10 +1,10 @@ PRGNAM="calc" -VERSION="2.12.9.1" +VERSION="2.14.1.5" HOMEPAGE="http://www.isthe.com/chongo/tech/comp/calc/" -DOWNLOAD="http://www.isthe.com/chongo/src/calc/calc-2.12.9.1.tar.bz2" -MD5SUM="e4abaecede9a9794474f3531550668f4" +DOWNLOAD="http://www.isthe.com/chongo/src/calc/calc-2.14.1.5.tar.bz2" +MD5SUM="57607be276a3998fa76376e41dc49a03" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Dave Woodfall" +MAINTAINER="D Woodfall" EMAIL="dave@slackbuilds.org" diff --git a/academic/calcoo/calcoo.info b/academic/calcoo/calcoo.info index e05dcb7ba6..cb01da56f7 100644 --- a/academic/calcoo/calcoo.info +++ b/academic/calcoo/calcoo.info @@ -5,6 +5,6 @@ DOWNLOAD="http://downloads.sourceforge.net/project/calcoo/calcoo/2.1.0/calcoo.ja MD5SUM="78880e375fb50cb6b945e43713c11065" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk8" MAINTAINER="Robby Workman" EMAIL="rworkman@slackbuilds.org" diff --git a/academic/camd/camd.SlackBuild b/academic/camd/camd.SlackBuild index 3b4c52de11..2823459a12 100644 --- a/academic/camd/camd.SlackBuild +++ b/academic/camd/camd.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/cap3/README b/academic/cap3/README index bd6e1fb491..a4023eccfa 100644 --- a/academic/cap3/README +++ b/academic/cap3/README @@ -13,3 +13,9 @@ This just repackages the binaries provided from upstream. If you use CAP3 in any published work, please cite: Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Genome Res., 9, 868-877. + +*NOTE* +The downloads are available here: +https://faculty.sites.iastate.edu/xqhuang/cap3-assembly-program + +Sources are also hosted by the maintainer to ease automatic download. diff --git a/academic/cap3/cap3.SlackBuild b/academic/cap3/cap3.SlackBuild index 2229bdd2d6..65359adf4b 100644 --- a/academic/cap3/cap3.SlackBuild +++ b/academic/cap3/cap3.SlackBuild @@ -22,25 +22,27 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220405 bkw: Modified by SlackBuilds.org, BUILD=3: fix doc permissions. + +# 20220318 bkw: Modified by SlackBuilds.org: fix 32-bit build when ARCH +# set to i586 or i686 in environment. + cd $(dirname $0) ; CWD=$(pwd) PRGNAM=cap3 VERSION=${VERSION:-20091029} # Use the last modification date as version -BUILD=${BUILD:-2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -52,17 +54,11 @@ OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - -# Determine the tarball arch -if [ "$ARCH" = "x86_64" ]; then - SRCARCH=".x86_64" -else - SRCARCH="" -fi +case "$ARCH" in + x86_64) SRCARCH=".x86_64" ;; + i?86) SRCARCH="" ;; + *) echo "Unsupported ARCH '$ARCH'"; exit 1 ;; +esac # Construct tarball name TARNAME=${PRGNAM}.linux${SRCARCH} @@ -77,18 +73,15 @@ cd $DIRNAM chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ + -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM -install -D -m755 formcon $PKG/usr/bin/formcon + -exec chmod 644 {} \+ -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +install -s -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -s -D -m755 formcon $PKG/usr/bin/formcon mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ +install -m0644 \ aceform doc README \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/cap3/cap3.info b/academic/cap3/cap3.info index 0ac9937cbe..e4293f8054 100644 --- a/academic/cap3/cap3.info +++ b/academic/cap3/cap3.info @@ -1,9 +1,9 @@ PRGNAM="cap3" VERSION="20091029" HOMEPAGE="http://seq.cs.iastate.edu/" -DOWNLOAD="http://seq.cs.iastate.edu/CAP3/cap3.linux.tar" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/cap3.linux.tar" MD5SUM="55f57f61e588d4de06c0506cf2696c29" -DOWNLOAD_x86_64="http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar" +DOWNLOAD_x86_64="https://raw.githubusercontent.com/slackalaxy/sources/main/cap3.linux.x86_64.tar" MD5SUM_x86_64="5393d937978ecc5f18fcb741140e1f02" REQUIRES="" MAINTAINER="Petar Petrov" diff --git a/academic/cblas/cblas.SlackBuild b/academic/cblas/cblas.SlackBuild index 6bd73f6c80..7334c23998 100644 --- a/academic/cblas/cblas.SlackBuild +++ b/academic/cblas/cblas.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CBLAS -# Copyright 2016-2021 Kyle Guinn <elyk03@gmail.com> +# Copyright 2016-2024 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=cblas SRCNAM=lapack -VERSION=${VERSION:-3.10.0} +VERSION=${VERSION:-3.12.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -39,22 +39,19 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="LICENSE CBLAS/README" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then diff --git a/academic/cblas/cblas.info b/academic/cblas/cblas.info index 08ecd567f0..ff8d8b3070 100644 --- a/academic/cblas/cblas.info +++ b/academic/cblas/cblas.info @@ -1,8 +1,8 @@ PRGNAM="cblas" -VERSION="3.10.0" +VERSION="3.12.0" HOMEPAGE="https://www.netlib.org/blas/" -DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.10.0/lapack-3.10.0.tar.gz" -MD5SUM="d70fc27a8bdebe00481c97c728184f09" +DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.12.0/lapack-3.12.0.tar.gz" +MD5SUM="c1b38bef123584d86a1bd8000784a7b2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="blas" diff --git a/academic/cblas/patches/cmake-piecewise.diff b/academic/cblas/patches/cmake-piecewise.diff index f8ee150b59..37cde2acaa 100644 --- a/academic/cblas/patches/cmake-piecewise.diff +++ b/academic/cblas/patches/cmake-piecewise.diff @@ -2,15 +2,15 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt --- a/CBLAS/CMakeLists.txt +++ b/CBLAS/CMakeLists.txt @@ -1,8 +1,6 @@ - message(STATUS "CBLAS enable") + message(STATUS "CBLAS enabled") enable_language(C) -set(LAPACK_INSTALL_EXPORT_NAME ${CBLASLIB}-targets) - # Create a header file cblas.h for the routines called in my C programs - include(FortranCInterface) - ## Ensure that the fortran compiler and c compiler specified are compatible -@@ -51,22 +49,3 @@ + include(CheckLanguage) + check_language(Fortran) +@@ -54,22 +52,3 @@ DESTINATION ${PKG_CONFIG_DIR} COMPONENT Development ) @@ -56,15 +56,12 @@ diff --git a/CBLAS/cmake/cblas-config-install.cmake.in b/CBLAS/cmake/cblas-confi deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-install.cmake.in +++ /dev/null -@@ -1,23 +0,0 @@ +@@ -1,19 +0,0 @@ -# Compute locations from <prefix>/@{LIBRARY_DIR@/cmake/lapacke-<v>/<self>.cmake -get_filename_component(_CBLAS_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_SELF_DIR}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_PREFIX}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_CBLAS_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") +-set(LAPACK_DIR "@CMAKE_INSTALL_FULL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. @@ -73,12 +70,11 @@ deleted file mode 100644 -endif() - -# Report lapacke header search locations. --set(CBLAS_INCLUDE_DIRS ${_CBLAS_PREFIX}/include) +-set(CBLAS_INCLUDE_DIRS @CMAKE_INSTALL_FULL_INCLUDEDIR@) - -# Report lapacke libraries. -set(CBLAS_LIBRARIES @CBLASLIB@) - --unset(_CBLAS_PREFIX) -unset(_CBLAS_SELF_DIR) diff --git a/CBLAS/cmake/cblas-config-version.cmake.in b/CBLAS/cmake/cblas-config-version.cmake.in deleted file mode 100644 @@ -96,15 +92,15 @@ deleted file mode 100644 diff --git a/CBLAS/src/CMakeLists.txt b/CBLAS/src/CMakeLists.txt --- a/CBLAS/src/CMakeLists.txt +++ b/CBLAS/src/CMakeLists.txt -@@ -123,9 +123,5 @@ +@@ -172,9 +172,5 @@ if(HAS_ATTRIBUTE_WEAK_SUPPORT) target_compile_definitions(${CBLASLIB} PRIVATE HAS_ATTRIBUTE_WEAK_SUPPORT) endif() -target_include_directories(${CBLASLIB} PUBLIC -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../include> +- $<BUILD_INTERFACE:${LAPACK_BINARY_DIR}/include> - $<INSTALL_INTERFACE:include> -) - target_link_libraries(${CBLASLIB} PRIVATE ${BLAS_LIBRARIES}) + target_link_libraries(${CBLASLIB} PUBLIC ${BLAS_LIBRARIES}) lapack_install_library(${CBLASLIB}) diff --git a/CMAKE/lapack-config-build.cmake.in b/CMAKE/lapack-config-build.cmake.in deleted file mode 100644 @@ -152,8 +148,8 @@ deleted file mode 100644 diff --git a/CMakeLists.txt b/CMakeLists.txt --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -157,11 +157,8 @@ - +@@ -155,11 +155,8 @@ + endif() # -------------------------------------------------- -set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKLIB}-targets) @@ -164,30 +160,8 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Development LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT RuntimeLibraries RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT RuntimeLibraries -@@ -201,21 +198,6 @@ - include(CheckLAPACKCompilerFlags) - CheckLAPACKCompilerFlags() +@@ -218,8 +215,9 @@ --# -------------------------------------------------- --# Check second function -- --include(CheckTimeFunction) --set(NONE ${TIME_FUNC}) --CHECK_TIME_FUNCTION(NONE TIME_FUNC) --CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) --CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) --CHECK_TIME_FUNCTION(EXT_ETIME_ TIME_FUNC) --CHECK_TIME_FUNCTION(INT_ETIME TIME_FUNC) --message(STATUS "--> Will use second_${TIME_FUNC}.f and dsecnd_${TIME_FUNC}.f as timing function.") -- --set(SECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/second_${TIME_FUNC}.f) --set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) -- - # deprecated LAPACK and LAPACKE routines - option(BUILD_DEPRECATED "Build deprecated routines" OFF) - message(STATUS "Build deprecated routines: ${BUILD_DEPRECATED}") -@@ -239,8 +221,9 @@ - endif() # -------------------------------------------------- -# Subdirectories that need to be processed @@ -197,7 +171,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided BLAS libraries if(BLAS_LIBRARIES) -@@ -251,131 +234,105 @@ +@@ -230,59 +228,41 @@ if(BLAS_FOUND) message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRARIES}.") else() @@ -268,21 +242,28 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided or automatically found LAPACK libraries if(LAPACK_LIBRARIES) - include(CheckFortranFunctionExists) - set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) - # Check if new routine of 3.4.0 is in LAPACK_LIBRARIES -- CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LATESTLAPACK_FOUND) -+ CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LAPACK_FOUND) - unset(CMAKE_REQUIRED_LIBRARIES) -- if(LATESTLAPACK_FOUND) -+ if(LAPACK_FOUND) - message(STATUS "--> LAPACK supplied by user is WORKING, will use ${LAPACK_LIBRARIES}.") +@@ -293,27 +273,28 @@ + include(CheckFortranFunctionExists) + set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) + # Check if new routine of 3.4.0 is in LAPACK_LIBRARIES +- CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LATESTLAPACK_FOUND) ++ CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LAPACK_FOUND) + unset(CMAKE_REQUIRED_LIBRARIES) +- if(LATESTLAPACK_FOUND) ++ if(LAPACK_FOUND) + message(STATUS "--> LAPACK supplied by user is WORKING, will use ${LAPACK_LIBRARIES}.") + else() +- message(ERROR "--> LAPACK supplied by user is not WORKING or is older than LAPACK 3.4.0, CANNOT USE ${LAPACK_LIBRARIES}.") +- message(ERROR "--> Will use REFERENCE LAPACK (by default)") +- message(ERROR "--> Or Correct your LAPACK_LIBRARIES entry ") +- message(ERROR "--> Or Consider checking USE_OPTIMIZED_LAPACK") ++ message(SEND_ERROR "--> LAPACK supplied by user is NOT WORKING or is older than LAPACK 3.4.0, cannot use ${LAPACK_LIBRARIES}.") + endif() else() -- message(ERROR "--> LAPACK supplied by user is not WORKING or is older than LAPACK 3.4.0, CANNOT USE ${LAPACK_LIBRARIES}.") -- message(ERROR "--> Will use REFERENCE LAPACK (by default)") -- message(ERROR "--> Or Correct your LAPACK_LIBRARIES entry ") -- message(ERROR "--> Or Consider checking USE_OPTIMIZED_LAPACK") -+ message(SEND_ERROR "--> LAPACK supplied by user is NOT WORKING or is older than LAPACK 3.4.0, cannot use ${LAPACK_LIBRARIES}.") + message(STATUS "--> LAPACK supplied by user is ${LAPACK_LIBRARIES}.") + message(STATUS "--> CMake couldn't find a Fortran compiler, so it cannot check if the provided LAPACK library works.") +- set(LATESTLAPACK_FOUND TRUE) ++ set(LAPACK_FOUND TRUE) endif() -endif() @@ -298,20 +279,12 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + set(LAPACK_FOUND TRUE) + + set(NEED_BLAS TRUE) -+ -+ # Check second function -+ include(CheckTimeFunction) -+ set(NONE ${TIME_FUNC}) -+ CHECK_TIME_FUNCTION(NONE TIME_FUNC) -+ CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) -+ CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) -+ CHECK_TIME_FUNCTION(EXT_ETIME_ TIME_FUNC) -+ CHECK_TIME_FUNCTION(INT_ETIME TIME_FUNC) -+ message(STATUS "--> Will use second_${TIME_FUNC}.f and dsecnd_${TIME_FUNC}.f as timing function.") -+ -+ set(SECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/second_${TIME_FUNC}.f) -+ set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) -+ + + enable_language(Fortran) + +@@ -336,67 +317,38 @@ + set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) + add_subdirectory(SRC) -else() - set(CMAKE_EXE_LINKER_FLAGS @@ -349,16 +322,17 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt option(LAPACKE_WITH_TMG "Build LAPACKE with tmglib routines" OFF) if(LAPACKE_WITH_TMG) - set(LAPACKE ON) -+ set(BUILD_LAPACKE ON) - endif() - +-endif() +- -# TMGLIB -# Cache export target -set(LAPACK_INSTALL_EXPORT_NAME_CACHE ${LAPACK_INSTALL_EXPORT_NAME}) -if(BUILD_TESTING OR LAPACKE_WITH_TMG) +- enable_language(Fortran) - if(LATESTLAPACK_FOUND AND LAPACKE_WITH_TMG) - set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) - # Check if dlatms (part of tmg) is found +- include(CheckFortranFunctionExists) - CHECK_FORTRAN_FUNCTION_EXISTS("dlatms" LAPACK_WITH_TMGLIB_FOUND) - unset(CMAKE_REQUIRED_LIBRARIES) - if(NOT LAPACK_WITH_TMGLIB_FOUND) @@ -368,18 +342,29 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt - endif() - endif() - add_subdirectory(TESTING/MATGEN) --endif() ++ set(BUILD_LAPACKE ON) + endif() -# Reset export target -set(LAPACK_INSTALL_EXPORT_NAME ${LAPACK_INSTALL_EXPORT_NAME_CACHE}) -unset(LAPACK_INSTALL_EXPORT_NAME_CACHE) - + +-#------------------------------------- +-# LAPACKE + # Include lapack.h and lapacke_mangling.h even if LAPACKE is not built + add_subdirectory(LAPACKE/include) + -if(LAPACKE) +if(BUILD_LAPACKE) + set(NEED_LAPACK TRUE) add_subdirectory(LAPACKE) endif() -@@ -428,111 +385,16 @@ +- + #------------------------------------- + # BLAS++ / LAPACK++ + option(BLAS++ "Build BLAS++" OFF) +@@ -446,111 +398,16 @@ ExternalProject_Add_StepDependencies(lapackpp build blaspp ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) endif() @@ -397,7 +382,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -set(CPACK_PACKAGE_INSTALL_DIRECTORY "LAPACK") -if(WIN32 AND NOT UNIX) - # There is a bug in NSI that does not handle full unix paths properly. Make -- # sure there is at least one set of four (4) backlasshes. +- # sure there is at least one set of four (4) backslashes. - set(CPACK_NSIS_HELP_LINK "http:\\\\\\\\http://icl.cs.utk.edu/lapack-forum") - set(CPACK_NSIS_URL_INFO_ABOUT "http:\\\\\\\\www.netlib.org/lapack") - set(CPACK_NSIS_CONTACT "lapack@eecs.utk.edu") @@ -501,20 +486,20 @@ diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt --- a/LAPACKE/CMakeLists.txt +++ b/LAPACKE/CMakeLists.txt @@ -1,8 +1,6 @@ - message(STATUS "LAPACKE enable") + message(STATUS "LAPACKE enabled") enable_language(C) -set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKELIB}-targets) - - # Create a header file lapacke_mangling.h for the routines called in my C programs - include(FortranCInterface) - ## Ensure that the fortran compiler and c compiler specified are compatible -@@ -79,14 +77,6 @@ + include_directories(include ${LAPACK_BINARY_DIR}/include) + add_subdirectory(src) + add_subdirectory(utils) +@@ -74,14 +72,6 @@ VERSION ${LAPACK_VERSION} SOVERSION ${LAPACK_MAJOR_VERSION} ) -target_include_directories(${LAPACKELIB} PUBLIC -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> +- $<BUILD_INTERFACE:${LAPACK_BINARY_DIR}/include> - $<INSTALL_INTERFACE:include> -) -if(WIN32 AND NOT UNIX) @@ -524,7 +509,7 @@ diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt if(LAPACKE_WITH_TMG) target_link_libraries(${LAPACKELIB} PRIVATE ${TMGLIB}) -@@ -111,22 +101,3 @@ +@@ -106,22 +96,3 @@ DESTINATION ${PKG_CONFIG_DIR} COMPONENT Development ) @@ -573,15 +558,12 @@ diff --git a/LAPACKE/cmake/lapacke-config-install.cmake.in b/LAPACKE/cmake/lapac deleted file mode 100644 --- a/LAPACKE/cmake/lapacke-config-install.cmake.in +++ /dev/null -@@ -1,26 +0,0 @@ +@@ -1,22 +0,0 @@ -# Compute locations from <prefix>/@{LIBRARY_DIR@/cmake/lapacke-<v>/<self>.cmake -get_filename_component(_LAPACKE_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_SELF_DIR}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_PREFIX}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_LAPACKE_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") +-set(LAPACK_DIR "@CMAKE_INSTALL_FULL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. @@ -593,12 +575,11 @@ deleted file mode 100644 -set(LAPACKE_Fortran_COMPILER_ID ${LAPACK_Fortran_COMPILER_ID}) - -# Report lapacke header search locations. --set(LAPACKE_INCLUDE_DIRS ${_LAPACKE_PREFIX}/include) +-set(LAPACKE_INCLUDE_DIRS @CMAKE_INSTALL_FULL_INCLUDEDIR@) - -# Report lapacke libraries. -set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) - --unset(_LAPACKE_PREFIX) -unset(_LAPACKE_SELF_DIR) diff --git a/LAPACKE/cmake/lapacke-config-version.cmake.in b/LAPACKE/cmake/lapacke-config-version.cmake.in deleted file mode 100644 @@ -613,3 +594,20 @@ deleted file mode 100644 - endif() -endif() - +diff --git a/LAPACKE/include/CMakeLists.txt b/LAPACKE/include/CMakeLists.txt +--- a/LAPACKE/include/CMakeLists.txt ++++ b/LAPACKE/include/CMakeLists.txt +@@ -1,5 +1,5 @@ + set(LAPACKE_INCLUDE lapack.h) +-IF(LAPACKE) ++IF(BUILD_LAPACKE) + list(APPEND LAPACKE_INCLUDE lapacke.h lapacke_config.h lapacke_utils.h) + endif() + +@@ -23,4 +23,4 @@ + message(WARNING "Reverting to pre-defined include/lapacke_mangling.h") + configure_file(lapacke_mangling_with_flags.h.in + ${LAPACK_BINARY_DIR}/include/lapacke_mangling.h) +-endif() +\ No newline at end of file ++endif() diff --git a/academic/ccolamd/ccolamd.SlackBuild b/academic/ccolamd/ccolamd.SlackBuild index 11ecdf6549..504b1668e9 100644 --- a/academic/ccolamd/ccolamd.SlackBuild +++ b/academic/ccolamd/ccolamd.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/cdo/README b/academic/cdo/README index e767d4ea31..a7fcde9c55 100644 --- a/academic/cdo/README +++ b/academic/cdo/README @@ -5,3 +5,12 @@ Climate and NWP model Data. Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. + +REQUIRES: proj udunits netcdf eccodes + +By default, the script does not build nor run the tests. You can use the +option TESTBUILD=YES to build and run the tests before the make install +part. Note that the hdf5 slackbuild builds the library in a +non-thread-safe manner so one of the test will fail with a note in the +test log about requiring the use of the -L flag to compensate, but the +tests themself to not use that flag so fails. diff --git a/academic/cdo/cdo.SlackBuild b/academic/cdo/cdo.SlackBuild index bd7e924a3d..bc0583a4da 100644 --- a/academic/cdo/cdo.SlackBuild +++ b/academic/cdo/cdo.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cdo -# Copyright 2020-2021 Gregory J. L. Tourte <artourter@gmail.com> +# Copyright 2020-2024 Gregory J. L. Tourte <artourter@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=cdo -VERSION=${VERSION:-2.0.1} +VERSION=${VERSION:-2.4.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -66,6 +66,8 @@ fi set -e +TESTBUILD=${TESTBUILD:-NO} + rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP @@ -74,31 +76,31 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -perm /111 -a \! -perm 755 -a -exec chmod 755 {} + -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} + -# static. CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --disable-static \ + --with-eccodes=yes \ --with-szlib=yes \ --with-netcdf=yes \ --with-hdf5=yes \ - --with-udunits2 \ --with-threads=yes \ - --disable-static \ + --with-udunits2 \ --with-fftw3 \ --with-proj \ --with-curl \ --with-libxml2 \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ + --enable-silent-rules \ --build=$ARCH-slackware-linux make +[[ $TESTBUILD == "YES" ]] && make check make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ @@ -106,7 +108,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS COPYING ChangeLog INSTALL NEWS OPERATORS README \ + AUTHORS ChangeLog LICENSE NEWS OPERATORS README \ doc/*.pdf \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/cdo/cdo.info b/academic/cdo/cdo.info index d652547f6a..f3ca4cd66b 100644 --- a/academic/cdo/cdo.info +++ b/academic/cdo/cdo.info @@ -1,10 +1,10 @@ PRGNAM="cdo" -VERSION="2.0.1" +VERSION="2.4.0" HOMEPAGE="https://code.mpimet.mpg.de/projects/cdo" -DOWNLOAD="https://code.mpimet.mpg.de/attachments/download/26477/cdo-2.0.1.tar.gz" -MD5SUM="3db00835ab5b60802903995e4a80ce59" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="proj udunits netcdf" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://code.mpimet.mpg.de/attachments/download/29313/cdo-2.4.0.tar.gz" +MD5SUM_x86_64="797d3c2257f73937dc95b280dd21fd8b" +REQUIRES="proj udunits netcdf eccodes" MAINTAINER="ArTourter" EMAIL="artourter@gmail.com" diff --git a/academic/celestia/README b/academic/celestia/README index 038946a99d..1e99d61175 100644 --- a/academic/celestia/README +++ b/academic/celestia/README @@ -1,11 +1,11 @@ -A real-time space simulation that lets you experience our universe -in three dimensions. +A real-time space simulation that lets you experience our universe in +three dimensions. -There are four frontend possibilities to choose. The Glut one works out -of the box, the GTK one needs gtkglext, and the Gnome one is untested. -The KDE frontend hasn't been updated since kde3 times, so it's practically -non-functional. +There are four frontend possibilities to choose. The Glut one works +out of the box, the GTK one needs gtkglext, and the Gnome one is +untested. The KDE frontend hasn't been updated since kde3 times, so +it's practically non-functional. -Since the GTK frontend is the default, gtkglext is a required dependency. -Further, lua53 is listed as required dependency, but lua or lua52 will -work as well. +Since the GTK frontend is the default, gtkglext is a required +dependency. Further, lua53 is listed as required dependency, but lua +or lua52 will work as well. diff --git a/academic/chemtool/chemtool.SlackBuild b/academic/chemtool/chemtool.SlackBuild index a05d93d3f9..975235e59a 100644 --- a/academic/chemtool/chemtool.SlackBuild +++ b/academic/chemtool/chemtool.SlackBuild @@ -79,6 +79,10 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# Thanks, Debian +# https://salsa.debian.org/debichem-team/chemtool/-/blob/7d0413fe4f5bce35fe9c16fd196758319df05442/debian/patches/957084_gcc10.patch +patch -p1 < $CWD/gcc10.patch + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ diff --git a/academic/chemtool/gcc10.patch b/academic/chemtool/gcc10.patch new file mode 100644 index 0000000000..d782f8e4a6 --- /dev/null +++ b/academic/chemtool/gcc10.patch @@ -0,0 +1,37 @@ +--- a/ct1.h ++++ b/ct1.h +@@ -273,12 +273,12 @@ + extern float importfactor; + extern int importoffset; + +-char **intype; +-char **inmode; +-int babelin; +-char **outtype; +-char **outmode; +-int babelout; ++extern char **intype; ++extern char **inmode; ++extern int babelin; ++extern char **outtype; ++extern char **outmode; ++extern int babelout; + extern char *babel; + extern GdkGC *mygc[8],*background_gc,*hlgc; + extern int curpen; +--- a/inout.c ++++ b/inout.c +@@ -30,6 +30,13 @@ + extern GdkFont *font[7],*smallfont[7],*symbfont[7],*boldfont[7],*slfont[7]; + #endif + ++char **intype; ++char **inmode; ++int babelin; ++char **outtype; ++char **outmode; ++int babelout; ++ + static char babeloutp[4]; + + int diff --git a/academic/cholmod/cholmod.SlackBuild b/academic/cholmod/cholmod.SlackBuild index 17d2ddc9d6..4daabb7bf7 100644 --- a/academic/cholmod/cholmod.SlackBuild +++ b/academic/cholmod/cholmod.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Core/lesser.txt Modify/gpl.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/cholmod/cholmod.info b/academic/cholmod/cholmod.info index ddaabdec00..468deec03d 100644 --- a/academic/cholmod/cholmod.info +++ b/academic/cholmod/cholmod.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/Suit MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas lapack suitesparseconfig amd camd colamd ccolamd" +REQUIRES="lapack amd camd colamd ccolamd" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/cistrome-MACS/cistrome-MACS.SlackBuild b/academic/cistrome-MACS/cistrome-MACS.SlackBuild index eb00d4f261..98f279db3c 100644 --- a/academic/cistrome-MACS/cistrome-MACS.SlackBuild +++ b/academic/cistrome-MACS/cistrome-MACS.SlackBuild @@ -67,13 +67,20 @@ else LIBDIRSUFFIX="" fi +# 20220222 bkw: depending on what client was used to download the file, +# it may have CGI parameters in the filename. +TARBALL=$CWD/${SRCNAM}-$SRCVER.tar.gz +if [ ! -e $TARBALL ]; then + TARBALL="$( /bin/ls $TARBALL\?* | head -1 )" +fi + set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $SRCNAM-$VERSION -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz +tar xvf $TARBALL cd $SRCNAM-$VERSION chown -R root:root . find -L . \ diff --git a/academic/cistrome-MACS/cistrome-MACS.info b/academic/cistrome-MACS/cistrome-MACS.info index 02eb7b8547..7ca43c2935 100644 --- a/academic/cistrome-MACS/cistrome-MACS.info +++ b/academic/cistrome-MACS/cistrome-MACS.info @@ -1,7 +1,7 @@ PRGNAM="cistrome-MACS" VERSION="1.4.2" HOMEPAGE="https://github.com/taoliu/MACS/" -DOWNLOAD="https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/cistrome-MACS/MACS-1.4.2-1.tar.gz" MD5SUM="950dab09fe1335c8bbb34a896c21e3e2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/cistrome-mdseqpos/cistrome-mdseqpos.info b/academic/cistrome-mdseqpos/cistrome-mdseqpos.info index 3b19df7684..b1e6afd6e2 100644 --- a/academic/cistrome-mdseqpos/cistrome-mdseqpos.info +++ b/academic/cistrome-mdseqpos/cistrome-mdseqpos.info @@ -5,6 +5,6 @@ DOWNLOAD="https://bitbucket.org/cistrome/cistrome-applications-harvard/get/63346 MD5SUM="0441f0c1bb3ffa156dfe9ed0fccd5dc8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="numpy python-django R" +REQUIRES="python2-numpy python2-django R" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/clustalo/clustalo.SlackBuild b/academic/clustalo/clustalo.SlackBuild index a8870c0f57..828c94a785 100644 --- a/academic/clustalo/clustalo.SlackBuild +++ b/academic/clustalo/clustalo.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=clustalo VERSION=${VERSION:-1.2.4} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -107,6 +107,8 @@ cp -a \ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/clustalx/QT.patch b/academic/clustalx/QT.patch new file mode 100644 index 0000000000..72907ea824 --- /dev/null +++ b/academic/clustalx/QT.patch @@ -0,0 +1,200 @@ +diff -urN clustalx-2.1/AlignOutputFileNames.cpp clustalx-2.1-bak/AlignOutputFileNames.cpp +--- clustalx-2.1/AlignOutputFileNames.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/AlignOutputFileNames.cpp 2015-09-18 18:59:38.582405761 +0200 +@@ -13,6 +13,7 @@ + * 18-06-07,Nigel Brown(EMBL): Made the 'ok' button in each dialogue be the + * default instead of a Browse button. + */ ++#include <QtGui> + #include <QPushButton> + #include <QGroupBox> + #include <QCheckBox> +@@ -20,8 +21,8 @@ + #include <QGridLayout> + #include <QSizePolicy> + #include <QComboBox> +-#include <QtGui> + #include <QLabel> ++#include <QLineEdit> + #include <iostream> + #include "AlignOutputFileNames.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/AlignmentViewerWidget.cpp clustalx-2.1-bak/AlignmentViewerWidget.cpp +--- clustalx-2.1/AlignmentViewerWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/AlignmentViewerWidget.cpp 2015-09-18 18:50:09.762563103 +0200 +@@ -69,6 +69,11 @@ + #include "PSPrinter.h" + #include "FileDialog.h" + #include <QFontMetrics> ++#include <QVBoxLayout> ++#include <QScrollBar> ++#include <QScrollArea> ++#include <QMessageBox> ++#include <QGroupBox> + + AlignmentViewerWidget::AlignmentViewerWidget(QWidget *parent) + : QWidget(parent), +diff -urN clustalx-2.1/AlignmentWidget.cpp clustalx-2.1-bak/AlignmentWidget.cpp +--- clustalx-2.1/AlignmentWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/AlignmentWidget.cpp 2015-09-18 18:58:36.656119118 +0200 +@@ -46,6 +46,7 @@ + ****************************************************************************/ + + #include <QtGui> ++#include <QScrollArea> + #include "AlignmentWidget.h" + #include "clustalW/general/userparams.h" + #include "ClustalQtParams.h" +diff -urN clustalx-2.1/BootstrapTreeDialog.cpp clustalx-2.1-bak/BootstrapTreeDialog.cpp +--- clustalx-2.1/BootstrapTreeDialog.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/BootstrapTreeDialog.cpp 2015-09-18 19:00:09.782214298 +0200 +@@ -5,6 +5,7 @@ + * 12-4-07, Mark Larkin, Removed destructor. No need to delete QObjects. Also removed + * setAllPtrsToNull function. + */ ++#include <QtGui> + #include <QPushButton> + #include <QGroupBox> + #include <QCheckBox> +@@ -12,8 +13,8 @@ + #include <QGridLayout> + #include <QSizePolicy> + #include <QComboBox> +-#include <QtGui> + #include <QLabel> ++#include <QLineEdit> + #include <iostream> + #include "BootstrapTreeDialog.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/ColorFileXmlParser.cpp clustalx-2.1-bak/ColorFileXmlParser.cpp +--- clustalx-2.1/ColorFileXmlParser.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/ColorFileXmlParser.cpp 2015-09-18 19:00:42.695345653 +0200 +@@ -1,4 +1,5 @@ + #include <QtGui> ++#include <QMessageBox> + + #include "ColorFileXmlParser.h" + #include "ClustalQtParams.h" +@@ -202,4 +203,4 @@ + rule = rule.nextSiblingElement("resrule"); + } + return numOfRules; +-} +\ No newline at end of file ++} +diff -urN clustalx-2.1/HelpDisplayWidget.cpp clustalx-2.1-bak/HelpDisplayWidget.cpp +--- clustalx-2.1/HelpDisplayWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/HelpDisplayWidget.cpp 2015-09-18 19:34:51.692771579 +0200 +@@ -16,6 +16,8 @@ + #include <QTextEdit> + #include <iostream> + #include <fstream> ++#include <QPushButton> ++#include <QVBoxLayout> + #include <QtGui> + #include "Resources.h" + +diff -urN clustalx-2.1/PSPrinter.cpp clustalx-2.1-bak/PSPrinter.cpp +--- clustalx-2.1/PSPrinter.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/PSPrinter.cpp 2015-09-18 19:20:36.528019466 +0200 +@@ -17,6 +17,7 @@ + #include <iomanip> + #include <sstream> + #include <QtGui> ++#include <QMessageBox> + #include "PSPrinter.h" + #include "ColorFileXmlParser.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/ProteinGapParameters.cpp clustalx-2.1-bak/ProteinGapParameters.cpp +--- clustalx-2.1/ProteinGapParameters.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/ProteinGapParameters.cpp 2015-09-18 19:20:07.311532091 +0200 +@@ -9,6 +9,7 @@ + #include <QLabel> + #include <QString> + #include <QMessageBox> ++#include <QLineEdit> + #include "ProteinGapParameters.h" + #include "clustalW/general/userparams.h" + +diff -urN clustalx-2.1/SaveSeqFile.cpp clustalx-2.1-bak/SaveSeqFile.cpp +--- clustalx-2.1/SaveSeqFile.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/SaveSeqFile.cpp 2015-09-18 19:21:28.231035513 +0200 +@@ -20,6 +20,8 @@ + #include <QComboBox> + #include <QtGui> + #include <QLabel> ++#include <QMessageBox> ++#include <QLineEdit> + #include "SaveSeqFile.h" + #include "clustalW/general/userparams.h" + #include "clustalW/general/utils.h" +diff -urN clustalx-2.1/SeqNameWidget.cpp clustalx-2.1-bak/SeqNameWidget.cpp +--- clustalx-2.1/SeqNameWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/SeqNameWidget.cpp 2015-09-18 19:22:48.903873782 +0200 +@@ -56,6 +56,7 @@ + ****************************************************************************/ + + #include <QtGui> ++#include <QScrollArea> + #include "SeqNameWidget.h" + #include "KeyController.h" //- nige + #include "clustalW/alignment/Alignment.h" +diff -urN clustalx-2.1/TreeOutputFileNames.cpp clustalx-2.1-bak/TreeOutputFileNames.cpp +--- clustalx-2.1/TreeOutputFileNames.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/TreeOutputFileNames.cpp 2015-09-18 19:23:37.006911921 +0200 +@@ -13,6 +13,7 @@ + #include <QComboBox> + #include <QtGui> + #include <QLabel> ++#include <QLineEdit> + #include <iostream> + #include "TreeOutputFileNames.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/WritePostscriptFile.cpp clustalx-2.1-bak/WritePostscriptFile.cpp +--- clustalx-2.1/WritePostscriptFile.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/WritePostscriptFile.cpp 2015-09-18 19:24:30.429917414 +0200 +@@ -20,6 +20,8 @@ + #include <QComboBox> + #include <QtGui> + #include <QLabel> ++#include <QLineEdit> ++#include <QMessageBox> + #include <iostream> + #include "WritePostscriptFile.h" + #include "clustalW/general/userparams.h" +Binary files clustalx-2.1/clustalx and clustalx-2.1-bak/clustalx differ +diff -urN clustalx-2.1/clustalx.pro clustalx-2.1-bak/clustalx.pro +--- clustalx-2.1/clustalx.pro 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/clustalx.pro 2015-09-18 19:14:42.666857671 +0200 +@@ -4,8 +4,11 @@ + + TEMPLATE = app + TARGET = clustalx +-CONFIG += release static ++CONFIG += release + QT += xml ++QT += widgets ++DEFINES += QT_DISABLE_DEPRECATED_BEFORE=0x000000 ++ + VERSION = 2.1 + win32 { + DEFINES += OS_WINDOWS +diff -urN clustalx-2.1/mainwindow.cpp clustalx-2.1-bak/mainwindow.cpp +--- clustalx-2.1/mainwindow.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/mainwindow.cpp 2015-09-18 19:19:03.545256739 +0200 +@@ -94,6 +94,15 @@ + #include <cstdlib> + #include <QCheckBox> + #include <QStringList> ++#include <QMenu> ++#include <QMenuBar> ++#include <QAction> ++#include <QMessageBox> ++#include <QApplication> ++#include <QScrollBar> ++#include <QHBoxLayout> ++#include <QGroupBox> ++#include <QVBoxLayout> + #include "SecStructOptions.h" + #include "mainwindow.h" + #include "WritePostscriptFile.h" diff --git a/academic/clustalx/clustalx.SlackBuild b/academic/clustalx/clustalx.SlackBuild index f8c0d9d215..756d1eaff4 100644 --- a/academic/clustalx/clustalx.SlackBuild +++ b/academic/clustalx/clustalx.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for clustalx -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -29,13 +29,13 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=clustalx VERSION=${VERSION:-2.1} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) export ARCH=i486 ;; + i?86) export ARCH=i586 ;; arm*) export ARCH=arm ;; *) export ARCH=$( uname -m ) ;; esac @@ -53,8 +53,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -76,8 +76,9 @@ rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION -# The patch is from Archlinux AUR, as mentioned above. +# The patches are from Archlinux AUR, as mentioned above. patch -p1 < $CWD/fix-static.patch +patch -p1 < $CWD/QT.patch chown -R root:root . find -L . \ @@ -88,7 +89,7 @@ find -L . \ sed -i 's/static//g' clustalx.pro -qmake +qmake-qt5 #Use our CFLAGS/CXXFLAGS sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile diff --git a/academic/colamd/colamd.SlackBuild b/academic/colamd/colamd.SlackBuild index 9ebc5c4963..3f9a632954 100644 --- a/academic/colamd/colamd.SlackBuild +++ b/academic/colamd/colamd.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/colin/colin.SlackBuild b/academic/colin/colin.SlackBuild index 1231c3520b..4b3e3b0b5e 100644 --- a/academic/colin/colin.SlackBuild +++ b/academic/colin/colin.SlackBuild @@ -60,7 +60,7 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then exit 0 fi -TMP=${TMP:-/tmp} +TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -79,6 +79,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh qmake make diff --git a/academic/colin/colin.info b/academic/colin/colin.info index b8479e1a33..5a19ff7802 100644 --- a/academic/colin/colin.info +++ b/academic/colin/colin.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/colin2/files/colin-1.8.2.tar.xz" MD5SUM="e7260f262dbc563b40b6de529d6aa519" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="qt4" MAINTAINER="Prof. HORSTMANN" EMAIL="wmh@eipg.fr" diff --git a/academic/convertall/convertall.SlackBuild b/academic/convertall/convertall.SlackBuild index 13ca4c524a..c7cb4bf170 100644 --- a/academic/convertall/convertall.SlackBuild +++ b/academic/convertall/convertall.SlackBuild @@ -28,12 +28,15 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220405 bkw: Modified by SlackBuilds.org, BUILD=2: +# - remove /usr/share/doc and useless INSTALL instructions. + cd $(dirname $0) ; CWD=$(pwd) PRGNAM=convertall SRCNAM=ConvertAll VERSION=${VERSION:-0.8.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -45,9 +48,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -82,9 +82,9 @@ cd $SRCNAM chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ + -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + -exec chmod 644 {} \+ # Change installation directory to /usr and use LIBDIRSUFFIX sed -i -e "s/usr\/local/usr/" -e "s/'lib'/'lib$LIBDIRSUFFIX'/" install.py @@ -94,6 +94,8 @@ python3 install.py -b $PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +rm -rf doc/INSTALL $PKG/usr/share/doc + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ doc/* \ diff --git a/academic/copasi/README b/academic/copasi/README index c640a01c87..1ebe37a34d 100644 --- a/academic/copasi/README +++ b/academic/copasi/README @@ -1,17 +1,17 @@ -COPASI is a package for modeling and simulation of biochemical networks, -popular in the field of systems biology. +COPASI is a package for modeling and simulation of chemical reaction +networks and other dynamical systems. -COPASI is a stand-alone program that simulates models of biochemical -networks using ODE solvers or Gillespie's stochastic simulation -algorithm. COPASI is compatible with models in SBML format. It also -performs several analyses, such as steady state, stability, parameter -sensitivity, elementary modes, Lyapunov exponents, optimization, and -parameter estimation. Data can be visualized in plots, histograms and -animations of network diagrams. COPASI's GUI is based on QT, but a -command line version is also included that allows for processing -computations in batch mode. +COPASI is a stand-alone program that simulates models of chemical +reaction networks using ODE/SDE solvers or Gillespie's stochastic +simulation algorithm. COPASI is compatible with models in SBML format. +It also performs several analyses, such as steady state, stability, +parameter sensitivity, elementary modes, Lyapunov exponents, +optimization, and parameter estimation. Data can be visualized in +plots, histograms and animations of network diagrams. COPASI's GUI is +based on QT, but a command line version is also included that allows +for processing computations in batch mode. COPASI is a collaboration between research groups at the Biocomplexity -Institute and Initiative at University of Virginia, University of +Institute and Initiative at University of Virginia, University of Heidelberg, University of Connecticut, and previously the University of Manchester, Virginia Tech, and the EML-Research. diff --git a/academic/copasi/copasi.SlackBuild b/academic/copasi/copasi.SlackBuild index 69f308ccc7..0a6da4fcfd 100644 --- a/academic/copasi/copasi.SlackBuild +++ b/academic/copasi/copasi.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=copasi -VERSION=${VERSION:-4.28.226} +VERSION=${VERSION:-4.42.284} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -68,7 +68,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf COPASI-$VERSION-$BINNAME $PRGNAM-$VERSION -tar xvf $CWD/COPASI-$VERSION-$BINNAME.tar.gz +sh $CWD/COPASI-$VERSION-$BINNAME.sh -e . mv COPASI-$VERSION-$BINNAME $PRGNAM-$VERSION cd $PRGNAM-$VERSION chown -R root:root . diff --git a/academic/copasi/copasi.desktop b/academic/copasi/copasi.desktop index 80dcef7083..6690ec34a4 100644 --- a/academic/copasi/copasi.desktop +++ b/academic/copasi/copasi.desktop @@ -1,5 +1,5 @@ [Desktop Entry] -Exec=sh -c "COPASIDIR=/usr /usr/bin/CopasiUI" +Exec=/usr/bin/CopasiUI %u Icon=/usr/share/pixmaps/copasi.xpm Type=Application Name=COPASI diff --git a/academic/copasi/copasi.info b/academic/copasi/copasi.info index 93b7729f70..75e1b966a6 100644 --- a/academic/copasi/copasi.info +++ b/academic/copasi/copasi.info @@ -1,10 +1,10 @@ PRGNAM="copasi" -VERSION="4.28.226" -HOMEPAGE="http://copasi.org" -DOWNLOAD="https://github.com/copasi/COPASI/releases/download/Build-226/COPASI-4.28.226-Linux-32bit.tar.gz" -MD5SUM="3fd18c60296def1158295b4b39a41085" -DOWNLOAD_x86_64="https://github.com/copasi/COPASI/releases/download/Build-226/COPASI-4.28.226-Linux-64bit.tar.gz" -MD5SUM_x86_64="9709892e02b9ec7e9ccb0d9ec7e8b08b" +VERSION="4.42.284" +HOMEPAGE="https://copasi.org" +DOWNLOAD="https://github.com/copasi/COPASI/releases/download/Build-284/COPASI-4.42.284-Linux-32bit.sh" +MD5SUM="66ae94a23f8d7745835e3639f1c567f6" +DOWNLOAD_x86_64="https://github.com/copasi/COPASI/releases/download/Build-284/COPASI-4.42.284-Linux-64bit.sh" +MD5SUM_x86_64="87f09230f64ea4c69a6695963e4f2594" REQUIRES="" MAINTAINER="Pedro Mendes" EMAIL="pedro@gepasi.org" diff --git a/academic/copasi/slack-desc b/academic/copasi/slack-desc index 713b2c5d95..46fa181d4b 100644 --- a/academic/copasi/slack-desc +++ b/academic/copasi/slack-desc @@ -9,11 +9,11 @@ copasi: copasi (tool for modeling and simulation of biochemical networks) copasi: copasi: COPASI is a stand-alone program that simulates models of biochemical -copasi: networks using ODE solvers or Gillespie's stochastic simulation +copasi: networks using ODE/SDE solvers or Gillespie's stochastic simulation copasi: algorithm. COPASI is compatible with models in SBML format. It also copasi: performs several analyses: stability, parameter sensitivity, copasi: elementary modes, Lyapunov exponents, optimization, and parameter copasi: estimation. Data can be visualized in plots, histograms and animations copasi: of network diagrams. Both GUI and a command line version are included. copasi: -copasi: Homepage: http://www.copasi.org/ +copasi: Homepage: https://copasi.org/ diff --git a/academic/coq/README b/academic/coq/README deleted file mode 100644 index e21de9a5fa..0000000000 --- a/academic/coq/README +++ /dev/null @@ -1,7 +0,0 @@ -coq is a formal proof management system. It provides a formal language -to write mathematical definitions, executable algorithms and theorems -together with an environment for semi-interactive development of -machine-checked proofs. - -To build CoqIDE, add COQIDE=yes, e.g.: COQIDE=yes ./coq.SlackBuild. -You will need the lablgtk package built with gtksourceview support. diff --git a/academic/coq/coq.info b/academic/coq/coq.info deleted file mode 100644 index 93554ae125..0000000000 --- a/academic/coq/coq.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="coq" -VERSION="8.9.0" -HOMEPAGE="http://coq.inria.fr/" -DOWNLOAD="https://github.com/coq/coq/archive/V8.9.0/coq-8.9.0.tar.gz" -MD5SUM="490c89609c1271fe7f20e6ea1bd107b5" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="camlp5 ocaml-findlib" -MAINTAINER="Nick Smallbone" -EMAIL="nick@smallbone.se" diff --git a/academic/coq/gpl.txt.gz b/academic/coq/gpl.txt.gz Binary files differdeleted file mode 100644 index 0ef740a4c7..0000000000 --- a/academic/coq/gpl.txt.gz +++ /dev/null diff --git a/academic/cryptominisat/cryptominisat.SlackBuild b/academic/cryptominisat/cryptominisat.SlackBuild index 357e4ab133..74cbbb84e1 100644 --- a/academic/cryptominisat/cryptominisat.SlackBuild +++ b/academic/cryptominisat/cryptominisat.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cryptominisat -# Copyright 2019 Alan Aversa USA +# Copyright 2024 Caterino Tommaso, T.O.P. USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=cryptominisat -VERSION=${VERSION:-5.7.1} +VERSION=${VERSION:-5.11.21} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -89,12 +89,17 @@ cd build -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_INSTALL_LIBDIR=lib${LIBDIRSUFFIX} \ - -DUSE_GAUSS=ON \ + -DIPASIR=ON \ + -DSTATICCOMPILE=ON \ -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG cd .. +# include source code: +mkdir -p $PKG/usr/src +cp -a src $PKG/usr/src/$PRGNAM + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/cryptominisat/cryptominisat.info b/academic/cryptominisat/cryptominisat.info index ecbc9f24ff..cb39e89a62 100644 --- a/academic/cryptominisat/cryptominisat.info +++ b/academic/cryptominisat/cryptominisat.info @@ -1,10 +1,10 @@ PRGNAM="cryptominisat" -VERSION="5.7.1" +VERSION="5.11.21" HOMEPAGE="https://www.msoos.org/cryptominisat5/" -DOWNLOAD="https://github.com/msoos/cryptominisat/archive/5.7.1/cryptominisat-5.7.1.tar.gz" -MD5SUM="e4ff835bbfe1995cc5e62a6e464dfd98" +DOWNLOAD="https://github.com/msoos/cryptominisat/archive/5.11.21/cryptominisat-5.11.21.tar.gz" +MD5SUM="7f2fbe1975c9045d351a7921f4028b38" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Alan Aversa" -EMAIL="aveNOrsa@email.ariSPAMzona.edu" +MAINTAINER="Caterino Tommaso, T.O.P." +EMAIL="alaNOn_aversa@lavabSPAMit.com (remove NO and SPAM)" diff --git a/academic/csparse/csparse.SlackBuild b/academic/csparse/csparse.SlackBuild index d75ef5a125..9725887ad3 100644 --- a/academic/csparse/csparse.SlackBuild +++ b/academic/csparse/csparse.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/cufflinks/cufflinks.info b/academic/cufflinks/cufflinks.info index 6881614543..b35162c3e6 100644 --- a/academic/cufflinks/cufflinks.info +++ b/academic/cufflinks/cufflinks.info @@ -8,4 +8,3 @@ MD5SUM_x86_64="7e693d182dcfda8aeef8523219ea9ea7" REQUIRES="samtools-legacy" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" - diff --git a/academic/cvc4/cvc4.info b/academic/cvc4/cvc4.info index 4fc4ede8c6..379b15bffa 100644 --- a/academic/cvc4/cvc4.info +++ b/academic/cvc4/cvc4.info @@ -1,12 +1,12 @@ PRGNAM="cvc4" VERSION="1.8" HOMEPAGE="https://cvc4.cs.stanford.edu/" -DOWNLOAD="https://github.com/CVC4/CVC4/archive/1.8/CVC4-1.8.tar.gz \ +DOWNLOAD="https://ponce.cc/slackware/sources/repo/CVC4-1.8.tar.gz \ https://www.antlr3.org/download/antlr-3.4-complete.jar" MD5SUM="9f7657e21fec3c4042225b0b8f513c34 \ 1b91dea1c7d480b3223f7c8a9aa0e172" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk libantlr3c python-toml" +REQUIRES="zulu-openjdk8 libantlr3c python2-toml" MAINTAINER="Nick Smallbone" EMAIL="nick@smallbone.se" diff --git a/academic/cxsparse/cxsparse.SlackBuild b/academic/cxsparse/cxsparse.SlackBuild index ea960f7d72..4d8c288e24 100644 --- a/academic/cxsparse/cxsparse.SlackBuild +++ b/academic/cxsparse/cxsparse.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/dakota/README b/academic/dakota/README index 3a0d5dbe15..7a5783c44c 100644 --- a/academic/dakota/README +++ b/academic/dakota/README @@ -13,4 +13,4 @@ Optional dependency: openmpi (for distributed memory parallel capabilities) You can build with multiple jobs by setting the MAKEFLAGS environment -variable. +variable (e.g. export MAKEFLAGS="-j$(nproc)" at bash prompt). diff --git a/academic/dakota/dakota.SlackBuild b/academic/dakota/dakota.SlackBuild index 958c601ec1..2e907ef4f2 100644 --- a/academic/dakota/dakota.SlackBuild +++ b/academic/dakota/dakota.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for Dakota -# Copyright 2017, 2018, 2019, 2020 Lorenzo Trevisan, Caorle, Venice, Italy +# Copyright 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024 Lorenzo Trevisan, Caorle, Venice, Italy # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=dakota -VERSION=${VERSION:-6.11.0} +VERSION=${VERSION:-6.19.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -69,9 +69,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION-release-public.src-UI -tar xvf $CWD/$PRGNAM-$VERSION-release-public.src-UI.tar.gz -cd $PRGNAM-$VERSION-release-public.src-UI +rm -rf $PRGNAM-$VERSION-public-src-cli +tar xvf $CWD/$PRGNAM-$VERSION-public-src-cli.tar.gz + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -79,6 +79,10 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +cd $PRGNAM-$VERSION-public-src-cli + +sed -i -e '11 a #include <math.h>' ./src/unit/dakota_tolerance_intervals/test_tolerance_intervals.cpp + mkdir -p build cd build cmake \ @@ -97,7 +101,11 @@ install -D -m755 $CWD/$PRGNAM.sh $PKG/etc/profile.d/$PRGNAM.sh.new install -D -m755 $CWD/$PRGNAM.csh $PKG/etc/profile.d/$PRGNAM.csh.new mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYRIGHT LICENSE INSTALL README $PKG/usr/doc/$PRGNAM-$VERSION +cp -a COPYRIGHT LICENSE README $PKG/usr/doc/$PRGNAM-$VERSION +tar xvf $CWD/html-dev-${VERSION}.tar.gz -C $PKG/usr/doc/$PRGNAM-$VERSION +tar xvf $CWD/user-html-${VERSION}.tar.gz -C $PKG/usr/doc/$PRGNAM-$VERSION +chown -R root:root $PKG/usr/doc/$PRGNAM-$VERSION +chmod 755 $(find $PKG/usr/doc/$PRGNAM-$VERSION -type d) cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/dakota/dakota.info b/academic/dakota/dakota.info index 80d0d1cd01..9e43bb02f6 100644 --- a/academic/dakota/dakota.info +++ b/academic/dakota/dakota.info @@ -1,10 +1,14 @@ PRGNAM="dakota" -VERSION="6.11.0" +VERSION="6.19.0" HOMEPAGE="https://dakota.sandia.gov/" -DOWNLOAD="https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.11.0-release-public.src-UI.tar.gz" -MD5SUM="3a81ce3f6b0c3a9087a0cd8f53e16249" +DOWNLOAD="https://github.com/snl-dakota/dakota/releases/download/v6.19.0/dakota-6.19.0-public-src-cli.tar.gz \ + https://snl-dakota.github.io/docs/6.19.0/downloads/user-html-6.19.0.tar.gz \ + https://snl-dakota.github.io/docs/6.19.0/downloads/html-dev-6.19.0.tar.gz" +MD5SUM="78210b4aa56dc15b5e05054b83f265f0 \ + da5c00e92c271a451295e2ac26ee02f5 \ + 10fbfb5a564e79c3ffcbb8ee246c0973" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas lapack" +REQUIRES="lapack" MAINTAINER="Lorenzo Trevisan" EMAIL="lorenzo.trevisan@gmail.com" diff --git a/academic/datamash/datamash.SlackBuild b/academic/datamash/datamash.SlackBuild index 4fde6484d4..65806834f5 100644 --- a/academic/datamash/datamash.SlackBuild +++ b/academic/datamash/datamash.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for datamash -# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=datamash -VERSION=${VERSION:-1.7} +VERSION=${VERSION:-1.8} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -106,7 +106,7 @@ gzip -9 $PKG/usr/info/*.info* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS ChangeLog COPYING INSTALL NEWS README THANKS TODO \ + ABOUT-NLS AUTHORS ChangeLog COPYING INSTALL NEWS README THANKS \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/datamash/datamash.info b/academic/datamash/datamash.info index ff23e91fa2..bc70b16d84 100644 --- a/academic/datamash/datamash.info +++ b/academic/datamash/datamash.info @@ -1,8 +1,8 @@ PRGNAM="datamash" -VERSION="1.7" +VERSION="1.8" HOMEPAGE="https://www.gnu.org/software/datamash/" -DOWNLOAD="https://ftp.gnu.org/gnu/datamash/datamash-1.7.tar.gz" -MD5SUM="e5474d3bfee13e7ab1c44ebaec497a0d" +DOWNLOAD="https://ftp.gnu.org/gnu/datamash/datamash-1.8.tar.gz" +MD5SUM="b5f2dcfcefb2d41f88c54619b08727e3" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/dimod/README b/academic/dimod/README new file mode 100644 index 0000000000..23a53588f8 --- /dev/null +++ b/academic/dimod/README @@ -0,0 +1,12 @@ + dimod is a shared API for samplers. It provides: + + - classes for quadratic models---such as the binary quadratic model + (BQM) class that contains Ising and QUBO models used by samplers + such as the D-Wave system---and higher-order (non-quadratic) + models. + - reference examples of samplers and composed samplers. + - abstract base classes for constructing new samplers and composed + samplers. + + + If you want to run the tests set the environment variable TESTS=yes. diff --git a/academic/dimod/dimod.SlackBuild b/academic/dimod/dimod.SlackBuild new file mode 100644 index 0000000000..095c740e7e --- /dev/null +++ b/academic/dimod/dimod.SlackBuild @@ -0,0 +1,119 @@ +#!/bin/bash + +# Slackware build script for dimod + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dimod" +VERSION=${VERSION:-0.12.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + IGNORE_TESTS="test_(bqm|cyutilities|discrete_quadratic_model|lp|quadratic_model|serialization_fileview|variables).py" + PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + cd tests + for file in $(ls test_*.py | grep -v -E $IGNORE_TESTS); do + echo -n "$file " + PYTHONPATH=../build/lib.linux-$(uname -m)-$PYVER python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dimod/dimod.info b/academic/dimod/dimod.info new file mode 100644 index 0000000000..83925dbffe --- /dev/null +++ b/academic/dimod/dimod.info @@ -0,0 +1,10 @@ +PRGNAM="dimod" +VERSION="0.12.0" +HOMEPAGE="https://github.com/dwavesystems" +DOWNLOAD="https://github.com/dwavesystems/dimod/archive/0.12.0/dimod-0.12.0.tar.gz" +MD5SUM="20dfa5a1cb6f06b3f928c0538f8a021c" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-numpy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dimod/slack-desc b/academic/dimod/slack-desc new file mode 100644 index 0000000000..fb746b8f61 --- /dev/null +++ b/academic/dimod/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dimod: dimod (A shared API for samplers) +dimod: +dimod: dimod is a shared API for samplers. It provides: +dimod: +dimod: - classes for quadratic models---such as the binary quadratic +dimod: model (BQM) class that contains Ising and QUBO models used by +dimod: samplers such as the D-Wave system---and higher-order +dimod: (non-quadratic) models. +dimod: - reference examples of samplers and composed samplers. +dimod: - abstract base classes for constructing new samplers and composed +dimod: samplers. diff --git a/academic/drawtiming/InitializeMagick.diff b/academic/drawtiming/InitializeMagick.diff deleted file mode 100644 index d610544a76..0000000000 --- a/academic/drawtiming/InitializeMagick.diff +++ /dev/null @@ -1,30 +0,0 @@ -Description: Properly initialize GraphicsMagick - Quoting from GraphicsMagick's NEWS file " - 1.3.8 (January 21, 2010) - ======================== - [...] - Behavior Changes: - InitializeMagick() MUST be invoked prior to using any Magick API function. - Failure to do so will likely lead to an immediate application crash. This is - due to initialization and runtime changes intended to improve thread safety - and efficiency. Previously it was only strongly recommended to invoke - InitializeMagick(). - " -Author: Galland (https://launchpad.net/~victor-lopez) -Bug-Ubuntu: https://bugs.launchpad.net/bugs/636021 -Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=599915 -Bug: http://sourceforge.net/tracker/index.php?func=detail&aid=3136111&group_id=118983&atid=682742 -Forwarded: yes - ---- a/src/main.cc -+++ b/src/main.cc -@@ -97,6 +97,9 @@ - double scale = 1; - int flags = 0; - -+#ifndef LITE -+ InitializeMagick(NULL); -+#endif /* ! LITE */ - int k, c; - while ((c = getopt_long (argc, argv, "ac:f:hl:o:p:vVw:x:", opts, &k)) != -1) - switch (c) { diff --git a/academic/drawtiming/README b/academic/drawtiming/README deleted file mode 100644 index 32f4e261c2..0000000000 --- a/academic/drawtiming/README +++ /dev/null @@ -1,6 +0,0 @@ -DrawTiming provides a command line tool for documenting hardware and -software designs through timing diagrams. It reads signal descriptions -from a text file with an intuitive syntax, and outputs a timing diagram -to an image file. Notation typical of timing diagrams found in the -Electrical Engineering discipline is used, including arrows -indicating causal relationships between signal transitions. diff --git a/academic/drawtiming/drawtiming.info b/academic/drawtiming/drawtiming.info deleted file mode 100644 index 3e15375061..0000000000 --- a/academic/drawtiming/drawtiming.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="drawtiming" -VERSION="0.7.1" -HOMEPAGE="http://drawtiming.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/project/drawtiming/drawtiming/0.7.1/drawtiming-0.7.1.tar.gz" -MD5SUM="bc25f43f5301ee6cfb65ed8e151a2e1d" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="R. S. Ananda Murthy" -EMAIL="rsamurti@gmail.com" diff --git a/academic/drawtiming/manpage-fix.diff b/academic/drawtiming/manpage-fix.diff deleted file mode 100644 index 2aa56c124d..0000000000 --- a/academic/drawtiming/manpage-fix.diff +++ /dev/null @@ -1,62 +0,0 @@ -Description: Fix typos and hyphenation -Author: أحمد المحمودي (Ahmed El-Mahmoudy) <aelmahmoudy@sabily.org> -Forwarded: yes ---- a/doc/drawtiming.1 -+++ b/doc/drawtiming.1 -@@ -56,7 +56,7 @@ - .It Fl -pagesize Ar WidthxHeight - Scale the diagram to fit given image size. - .It Fl -aspect --Maintain fixed aspect ratio if --pagesize given. -+Maintain fixed aspect ratio if \-\-pagesize given. - .It Fl -cell-height Ar H - Height of the each signal in pixels. Default is 32. - .It Fl -cell-width Ar W -@@ -101,23 +101,23 @@ - changing its value. - .El - .Pp --Statements are seperated by the following symbols: -+Statements are separated by the following symbols: - .Bl -tag -width "-tD>" - .It , --The comma seperator is used to seperate statements without -+The comma separator is used to separate statements without - affecting the dependency list or clock (ie: the next statement will - add to the dependency list). - .It ; --The semicolon seperator resets the list of dependencies without -+The semicolon separator resets the list of dependencies without - incrementing the clock - .It . --The period seperator resets the list of dependencies and -+The period separator resets the list of dependencies and - increments the clock. - .It => --The "causes" seperator renders dependency arrows based on the -+The "causes" separator renders dependency arrows based on the - current list of dependencies and then resets the dependency list. - .It -tD> --The "delay" seperator renders a delay arrow from the last dependency -+The "delay" separator renders a delay arrow from the last dependency - with the annotation - .Em tD . - .El -@@ -173,7 +173,7 @@ - value if their initial value is not given. - .Pp - Independent signal transitions which occur simultaneously are normally --seperated by commas. Since signals aren't normally expected to change -+separated by commas. Since signals aren't normally expected to change - simultaneously, the initial state is a good example of this: - .Pp - .Dl POWER=0, FIRE=0, ARMED=0, LED=OFF, COUNT=N. -@@ -194,7 +194,7 @@ - .Pp - .Dl POWER=1 => LED=GREEN. - .Pp --For signal state changes with multiple dependencies, seperate the -+For signal state changes with multiple dependencies, separate the - dependencies with commas: - .Pp - .Dl FIRE, ARMED => LED=RED. diff --git a/academic/drawtiming/missing-includes.diff b/academic/drawtiming/missing-includes.diff deleted file mode 100644 index 7dbad2192e..0000000000 --- a/academic/drawtiming/missing-includes.diff +++ /dev/null @@ -1,13 +0,0 @@ -Description: Add missing string.h include. -Author: Wesley J. Landaker <wjl@icecavern.net> -Forwarded: yes ---- a/src/timing.cc -+++ b/src/timing.cc -@@ -23,6 +23,7 @@ - #include "timing.h" - #include <map> - #include <fstream> -+#include <string.h> - using namespace std; - using namespace timing; - using namespace Magick; diff --git a/academic/drawtiming/slack-desc b/academic/drawtiming/slack-desc deleted file mode 100644 index a406fa95ca..0000000000 --- a/academic/drawtiming/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -drawtiming: drawtiming (tool for drawing timing diagrams) -drawtiming: -drawtiming: DrawTiming provides a command line tool for documenting hardware and -drawtiming: software designs through timing diagrams. It reads signal -drawtiming: descriptions from a text file with an intuitive syntax, -drawtiming: and outputs a timing diagram to an image file. Notation typical -drawtiming: of timing diagrams found in the Electrical Engineering discipline -drawtiming: is used, including arrows indicating causal relationships between -drawtiming: signal transitions. -drawtiming: -drawtiming: diff --git a/academic/drawtiming/switch_LDFLAGS_LDADD.diff b/academic/drawtiming/switch_LDFLAGS_LDADD.diff deleted file mode 100644 index 8ae536630d..0000000000 --- a/academic/drawtiming/switch_LDFLAGS_LDADD.diff +++ /dev/null @@ -1,36 +0,0 @@ -Description: Switch LDADD with LDFLAGS - This change is to move the objects before the libs. to fix an FTBFS when - --as-needed is passed to gcc. -Author: أحمد المحمودي (Ahmed El-Mahmoudy) <aelmahmoudy@sabily.org> -Forwarded: yes ---- drawtiming-0.7.1.orig/src/Makefile.am -+++ drawtiming-0.7.1/src/Makefile.am -@@ -3,7 +3,7 @@ - - bin_PROGRAMS = drawtiming - drawtiming_SOURCES = main.cc globals.h parser.yy scanner.ll timing.cc timing.h --drawtiming_LDFLAGS = @MAGICK_LIBS@ -+drawtiming_LDADD = @MAGICK_LIBS@ - - EXTRA_DIST = parser.h - BUILT_SOURCES = parser.h ---- drawtiming-0.7.1.orig/src/Makefile.in -+++ drawtiming-0.7.1/src/Makefile.in -@@ -51,7 +51,7 @@ - am_drawtiming_OBJECTS = main.$(OBJEXT) parser.$(OBJEXT) \ - scanner.$(OBJEXT) timing.$(OBJEXT) - drawtiming_OBJECTS = $(am_drawtiming_OBJECTS) --drawtiming_LDADD = $(LDADD) -+drawtiming_LDADD = @MAGICK_LIBS@ $(LDADD) - DEFAULT_INCLUDES = -I. -I$(srcdir) -I$(top_builddir) - depcomp = $(SHELL) $(top_srcdir)/depcomp - am__depfiles_maybe = depfiles -@@ -159,7 +159,7 @@ - AM_CXXFLAGS = @MAGICK_CFLAGS@ -DYYDEBUG=1 - AM_YFLAGS = -d - drawtiming_SOURCES = main.cc globals.h parser.yy scanner.ll timing.cc timing.h --drawtiming_LDFLAGS = @MAGICK_LIBS@ -+drawtiming_LDFLAGS = @LDFLAGS@ - EXTRA_DIST = parser.h - BUILT_SOURCES = parser.h - all: $(BUILT_SOURCES) diff --git a/academic/ds9/README b/academic/ds9/README index bab29ee863..3569e0678c 100644 --- a/academic/ds9/README +++ b/academic/ds9/README @@ -1,10 +1,13 @@ -SAOImageDS9 is an astronomical imaging and data visualization application. DS9 -is a stand-alone application which supports FITS images and binary tables, -multiple frame buffers, region manipulation, and many scale algorithms and -colormaps. DS9 supports a consistent set of GUI and functional capabilities, -as well as advanced features such as 2-D, 3-D and RGB frame buffers, mosaic -images, tiling, blinking, geometric markers, colormap manipulation, scaling, -arbitrary zoom, cropping, rotation, pan, and a variety of coordinate systems. -The GUI for DS9 is user configurable. GUI elements such as the coordinate -display, panner, magnifier, horizontal and vertical graphs, button bar, and -color bar can be configured via menus or the command line. +SAOImageDS9 is an astronomical imaging and data visualization +application. DS9 supports FITS images and binary tables, multiple +frame buffers, region manipulation, and many scale algorithms and +colormaps. All versions and platforms support a consistent set of GUI +and functional capabilities. DS9 supports advanced features such as +2-D, 3-D and RGB frame buffers, mosaic images, tiling, blinking, +geometric markers, colormap manipulation, scaling, arbitrary zoom, +cropping, rotation, pan, and a variety of coordinate systems. +Furthermore, the application is stand-alone and requires no +installation or support files. The GUI for DS9 is user configurable. +GUI elements such as the coordinate display, panner, magnifier, +horizontal and vertical graphs, button bar, and color bar can be +configured via menus or the command line. diff --git a/academic/ds9/ds9-icon.png b/academic/ds9/ds9-icon.png Binary files differdeleted file mode 100644 index 09254821f3..0000000000 --- a/academic/ds9/ds9-icon.png +++ /dev/null diff --git a/academic/ds9/ds9.SlackBuild b/academic/ds9/ds9.SlackBuild index ceb9d596c5..096402f85e 100644 --- a/academic/ds9/ds9.SlackBuild +++ b/academic/ds9/ds9.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for ds9 (SAOImageDS9) -# Copyright 2021 Nitish Ragoomundun, Mauritius +# Copyright 2022 Nitish Ragoomundun, Mauritius # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ds9 -VERSION=${VERSION:-8.2.1} +VERSION=${VERSION:-8.4.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -82,7 +82,7 @@ find -L . \ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ -./unix/configure \ +unix/configure \ --prefix=/usr \ --bindir=/usr/bin \ --sysconfdir=/etc \ @@ -102,8 +102,8 @@ install -D -m755 bin/ds9 $PKG/usr/bin/ # Install icon mkdir -p $PKG/usr/share/applications mkdir -p $PKG/usr/share/pixmaps +install -m 644 ds9/doc/sun.png $PKG/usr/share/pixmaps/ds9-icon.png install -m 644 $CWD/ds9.desktop $PKG/usr/share/applications -install -m 644 $CWD/ds9-icon.png $PKG/usr/share/pixmaps # Copy documentation cp -a BUILD.txt LICENSE README.md ds9/doc/* $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/ds9/ds9.desktop b/academic/ds9/ds9.desktop index 08b18e0bbd..d942e73988 100644 --- a/academic/ds9/ds9.desktop +++ b/academic/ds9/ds9.desktop @@ -1,9 +1,10 @@ [Desktop Entry] -Name=ds9 -GenericName=SAOImageDS9 -Comment=Astronomical Software and FITS viewing program Exec=ds9 Icon=ds9-icon -Terminal=false Type=Application Categories=Education;Science;Astronomy; +Name=ds9 +GenericName=SAOImageDS9 +Comment=Astronomical Software and FITS viewing program +MimeType=image/fits; +Terminal=false diff --git a/academic/ds9/ds9.info b/academic/ds9/ds9.info index 475fe53290..59d26462bc 100644 --- a/academic/ds9/ds9.info +++ b/academic/ds9/ds9.info @@ -1,8 +1,8 @@ PRGNAM="ds9" -VERSION="8.2.1" +VERSION="8.4.1" HOMEPAGE="https://sites.google.com/cfa.harvard.edu/saoimageds9/home" -DOWNLOAD="https://ds9.si.edu/archive/source/ds9.8.2.1.tar.gz" -MD5SUM="99afcdc4a72e2ca15fda0b5f9af945af" +DOWNLOAD="https://ds9.si.edu/archive/source/ds9.8.4.1.tar.gz" +MD5SUM="b227d7ce367d3d7901d88cd5fccd23f7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/ds9/slack-desc b/academic/ds9/slack-desc index b4bd41a641..713bb9386a 100644 --- a/academic/ds9/slack-desc +++ b/academic/ds9/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| ds9: ds9 (Astronomical tool) ds9: -ds9: DS9 is an astronomical imaging and visualization tool. It supports -ds9: the FITS format and binary tables. It includes many imaging features -ds9: such as tiling, cropping, as well as advanced features such as -ds9: multiple 2D, 3D, RGB frame buffers, colormap manipulation and mosaic -ds9: images. DS9 also supports a variety of coordinate systems and has a -ds9: user configurable interface. -ds9: +ds9: SAOImageDS9 is an astronomical imaging and data visualization tool. +ds9: It supports FITS images and binary tables. It also includes many +ds9: advanced imaging features such as 2-D, 3-D and RGB frame buffers, +ds9: mosaic images, tiling, blinking, geometric markers, colormap +ds9: manipulation, scaling, arbitrary zoom, cropping, rotation, pan, and a +ds9: variety of coordinate systems. DS9 also has user configurable GUI +ds9: elements. ds9: Homepage: https://sites.google.com/cfa.harvard.edu/saoimageds9/home ds9: diff --git a/academic/dwave-cloud-client/README b/academic/dwave-cloud-client/README new file mode 100644 index 0000000000..d37eefb206 --- /dev/null +++ b/academic/dwave-cloud-client/README @@ -0,0 +1,8 @@ + A minimal implementation of the REST interface used to communicate +with D-Wave Solver API (SAPI) servers. + + SAPI is an application layer built to provide resource discovery, +permissions, and scheduling for quantum annealing resources at +D-Wave Systems. This package provides a minimal Python interface to +that layer without compromising the quality of interactions and +workflow. diff --git a/academic/dwave-cloud-client/dwave-cloud-client.SlackBuild b/academic/dwave-cloud-client/dwave-cloud-client.SlackBuild new file mode 100644 index 0000000000..61e4e1cf71 --- /dev/null +++ b/academic/dwave-cloud-client/dwave-cloud-client.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for dwave-cloud-client + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-cloud-client" +VERSION=${VERSION:-0.10.3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-cloud-client/dwave-cloud-client.info b/academic/dwave-cloud-client/dwave-cloud-client.info new file mode 100644 index 0000000000..170b17eb99 --- /dev/null +++ b/academic/dwave-cloud-client/dwave-cloud-client.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-cloud-client" +VERSION="0.10.3" +HOMEPAGE="https://github.com/dwavesystems/dwave-cloud-client" +DOWNLOAD="https://github.com/dwavesystems/dwave-cloud-client/archive/0.10.3/dwave-cloud-client-0.10.3.tar.gz" +MD5SUM="00a192d9aa86c07ed7b5a42a2011d78f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-cloud-client/slack-desc b/academic/dwave-cloud-client/slack-desc new file mode 100644 index 0000000000..b3a744ce10 --- /dev/null +++ b/academic/dwave-cloud-client/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-cloud-client: dwave-cloud-client (REST interface for communicating to D-Wave API) +dwave-cloud-client: +dwave-cloud-client: +dwave-cloud-client: +dwave-cloud-client: A minimal implementation of the REST interface used to communicate +dwave-cloud-client: with D-Wave Solver API (SAPI) servers. +dwave-cloud-client: +dwave-cloud-client: +dwave-cloud-client: +dwave-cloud-client: +dwave-cloud-client: diff --git a/academic/dwave-greedy/README b/academic/dwave-greedy/README new file mode 100644 index 0000000000..3e3fb8d475 --- /dev/null +++ b/academic/dwave-greedy/README @@ -0,0 +1,13 @@ + An implementation of a steepest descent solver for binary quadratic +models. + + Steepest descent is the discrete analogue of gradient descent, but +the best move is computed using a local minimization rather rather +than computing a gradient. At each step, we determine the dimension +along which to descend based on the highest energy drop caused by a +variable flip. + + + Optional building mode set with environment variables: + - TESTS=yes (performs tests, requires dimod) + diff --git a/academic/dwave-greedy/dwave-greedy.SlackBuild b/academic/dwave-greedy/dwave-greedy.SlackBuild new file mode 100644 index 0000000000..62db8ce464 --- /dev/null +++ b/academic/dwave-greedy/dwave-greedy.SlackBuild @@ -0,0 +1,120 @@ +#!/bin/bash + +# Slackware build script for dwave-greedy + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-greedy" +VERSION=${VERSION:-0.2.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +make -C tests +if [ "${TESTS:-no}" == "yes" ]; then + IGNORE_TESTS="test_(composite|sampler).py" + PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + cd tests + for file in $(ls test_*.py | grep -v -E $IGNORE_TESTS); do + echo -n "$file " + PYTHONPATH=../build/lib.linux-$(uname -m)-$PYVER python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-greedy/dwave-greedy.info b/academic/dwave-greedy/dwave-greedy.info new file mode 100644 index 0000000000..a3c9b5ee9e --- /dev/null +++ b/academic/dwave-greedy/dwave-greedy.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-greedy" +VERSION="0.2.5" +HOMEPAGE="https://github.com/dwavesystems/dwave-greedy" +DOWNLOAD="https://github.com/dwavesystems/dwave-greedy/archive/0.2.5/dwave-greedy-0.2.5.tar.gz" +MD5SUM="8805c6bfa59c9b33d1e00e713e62fb98" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-numpy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-greedy/slack-desc b/academic/dwave-greedy/slack-desc new file mode 100644 index 0000000000..15d483f32f --- /dev/null +++ b/academic/dwave-greedy/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-greedy: dwave-greedy (Implementation of a steepest descent solver for (BQM)) +dwave-greedy: +dwave-greedy: An implementation of a steepest descent solver for binary +dwave-greedy: quadratic models. +dwave-greedy: Steepest descent is the discrete analogue of gradient descent, +dwave-greedy: but the best move is computed using a local minimization rather +dwave-greedy: rather than computing a gradient. At each step, we determine the +dwave-greedy: dimension along which to descend based on the highest energy drop +dwave-greedy: caused by a variable flip. +dwave-greedy: +dwave-greedy: diff --git a/academic/dwave-hybrid/README b/academic/dwave-hybrid/README new file mode 100644 index 0000000000..d1b5b77883 --- /dev/null +++ b/academic/dwave-hybrid/README @@ -0,0 +1,15 @@ + A general, minimal Python framework for building hybrid asynchronous +decomposition samplers for quadratic unconstrained binary optimization +(QUBO) problems. + + dwave-hybrid facilitates three aspects of solution development: + + - Hybrid approaches to combining quantum and classical compute + resources + - Evaluating a portfolio of algorithmic components and + problem-decomposition trategies + - Experimenting with workflow structures and parameters to obtain + the best application results + + The framework enables rapid development and insight into expected +performance of productized versions of its experimental prototypes. diff --git a/academic/dwave-hybrid/dwave-hybrid.SlackBuild b/academic/dwave-hybrid/dwave-hybrid.SlackBuild new file mode 100644 index 0000000000..48f688e505 --- /dev/null +++ b/academic/dwave-hybrid/dwave-hybrid.SlackBuild @@ -0,0 +1,112 @@ +#!/bin/bash + +# Slackware build script for dwave-hybrid + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-hybrid" +VERSION=${VERSION:-0.6.9} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +# install libexec +mkdir -p $PKG/usr/libexec/$PRGNAM +cp -av scripts/* $PKG/usr/libexec/$PRGNAM + +# install examples and problems +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -av examples $PKG/usr/share/$PRGNAM-$VERSION +cp -av problems $PKG/usr/share/$PRGNAM-$VERSION + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-hybrid/dwave-hybrid.info b/academic/dwave-hybrid/dwave-hybrid.info new file mode 100644 index 0000000000..c45b1d0cf0 --- /dev/null +++ b/academic/dwave-hybrid/dwave-hybrid.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-hybrid" +VERSION="0.6.9" +HOMEPAGE="https://github.com/dwavesystems/dwave-hybrid" +DOWNLOAD="https://github.com/dwavesystems/dwave-hybrid/archive/0.6.9/dwave-hybrid-0.6.9.tar.gz" +MD5SUM="406d8439c122b7e6f1dd6b3427f5c954" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-hybrid/slack-desc b/academic/dwave-hybrid/slack-desc new file mode 100644 index 0000000000..025491ccfe --- /dev/null +++ b/academic/dwave-hybrid/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-hybrid: dwave-hybrid (Hybrid Async Decomposition Sampler prototype framework) +dwave-hybrid: +dwave-hybrid: +dwave-hybrid: +dwave-hybrid: A general, minimal Python framework for building hybrid +dwave-hybrid: asynchronous decomposition samplers for quadratic unconstrained +dwave-hybrid: binary optimization (QUBO) problems. +dwave-hybrid: +dwave-hybrid: +dwave-hybrid: +dwave-hybrid: diff --git a/academic/dwave-inspector/README b/academic/dwave-inspector/README new file mode 100644 index 0000000000..ed70d96276 --- /dev/null +++ b/academic/dwave-inspector/README @@ -0,0 +1,2 @@ + A tool for visualizing problems submitted to, and answers received +from, a D-Wave structured solver such as an Advantage quantum computer. diff --git a/academic/dwave-inspector/dwave-inspector.SlackBuild b/academic/dwave-inspector/dwave-inspector.SlackBuild new file mode 100644 index 0000000000..0aac87aea0 --- /dev/null +++ b/academic/dwave-inspector/dwave-inspector.SlackBuild @@ -0,0 +1,107 @@ +#!/bin/bash + +# Slackware build script for dwave-inspector + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-inspector" +VERSION=${VERSION:-0.3.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +# install examples +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -av examples $PKG/usr/share/$PRGNAM-$VERSION + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-inspector/dwave-inspector.info b/academic/dwave-inspector/dwave-inspector.info new file mode 100644 index 0000000000..a501f460c4 --- /dev/null +++ b/academic/dwave-inspector/dwave-inspector.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-inspector" +VERSION="0.3.0" +HOMEPAGE="https://github.com/dwavesystems/dwave-inspector" +DOWNLOAD="https://github.com/dwavesystems/dwave-inspector/archive/0.3.0/dwave-inspector-0.3.0.tar.gz" +MD5SUM="db97afcfbf90e989859737954f2786cc" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-inspector/slack-desc b/academic/dwave-inspector/slack-desc new file mode 100644 index 0000000000..17dfab47eb --- /dev/null +++ b/academic/dwave-inspector/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-inspector: dwave-inspector (Tool for visualizing D-Wave structured solver) +dwave-inspector: +dwave-inspector: +dwave-inspector: +dwave-inspector: A tool for visualizing problems submitted to, and answers +dwave-inspector: received from, a D-Wave structured solver such as an Advantage +dwave-inspector: quantum computer. +dwave-inspector: +dwave-inspector: +dwave-inspector: +dwave-inspector: diff --git a/academic/dwave-neal/README b/academic/dwave-neal/README new file mode 100644 index 0000000000..45dd6fdd1d --- /dev/null +++ b/academic/dwave-neal/README @@ -0,0 +1,11 @@ + An implementation of a simulated annealing sampler. + + A simulated annealing sampler can be used for approximate Boltzmann +sampling or heuristic optimization. This implementation approaches +the equilibrium distribution by performing updates at a sequence of +increasing beta values, beta_schedule, terminating at the target +beta. Each spin is updated once in a fixed order per point in the +beta_schedule according to a Metropolis- Hastings update. When beta +is large the target distribution concentrates, at equilibrium, +over ground states of the model. Samples are guaranteed to match +the equilibrium for long 'smooth' beta schedules. diff --git a/academic/dwave-neal/dwave-neal.SlackBuild b/academic/dwave-neal/dwave-neal.SlackBuild new file mode 100644 index 0000000000..a6f1fe8909 --- /dev/null +++ b/academic/dwave-neal/dwave-neal.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/bash + +# Slackware build script for dwave-neal + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-neal" +VERSION=${VERSION:-0.5.9} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) +cd tests + for file in $(ls test_*.py); do + echo -n "$file " + PYTHONPATH=../build/lib.linux-$(uname -m)-$PYVER python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done +cd .. + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-neal/dwave-neal.info b/academic/dwave-neal/dwave-neal.info new file mode 100644 index 0000000000..3f928a533d --- /dev/null +++ b/academic/dwave-neal/dwave-neal.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-neal" +VERSION="0.5.9" +HOMEPAGE="https://github.com/dwavesystems/dwave-neal" +DOWNLOAD="https://github.com/dwavesystems/dwave-neal/archive/0.5.9/dwave-neal-0.5.9.tar.gz" +MD5SUM="f01bae63001966835a0677e8b9b07ea8" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="dimod" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-neal/slack-desc b/academic/dwave-neal/slack-desc new file mode 100644 index 0000000000..da4cd80d24 --- /dev/null +++ b/academic/dwave-neal/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-neal: dwave-neal (An implementation of a simulated annealing sampler) +dwave-neal: +dwave-neal: An implementation of a simulated annealing sampler. +dwave-neal: +dwave-neal: A simulated annealing sampler can be used for approximate Boltzmann +dwave-neal: sampling or heuristic optimization. This implementation approaches +dwave-neal: the equilibrium distribution by performing updates at a sequence of +dwave-neal: increasing beta values, beta_schedule, terminating at the target +dwave-neal: beta. +dwave-neal: +dwave-neal: diff --git a/academic/dwave-networkx/README b/academic/dwave-networkx/README new file mode 100644 index 0000000000..9c0129351a --- /dev/null +++ b/academic/dwave-networkx/README @@ -0,0 +1,10 @@ + D-Wave NetworkX is an extension of NetworkX---a Python language +package for exploration and analysis of networks and network +algorithms---for users of D-Wave Systems. It provides tools for +working with Chimera graphs and implementations of graph-theory +algorithms on the D-Wave system and other binary quadratic model +samplers. + + + If you want to run the tests set the environment variable TESTS=yes, +this requires networkx, dimod and numpy3. diff --git a/academic/dwave-networkx/dwave-networkx.SlackBuild b/academic/dwave-networkx/dwave-networkx.SlackBuild new file mode 100644 index 0000000000..3c1570af2e --- /dev/null +++ b/academic/dwave-networkx/dwave-networkx.SlackBuild @@ -0,0 +1,119 @@ +#!/bin/bash + +# Slackware build script for dwave-networkx + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-networkx" +VERSION=${VERSION:-0.8.12} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + IGNORE_TESTS="test_(matching).py" + PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + cd tests + for file in $(ls test_*.py | grep -v -E $IGNORE_TESTS); do + echo -n "$file " + PYTHONPATH=../build/lib python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE.txt README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-networkx/dwave-networkx.info b/academic/dwave-networkx/dwave-networkx.info new file mode 100644 index 0000000000..25a6ac6260 --- /dev/null +++ b/academic/dwave-networkx/dwave-networkx.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-networkx" +VERSION="0.8.12" +HOMEPAGE="https://www.dwavesys.com" +DOWNLOAD="https://github.com/dwavesystems/dwave-networkx/archive/0.8.12/dwave-networkx-0.8.12.tar.gz" +MD5SUM="5bd9d71bc6ebd723d1b741debc4abcef" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-networkx/slack-desc b/academic/dwave-networkx/slack-desc new file mode 100644 index 0000000000..db55ee6e77 --- /dev/null +++ b/academic/dwave-networkx/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-networkx: dwave-networkx (Network exploration and analysis for D-Wave Systems) +dwave-networkx: +dwave-networkx: +dwave-networkx: D-Wave NetworkX is an extension of NetworkX---a Python language +dwave-networkx: package for exploration and analysis of networks and network +dwave-networkx: algorithms---for users of D-Wave Systems. It provides tools for +dwave-networkx: working with Chimera graphs and implementations of graph-theory +dwave-networkx: algorithms on the D-Wave system and other binary quadratic model +dwave-networkx: samplers. +dwave-networkx: +dwave-networkx: diff --git a/academic/dwave-ocean-sdk/README b/academic/dwave-ocean-sdk/README new file mode 100644 index 0000000000..fc830b8659 --- /dev/null +++ b/academic/dwave-ocean-sdk/README @@ -0,0 +1,23 @@ + Ocean is D-Wave's suite of tools for solving hard problems with +quantum computers. + + After installing you can run "dwave setup" to configure your +system. If you don't have yet you shall get an API token after +registering at dwavesystem's webpage. + + +NOTE: slackbuilds.org, doesn't request to include packages that isn't +necessary to build the package nonetheless there is a few packages +required for running the dwave ocean sdk: + - python3-dateutil + - python3-plucky + - python-diskcache + - click + - homebase + - python3-pydantic + - PySocks + - rectangle-packer + +Other packages for development + - scipy3 + - fasteners diff --git a/academic/dwave-ocean-sdk/dwave-ocean-sdk.SlackBuild b/academic/dwave-ocean-sdk/dwave-ocean-sdk.SlackBuild new file mode 100644 index 0000000000..cfad5737ba --- /dev/null +++ b/academic/dwave-ocean-sdk/dwave-ocean-sdk.SlackBuild @@ -0,0 +1,134 @@ +#!/bin/bash + +# Slackware build script for dwave-ocean-sdk + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=dwave-ocean-sdk +VERSION=${VERSION:-6.0.0} +BUILD=${BUILD:-2} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION + +# unpack components +for source_file in $(ls $CWD/{dimod,dwave-{cloud-client,greedy,hybrid,inspector,neal,networkx,preprocessing,system,tabu},dwavebinarycsp,minorminer,penaltymodel,dwavebinarycsp}-*.tar.gz); do + dir_name=$(basename $source_file | sed 's/-[0-9].*//') + tar xvf $source_file -C $dir_name --strip-component 1 +done + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + +for source_file in $(ls $CWD/{dimod,dwave-{cloud-client,greedy,hybrid,inspector,neal,networkx,preprocessing,system,tabu},dwavebinarycsp,minorminer,penaltymodel,dwavebinarycsp}-*.tar.gz); do + dir_name=$(basename $source_file | sed 's/-[0-9].*//') + echo "Installing: $dir_name" + cd $dir_name + + # set path to installed package modules + PYTHONPATH=$PKG/usr/lib${LIBDIRSUFFIX}/python$PYVER/site-packages \ + python3 setup.py install --root=$PKG + + # install documentation + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/$dir_name + cp -avL docs $PKG/usr/doc/$PRGNAM-$VERSION/$dir_name + + # install examples if exists + if [ -d examples ]; then + mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/$dir_name + cp -av examples $PKG/usr/share/$PRGNAM-$VERSION/$dir_name + fi + cd .. +done + +# install dwave-ocean-sdk +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CONTRIBUTING.rst LICENSE README.rst \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-ocean-sdk/dwave-ocean-sdk.info b/academic/dwave-ocean-sdk/dwave-ocean-sdk.info new file mode 100644 index 0000000000..0a3328a777 --- /dev/null +++ b/academic/dwave-ocean-sdk/dwave-ocean-sdk.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-ocean-sdk" +VERSION="6.0.0" +HOMEPAGE="https://www.dwavesys.com/solutions-and-products/ocean" +DOWNLOAD="https://github.com/dwavesystems/dwave-ocean-sdk/archive/6.0.0/dwave-ocean-sdk-6.0.0.tar.gz https://github.com/dwavesystems/dimod/archive/0.12.0/dimod-0.12.0.tar.gz https://github.com/dwavesystems/dwave-cloud-client/archive/0.10.3/dwave-cloud-client-0.10.3.tar.gz https://github.com/dwavesystems/dwave-greedy/archive/0.2.5/dwave-greedy-0.2.5.tar.gz https://github.com/dwavesystems/dwave-hybrid/archive/0.6.9/dwave-hybrid-0.6.9.tar.gz https://github.com/dwavesystems/dwave-inspector/archive/0.3.0/dwave-inspector-0.3.0.tar.gz https://github.com/dwavesystems/dwave-neal/archive/0.5.9/dwave-neal-0.5.9.tar.gz https://github.com/dwavesystems/dwave-networkx/archive/0.8.12/dwave-networkx-0.8.12.tar.gz https://github.com/dwavesystems/dwave-preprocessing/archive/0.5.0/dwave-preprocessing-0.5.0.tar.gz https://github.com/dwavesystems/dwave-system/archive/1.16.0/dwave-system-1.16.0.tar.gz https://github.com/dwavesystems/dwave-tabu/archive/0.4.5/dwave-tabu-0.4.5.tar.gz https://github.com/dwavesystems/dwavebinarycsp/archive/0.2.0/dwavebinarycsp-0.2.0.tar.gz https://github.com/dwavesystems/minorminer/archive/0.2.9/minorminer-0.2.9.tar.gz https://github.com/dwavesystems/penaltymodel/archive/1.0.2/penaltymodel-1.0.2.tar.gz" +MD5SUM="23c03fae1a25ca9246b46fdf01e36a88 20dfa5a1cb6f06b3f928c0538f8a021c 00a192d9aa86c07ed7b5a42a2011d78f 8805c6bfa59c9b33d1e00e713e62fb98 406d8439c122b7e6f1dd6b3427f5c954 db97afcfbf90e989859737954f2786cc f01bae63001966835a0677e8b9b07ea8 5bd9d71bc6ebd723d1b741debc4abcef 68de0e23a6c8023f30f056e5aae2cbfb 450b6fbdf0829ec7e2dddec4e9d0b23b 861fe9eb8b0771b97c6240e228ac5e50 59fe60257afe4725a50dc7cf4fb7b972 de59a2d16a94ee5853938cbf19d61a6f 26c6d33ac5a17620c4d6de76985cc552" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-numpy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-ocean-sdk/slack-desc b/academic/dwave-ocean-sdk/slack-desc new file mode 100644 index 0000000000..8aad645d3e --- /dev/null +++ b/academic/dwave-ocean-sdk/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-ocean-sdk: dwave-ocean-sdk (D-Wave Ocean SDK) +dwave-ocean-sdk: +dwave-ocean-sdk: +dwave-ocean-sdk: +dwave-ocean-sdk: Ocean is D-Wave's suite of tools for solving hard problems with +dwave-ocean-sdk: quantum computers. +dwave-ocean-sdk: +dwave-ocean-sdk: +dwave-ocean-sdk: +dwave-ocean-sdk: +dwave-ocean-sdk: diff --git a/academic/dwave-preprocessing/README b/academic/dwave-preprocessing/README new file mode 100644 index 0000000000..b0f9a0feab --- /dev/null +++ b/academic/dwave-preprocessing/README @@ -0,0 +1,2 @@ + dwave-preprocessing is a package of common preprocessing tools that +can aid in solving binary quadratic models (BQM). diff --git a/academic/dwave-preprocessing/dwave-preprocessing.SlackBuild b/academic/dwave-preprocessing/dwave-preprocessing.SlackBuild new file mode 100644 index 0000000000..4314c1f173 --- /dev/null +++ b/academic/dwave-preprocessing/dwave-preprocessing.SlackBuild @@ -0,0 +1,117 @@ +#!/bin/bash + +# Slackware build script for dwave-preprocessing + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-preprocessing" +VERSION=${VERSION:-0.5.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +# run tests +PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) +cd tests + for file in $(ls test_*.py); do + echo -n "$file " + PYTHONPATH=../build/lib.linux-$(uname -m)-$PYVER python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done +cd .. + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-preprocessing/dwave-preprocessing.info b/academic/dwave-preprocessing/dwave-preprocessing.info new file mode 100644 index 0000000000..6b4a6f3e81 --- /dev/null +++ b/academic/dwave-preprocessing/dwave-preprocessing.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-preprocessing" +VERSION="0.5.0" +HOMEPAGE="https://www.dwavesys.com" +DOWNLOAD="https://github.com/dwavesystems/dwave-preprocessing/archive/0.5.0/dwave-preprocessing-0.5.0.tar.gz" +MD5SUM="68de0e23a6c8023f30f056e5aae2cbfb" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="dimod" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-preprocessing/slack-desc b/academic/dwave-preprocessing/slack-desc new file mode 100644 index 0000000000..fbf08c0c18 --- /dev/null +++ b/academic/dwave-preprocessing/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-preprocessing: dwave-preprocessing (preprocessing tools for binary quadratic models) +dwave-preprocessing: +dwave-preprocessing: +dwave-preprocessing: dwave-preprocessing is a package of common preprocessing tools +dwave-preprocessing: that can aid in solving binary quadratic models (BQM). +dwave-preprocessing: +dwave-preprocessing: +dwave-preprocessing: +dwave-preprocessing: +dwave-preprocessing: +dwave-preprocessing: diff --git a/academic/dwave-system/README b/academic/dwave-system/README new file mode 100644 index 0000000000..4ff6726c99 --- /dev/null +++ b/academic/dwave-system/README @@ -0,0 +1,9 @@ + dwave-system is a basic API for easily incorporating the D-Wave +system as a sampler in the D-Wave Ocean software stack, directly +or through Leap's cloud-based hybrid solvers. It includes +DWaveSampler, a dimod sampler that accepts and passes system +parameters such as system identification and authentication down +the stack, LeapHybridSampler, for Leap's hybrid solvers, and other. +It also includes several useful composites---layers of pre- and +post-processing---that can be used with DWaveSampler to handle +minor-embedding, optimize chain strength, etc. diff --git a/academic/dwave-system/dwave-system.SlackBuild b/academic/dwave-system/dwave-system.SlackBuild new file mode 100644 index 0000000000..c2f1f2e2c0 --- /dev/null +++ b/academic/dwave-system/dwave-system.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for dwave-system + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-system" +VERSION=${VERSION:-1.16.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-system/dwave-system.info b/academic/dwave-system/dwave-system.info new file mode 100644 index 0000000000..260dccfdf2 --- /dev/null +++ b/academic/dwave-system/dwave-system.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-system" +VERSION="1.16.0" +HOMEPAGE="https://www.dwavesys.com" +DOWNLOAD="https://github.com/dwavesystems/dwave-system/archive/1.16.0/dwave-system-1.16.0.tar.gz" +MD5SUM="450b6fbdf0829ec7e2dddec4e9d0b23b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-system/slack-desc b/academic/dwave-system/slack-desc new file mode 100644 index 0000000000..60573eac9d --- /dev/null +++ b/academic/dwave-system/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-system: dwave-system (basic API for D-Wave system) +dwave-system: +dwave-system: dwave-system is a basic API for easily incorporating the D-Wave +dwave-system: system as a sampler in the D-Wave Ocean software stack, directly or +dwave-system: through Leap's cloud-based hybrid solvers. It includes DWaveSampler, +dwave-system: a dimod sampler that accepts and passes system parameters such as +dwave-system: system identification and authentication down the stack, +dwave-system: LeapHybridSampler, for Leap's hybrid solvers, and other. It also +dwave-system: includes several useful composites---layers of pre- and +dwave-system: post-processing---that can be used with DWaveSampler to handle +dwave-system: minor-embedding, optimize chain strength, etc. diff --git a/academic/dwave-tabu/README b/academic/dwave-tabu/README new file mode 100644 index 0000000000..0a82867af8 --- /dev/null +++ b/academic/dwave-tabu/README @@ -0,0 +1,7 @@ + A C/C++ implementation of the MST2 multistart tabu search algorithm +for quadratic unconstrained binary optimization (QUBO) problems with +a dimod sampler Python interface. + + + For running tests set the environment variable TESTS=yes, this +requires dimod. diff --git a/academic/dwave-tabu/dwave-tabu.SlackBuild b/academic/dwave-tabu/dwave-tabu.SlackBuild new file mode 100644 index 0000000000..fe9ce1a14b --- /dev/null +++ b/academic/dwave-tabu/dwave-tabu.SlackBuild @@ -0,0 +1,118 @@ +#!/bin/bash + +# Slackware build script for dwave-tabu + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-tabu" +VERSION=${VERSION:-0.4.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + cd tests + for file in $(ls test_*.py); do + echo -n "$file " + PYTHONPATH=../build/lib.linux-$(uname -m)-$PYVER python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-tabu/dwave-tabu.info b/academic/dwave-tabu/dwave-tabu.info new file mode 100644 index 0000000000..ffc2d1fb68 --- /dev/null +++ b/academic/dwave-tabu/dwave-tabu.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-tabu" +VERSION="0.4.5" +HOMEPAGE="https://github.com/dwavesystems/dwave-tabu" +DOWNLOAD="https://github.com/dwavesystems/dwave-tabu/archive/0.4.5/dwave-tabu-0.4.5.tar.gz" +MD5SUM="861fe9eb8b0771b97c6240e228ac5e50" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-numpy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-tabu/slack-desc b/academic/dwave-tabu/slack-desc new file mode 100644 index 0000000000..cfea47c422 --- /dev/null +++ b/academic/dwave-tabu/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-tabu: dwave-tabu (C/C++ implementation of MST2 for QUBO) +dwave-tabu: +dwave-tabu: +dwave-tabu: +dwave-tabu: A C/C++ implementation of the MST2 multistart tabu search algorithm +dwave-tabu: for quadratic unconstrained binary optimization (QUBO) problems with +dwave-tabu: a dimod sampler Python interface. +dwave-tabu: +dwave-tabu: +dwave-tabu: +dwave-tabu: diff --git a/academic/dwavebinarycsp/README b/academic/dwavebinarycsp/README new file mode 100644 index 0000000000..9f177497e7 --- /dev/null +++ b/academic/dwavebinarycsp/README @@ -0,0 +1,7 @@ + Library to construct a binary quadratic model from a constraint +satisfaction problem with small constraints over binary variables. + + + If you want to run the tests set the environment variable TESTS=yes +this requires: blas, lapack, dimod, homebase, networkx, numpy3, +penaltymodel and scipy3. diff --git a/academic/dwavebinarycsp/dwavebinarycsp.SlackBuild b/academic/dwavebinarycsp/dwavebinarycsp.SlackBuild new file mode 100644 index 0000000000..d5951f4fbc --- /dev/null +++ b/academic/dwavebinarycsp/dwavebinarycsp.SlackBuild @@ -0,0 +1,118 @@ +#!/bin/bash + +# Slackware build script for dwavebinarycsp + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwavebinarycsp" +VERSION=${VERSION:-0.2.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + cd tests + for file in $(ls test_*.py); do + echo -n "$file " + PYTHONPATH=../build/lib python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwavebinarycsp/dwavebinarycsp.info b/academic/dwavebinarycsp/dwavebinarycsp.info new file mode 100644 index 0000000000..084a44c3e7 --- /dev/null +++ b/academic/dwavebinarycsp/dwavebinarycsp.info @@ -0,0 +1,10 @@ +PRGNAM="dwavebinarycsp" +VERSION="0.2.0" +HOMEPAGE="https://github.com/dwavesystems" +DOWNLOAD="https://github.com/dwavesystems/dwavebinarycsp/archive/0.2.0/dwavebinarycsp-0.2.0.tar.gz" +MD5SUM="59fe60257afe4725a50dc7cf4fb7b972" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwavebinarycsp/slack-desc b/academic/dwavebinarycsp/slack-desc new file mode 100644 index 0000000000..d288947374 --- /dev/null +++ b/academic/dwavebinarycsp/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwavebinarycsp: dwavebinarycsp (Library for contructing binary quadratic models) +dwavebinarycsp: +dwavebinarycsp: +dwavebinarycsp: +dwavebinarycsp: Library to construct a binary quadratic model from a constraint +dwavebinarycsp: satisfaction problem with small constraints over binary variables. +dwavebinarycsp: +dwavebinarycsp: +dwavebinarycsp: +dwavebinarycsp: +dwavebinarycsp: diff --git a/academic/ed-v6/ed-v6.SlackBuild b/academic/ed-v6/ed-v6.SlackBuild index d52282c25f..ab0b073b0e 100644 --- a/academic/ed-v6/ed-v6.SlackBuild +++ b/academic/ed-v6/ed-v6.SlackBuild @@ -70,7 +70,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$SRCVERSION -tar xvf $CWD/$SRCVERSION.tar.gz +tar xvf $CWD/$PRGNAM-$SRCVERSION.tar.gz cd $PRGNAM-$SRCVERSION chown -R root:root . find -L . \ diff --git a/academic/ed-v6/ed-v6.info b/academic/ed-v6/ed-v6.info index 35e5735a5a..c7d239ec09 100644 --- a/academic/ed-v6/ed-v6.info +++ b/academic/ed-v6/ed-v6.info @@ -1,10 +1,10 @@ PRGNAM="ed-v6" VERSION="c72c0e" HOMEPAGE="https://github.com/geocar/ed-v6" -DOWNLOAD="https://github.com/geocar/ed-v6/archive/c72c0e9/c72c0e9445af26bd9fde2d39da5628e6dabf36dd.tar.gz" +DOWNLOAD="https://github.com/geocar/ed-v6/archive/c72c0e9/ed-v6-c72c0e9445af26bd9fde2d39da5628e6dabf36dd.tar.gz" MD5SUM="797a81796fdaf0b35bbce721d08d7bd7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Dave Woodfall" +MAINTAINER="D Woodfall" EMAIL="dave@slackbuilds.org" diff --git a/academic/edsim51di/edsim51di.info b/academic/edsim51di/edsim51di.info index ff9f94cec3..03325ce1ce 100644 --- a/academic/edsim51di/edsim51di.info +++ b/academic/edsim51di/edsim51di.info @@ -1,10 +1,10 @@ PRGNAM="edsim51di" VERSION="2.1.20" -HOMEPAGE="http://www.edsim51.com/" -DOWNLOAD="http://www.edsim51.com/8051simulator/edsim51di.zip" -MD5SUM="b97b326e8d74a2f5ade7f30e617d8ce8" +HOMEPAGE="https://www.edsim51.com/" +DOWNLOAD="https://www.edsim51.com/8051simulator/edsim51di.zip" +MD5SUM="b72c84a29560237e310b3eacfd61e9b7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="openjdk7" +REQUIRES="zulu-openjdk11" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/elk/README b/academic/elk/README new file mode 100644 index 0000000000..2acde1734e --- /dev/null +++ b/academic/elk/README @@ -0,0 +1,20 @@ +An all-electron full-potential linearised augmented-plane wave +(LAPW) code with many advanced features. Written originally at +Karl-Franzens-Universitat Graz as a milestone of the EXCITING EU +Research and Training Network, the code is designed to be as simple +as possible so that new developments in the field of density +functional theory (DFT) can be added quickly and reliably. The code +is freely available under the GNU General Public License. + + + The code is made to use OpenMP and only build with -fopenmp flag, +although the default building doesn't use additional optimization +flags to OpenMP. + However there is some building options available, that can be set +using the environment variables as following: + If you want to enable more optimizations to OpenMP set OMP_OPT=yes + You can also enable MPI, set MPI=yes and install openmpi or mpich. + It's also possible to use OMP_OPT=yes and MPI=yes together. + + Optional dependence: libxc + To use libxc set LIBXC=yes, this requires libxc diff --git a/academic/elk/elk.SlackBuild b/academic/elk/elk.SlackBuild new file mode 100644 index 0000000000..fdcc077a89 --- /dev/null +++ b/academic/elk/elk.SlackBuild @@ -0,0 +1,154 @@ +#!/bin/bash + +# Slackware build script for elk + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=elk +VERSION=${VERSION:-8.5.10} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tgz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# set default compiler flags to all modes +# NOTE: doesn't compile without openmp +FORTRAN_COMPILER="gfortran" +BUILD_FLAGS="-Wall -std=legacy -fopenmp" + +if [ "${OMP_OPT:-no}" == "yes" ]; then + BUILD_FLAGS="$BUILD_FLAGS -ffast-math -funroll-loops -fopenmp" +fi + +if [ "${MPI:-no}" == "yes" ]; then + FORTRAN_COMPILER="mpif90" +fi + +# configure building +echo > make.inc +echo "MAKE = make" >> make.inc +echo "F90 = $FORTRAN_COMPILER" >> make.inc +echo "F90_OPTS = -O2 $BUILD_FLAGS" >> make.inc +echo "F77 = $FORTRAN_COMPILER" >> make.inc +echo "F77_OPTS = -O2 $BUILD_FLAGS" >> make.inc +echo "AR = ar" >> make.inc +echo "LIB_LPK = lapack.a blas.a" >> make.inc +echo "LIB_FFT = fftlib.a" >> make.inc +cat make.def >> make.inc + +if [ "${LIBXC:-no}" == "yes" ]; then + sed -i '47aLIB_libxc = /usr/lib'${LIBDIRSUFFIX}'/libxc.so' make.inc + sed -i 's/^#SRC_libxc/SRC_libxc/' make.inc +fi + +# fix eos and spacegroup makefile "cannot open module file modmain.mod" +sed -i '20s/$(OBJ)/$(SRC)/' src/eos/Makefile +sed -i '20a\\t$(F90) $(F90_OPTS) -c $(SRC)' src/eos/Makefile +sed -i '28s/$(OBJ)/$(SRC)/' src/spacegroup/Makefile +sed -i '28a\\t$(F90) $(F90_OPTS) -c $(SRC)' src/spacegroup/Makefile + +make all + +# not rule to install, so perform it manually +install -d $PKG/usr/bin +install -m 755 src/elk $PKG/usr/bin + +install -d $PKG/usr/libexec/$PRGNAM +install -m 755 src/{grepelk,protex,rmspaces,vimelk} $PKG/usr/libexec/$PRGNAM +install -m 755 src/eos/eos $PKG/usr/libexec/$PRGNAM +install -m 755 src/spacegroup/spacegroup $PKG/usr/libexec/$PRGNAM + +# install examples and some tools +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a examples species utilities $PKG/usr/share/$PRGNAM-$VERSION + +# update examples to search expecies at system installation path +for file in $(grep -lr "" $PKG/usr/share/$PRGNAM-$VERSION/examples); do + sed -i 's#\(../../..\)\(/species\)#/usr/share/'$PRGNAM-$VERSION'\2#' $file +done + + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + COPYING docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/elk/elk.info b/academic/elk/elk.info new file mode 100644 index 0000000000..5e2bbbb368 --- /dev/null +++ b/academic/elk/elk.info @@ -0,0 +1,10 @@ +PRGNAM="elk" +VERSION="8.5.10" +HOMEPAGE="https://elk.sourceforge.io" +DOWNLOAD="https://sourceforge.net/projects/elk/files/elk-8.5.10.tgz" +MD5SUM="31666536723d352b07c9df3af4b9ac12" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/elk/slack-desc b/academic/elk/slack-desc new file mode 100644 index 0000000000..341d56c177 --- /dev/null +++ b/academic/elk/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +elk: elk (linearized augmented-plane-wave (LAPW) software) +elk: +elk: An all-electron full-potential linearised augmented-plane wave +elk: (LAPW) code with many advanced features. Written originally at +elk: Karl-Franzens-Universitat Graz as a milestone of the EXCITING EU +elk: Research and Training Network, the code is designed to be as simple +elk: as possible so that new developments in the field of density +elk: functional theory (DFT) can be added quickly and reliably. The code +elk: is freely available under the GNU General Public License. +elk: +elk: diff --git a/academic/engauge/engauge.SlackBuild b/academic/engauge/engauge.SlackBuild index 395fe78e5c..2840fef1ae 100644 --- a/academic/engauge/engauge.SlackBuild +++ b/academic/engauge/engauge.SlackBuild @@ -24,7 +24,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=engauge -VERSION=${VERSION:-10.10} +VERSION=${VERSION:-12.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -81,7 +81,7 @@ find -L . \ POPPLER_INCLUDE=/usr/include/poppler/qt5 \ POPPLER_LIB=/usr/lib${LIBDIRSUFFIX} \ -OPENJPEG_INCLUDE=/usr/include/openjpeg-2.3 \ +OPENJPEG_INCLUDE=/usr/include/openjpeg-2.4 \ OPENJPEG_LIB=/usr/lib${LIBDIRSUFFIX} \ qmake-qt5 \ QMAKE_CFLAGS+="$SLKCFLAGS" \ diff --git a/academic/engauge/engauge.info b/academic/engauge/engauge.info index ff9fb67efe..baec06a791 100644 --- a/academic/engauge/engauge.info +++ b/academic/engauge/engauge.info @@ -1,8 +1,8 @@ PRGNAM="engauge" -VERSION="10.10" +VERSION="12.1" HOMEPAGE="http://markummitchell.github.io/engauge-digitizer/" -DOWNLOAD="https://github.com/markummitchell/engauge-digitizer/archive/v10.10/engauge-digitizer-10.10.tar.gz" -MD5SUM="fe00faf453ff25f355fc46f81280d69a" +DOWNLOAD="https://github.com/markummitchell/engauge-digitizer/archive/v12.1/engauge-digitizer-12.1.tar.gz" +MD5SUM="842ec1769723018845b0a1acb3f1484c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="log4cpp" diff --git a/academic/ent/ent.SlackBuild b/academic/ent/ent.SlackBuild index 74608571e8..90786516a8 100644 --- a/academic/ent/ent.SlackBuild +++ b/academic/ent/ent.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for ent -# Written by B. Watson (yalhcru@gmail.com) +# Written by B. Watson (urchlay@slackware.uk) # Licensed under the WTFPL. See http://www.wtfpl.net/txt/copying/ for details. @@ -35,16 +35,12 @@ OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" - LIBDIRSUFFIX="" fi set -e diff --git a/academic/ent/ent.info b/academic/ent/ent.info index 6e12c713a0..fc59242126 100644 --- a/academic/ent/ent.info +++ b/academic/ent/ent.info @@ -1,10 +1,10 @@ PRGNAM="ent" VERSION="20080128" -HOMEPAGE="http://www.fourmilab.ch/random/" -DOWNLOAD="http://www.fourmilab.ch/random/random.zip" +HOMEPAGE="https://www.fourmilab.ch/random/" +DOWNLOAD="https://www.fourmilab.ch/random/random.zip" MD5SUM="8104a83af1ea5b280da96c92da18eae4" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="B. Watson" -EMAIL="yalhcru@gmail.com" +EMAIL="urchlay@slackware.uk" diff --git a/academic/ephem/README b/academic/ephem/README new file mode 100644 index 0000000000..3a9ea4f24c --- /dev/null +++ b/academic/ephem/README @@ -0,0 +1,7 @@ +Ephem is a program that displays ephemerides for all the planets plus +any two additional objects. The additional objects may be fixed or +specified via heliocentric elliptical, hyperbolic or parabolic orbital +elements to accommodate solar system objects such as asteroids or +comets. + +The user manual can be found at /usr/share/doc/ephem-4.32/Man.txt. diff --git a/academic/ephem/ephem.SlackBuild b/academic/ephem/ephem.SlackBuild new file mode 100644 index 0000000000..207f8a9ec3 --- /dev/null +++ b/academic/ephem/ephem.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for ephem + +# Copyright 2023 Dario Nicodemi Italy +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=ephem +VERSION=${VERSION:-4.32} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +make CFLAGS="$SLKCFLAGS -DANSI_COLORS -DGLOBE_PHOON -fcommon" +mkdir -p $PKG/usr/bin +cp $PRGNAM $PKG/usr/bin + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + Man.txt \ + README \ + ephem.cfg \ + ephem.db \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ephem/ephem.info b/academic/ephem/ephem.info new file mode 100644 index 0000000000..88a3337d51 --- /dev/null +++ b/academic/ephem/ephem.info @@ -0,0 +1,10 @@ +PRGNAM="ephem" +VERSION="4.32" +HOMEPAGE="http://www.clearskyinstitute.com/ephem/" +DOWNLOAD="http://www.clearskyinstitute.com/ephem/ephem-4.32.tar.gz" +MD5SUM="953e5f97c610140b29d729c44aecd6b8" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Dario Nicodemi" +EMAIL="dario.sbo@gmail.com" diff --git a/academic/ephem/slack-desc b/academic/ephem/slack-desc new file mode 100644 index 0000000000..48c0038ad2 --- /dev/null +++ b/academic/ephem/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +ephem: ephem (ephemeris program for 24x80 character display) +ephem: +ephem: Ephem is a program that displays ephemerides for all the planets plus +ephem: any two additional objects. The additional objects may be fixed or +ephem: specified via heliocentric elliptical, hyperbolic or parabolic +ephem: orbital elements accommodate solar system objects such as asteroids +ephem: or comets. +ephem: +ephem: +ephem: +ephem: diff --git a/academic/equalx/equalx.SlackBuild b/academic/equalx/equalx.SlackBuild index e827277920..21a6bc3c6b 100644 --- a/academic/equalx/equalx.SlackBuild +++ b/academic/equalx/equalx.SlackBuild @@ -23,7 +23,7 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# Now maintained by B. Watson <yalhcru@gmail.com> +# Now maintained by B. Watson <urchlay@slackware.uk> # 20210802 bkw: BUILD=3, update for qt5 on -current. diff --git a/academic/equalx/equalx.info b/academic/equalx/equalx.info index c99a016018..5b43393881 100644 --- a/academic/equalx/equalx.info +++ b/academic/equalx/equalx.info @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="exempi" MAINTAINER="B. Watson" -EMAIL="yalhcru@gmail.com" +EMAIL="urchlay@slackware.uk" diff --git a/academic/evopedia_qt/evopedia_qt.SlackBuild b/academic/evopedia_qt/evopedia_qt.SlackBuild index 7092baa732..b146f57090 100644 --- a/academic/evopedia_qt/evopedia_qt.SlackBuild +++ b/academic/evopedia_qt/evopedia_qt.SlackBuild @@ -14,7 +14,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -47,6 +47,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh # uncomment NO_GUI option for a gui less installation qmake PREFIX=$PKG/usr #DEFINES+=NO_GUI make diff --git a/academic/evopedia_qt/evopedia_qt.info b/academic/evopedia_qt/evopedia_qt.info index a918ec4dd3..8f212fa1c6 100644 --- a/academic/evopedia_qt/evopedia_qt.info +++ b/academic/evopedia_qt/evopedia_qt.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/evopedia/evopedia_qt/archive/v0.4.4/evopedia_qt-0.4 MD5SUM="3418c22e5d69baa06fe0de7de7c57110" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="qt4" MAINTAINER="Dan-Simon Myrland" EMAIL="dansimon@radiotube.org" diff --git a/academic/extrema/extrema.SlackBuild b/academic/extrema/extrema.SlackBuild index 68178383b3..66760b5c5d 100644 --- a/academic/extrema/extrema.SlackBuild +++ b/academic/extrema/extrema.SlackBuild @@ -29,7 +29,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=extrema VERSION=${VERSION:-4.4.5} -BUILD=${BUILD:-2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -120,6 +120,8 @@ cp -a doc/* AUTHORS COPYING ChangeLog INSTALL NEWS README THANKS \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh diff --git a/academic/fann/fann.SlackBuild b/academic/fann/fann.SlackBuild index 6706d67150..d57e66a8e0 100644 --- a/academic/fann/fann.SlackBuild +++ b/academic/fann/fann.SlackBuild @@ -16,7 +16,7 @@ SRCNAME=FANN-$VERSION-Source if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -34,8 +34,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/fastqc/doinst.sh b/academic/fastqc/doinst.sh index d9483a16ab..5fb28930db 100644 --- a/academic/fastqc/doinst.sh +++ b/academic/fastqc/doinst.sh @@ -1,8 +1,3 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi - -( cd usr/bin ; rm -rf fastqc ) -( cd usr/bin ; ln -sf ../share/java/fastqc/fastqc fastqc ) -( cd usr/doc/fastqc-0.11.8 ; rm -rf Help ) -( cd usr/doc/fastqc-0.11.8 ; ln -sf ../../share/java/fastqc/Help Help ) diff --git a/academic/fastqc/fastqc.SlackBuild b/academic/fastqc/fastqc.SlackBuild index e1e1cf5a59..c8127dac3f 100644 --- a/academic/fastqc/fastqc.SlackBuild +++ b/academic/fastqc/fastqc.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for fastqc -# Copyright 2015-2018 Petar Petrov slackalaxy@gmail.com; 2018-2020 Rob van Nues sborg63.org +# Copyright 2015-2018 Petar Petrov slackalaxy@gmail.com; 2018-2023 Rob van Nues sborg63.org # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,10 +26,10 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=fastqc SRCNAM=FastQC -VERSION=${VERSION:-0.11.9} -SRCVER=${SRCVER:-v0.11.9} +VERSION=${VERSION:-0.12.1} +SRCVER=${SRCVER:-v0.12.1} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -37,7 +37,7 @@ ARCH=noarch # Jar files names and versions JBZIP=jbzip2-0.9.jar -SAM=sam-1.103.jar +HTS=htsjdk.jar CISD=cisd-jhdf5.jar # If the variable PRINT_PACKAGE_NAME is set, then this script will report what @@ -67,8 +67,11 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# remove .svn folders causing java errors e.g. when using help +find -d -name .svn -exec rm -r '{}' ';' + install -D -m755 $PRGNAM $PKG/usr/share/java/$PRGNAM/$PRGNAM -cp -a Configuration net org Templates Help uk $JBZIP $SAM $CISD $PKG/usr/share/java/$PRGNAM +cp -a Configuration net org Templates Help uk $JBZIP $HTS $CISD $PKG/usr/share/java/$PRGNAM mkdir -p $PKG/usr/bin cd $PKG/usr/bin diff --git a/academic/fastqc/fastqc.info b/academic/fastqc/fastqc.info index a84ec6f99d..e043400da1 100644 --- a/academic/fastqc/fastqc.info +++ b/academic/fastqc/fastqc.info @@ -1,10 +1,10 @@ PRGNAM="fastqc" -VERSION="0.11.9" -HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" -DOWNLOAD="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip" -MD5SUM="ee7901b681bb2762d75d5a56c7ec6958" +VERSION="0.12.1" +HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" +DOWNLOAD="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip" +MD5SUM="a628c84cf19235d47fd979d4bb786a60" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/fet/README b/academic/fet/README index 3021e9183e..d32c44ad69 100644 --- a/academic/fet/README +++ b/academic/fet/README @@ -3,4 +3,5 @@ FET (A free software for automatic generation of timetable) This is a free software for automatically scheduling the timetable of a school, high-school or university. It uses a fast and efficient timetabling algorithm. -It is licensed under GNU GPL. +It is licensed under GNU Affero General Public License +version 3 or later. diff --git a/academic/fet/fet.SlackBuild b/academic/fet/fet.SlackBuild index 3c707e3465..6962abec49 100644 --- a/academic/fet/fet.SlackBuild +++ b/academic/fet/fet.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=fet -VERSION=${VERSION:-5.49.1} +VERSION=${VERSION:-6.19.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/fet/fet.info b/academic/fet/fet.info index d111ec04b5..2093219a59 100644 --- a/academic/fet/fet.info +++ b/academic/fet/fet.info @@ -1,8 +1,8 @@ PRGNAM="fet" -VERSION="5.49.1" +VERSION="6.19.3" HOMEPAGE="https://www.lalescu.ro/liviu/fet/" -DOWNLOAD="https://www.lalescu.ro/liviu/fet/download/fet-5.49.1.tar.bz2" -MD5SUM="063d3e4fa30c93820737fe8dbb28f55c" +DOWNLOAD="https://www.lalescu.ro/liviu/fet/download/fet-6.19.3.tar.bz2" +MD5SUM="5af48c9d1fdf303d7f2ed8ec306a257d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/fiji/ImageJ2.desktop b/academic/fiji/ImageJ2.desktop index 6ea0bc5041..404207c1ec 100644 --- a/academic/fiji/ImageJ2.desktop +++ b/academic/fiji/ImageJ2.desktop @@ -2,7 +2,7 @@ Name=Fiji (ImageJ 2) Comment=Fiji is just ImageJ Type=Application -Categories=Graphics; +Categories=Graphics;Education; Exec=fiji Terminal=false Icon=fiji diff --git a/academic/fiji/fiji.SlackBuild b/academic/fiji/fiji.SlackBuild index 4626a80a59..137669d5c6 100644 --- a/academic/fiji/fiji.SlackBuild +++ b/academic/fiji/fiji.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for fiji -# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=fiji -VERSION=${VERSION:-20200902_2101} +VERSION=${VERSION:-20230801_1717} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -33,11 +33,14 @@ PKGTYPE=${PKGTYPE:-tgz} DIRNAM=Fiji.app if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac + ARCH=$( uname -m ) +fi + +# Stop if arch is not supported +# 2023-05-16 DW: better if it's before PRINT_PACKAGE_NAME +if [ "$ARCH" != "x86_64" ]; then + printf "\n$ARCH is not supported... \n" + exit 1 fi # If the variable PRINT_PACKAGE_NAME is set, then this script will report what @@ -54,24 +57,12 @@ OUTPUT=${OUTPUT:-/tmp} set -e -# Stop if arch is not supported -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - -# Determine suffix -if [ "$ARCH" = "x86_64" ]; then - SUFFIX=linux64 -else - SUFFIX=inux32 -fi - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $DIRNAM -tar xvf $CWD/${PRGNAM}-$SUFFIX.tar.gz +#tar xvf $CWD/${PRGNAM}-linux64.tar.gz +unzip $CWD/${PRGNAM}-linux64.zip cd $DIRNAM chown -R root:root . find -L . \ @@ -81,7 +72,7 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Rename the binary we need -mv ImageJ-$SUFFIX $PRGNAM +mv ImageJ-linux64 $PRGNAM # We will put here two tools, so they are not run at startup. mkdir -p unused @@ -134,7 +125,7 @@ $PKG/opt/$PRGNAM cp $CWD/ImageJ2.desktop $PKG/opt/$PRGNAM # Install the simple wrapper -install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m 755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/fiji/fiji.info b/academic/fiji/fiji.info index 9e3928ff4b..ac7d400024 100644 --- a/academic/fiji/fiji.info +++ b/academic/fiji/fiji.info @@ -1,10 +1,10 @@ PRGNAM="fiji" -VERSION="20201104_1356" +VERSION="20230801_1717" HOMEPAGE="https://fiji.sc/" -DOWNLOAD="https://downloads.imagej.net/fiji/archive/20201104-1356/fiji-linux32.tar.gz" -MD5SUM="bff409ed4b683d67e3b3ac0d38423f0d" -DOWNLOAD_x86_64="https://downloads.imagej.net/fiji/archive/20201104-1356/fiji-linux64.tar.gz" -MD5SUM_x86_64="7141a774a0c759f6fea0875a6cbf58b9" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://downloads.imagej.net/fiji/archive/20230801-1717/fiji-linux64.zip" +MD5SUM_x86_64="9965c8c1c101866c66019a0a511da143" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/finchtv/finchtv.SlackBuild b/academic/finchtv/finchtv.SlackBuild index 8493e202c8..0a8f1321a9 100644 --- a/academic/finchtv/finchtv.SlackBuild +++ b/academic/finchtv/finchtv.SlackBuild @@ -31,7 +31,19 @@ TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} SRCVER=1_3_1 -ARCH=i386 # This will work on a stock Slackware64 as well. + +# 2023-05-16 DW: check for ARCH and kick wronguns +if [ -z "$ARCH" ]; then + case "$ARCH" in + i?86) ARCH=i586 ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if ! [ "$ARCH" = "x86_64" ] && ! [[ $ARCH =~ i?86 ]]; then + printf "\n$ARCH is not supported... \n" >/dev/stderr + exit 1 +fi # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information @@ -60,7 +72,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m 755 $PRGNAM $PKG/usr/bin/$PRGNAM find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/fityk/README b/academic/fityk/README index 7eb0de3a52..0217e00966 100644 --- a/academic/fityk/README +++ b/academic/fityk/README @@ -15,3 +15,6 @@ Pearson VII, bifurcated Gaussian, EMG, Doniach-Sunjic, etc.); but it is suitable for fitting any curve to 2D (x,y) data. Fityk is distributed under an open source licence (GPLv2+). + +Optional dependency: Sphinx. If installed, it will be used to generate +HTML documentation, which will be installed in /usr/share/fityk/html. diff --git a/academic/fityk/fityk.SlackBuild b/academic/fityk/fityk.SlackBuild index be395693d4..adc1ee2c44 100644 --- a/academic/fityk/fityk.SlackBuild +++ b/academic/fityk/fityk.SlackBuild @@ -1,8 +1,8 @@ #!/bin/bash # Slackware build script for fityk -# Based on Slackware 14.2 SlackBuild +# Based on Slackware 15.0 SlackBuild # -# Copyright 2017, Fellype do Nascimento, Campinas - Brazil +# Copyright 2017-2023, Fellype do Nascimento, Guaratinguetá - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# The SlackBuilds.org team contributed with improvements and maintenance of +# this script cd $(dirname $0) ; CWD=$(pwd) PRGNAM=fityk -VERSION=${VERSION:-1.3.1} +VERSION=${VERSION:-1.3.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -39,9 +41,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -71,35 +70,37 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 +tar xvf $CWD/$PRGNAM-$VERSION.tar.?z* cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS -std=c++14" \ ./configure \ --prefix=/usr \ --bindir=/usr/bin \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --mandir=/usr/man \ --enable-python \ + --with-wx-config=/usr/lib$LIBDIRSUFFIX/wx/config/gtk3-unicode-3.0 \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +make DESTDIR=$PKG install-strip mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING INSTALL NEWS README.md TODO $PKG/usr/doc/$PRGNAM-$VERSION +cp -a COPYING NEWS README.md TODO $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild gzip -9 $PKG/usr/man/man1/fityk.1 +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh diff --git a/academic/fityk/fityk.info b/academic/fityk/fityk.info index 76de4f6ab5..c9bdbeba0a 100644 --- a/academic/fityk/fityk.info +++ b/academic/fityk/fityk.info @@ -1,10 +1,10 @@ PRGNAM="fityk" -VERSION="1.3.1" +VERSION="1.3.2" HOMEPAGE="http://fityk.nieto.pl/" -DOWNLOAD="https://github.com/wojdyr/fityk/releases/download/v1.3.1/fityk-1.3.1.tar.bz2" -MD5SUM="41c9a2589e2eac4317a480b364ff493a" +DOWNLOAD="https://github.com/wojdyr/fityk/releases/download/v1.3.2/fityk-1.3.2.tar.bz2" +MD5SUM="b5c24bc3cafd0e30f32f6daf56375fac" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="lua xylib" MAINTAINER="Fellype do Nascimento" -EMAIL="fellype(at)gmail.com" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/flann/flann.SlackBuild b/academic/flann/flann.SlackBuild index c9be97ef6e..eadcc1568c 100644 --- a/academic/flann/flann.SlackBuild +++ b/academic/flann/flann.SlackBuild @@ -82,6 +82,12 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +sed -i "s|setup\.py install|setup.py install --root=$PKG --optimize=1|" src/python/CMakeLists.txt + +touch src/cpp/empty.cpp +sed -i -e 's/flann_cpp SHARED \"\"/flann_cpp SHARED \"empty\.cpp\"/g' src/cpp/CMakeLists.txt +sed -i -e 's/flann SHARED \"\"/flann SHARED \"empty\.cpp\"/g' src/cpp/CMakeLists.txt + mkdir -p build cd build cmake \ @@ -89,15 +95,23 @@ cd build -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DBUILD_MATLAB_BINDINGS=OFF \ + -DBUILD_PYTHON_BINDINGS=ON \ + -DPYTHON_EXECUTABLE=/usr/bin/python3 \ + -DBUILD_TESTS=OFF \ + -DBUILD_EXAMPLES=OFF \ -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG cd .. +rm -fR $PKG/usr/share/$PRGNAM find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +rm -fR $PKG/usr/share/doc mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp COPYING ChangeLog README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/flashqard/README b/academic/flashqard/README deleted file mode 100644 index 0e0fa5eaaf..0000000000 --- a/academic/flashqard/README +++ /dev/null @@ -1,8 +0,0 @@ -FlashQard is an educational software to improve your learning process. -It is designed to help you learn not only a new language but anything -that can be learned! This aim is achieved by using the widely used -method called the Leitner System and the idea of "different card types -for different purposes". Leitner System (proposed by Sebastian Leitner -in the 1970s) is one the most efficient methods for learning, which -allows you to focus on the most difficult flashcards and not waste your -time on what you have already learned. diff --git a/academic/flashqard/flashqard-0.15.0_qt-4.8.7.patch b/academic/flashqard/flashqard-0.15.0_qt-4.8.7.patch deleted file mode 100644 index 57bce20dce..0000000000 --- a/academic/flashqard/flashqard-0.15.0_qt-4.8.7.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff -u -r flashqard-0.15.0/src/PrettyButton.cpp flashqard-0.15.0-patched/src/PrettyButton.cpp ---- flashqard-0.15.0/src/PrettyButton.cpp 2009-09-08 22:56:54.000000000 +0100 -+++ flashqard-0.15.0-patched/src/PrettyButton.cpp 2015-07-28 11:49:56.506872447 +0100 -@@ -25,6 +25,7 @@ - #include "PrettyButton.h" - #include "TextEditor.h" - #include "MimeData.h" -+#include <QApplication> - #include <QPainter> - #include <QTimerEvent> - #include <QDropEvent> -diff -u -r flashqard-0.15.0/src/Utilities.cpp flashqard-0.15.0-patched/src/Utilities.cpp ---- flashqard-0.15.0/src/Utilities.cpp 2009-09-08 22:56:54.000000000 +0100 -+++ flashqard-0.15.0-patched/src/Utilities.cpp 2015-07-28 11:45:33.484870666 +0100 -@@ -22,6 +22,7 @@ - // | Author: Shahab Shirazi <shahab@flashqard-project.org> | - // +-------------------------------------------------------------------------+ - -+#include <QDir> - #include <QRegExp> - #include <QToolBar> - #include <QMessageBox> diff --git a/academic/flashqard/flashqard.SlackBuild b/academic/flashqard/flashqard.SlackBuild deleted file mode 100644 index c7ca3fb4a5..0000000000 --- a/academic/flashqard/flashqard.SlackBuild +++ /dev/null @@ -1,93 +0,0 @@ -#!/bin/bash - -# Slackware build script for flashqard -# written by Mehdi Esmaeelpour ariarat@gmail.com www.slack-world.com - -cd $(dirname $0) ; CWD=$(pwd) - -PRGNAM=flashqard -VERSION=${VERSION:-0.15.0} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} -PKGTYPE=${PKGTYPE:-tgz} - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i486 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. -if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then - echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" - exit 0 -fi - -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -# Patch for missing includes with qt-4.8.7 -patch -p1 < $CWD/flashqard-0.15.0_qt-4.8.7.patch - -mkdir -p build -cd build - cmake \ - -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_INSTALL_PREFIX=/usr \ - -DLIB_SUFFIX=${LIBDIRSUFFIX} \ - -DMAN_INSTALL_DIR=/usr/man \ - -DCMAKE_BUILD_TYPE=Release .. - make - make install DESTDIR=$PKG -cd .. - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - COPYING ChangeLog README AUTHORS INSTALL \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/flashqard/flashqard.info b/academic/flashqard/flashqard.info deleted file mode 100644 index 85b44828be..0000000000 --- a/academic/flashqard/flashqard.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="flashqard" -VERSION="0.15.0" -HOMEPAGE="http://www.flashqard-project.org/" -DOWNLOAD="http://downloads.sourceforge.net/flashqard/flashqard-0.15.0.tar.gz" -MD5SUM="aa2c58d3b18f0ce8d2a31ece9d299647" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="ariarat" -EMAIL="ariarat@gmail.com" diff --git a/academic/flexbar/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch b/academic/flexbar/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch new file mode 100644 index 0000000000..12068e9337 --- /dev/null +++ b/academic/flexbar/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch @@ -0,0 +1,710 @@ +From 195a1ab2c2715b07df5acff58dc2a0396d9cd52d Mon Sep 17 00:00:00 2001 +From: Liam Keegan <liam@keegan.ch> +Date: Thu, 9 Feb 2023 16:27:37 +0100 +Subject: [PATCH 1/4] Migrate from tbb to onetbb + +- add `FlexbarAtomic` + - a simple wrapper around `std::atomic` which adds a copy constructor + - to replace `tbb::atomic` member variables in classes with default copy constructors +- replace removed `tbb::atomic` + - with `FlexbarAtomic` if copy constructor was assumed + - with `std::atomic` otherwise +- filters (PairedAlign, PairedInput, PairedOutput) + - no longer inherit from tbb::filter + - take and return pointers to actual type instead of void* + - operator() is now const +- pipeline + - use parallel_pipeline and make_filter +- use global_control to set max threads +- use `oneapi::tbb` namespace +- add find_package for TBB to CMakeLists.txt +--- + src/CMakeLists.txt | 9 ++------- + src/Flexbar.h | 27 +++++++++++++++------------ + src/FlexbarTypes.h | 16 +++++++++++++++- + src/LoadAdapters.h | 4 ++-- + src/LoadFasta.h | 6 +++--- + src/Options.h | 2 +- + src/PairedAlign.h | 23 ++++++++++------------- + src/PairedInput.h | 10 ++++------ + src/PairedOutput.h | 29 ++++++++++++----------------- + src/SeqAlign.h | 12 ++++++------ + src/SeqAlignPair.h | 6 +++--- + src/SeqInput.h | 2 +- + src/SeqOutput.h | 6 +++--- + src/SeqOutputFiles.h | 2 +- + 14 files changed, 78 insertions(+), 76 deletions(-) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index a5643ca..ca4e5db 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -32,9 +32,9 @@ else() + endif() + + add_executable( flexbar Flexbar.cpp ) +-target_link_libraries( flexbar tbb -lpthread ) +- + ++find_package(TBB CONFIG REQUIRED) ++target_link_libraries(flexbar TBB::tbb) + find_package( ZLIB ) + if( ZLIB_FOUND ) + include_directories( ${ZLIB_INCLUDE_DIRS} ) +@@ -53,9 +53,4 @@ else() + message( STATUS "Build will not support bzip2." ) + endif() + +-# find_package( TBB REQUIRED ) +-# if( NOT TBB_FOUND ) +-# message( FATAL_ERROR "TBB library not found." ) +-# endif() +- + set( SEQAN_CTD_EXECUTABLES ${SEQAN_CTD_EXECUTABLES} flexbar CACHE INTERNAL "" ) +diff --git a/src/Flexbar.h b/src/Flexbar.h +index 67c07d7..d1a8f31 100644 +--- a/src/Flexbar.h ++++ b/src/Flexbar.h +@@ -12,10 +12,9 @@ + #include <iostream> + #include <vector> + +-#include <tbb/pipeline.h> +-#include <tbb/task_scheduler_init.h> +-#include <tbb/concurrent_vector.h> +-#include <tbb/mutex.h> ++#include <oneapi/tbb/parallel_pipeline.h> ++#include <oneapi/tbb/global_control.h> ++#include <oneapi/tbb/concurrent_vector.h> + + #include <seqan/basic.h> + #include <seqan/sequence.h> +@@ -240,14 +239,18 @@ void startProcessing(Options &o){ + PairedAlign<TSeqStr, TString> alignFilter(o); + PairedOutput<TSeqStr, TString> outputFilter(o); + +- tbb::task_scheduler_init init_serial(o.nThreads); +- tbb::pipeline pipe; +- +- pipe.add_filter(inputFilter); +- pipe.add_filter(alignFilter); +- pipe.add_filter(outputFilter); +- pipe.run(o.nThreads); +- ++ oneapi::tbb::global_control control( ++ oneapi::tbb::global_control::max_allowed_parallelism, o.nThreads); ++ oneapi::tbb::parallel_pipeline(o.nThreads, ++ oneapi::tbb::make_filter<void, TPairedReadBundle *>( ++ oneapi::tbb::filter_mode::serial_in_order, inputFilter) ++ & ++ oneapi::tbb::make_filter<TPairedReadBundle *, TPairedReadBundle *>( ++ oneapi::tbb::filter_mode::parallel, alignFilter) ++ & ++ oneapi::tbb::make_filter<TPairedReadBundle *, void>( ++ oneapi::tbb::filter_mode::serial_in_order, outputFilter) ++ ); + if(o.logAlign == TAB) *out << "\n"; + *out << "done.\n" << endl; + +diff --git a/src/FlexbarTypes.h b/src/FlexbarTypes.h +index 8abdf66..f1bce0f 100644 +--- a/src/FlexbarTypes.h ++++ b/src/FlexbarTypes.h +@@ -3,6 +3,20 @@ + #ifndef FLEXBAR_FLEXBARTYPES_H + #define FLEXBAR_FLEXBARTYPES_H + ++#include <atomic> ++ ++// A simple wrapper around std::atomic<T> with a copy-constructor ++// This is a drop-in replacement for the previously used tbb::atomic (which is copyable), ++// to avoid having to add copy-constructors to classes that used it ++template<typename T> ++struct FlexbarAtomic : public std::atomic<T> { ++ FlexbarAtomic() = default; ++ explicit constexpr FlexbarAtomic(T t) : std::atomic<T>(t) {} ++ constexpr FlexbarAtomic(const FlexbarAtomic<T>& other) : ++ FlexbarAtomic(other.load(std::memory_order_acquire)) ++ {} ++}; ++ + + template <typename TSeqStr, typename TString> + class SeqRead { +@@ -126,7 +140,7 @@ namespace flexbar{ + FSeqStr seq; + bool rcAdapter; + +- tbb::atomic<unsigned long> rmOverlap, rmFull; ++ FlexbarAtomic<unsigned long> rmOverlap, rmFull; + + TBar() : + rmOverlap(0), +diff --git a/src/LoadAdapters.h b/src/LoadAdapters.h +index 046e799..6168775 100644 +--- a/src/LoadAdapters.h ++++ b/src/LoadAdapters.h +@@ -10,7 +10,7 @@ class LoadAdapters { + private: + + std::ostream *out; +- tbb::concurrent_vector<flexbar::TBar> adapters; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> adapters; + + flexbar::Adapters a; + +@@ -134,7 +134,7 @@ class LoadAdapters { + }; + + +- tbb::concurrent_vector<flexbar::TBar> getAdapters(){ ++ oneapi::tbb::concurrent_vector<flexbar::TBar> getAdapters(){ + return adapters; + } + +diff --git a/src/LoadFasta.h b/src/LoadFasta.h +index 3e69594..ccd0550 100644 +--- a/src/LoadFasta.h ++++ b/src/LoadFasta.h +@@ -10,7 +10,7 @@ class LoadFasta { + private: + + std::ostream *out; +- tbb::concurrent_vector<flexbar::TBar> bars; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> bars; + + const bool m_isAdapter; + const flexbar::RevCompMode m_rcMode; +@@ -94,12 +94,12 @@ class LoadFasta { + }; + + +- tbb::concurrent_vector<flexbar::TBar> getBars(){ ++ oneapi::tbb::concurrent_vector<flexbar::TBar> getBars(){ + return bars; + } + + +- void setBars(tbb::concurrent_vector<flexbar::TBar> &newBars){ ++ void setBars(oneapi::tbb::concurrent_vector<flexbar::TBar> &newBars){ + bars = newBars; + } + +diff --git a/src/Options.h b/src/Options.h +index 6299c50..21d7710 100644 +--- a/src/Options.h ++++ b/src/Options.h +@@ -46,7 +46,7 @@ struct Options{ + flexbar::AdapterPreset aPreset; + flexbar::AdapterTrimmed aTrimmed; + +- tbb::concurrent_vector<flexbar::TBar> barcodes, adapters, barcodes2, adapters2; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> barcodes, adapters, barcodes2, adapters2; + + std::ostream *out; + std::fstream fstrmOut; +diff --git a/src/PairedAlign.h b/src/PairedAlign.h +index d6f9956..59c4473 100644 +--- a/src/PairedAlign.h ++++ b/src/PairedAlign.h +@@ -9,7 +9,7 @@ + + + template <typename TSeqStr, typename TString> +-class PairedAlign : public tbb::filter { ++class PairedAlign { + + private: + +@@ -31,9 +31,9 @@ class PairedAlign : public tbb::filter { + const flexbar::TrimEnd m_aTrimEnd, m_arcTrimEnd, m_bTrimEnd; + const flexbar::PairOverlap m_poMode; + +- tbb::atomic<unsigned long> m_unassigned; +- tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_adapters2; +- tbb::concurrent_vector<flexbar::TBar> *m_barcodes, *m_barcodes2; ++ mutable FlexbarAtomic<unsigned long> m_unassigned; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_adapters2; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *m_barcodes, *m_barcodes2; + + typedef SeqAlign<TSeqStr, TString, SeqAlignAlgo<TSeqStr> > TSeqAlign; + TSeqAlign *m_a1, *m_b1, *m_a2, *m_b2; +@@ -47,7 +47,6 @@ class PairedAlign : public tbb::filter { + + PairedAlign(Options &o) : + +- filter(parallel), + m_format(o.format), + m_log(o.logAlign), + m_runType(o.runType), +@@ -102,7 +101,7 @@ class PairedAlign : public tbb::filter { + }; + + +- void alignPairedReadToBarcodes(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode){ ++ void alignPairedReadToBarcodes(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode) const { + + using namespace flexbar; + +@@ -122,7 +121,7 @@ class PairedAlign : public tbb::filter { + } + + +- void alignPairedReadToAdapters(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode, const flexbar::TrimEnd trimEnd){ ++ void alignPairedReadToAdapters(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode, const flexbar::TrimEnd trimEnd) const { + + using namespace flexbar; + +@@ -173,7 +172,7 @@ class PairedAlign : public tbb::filter { + } + + +- void trimLeftHPS(flexbar::TSeqRead* seqRead){ ++ void trimLeftHPS(flexbar::TSeqRead* seqRead) const{ + + using namespace std; + using namespace flexbar; +@@ -223,7 +222,7 @@ class PairedAlign : public tbb::filter { + } + + +- void trimRightHPS(flexbar::TSeqRead* seqRead){ ++ void trimRightHPS(flexbar::TSeqRead* seqRead) const{ + + using namespace std; + using namespace flexbar; +@@ -275,13 +274,11 @@ class PairedAlign : public tbb::filter { + + + // tbb filter operator +- void* operator()(void* item){ ++ flexbar::TPairedReadBundle* operator()(flexbar::TPairedReadBundle* prBundle) const{ + + using namespace flexbar; + +- if(item != NULL){ +- +- TPairedReadBundle *prBundle = static_cast<TPairedReadBundle* >(item); ++ if(prBundle != NULL){ + + if(m_umiTags){ + for(unsigned int i = 0; i < prBundle->size(); ++i){ +diff --git a/src/PairedInput.h b/src/PairedInput.h +index 94a54e5..f7a6c9e 100644 +--- a/src/PairedInput.h ++++ b/src/PairedInput.h +@@ -7,7 +7,7 @@ + + + template <typename TSeqStr, typename TString> +-class PairedInput : public tbb::filter { ++class PairedInput { + + private: + +@@ -15,14 +15,13 @@ class PairedInput : public tbb::filter { + const bool m_isPaired, m_useBarRead, m_useNumberTag, m_interleaved; + const unsigned int m_bundleSize; + +- tbb::atomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles; ++ mutable FlexbarAtomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles; + SeqInput<TSeqStr, TString> *m_f1, *m_f2, *m_b; + + public: + + PairedInput(const Options &o) : + +- filter(serial_in_order), + m_format(o.format), + m_useNumberTag(o.useNumberTag), + m_interleaved(o.interleavedInput), +@@ -55,7 +54,7 @@ class PairedInput : public tbb::filter { + } + + +- void* loadPairedReadBundle(){ ++ void* loadPairedReadBundle() const{ + + using namespace std; + using namespace flexbar; +@@ -207,8 +206,7 @@ class PairedInput : public tbb::filter { + + + // tbb filter operator +- void* operator()(void*){ +- ++ flexbar::TPairedReadBundle* operator()(oneapi::tbb::flow_control& fc) const { + using namespace flexbar; + + TPairedReadBundle *prBundle = NULL; +diff --git a/src/PairedOutput.h b/src/PairedOutput.h +index 6c3fad7..c0d3626 100644 +--- a/src/PairedOutput.h ++++ b/src/PairedOutput.h +@@ -9,7 +9,7 @@ + + + template <typename TSeqStr, typename TString> +-class PairedOutput : public tbb::filter { ++class PairedOutput { + + private: + +@@ -18,8 +18,8 @@ class PairedOutput : public tbb::filter { + const bool m_isPaired, m_writeUnassigned, m_writeSingleReads, m_writeSingleReadsP; + const bool m_twoBarcodes, m_qtrimPostRm; + +- tbb::atomic<unsigned long> m_nSingleReads, m_nLowPhred; +- ++ mutable FlexbarAtomic<unsigned long> m_nSingleReads, m_nLowPhred; ++ + const std::string m_target; + + const flexbar::FileFormat m_format; +@@ -34,14 +34,13 @@ class PairedOutput : public tbb::filter { + TOutFiles *m_outMap; + std::ostream *out; + +- tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_barcodes; +- tbb::concurrent_vector<flexbar::TBar> *m_adapters2, *m_barcodes2; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_barcodes; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters2, *m_barcodes2; + + public: + + PairedOutput(Options &o) : + +- filter(serial_in_order), + m_target(o.targetName), + m_format(o.format), + m_runType(o.runType), +@@ -57,6 +56,8 @@ class PairedOutput : public tbb::filter { + m_writeSingleReads(o.writeSingleReads), + m_writeSingleReadsP(o.writeSingleReadsP), + m_twoBarcodes(o.barDetect == flexbar::WITHIN_READ_REMOVAL2 || o.barDetect == flexbar::WITHIN_READ2), ++ m_nSingleReads(0), ++ m_nLowPhred(0), + out(o.out){ + + using namespace std; +@@ -68,9 +69,7 @@ class PairedOutput : public tbb::filter { + m_adapters2 = &o.adapters2; + + m_mapsize = 0; +- m_nSingleReads = 0; +- m_nLowPhred = 0; +- ++ + switch(m_runType){ + + case PAIRED_BARCODED:{ +@@ -237,7 +236,7 @@ class PairedOutput : public tbb::filter { + }; + + +- void writePairedRead(flexbar::TPairedRead* pRead){ ++ void writePairedRead(flexbar::TPairedRead* pRead) const{ + + using namespace flexbar; + +@@ -346,13 +345,11 @@ class PairedOutput : public tbb::filter { + + + // tbb filter operator +- void* operator()(void* item){ ++ void operator()(flexbar::TPairedReadBundle* prBundle) const{ + + using namespace flexbar; + +- if(item != NULL){ +- +- TPairedReadBundle *prBundle = static_cast< TPairedReadBundle* >(item); ++ if(prBundle != NULL){ + + for(unsigned int i = 0; i < prBundle->size(); ++i){ + +@@ -361,8 +358,6 @@ class PairedOutput : public tbb::filter { + } + delete prBundle; + } +- +- return NULL; + } + + +@@ -457,7 +452,7 @@ class PairedOutput : public tbb::filter { + + using namespace std; + +- tbb::concurrent_vector<flexbar::TBar> *adapters; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *adapters; + const unsigned int maxSpaceLen = 20; + + int startLen = 8; +diff --git a/src/SeqAlign.h b/src/SeqAlign.h +index 221a901..b10aafa 100644 +--- a/src/SeqAlign.h ++++ b/src/SeqAlign.h +@@ -3,7 +3,7 @@ + #ifndef FLEXBAR_SEQALIGN_H + #define FLEXBAR_SEQALIGN_H + +-tbb::mutex ouputMutex; ++std::mutex ouputMutex; + + template <typename TSeqStr, typename TString, class TAlgorithm> + class SeqAlign { +@@ -21,16 +21,16 @@ class SeqAlign { + const float m_errorRate; + const unsigned int m_bundleSize; + +- tbb::atomic<unsigned long> m_nPreShortReads, m_modified; +- tbb::concurrent_vector<flexbar::TBar> *m_queries; +- tbb::concurrent_vector<unsigned long> m_rmOverlaps; ++ std::atomic<unsigned long> m_nPreShortReads, m_modified; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *m_queries; ++ oneapi::tbb::concurrent_vector<unsigned long> m_rmOverlaps; + + std::ostream *m_out; + TAlgorithm m_algo; + + public: + +- SeqAlign(tbb::concurrent_vector<flexbar::TBar> *queries, const Options &o, int minOverlap, float errorRate, const int tailLength, const int match, const int mismatch, const int gapCost, const bool isBarcoding): ++ SeqAlign(oneapi::tbb::concurrent_vector<flexbar::TBar> *queries, const Options &o, int minOverlap, float errorRate, const int tailLength, const int match, const int mismatch, const int gapCost, const bool isBarcoding): + + m_minOverlap(minOverlap), + m_errorRate(errorRate), +@@ -51,7 +51,7 @@ class SeqAlign { + m_algo(TAlgorithm(o, match, mismatch, gapCost, ! isBarcoding)){ + + m_queries = queries; +- m_rmOverlaps = tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0); ++ m_rmOverlaps = oneapi::tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0); + }; + + +diff --git a/src/SeqAlignPair.h b/src/SeqAlignPair.h +index d5d1079..2479242 100644 +--- a/src/SeqAlignPair.h ++++ b/src/SeqAlignPair.h +@@ -20,8 +20,8 @@ class SeqAlignPair { + const float m_errorRate; + const unsigned int m_bundleSize; + +- tbb::atomic<unsigned long> m_nPreShortReads, m_overlaps, m_modified; +- tbb::concurrent_vector<unsigned long> m_overlapLengths; ++ std::atomic<unsigned long> m_nPreShortReads, m_overlaps, m_modified; ++ oneapi::tbb::concurrent_vector<unsigned long> m_overlapLengths; + + std::ostream *m_out; + TAlgorithm m_algo; +@@ -45,7 +45,7 @@ class SeqAlignPair { + m_modified(0), + m_algo(TAlgorithm(o, match, mismatch, gapCost, true)){ + +- m_overlapLengths = tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0); ++ m_overlapLengths = oneapi::tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0); + }; + + +diff --git a/src/SeqInput.h b/src/SeqInput.h +index 4dcbe74..7a8f8d0 100644 +--- a/src/SeqInput.h ++++ b/src/SeqInput.h +@@ -18,7 +18,7 @@ class SeqInput { + + const bool m_preProcess, m_useStdin, m_qtrimPostRm, m_iupacInput; + const int m_maxUncalled, m_preTrimBegin, m_preTrimEnd, m_qtrimThresh, m_qtrimWinSize; +- tbb::atomic<unsigned long> m_nrReads, m_nrChars, m_nLowPhred; ++ std::atomic<unsigned long> m_nrReads, m_nrChars, m_nLowPhred; + + public: + +diff --git a/src/SeqOutput.h b/src/SeqOutput.h +index 9a63e6a..64cab91 100644 +--- a/src/SeqOutput.h ++++ b/src/SeqOutput.h +@@ -18,8 +18,8 @@ class SeqOutput { + const bool m_switch2Fasta, m_writeLenDist, m_useStdout; + const unsigned int m_minLength, m_cutLen_read; + +- tbb::atomic<unsigned long> m_countGood, m_countGoodChars; +- tbb::concurrent_vector<unsigned long> m_lengthDist; ++ std::atomic<unsigned long> m_countGood, m_countGoodChars; ++ oneapi::tbb::concurrent_vector<unsigned long> m_lengthDist; + + public: + +@@ -48,7 +48,7 @@ class SeqOutput { + } + m_filePath += o.outCompression; + +- m_lengthDist = tbb::concurrent_vector<unsigned long>(MAX_READLENGTH + 1, 0); ++ m_lengthDist = oneapi::tbb::concurrent_vector<unsigned long>(MAX_READLENGTH + 1, 0); + + if(m_useStdout){ + +diff --git a/src/SeqOutputFiles.h b/src/SeqOutputFiles.h +index fe6b50e..8ece58c 100644 +--- a/src/SeqOutputFiles.h ++++ b/src/SeqOutputFiles.h +@@ -14,7 +14,7 @@ class SeqOutputFiles { + typedef SeqOutput<TSeqStr, TString> TSeqOutput; + + TSeqOutput *f1, *f2, *single1, *single2; +- tbb::atomic<unsigned long> m_nShort_1, m_nShort_2; ++ std::atomic<unsigned long> m_nShort_1, m_nShort_2; + + SeqOutputFiles() : + f1(0), + +From 1c872fa10d474f090633fc95d409aa60607a3f96 Mon Sep 17 00:00:00 2001 +From: Liam Keegan <liam@keegan.ch> +Date: Fri, 10 Feb 2023 09:55:58 +0100 +Subject: [PATCH 2/4] Fix parallel_pipeline issues + +- pass a lambda with a reference to the filter instead of directly passing the filter to parallel_pipeline + - passed filters may be copied and/or deleted by tbb + - flexbar continues to use the filter objects after the pipeline is finished +- call fc.stop() in PairedInput when there is no more input + - required control flow for first filter in parallel_pipeline that was previously missing +--- + src/Flexbar.h | 9 ++++++--- + src/PairedInput.h | 9 +++++++-- + 2 files changed, 13 insertions(+), 5 deletions(-) + +diff --git a/src/Flexbar.h b/src/Flexbar.h +index d1a8f31..46261cf 100644 +--- a/src/Flexbar.h ++++ b/src/Flexbar.h +@@ -243,13 +243,16 @@ void startProcessing(Options &o){ + oneapi::tbb::global_control::max_allowed_parallelism, o.nThreads); + oneapi::tbb::parallel_pipeline(o.nThreads, + oneapi::tbb::make_filter<void, TPairedReadBundle *>( +- oneapi::tbb::filter_mode::serial_in_order, inputFilter) ++ oneapi::tbb::filter_mode::serial_in_order, ++ [&inputFilter](auto &fc) { return inputFilter(fc); }) + & + oneapi::tbb::make_filter<TPairedReadBundle *, TPairedReadBundle *>( +- oneapi::tbb::filter_mode::parallel, alignFilter) ++ oneapi::tbb::filter_mode::parallel, ++ [&alignFilter](TPairedReadBundle *tprb) { return alignFilter(tprb); }) + & + oneapi::tbb::make_filter<TPairedReadBundle *, void>( +- oneapi::tbb::filter_mode::serial_in_order, outputFilter) ++ oneapi::tbb::filter_mode::serial_in_order, ++ [&outputFilter](TPairedReadBundle *tprb) { return outputFilter(tprb); }) + ); + if(o.logAlign == TAB) *out << "\n"; + *out << "done.\n" << endl; +diff --git a/src/PairedInput.h b/src/PairedInput.h +index f7a6c9e..4fc4441 100644 +--- a/src/PairedInput.h ++++ b/src/PairedInput.h +@@ -221,9 +221,14 @@ class PairedInput { + + prBundle = static_cast< TPairedReadBundle* >(loadPairedReadBundle()); + +- if(prBundle == NULL) return prBundle; ++ if(prBundle == NULL){ ++ fc.stop(); ++ return prBundle; ++ } + } +- } ++ } else { ++ fc.stop(); ++ } + + return prBundle; + } + +From 19722f2743c96235ff57948eda82f963cf734131 Mon Sep 17 00:00:00 2001 +From: Liam Keegan <liam@keegan.ch> +Date: Fri, 10 Feb 2023 10:21:22 +0100 +Subject: [PATCH 3/4] revert accidental removal of pthread linking in + src/CMakeLists.txt + +--- + src/CMakeLists.txt | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index ca4e5db..fb42cc4 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -32,6 +32,7 @@ else() + endif() + + add_executable( flexbar Flexbar.cpp ) ++target_link_libraries( flexbar -lpthread ) + + find_package(TBB CONFIG REQUIRED) + target_link_libraries(flexbar TBB::tbb) + +From a9b0eb87a391aeaf760f8116dca777749c8b4f96 Mon Sep 17 00:00:00 2001 +From: Liam Keegan <liam@keegan.ch> +Date: Fri, 10 Feb 2023 10:52:35 +0100 +Subject: [PATCH 4/4] use `std::atomic` instead of `FlexbarAtomic` in filters + as they are no longer require copy constructors + +--- + src/FlexbarTypes.h | 2 +- + src/PairedAlign.h | 2 +- + src/PairedInput.h | 2 +- + src/PairedOutput.h | 2 +- + 4 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/src/FlexbarTypes.h b/src/FlexbarTypes.h +index f1bce0f..3cf241e 100644 +--- a/src/FlexbarTypes.h ++++ b/src/FlexbarTypes.h +@@ -139,7 +139,7 @@ namespace flexbar{ + FString id; + FSeqStr seq; + bool rcAdapter; +- ++ + FlexbarAtomic<unsigned long> rmOverlap, rmFull; + + TBar() : +diff --git a/src/PairedAlign.h b/src/PairedAlign.h +index 59c4473..d3b50ae 100644 +--- a/src/PairedAlign.h ++++ b/src/PairedAlign.h +@@ -31,7 +31,7 @@ class PairedAlign { + const flexbar::TrimEnd m_aTrimEnd, m_arcTrimEnd, m_bTrimEnd; + const flexbar::PairOverlap m_poMode; + +- mutable FlexbarAtomic<unsigned long> m_unassigned; ++ mutable std::atomic<unsigned long> m_unassigned; + oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_adapters2; + oneapi::tbb::concurrent_vector<flexbar::TBar> *m_barcodes, *m_barcodes2; + +diff --git a/src/PairedInput.h b/src/PairedInput.h +index 4fc4441..230474b 100644 +--- a/src/PairedInput.h ++++ b/src/PairedInput.h +@@ -15,7 +15,7 @@ class PairedInput { + const bool m_isPaired, m_useBarRead, m_useNumberTag, m_interleaved; + const unsigned int m_bundleSize; + +- mutable FlexbarAtomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles; ++ mutable std::atomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles; + SeqInput<TSeqStr, TString> *m_f1, *m_f2, *m_b; + + public: +diff --git a/src/PairedOutput.h b/src/PairedOutput.h +index c0d3626..fae5d3f 100644 +--- a/src/PairedOutput.h ++++ b/src/PairedOutput.h +@@ -18,7 +18,7 @@ class PairedOutput { + const bool m_isPaired, m_writeUnassigned, m_writeSingleReads, m_writeSingleReadsP; + const bool m_twoBarcodes, m_qtrimPostRm; + +- mutable FlexbarAtomic<unsigned long> m_nSingleReads, m_nLowPhred; ++ mutable std::atomic<unsigned long> m_nSingleReads, m_nLowPhred; + + const std::string m_target; + diff --git a/academic/flexbar/flexbar.SlackBuild b/academic/flexbar/flexbar.SlackBuild index 69ec0db8d0..803163e046 100644 --- a/academic/flexbar/flexbar.SlackBuild +++ b/academic/flexbar/flexbar.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for flexbar -# Copyright 2017-2021 Rob van Nues +# Copyright 2017-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=flexbar VERSION=${VERSION:-3.5.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -41,9 +41,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -83,6 +80,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +patch -p 1 < $CWD/seqan_flexbar_pull_20.patch +patch -p 1 < $CWD/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch + mkdir -p build cd build cmake \ diff --git a/academic/flexbar/flexbar.info b/academic/flexbar/flexbar.info index 23efa136d8..6ac4dd0920 100644 --- a/academic/flexbar/flexbar.info +++ b/academic/flexbar/flexbar.info @@ -1,12 +1,12 @@ PRGNAM="flexbar" VERSION="3.5.0" HOMEPAGE="https://github.com/seqan/flexbar" -DOWNLOAD="https://github.com/seqan/flexbar/archive/v3.5.0/flexbar-3.5.0.tar.gz \ +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/seqan/flexbar/archive/v3.5.0/flexbar-3.5.0.tar.gz \ https://github.com/seqan/seqan/releases/download/seqan-v2.4.0/seqan-library-2.4.0.tar.xz" -MD5SUM="0e07bf4afebfd731c4718b401383224a \ +MD5SUM_x86_64="0e07bf4afebfd731c4718b401383224a \ eeadf5544555c1e196537a888d02d09f" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" REQUIRES="tbb" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/flexbar/seqan_flexbar_pull_20.patch b/academic/flexbar/seqan_flexbar_pull_20.patch new file mode 100644 index 0000000000..96db258a6b --- /dev/null +++ b/academic/flexbar/seqan_flexbar_pull_20.patch @@ -0,0 +1,44 @@ +From 707f9381be5d42c6acd122a3c268deb66600cf9a Mon Sep 17 00:00:00 2001 +From: svnbgnk <swb@live.de> +Date: Thu, 25 Jul 2019 16:35:47 +0200 +Subject: [PATCH] added mutex lock to log output + +--- + src/Flexbar.h | 1 + + src/SeqAlign.h | 3 +++ + 2 files changed, 4 insertions(+) + +diff --git a/src/Flexbar.h b/src/Flexbar.h +index 2f82f18..67c07d7 100644 +--- a/src/Flexbar.h ++++ b/src/Flexbar.h +@@ -15,6 +15,7 @@ + #include <tbb/pipeline.h> + #include <tbb/task_scheduler_init.h> + #include <tbb/concurrent_vector.h> ++#include <tbb/mutex.h> + + #include <seqan/basic.h> + #include <seqan/sequence.h> +diff --git a/src/SeqAlign.h b/src/SeqAlign.h +index 979d05f..221a901 100644 +--- a/src/SeqAlign.h ++++ b/src/SeqAlign.h +@@ -3,6 +3,7 @@ + #ifndef FLEXBAR_SEQALIGN_H + #define FLEXBAR_SEQALIGN_H + ++tbb::mutex ouputMutex; + + template <typename TSeqStr, typename TString, class TAlgorithm> + class SeqAlign { +@@ -305,7 +306,9 @@ class SeqAlign { + << "read seq " << seqRead.seq << "\n\n" << endl; + } + ++ ouputMutex.lock(); + *m_out << s.str(); ++ ouputMutex.unlock(); + + return ++qIndex; + } diff --git a/academic/g3data/g3data.SlackBuild b/academic/g3data/g3data.SlackBuild index c188881d18..c877a3fe84 100644 --- a/academic/g3data/g3data.SlackBuild +++ b/academic/g3data/g3data.SlackBuild @@ -71,7 +71,12 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +# respecting content-disposition may include cgi params in the filename +TARBALL=$CWD/$PRGNAM-$VERSION.tar.gz +if [ ! -e $TARBALL ]; then + TARBALL="$(/bin/ls $TARBALL\?* | head -1)" +fi +tar xvf $TARBALL cd $PRGNAM-$VERSION chown -R root:root . find -L . \ diff --git a/academic/g3data/g3data.info b/academic/g3data/g3data.info index c85e2d1a5a..e19e7437af 100644 --- a/academic/g3data/g3data.info +++ b/academic/g3data/g3data.info @@ -1,7 +1,7 @@ PRGNAM="g3data" VERSION="1.5.4" HOMEPAGE="https://github.com/pn2200/g3data" -DOWNLOAD="https://github.com/downloads/pn2200/g3data/g3data-1.5.4.tar.gz" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/g3data/g3data-1.5.4.tar.gz" MD5SUM="acb41e54ee5fbf167413218f209c4e3f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/gaiasky/README b/academic/gaiasky/README new file mode 100644 index 0000000000..ba6a28970a --- /dev/null +++ b/academic/gaiasky/README @@ -0,0 +1,37 @@ +Gaia Sky is a real-time, 3D, astronomy visualisation software free +and open source that provides a number of features that allows people +to observe and study the space in Virtual Reality. This slackbuild +install the prebuilt package released for Ubuntu. + +Gaia Sky is developed in the framework of ESA's Gaia mission to chart +about 1 billion stars of our Galaxy in the Gaia group of the +Astronomisches Rechen-Institut (ZAH, Universität Heidelberg). + +Hardware requirements: CPU 4 core or higher, GPU with 1 GB RAM with +support for OpenGL (at least 3.2) and GLSL 3.3, memory with 2-6 GB RAM +depending on catalog, and at least 1 GB of free disk space depending +on datasets. + +*** WARNING *** +1. Datasets +Gaia Sky requires pre-packed datasets (Gaia eDR3, NBG, SDSS, OCDR2, +ecc.) provided by the project, but can be used with other datasets in +VOTable, FITS, CSV and other formats (STIL). +When Gaia Sky starts for the first time, the application searches the +default dataset in ~/.local/share/gaiasky/data. If any dataset is not +found, Gaia Sky launches the Download Manager, a graphic interface +that allows to users to download the default dataset required. The +repository provides also other optional datasets which improve the +features of Gaia Sky (some datasets have very large size). For further +information, please read the README.SBo file. + +2. How to start Gaia Sky +A Desktop entry which launches the GUI is provided with the +installation (in Education > Science), but Gaia Sky can be started by +command-line if you want apply some flags. About this mode please read +the README.SBo file. + +3. Virtual Reality +The VR rendering is still in alpha mode: it is uncomplete and may +cause issues depending on the configuration. + diff --git a/academic/gaiasky/README.SBo b/academic/gaiasky/README.SBo new file mode 100644 index 0000000000..ce5288a0de --- /dev/null +++ b/academic/gaiasky/README.SBo @@ -0,0 +1,43 @@ +Further information + +1. About datasets +The Graphic Interface of the Download Manager starts if no datasets +are found in ~/.local/gaiasky/data, otherwise Gaia Sky won't start. + +The datasets available for download are the following: + +Data Packs: +- Basic data pack (REQUIRED): size 88,5 MB. It is the default-data + with 2,573 objects (Solar System objects as planets, satellites, + asteroids, eccetera, Milk Way, Constellations, orbits, ecc.) + +Texture Packs: +- High resolution textures: size 258 MB. + +Gaia stars catalogs: +- Gaia DR3 default: size 1 GB +- Gaia DR3 small: size 560 MB +- Gaia DR3 medium: size 3,3 GB +- Gaia DR3 large: size 8 GB +- Gaia DR3 very large: size 30 GB +- Gaia DR3 extra large: size 45 GB +- Gaia DR3 bright: 566 MB + +These datasets may be downloaded also manually through a web browser: +the Download Manager window provides a link (Manual Download) which +opens the default web browser at the address of the repository. + +Users can install also own or third part datasets. About this please +refer to the documentation on line. + +2. Start with a command-line from a console +This is needed if you want to apply some flags. This is needed if you +want to launch Gaia Sky in Virtual Reality mode: you have to open a +terminal and digit the command + + $ gaiasky -vr (or --openvr) + +Other available flags may be listed with the command + + $ gaiasky -h + diff --git a/academic/gaiasky/doinst.sh b/academic/gaiasky/doinst.sh new file mode 100644 index 0000000000..91a7c14948 --- /dev/null +++ b/academic/gaiasky/doinst.sh @@ -0,0 +1,7 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -x /sbin/setcap ]; then + /sbin/setcap cap_ipc_lock,cap_sys_nice=ep /usr/lib64/zulu-openjdk17/bin/java +fi diff --git a/academic/gaiasky/gaiasky.SlackBuild b/academic/gaiasky/gaiasky.SlackBuild new file mode 100644 index 0000000000..a736f4b832 --- /dev/null +++ b/academic/gaiasky/gaiasky.SlackBuild @@ -0,0 +1,135 @@ +#!/bin/bash + +# Slackware build script for gaiasky + +# Copyright 2023-2024 Giancarlo Dessì, Cagliari, IT +# Based on Booktab.SlackBuild written by Matteo Bernardini +# at https://ponce.cc/slackware/testing/Booktab/ +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gaiasky +VERSION=${VERSION:-"3.6.0"} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCVERSION=$( echo ${VERSION//./_} ) + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "x86_64" ]; then + SRCARCH="x86-64" + PKGARCH="$ARCH" +elif [ "$ARCH" = "arm" ]; then + printf "\n$ARCH is unsupported for gaiasky...\n\n" + exit 1 +else + SRCARCH="x86" + PKGARCH="i586" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +rm -rf $TMP/$PRGNAM-$VERSION +mkdir $TMP/$PRGNAM-$VERSION + +#Extract the application from the Ubuntu package +ar xv $CWD/${PRGNAM}_linux_$SRCVERSION.deb data.tar.gz +tar xvf data.tar.gz -C $TMP/$PRGNAM-$VERSION +rm -f data.tar.gz + +cd $TMP/$PRGNAM-$VERSION + +# patch the application entry: as is provided it won't work +# in Slackware/KDE +patch -p0 << 'EOF' +--- opt/gaiasky/gaiasky.desktop 2023-04-05 16:00:00.000000000 +0200 ++++ opt/gaiasky/gaiasky.desktop 2023-04-05 16:00:01.000000000 +0200 +@@ -3,6 +3,8 @@ + Name=Gaia Sky + Comment=3D universe simulator for desktop and VR with support for more than a billion objects +-Exec=gaiasky ++Exec=/opt/gaiasky/gaiasky ++GenericName=Desktop 3D universe viewer + Icon=/opt/gaiasky/gs_icon.svg + Terminal=false +-Categories=Science; ++Categories=Education;Science;Astronomy; ++StartupNotify=true + +EOF + +chown -R root:root . + +# The application will be installed in /opt but some files will be moved or +# linked in /usr according to the standard of Slackware installations +mkdir -p usr/share/applications +mkdir -p usr/doc/$PRGNAM-$VERSION +mkdir -p usr/bin + +# link the executable in /usr/bin +cd usr/bin +ln -s ../../opt/gaiasky/gaiasky gaiasky +cd ../../ + +# link the application desktop entry +cp -a opt/gaiasky/gaiasky.desktop usr/share/applications/gaiasky.desktop + +# move the entire tree in package-gaiasky +cp -a * $PKG/ + +# strip ELF objects +find $PKG/opt/gaiasky -type f -print0 | \ + xargs -0 file -m /etc/file/magic/elf | \ + grep 'ELF.*dynamic.*not stripped' | \ + cut -d: -f1 | xargs strip + +chmod 755 $PKG/opt/gaiasky/jre/lib/*.so +chmod 755 $PKG/opt/gaiasky/jre/lib/server/*.so + +# move some documentation files in /usr/doc/gaiasky-x.y.z +mv opt/gaiasky/*.md opt/gaiasky/releasenotes.txt $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gaiasky/gaiasky.info b/academic/gaiasky/gaiasky.info new file mode 100644 index 0000000000..ecb5220e4e --- /dev/null +++ b/academic/gaiasky/gaiasky.info @@ -0,0 +1,10 @@ +PRGNAM="gaiasky" +VERSION="3.6.0" +HOMEPAGE="https://zah.uni-heidelberg.de/gaia/outreach/gaiasky" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://gaia.ari.uni-heidelberg.de/gaiasky/releases/3.6.0.afdd9547d/gaiasky_linux_3_6_0.deb" +MD5SUM_x86_64="f681a23056f157d1a7dc4257318dd16c" +REQUIRES="zulu-openjdk17" +MAINTAINER="Giancarlo Dessi" +EMAIL="slack@giand.it" diff --git a/academic/gaiasky/slack-desc b/academic/gaiasky/slack-desc new file mode 100644 index 0000000000..cc7ca93657 --- /dev/null +++ b/academic/gaiasky/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gaiasky: gaiasky (3D universe simulator for desktop and VR) +gaiasky: +gaiasky: Gaia Sky is a real-time, 3D, astronomy visualisation software +gaiasky: developed in the framework of ESA's Gaia mission to chart about +gaiasky: 1 billion stars of our Galaxy in the Gaia group of the +gaiasky: Astronomisches Rechen-Institut (ZAH, Universitat Heidelberg). +gaiasky: +gaiasky: +gaiasky: https://zah.uni-heidelberg.de/gaia/outreach/gaiasky +gaiasky: +gaiasky: diff --git a/academic/gaw3/gaw3.SlackBuild b/academic/gaw3/gaw3.SlackBuild index 91a3888a90..3227c027ea 100644 --- a/academic/gaw3/gaw3.SlackBuild +++ b/academic/gaw3/gaw3.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gaw3 -VERSION=${VERSION:-20170716} +VERSION=${VERSION:-20220315} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/gaw3/gaw3.info b/academic/gaw3/gaw3.info index b829c40a98..fdcb7422af 100644 --- a/academic/gaw3/gaw3.info +++ b/academic/gaw3/gaw3.info @@ -1,8 +1,8 @@ PRGNAM="gaw3" -VERSION="20170716" +VERSION="20220315" HOMEPAGE="http://www.rvq.fr/linux/gaw.php" -DOWNLOAD="http://download.tuxfamily.org/gaw/download/gaw3-20170716.tar.gz" -MD5SUM="e9870cf8859cd4d99461e2351c34a2ff" +DOWNLOAD="http://download.tuxfamily.org/gaw/download/gaw3-20220315.tar.gz" +MD5SUM="725382012612626a79149685364d5886" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/gchemutils/README b/academic/gchemutils/README index 9b7f1eeb7f..f8efabc980 100644 --- a/academic/gchemutils/README +++ b/academic/gchemutils/README @@ -9,14 +9,10 @@ Six programs are available: 5) A Spectrum viewer (GSpectrum) 6) A periodic table of the elements application (GChemTable) -Three plugins for external programs are included: -1) A GOffice plugin allows embedding GChemPaint supported files in - programs supporting the GOffice component framework -2) A Gnumeric plugin provides a molar mass function for the spreadsheet -3) A Mozilla plugin allows embedding 2D, 3D and crystal structures as - well as spectra in web pages +A GOffice plugin is included, which allows embedding GChemPaint +supported files in programs supporting the GOffice component +framework. -An optional build-time dependency is gnumeric for building its plugin. - -NOTES: The Mozilla plugin might not be very stable, so if you want -to prevent it from building, pass MOZILLA=NO to the script. +Note: previously, there were also plugins for Mozilla and Gnumeric. +These have been removed because they no longer build with modern +versions of Mozilla and Gnumeric. diff --git a/academic/gchemutils/gchemutils.SlackBuild b/academic/gchemutils/gchemutils.SlackBuild index 72696658c8..c06dfb9ab6 100644 --- a/academic/gchemutils/gchemutils.SlackBuild +++ b/academic/gchemutils/gchemutils.SlackBuild @@ -22,16 +22,22 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220308 bkw: Modified by SlackBuilds.org, BUILD=3: +# - disable the mozilla plugin, since it doesn't build. +# - disable the gnumeric plugin, since it doesn't build either. +# - update the README to explain the above. +# - do not install useless INSTALL in doc dir. + cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gchemutils VERSION=${VERSION:-0.14.17} -BUILD=${BUILD:-1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} SRCNAM=gnome-chemistry-utils -MOZILLA=${MOZILLA:-YES} # Build the Mozilla plugin +MOZILLA=${MOZILLA:-NO} # Don't build the Mozilla plugin (it doesn't build) if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -41,9 +47,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -79,16 +82,22 @@ cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ # Disable Mozilla plugin building if anything other than YES # was given as an argument to MOZILLA= at runtime -[ ! "$MOZILLA" = "YES" ] && mozplug="disable" || mozplug="enable" +#[ ! "$MOZILLA" = "YES" ] && mozplug="disable" || mozplug="enable" + +# 20220308 bkw: force-disable, it no longer builds. +mozplug=disable + +# 20220308 bkw: dike out the gnumeric support, since it's broken. +sed -i.bak '/\(ver\|libspreadsheet\)/s,1\.12,999.99,g' configure CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS -std=c++14" \ ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ @@ -103,20 +112,17 @@ CXXFLAGS="$SLKCFLAGS" \ --build=$ARCH-slackware-linux make -make install DESTDIR=$PKG - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +make install-strip DESTDIR=$PKG +gzip -9 $PKG/usr/man/man*/* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS ChangeLog COPYING* INSTALL NEWS README TODO \ + AUTHORS ChangeLog COPYING* NEWS README TODO \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh diff --git a/academic/gcompris-qt/gcompris-qt.SlackBuild b/academic/gcompris-qt/gcompris-qt.SlackBuild index a4c7c7151d..01ad6255dc 100644 --- a/academic/gcompris-qt/gcompris-qt.SlackBuild +++ b/academic/gcompris-qt/gcompris-qt.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for gcompris-qt -# Copyright 2020 Willy Sudiarto Raharjo <willysr@slackbuilds.org> +# Copyright 2020-2024 Willy Sudiarto Raharjo <willysr@slackbuilds.org> # All rights reserved. # # Redistribution and use in source and binary forms, with or without modification, @@ -26,16 +26,10 @@ # NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# This software is licensed under the GNU GENERAL PUBLIC LICENSE Version 3, -# 29 June 2007 -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see <https://www.gnu.org/licenses/>. - cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gcompris-qt -VERSION=${VERSION:-1.1} +VERSION=${VERSION:-4.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -59,9 +53,6 @@ case "$ARCH" in ;; esac -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 diff --git a/academic/gcompris-qt/gcompris-qt.info b/academic/gcompris-qt/gcompris-qt.info index 5ff869de90..835328b6ce 100644 --- a/academic/gcompris-qt/gcompris-qt.info +++ b/academic/gcompris-qt/gcompris-qt.info @@ -1,10 +1,10 @@ PRGNAM="gcompris-qt" -VERSION="1.1" +VERSION="4.0" HOMEPAGE="https://gcompris.net/" -DOWNLOAD="https://gcompris.net/download/qt/linux/gcompris-qt-1.1-Linux32.sh" -MD5SUM="381f16e7f476a479e663e55c0f386c13" -DOWNLOAD_x86_64="https://gcompris.net/download/qt/linux/gcompris-qt-1.1-Linux64.sh" -MD5SUM_x86_64="06e571bb48a1fb30edeb00c5e6295cd9" +DOWNLOAD="https://gcompris.net/download/qt/linux/gcompris-qt-4.0-Linux32.sh" +MD5SUM="c28334c56e8c7f74888a2b641cbcca6f" +DOWNLOAD_x86_64="https://gcompris.net/download/qt/linux/gcompris-qt-4.0-Linux64.sh" +MD5SUM_x86_64="3f0714ef303ea3bc3799b614bcbd5857" REQUIRES="" MAINTAINER="Willy Sudiarto Raharjo" EMAIL="willysr@slackbuilds.org" diff --git a/academic/gcompris/README b/academic/gcompris/README deleted file mode 100644 index 63345e597b..0000000000 --- a/academic/gcompris/README +++ /dev/null @@ -1,5 +0,0 @@ -GCompris is an educational software suite comprising of numerous -activities for children aged 2 to 10. Some of the activities are game -oriented, but nonetheless still educational. Currently GCompris offers -in excess of 140 activities and more are being developed. GCompris -currently is translated into more than 40 languages. diff --git a/academic/gcompris/doinst.sh b/academic/gcompris/doinst.sh deleted file mode 100644 index 3857649f50..0000000000 --- a/academic/gcompris/doinst.sh +++ /dev/null @@ -1,3 +0,0 @@ -if [ -x /usr/bin/update-desktop-database ]; then - /usr/bin/update-desktop-database -q usr/share/applications &> /dev/null -fi diff --git a/academic/gcompris/gcompris.SlackBuild b/academic/gcompris/gcompris.SlackBuild deleted file mode 100644 index e4b1c0a7c2..0000000000 --- a/academic/gcompris/gcompris.SlackBuild +++ /dev/null @@ -1,114 +0,0 @@ -#!/bin/bash - -# Slackware build script for gcompris - -# Copyright (c) 2009, Paul Liconti -# Copyright 2013-2017 Willy Sudiarto Raharjo <willysr@slackbuilds.org> -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, -# this list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright -# notice, this list of conditions and the following disclaimer in the -# documentation and/or other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED -# TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -cd $(dirname $0) ; CWD=$(pwd) - -PRGNAM=gcompris -VERSION=${VERSION:-17.05} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} -PKGTYPE=${PKGTYPE:-tgz} - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. -if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then - echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" - exit 0 -fi - -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 -cd $PRGNAM-$VERSION -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux - -make -make install DESTDIR=$PKG - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING INSTALL NEWS README TODO $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gcompris/gcompris.info b/academic/gcompris/gcompris.info deleted file mode 100644 index b7710c8c8d..0000000000 --- a/academic/gcompris/gcompris.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="gcompris" -VERSION="17.05" -HOMEPAGE="https://gcompris.net/" -DOWNLOAD="https://gcompris.net/download/gtk/src/gcompris-17.05.tar.bz2" -MD5SUM="6c0733db29ca3d6b4100cdccc7a7a720" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Willy Sudiarto Raharjo" -EMAIL="willysr@slackbuilds.org" diff --git a/academic/gcompris/slack-desc b/academic/gcompris/slack-desc deleted file mode 100644 index fa37de57dc..0000000000 --- a/academic/gcompris/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -gcompris: gcompris (an educational software suite for children ages 2 to 10) -gcompris: -gcompris: GCompris is an educational software suite comprising of numerous -gcompris: activities for children aged 2 to 10. Some of the activities are game -gcompris: orientated, but nonetheless still educational. Currently GCompris -gcompris: offers in excess of 140 activities and more are being developed. -gcompris: GCompris currently is translated in more than 40 languages. -gcompris: -gcompris: Homepage: http://gcompris.net/ -gcompris: -gcompris: diff --git a/academic/gdstk/README b/academic/gdstk/README new file mode 100644 index 0000000000..2d5a39f1c5 --- /dev/null +++ b/academic/gdstk/README @@ -0,0 +1,12 @@ +gdstk (C++ library for manipulation of GDSII and OASIS files. ) + +Gdstk (GDSII Tool Kit) is a C++ library for creation and +manipulation of GDSII and OASIS files. It is also available as a +Python module meant to be a successor to Gdspy. Key features for the +creation of complex CAD layouts are included: Boolean operations on +polygons (AND, OR, NOT, XOR) based on clipping algorithm, Polygon +offset (inward and outward rescaling of polygons), Efficient +point-in-polygon solutions for large array sets. +Typical applications of Gdstk are in the fields of electronic chip +design, planar lightwave circuit design, and mechanical engineering. + diff --git a/academic/avogadro/avogadro.SlackBuild b/academic/gdstk/gdstk.SlackBuild index ab79957b1a..7a14390770 100644 --- a/academic/avogadro/avogadro.SlackBuild +++ b/academic/gdstk/gdstk.SlackBuild @@ -1,8 +1,8 @@ #!/bin/bash -# Slackware build script for Avogadro +# Slackware build script for gdstk -# Copyright 2010-2016 Larry Hajali <larryhaja[at]gmail[dot]com> +# Copyright 2023, Lockywolf # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,15 +24,15 @@ cd $(dirname $0) ; CWD=$(pwd) -PRGNAM=avogadro -VERSION=${VERSION:-1.2.0} +PRGNAM=gdstk +VERSION=${VERSION:-0.9.46} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -50,8 +50,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -59,6 +59,9 @@ elif [ "$ARCH" = "i686" ]; then elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" LIBDIRSUFFIX="" @@ -75,54 +78,42 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} + -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + -# Fix manpage directory. -sed -i 's|share/man|man|' doc/CMakeLists.txt -# Fix install directory and linking for libmsym library. -patch -p1 < $CWD/avogadro-1.2.0-libmsym.patch +#sed -i 's/qh_nextfacet2d/qh_nextfacet/g' src/utils.cpp -# fix build (with recent swig/linker/python?) -# http://pkgs.fedoraproject.org/cgit/rpms/avogadro.git/tree/avogadro-1.1.1-python_openbabel.patch -patch -p1 < $CWD/avogadro-1.1.1-python_openbabel.patch +sed -i 's|add_library(gdstk|add_library(gdstk SHARED|g' src/CMakeLists.txt mkdir -p build cd build cmake \ - -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ -DLIB_SUFFIX=${LIBDIRSUFFIX} \ - -DENABLE_RPATH=OFF \ - -DCMAKE_SKIP_RPATH=YES \ - -DENABLE_GLSL:BOOL=ON \ - -DENABLE_UPDATE_CHECKER=OFF \ - -DENABLE_VERSIONED_PLUGIN_DIR:BOOL=OFF \ - -DBUILD_SHARED_LIBS:BOOL=ON \ - -DQT_MKSPECS_RELATIVE=lib${LIBDIRSUFFIX}/qt/mkspecs \ + -DMAN_INSTALL_DIR=/usr/man \ + -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ + -DCMAKE_C_COMPILER_LAUNCHER=ccache \ -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. - make VERBOSE=1 - make install DESTDIR=$PKG -cd - +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -find $PKG/usr/man -type f -exec gzip -9 {} \; - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS COPYING INSTALL README \ - libavogadro/src/extensions/gl2ps/{COPYING*,*.txt,*.pdf} \ + README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gdstk/gdstk.info b/academic/gdstk/gdstk.info new file mode 100644 index 0000000000..4634504c1c --- /dev/null +++ b/academic/gdstk/gdstk.info @@ -0,0 +1,10 @@ +PRGNAM="gdstk" +VERSION="0.9.46" +HOMEPAGE="https://heitzmann.github.io/gdstk/" +DOWNLOAD="https://github.com/heitzmann/gdstk/archive/v0.9.46/gdstk-0.9.46.tar.gz" +MD5SUM="618e717dde0a136612254d3f0022d510" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="qhull" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.gdstk_2023-11-19@lockywolf.net" diff --git a/academic/gdstk/slack-desc b/academic/gdstk/slack-desc new file mode 100644 index 0000000000..fe5d87eea6 --- /dev/null +++ b/academic/gdstk/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gdstk: gdstk (C++ library for manipulation of GDSII and OASIS files. ) +gdstk: +gdstk: Gdstk (GDSII Tool Kit) is a C++ library for creation and +gdstk: manipulation of GDSII and OASIS files. It is also available as a +gdstk: Python module meant to be a successor to Gdspy. Key features for the +gdstk: creation of complex CAD layouts are included: Boolean operations on +gdstk: polygons (AND, OR, NOT, XOR) based on clipping algorithm, Polygon +gdstk: offset (inward and outward rescaling of polygons), Efficient +gdstk: point-in-polygon solutions for large array sets. +gdstk: Typical applications of Gdstk are in the fields of electronic chip +gdstk: design, planar lightwave circuit design, and mechanical engineering. diff --git a/academic/geda-gaf/geda-gaf.SlackBuild b/academic/geda-gaf/geda-gaf.SlackBuild index a3edd0b2a3..0feae7e775 100644 --- a/academic/geda-gaf/geda-gaf.SlackBuild +++ b/academic/geda-gaf/geda-gaf.SlackBuild @@ -9,7 +9,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=geda-gaf VERSION=${VERSION:-1.10.2} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -90,6 +90,8 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a $DOCS $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh diff --git a/academic/gelemental/gelemental.SlackBuild b/academic/gelemental/gelemental.SlackBuild index 74eb6046b6..7541dfe91b 100644 --- a/academic/gelemental/gelemental.SlackBuild +++ b/academic/gelemental/gelemental.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for gelemental -# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gelemental -VERSION=${VERSION:-2.0.0} +VERSION=${VERSION:-2.0.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -100,12 +100,17 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +# Only one category... +sed -i "s:GTK;Education;Science;Chemistry;:Education:" $PKG/usr/share/applications/$PRGNAM.desktop + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS ChangeLog COPYING COPYING.DATA INSTALL README NEWS NEWS-GPeriodic TODO TRANSLATORS \ + AUTHORS ChangeLog COPYING COPYING.DATA README NEWS NEWS-GPeriodic TODO TRANSLATORS \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh diff --git a/academic/gelemental/gelemental.info b/academic/gelemental/gelemental.info index 59fdeb15ae..5b79c725b8 100644 --- a/academic/gelemental/gelemental.info +++ b/academic/gelemental/gelemental.info @@ -1,8 +1,8 @@ PRGNAM="gelemental" -VERSION="2.0.0" +VERSION="2.0.2" HOMEPAGE="https://github.com/ginggs/gelemental/" -DOWNLOAD="https://github.com/ginggs/gelemental/archive/v2.0.0/gelemental-2.0.0.tar.gz" -MD5SUM="8d38d7599b0f2fc96e2bd622cd762b9a" +DOWNLOAD="https://github.com/ginggs/gelemental/archive/v2.0.2/gelemental-2.0.2.tar.gz" +MD5SUM="cbbc25d9648c76d8f17a96db3fa30314" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/gem5/README b/academic/gem5/README new file mode 100644 index 0000000000..c3de9f48c4 --- /dev/null +++ b/academic/gem5/README @@ -0,0 +1,20 @@ + The gem5 simulator is a modular platform for computer-system +architecture research, encompassing system-level architecture as +well as processor microarchitecture. gem5 is a community led project + with an open governance model. + + gem5 was originally conceived for computer architecture research +in academia, but it has grown to be used in computer system design +by academia, industry for research, and in teaching. + +By default it's build the X86 simulator, you can set to other +architectures with a environment variable as following: + - MIPS=yes + - POWER=yes + - RISCV=yes + - SPARC=yes + +Optional: + - protobuf-c (for tracing support) + - hdf5 + diff --git a/academic/gem5/gem5.SlackBuild b/academic/gem5/gem5.SlackBuild new file mode 100644 index 0000000000..81ce3cbb77 --- /dev/null +++ b/academic/gem5/gem5.SlackBuild @@ -0,0 +1,160 @@ +#!/bin/bash + +# Slackware build script for gem5 + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gem5 +VERSION=${VERSION:-20.1.0.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +if [ "${ARM:-no}" == "yes" ]; then + GEM5_ISA="ARM" + SCONS_OPTS="USE_SYSTEMC=no" +fi + +if [ "${MIPS:-no}" == "yes" ]; then + GEM5_ISA="$GEM5_ISA MIPS" +fi + +if [ "${POWER:-no}" == "yes" ]; then + GEM5_ISA="$GEM5_ISA POWER" +fi + +if [ "${RISCV:-no}" == "yes" ]; then + GEM5_ISA="$GEM5_ISA RISCV" +fi + +if [ "${RISCV:-no}" == "yes" ]; then + GEM5_ISA="$GEM5_ISA SPARC" +fi + +if [ ! "${X86:-yes}" == "no" ]; then + GEM5_ISA="$GEM5_ISA X86" +elif [ -z $GEM5_ISA ]; then + echo "At least one ISA must be enabled" + echo "The following ISA are available" + echo "X86 ARM MIPS POWER RISCV SPARC" +fi + +if [ "${DEBUG:-no}" == "yes" ]; then + VARIANT=debug +elif [ "${OPT:-no}" == "yes" ]; then + VARIANT=opt +else + VARIANT=fast +fi + +for gem5_isa in $GEM5_ISA; do + CCFLAGS_EXTRA="$SLKCFLAGS" \ + scons $SCONS_OPTS build/$gem5_isa/gem5.$VARIANT +done + +INSTALL_DIR=$PKG/opt/gem5-$VERSION + +# install binary +mkdir -p $INSTALL_DIR/bin +for gem5_isa in $GEM5_ISA; do + cp -a build/$gem5_isa/gem5.$VARIANT \ + $INSTALL_DIR/bin/gem5-$gem5_isa\.$VARIANT +done + +# install auxiliar files/tools +cp -a configs $INSTALL_DIR +cp -a system $INSTALL_DIR +cp -a tests $INSTALL_DIR +cp -a util $INSTALL_DIR + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a CODE-OF-CONDUCT.md CONTRIBUTING.md COPYING LICENSE \ + MAINTAINERS RELEASE-NOTES.md $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gem5/gem5.info b/academic/gem5/gem5.info new file mode 100644 index 0000000000..6855672c44 --- /dev/null +++ b/academic/gem5/gem5.info @@ -0,0 +1,10 @@ +PRGNAM="gem5" +VERSION="20.1.0.5" +HOMEPAGE="https://www.gem5.org" +DOWNLOAD="https://github.com/gem5/gem5/archive/v20.1.0.5/gem5-20.1.0.5.tar.gz" +MD5SUM="323f9a6eab649fbf7e12746695c0aeed" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/gem5/slack-desc b/academic/gem5/slack-desc new file mode 100644 index 0000000000..2654f3f312 --- /dev/null +++ b/academic/gem5/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gem5: gem5 (gem5 is an open-source system-level and processor simulator) +gem5: +gem5: The gem5 simulator is a modular platform for computer-system +gem5: architecture research, encompassing system-level architecture as +gem5: well as processor microarchitecture. gem5 is a community led project +gem5: with an open governance model. +gem5: gem5 was originally conceived for computer architecture research +gem5: in academia, but it has grown to be used in computer system design +gem5: by academia, industry for research, and in teaching. +gem5: +gem5: diff --git a/academic/genius/README b/academic/genius/README index fa2fa4b67b..844fbd0219 100644 --- a/academic/genius/README +++ b/academic/genius/README @@ -5,7 +5,3 @@ in some aspects to BC, Matlab, Maple or Mathematica. It is useful both as a simple calculator and as a research or educational tool. The syntax is very intuitive and is designed to mimic how mathematics is usually written. - -If you would like the GUI interface as well, it requires -libgnomeui, gtksourceview and vte2. If you have these dependencies, -pass the variable of GNOME=YES (or anything that isn't NO ;) diff --git a/academic/genius/genius.SlackBuild b/academic/genius/genius.SlackBuild index dd8974c60b..6170b1f2c0 100644 --- a/academic/genius/genius.SlackBuild +++ b/academic/genius/genius.SlackBuild @@ -25,14 +25,14 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=genius -VERSION=${VERSION:-1.0.23} +VERSION=${VERSION:-1.0.27} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -50,14 +50,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -GNOME=${GNOME:-NO} -GNOME_FLAGS="--disable-gtksourceview --disable-gnome" -if [ "$GNOME" != "NO" ] ; then - GNOME_FLAGS="" -fi - -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -85,8 +79,10 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -CFLAGS="$SLKCFLAGS -std=gnu89" \ -CXXFLAGS="$SLKCFLAGS -std=gnu89" \ +autoreconf -vif + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ @@ -94,9 +90,7 @@ CXXFLAGS="$SLKCFLAGS -std=gnu89" \ --localstatedir=/var \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ - --disable-scrollkeeper \ --disable-update-mimedb \ - $GNOME_FLAGS \ --build=$ARCH-slackware-linux make diff --git a/academic/genius/genius.info b/academic/genius/genius.info index b072a17292..f4eaec93fb 100644 --- a/academic/genius/genius.info +++ b/academic/genius/genius.info @@ -1,10 +1,10 @@ PRGNAM="genius" -VERSION="1.0.23" +VERSION="1.0.27" HOMEPAGE="http://www.5z.com/jirka/genius.html" -DOWNLOAD="http://ftp.5z.com/pub/genius/genius-1.0.23.tar.xz" -MD5SUM="3e94a5898e59c069c564f00136c2450d" +DOWNLOAD="https://download.gnome.org/sources/genius/1.0/genius-1.0.27.tar.xz" +MD5SUM="d510beed59c2b9ad52a56153e5825fb8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="rarian" +REQUIRES="gtksourceview4" MAINTAINER="Vincent Batts" EMAIL="vbatts@hashbangbash.com" diff --git a/academic/genometools/gcc10.patch b/academic/genometools/gcc10.patch deleted file mode 100644 index 2c4edf1b74..0000000000 --- a/academic/genometools/gcc10.patch +++ /dev/null @@ -1,88 +0,0 @@ -From 51205942b1f41abdf841771deac4e0e35d7d5016 Mon Sep 17 00:00:00 2001 -From: Sascha Steinbiss <satta@debian.org> -Date: Wed, 22 Apr 2020 21:59:57 +0200 -Subject: [PATCH 1/2] make sure to not ignore snprintf output - -GCC 10 will warn about the (here intended) silent string truncation -done by snprintf() unless the return value is handled. -Obviously this will break the build as we use -Werror. We -circumvent the problem by checking the output value and printing a -warning if we notice a truncation. ---- - src/ltr/ltrdigest_file_out_stream.c | 17 ++++++++++++----- - 1 file changed, 12 insertions(+), 5 deletions(-) - -diff --git a/src/ltr/ltrdigest_file_out_stream.c b/src/ltr/ltrdigest_file_out_stream.c -index 723b8cf9a..61325b693 100644 ---- a/src/ltr/ltrdigest_file_out_stream.c -+++ b/src/ltr/ltrdigest_file_out_stream.c -@@ -1,5 +1,5 @@ - /* -- Copyright (c) 2008-2015 Sascha Steinbiss <sascha@steinbiss.name> -+ Copyright (c) 2008-2020 Sascha Steinbiss <sascha@steinbiss.name> - Copyright (c) 2008-2013 Center for Bioinformatics, University of Hamburg - - Permission to use, copy, modify, and distribute this software for any -@@ -33,6 +33,7 @@ - #include "core/symbol.h" - #include "core/undef_api.h" - #include "core/unused_api.h" -+#include "core/warning_api.h" - #include "extended/extract_feature_sequence.h" - #include "extended/feature_node.h" - #include "extended/feature_node_iterator_api.h" -@@ -416,6 +417,8 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) - - if (!had_err) { - GtRange rng; -+ int ret = 0; -+ - ls->element.seqid = gt_calloc((size_t) ls->seqnamelen+1, sizeof (char)); - (void) snprintf(ls->element.seqid, - GT_MIN((size_t) gt_str_length(sdesc), -@@ -425,12 +428,16 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) - if (gt_str_length(sdesc) > (GtUword) ls->seqnamelen) - ls->element.seqid[ls->seqnamelen] = '\0'; - -- (void) gt_ltrelement_format_description(&ls->element, -- ls->seqnamelen, -- desc, -- (size_t) (GT_MAXFASTAHEADER-1)); -+ ret = gt_ltrelement_format_description(&ls->element, -+ ls->seqnamelen, -+ desc, -+ (size_t) (GT_MAXFASTAHEADER-1)); -+ if (ret < 0) { -+ gt_warning("FASTA header truncated: %s", desc); -+ } - gt_str_delete(sdesc); - -+ - /* output basic retrotransposon data */ - lltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftLTR); - rltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightLTR); - -From 30ae36037228dc4ed174e8462f3489638e6f5e76 Mon Sep 17 00:00:00 2001 -From: Sascha Steinbiss <satta@debian.org> -Date: Wed, 22 Apr 2020 22:01:00 +0200 -Subject: [PATCH 2/2] declare hashmap type as extern - -This fixes a build issue with GCC 10. -Closes #941. ---- - src/mgth/metagenomethreader.h | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/mgth/metagenomethreader.h b/src/mgth/metagenomethreader.h -index 92f16d498..7f76fffb9 100644 ---- a/src/mgth/metagenomethreader.h -+++ b/src/mgth/metagenomethreader.h -@@ -221,7 +221,7 @@ typedef struct - } ParseStruct; - - /* specific access mode of queryhash */ --DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp,,) -+DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp, extern,) - DECLARE_SAFE_DEREF(GtUword *, ulp) - - /* Funktion, mit der der Metagenomethreader gestartet wird diff --git a/academic/genometools/genometools.SlackBuild b/academic/genometools/genometools.SlackBuild index 9e55523524..47f6ca9adf 100644 --- a/academic/genometools/genometools.SlackBuild +++ b/academic/genometools/genometools.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for genometools -# Copyright 2014-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2014-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=genometools -VERSION=${VERSION:-1.6.1} +VERSION=${VERSION:-1.6.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -90,9 +90,6 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Thanks Debian for the patch -patch -p1 -i $CWD/gcc10.patch - # Fix library and man pages path sed -i "s:lib/libgenometools:lib${LIBDIRSUFFIX}/libgenometools:g" Makefile sed -i "s:\$(prefix)/lib:\$(prefix)/lib${LIBDIRSUFFIX}:g" Makefile diff --git a/academic/genometools/genometools.info b/academic/genometools/genometools.info index 7692e762e8..cac6f3b826 100644 --- a/academic/genometools/genometools.info +++ b/academic/genometools/genometools.info @@ -1,8 +1,8 @@ PRGNAM="genometools" -VERSION="1.6.1" +VERSION="1.6.2" HOMEPAGE="http://genometools.org/" -DOWNLOAD="http://genometools.org/pub/genometools-1.6.1.tar.gz" -MD5SUM="1dc80df17be32973266f5a3601fc64b8" +DOWNLOAD="http://genometools.org/pub/genometools-1.6.2.tar.gz" +MD5SUM="431e34d5490148dbcbc95e3de7ac4b78" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/genpak/genpak.SlackBuild b/academic/genpak/genpak.SlackBuild index ca05fd25f3..0a6ecb902c 100644 --- a/academic/genpak/genpak.SlackBuild +++ b/academic/genpak/genpak.SlackBuild @@ -22,11 +22,15 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220408 bkw: Modified by SlackBuilds.org, BUILD=7: +# - get rid of /usr/doc/gp symlink. +# - remove useless INSTALL.TXT from doc dir. + cd $(dirname $0) ; CWD=$(pwd) PRGNAM=genpak VERSION=${VERSION:-0.26} -BUILD=${BUILD:-6} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,9 +42,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -75,9 +76,9 @@ cd gp-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ # arch-independent data files belong in /usr/share: sed -i "s,usr/lib/,usr/share/,g" src/* man1/* html/* *.TXT @@ -102,10 +103,9 @@ make install docs \ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +gzip -9 $PKG/usr/man/man*/* -( cd $PKG/usr/doc ; mv gp $PRGNAM-$VERSION ; ln -s $PRGNAM-$VERSION gp ) +( cd $PKG/usr/doc ; rm gp/INSTALL.TXT ; mv gp $PRGNAM-$VERSION ) cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/geomview/README b/academic/geomview/README index 07f1a998fa..2a98653434 100644 --- a/academic/geomview/README +++ b/academic/geomview/README @@ -1,9 +1,9 @@ Geomview is an interactive 3D viewing program for Unix. -Geomview lets you view and manipulate three-dimensional objects: you -use the mouse to rotate, translate, zoom in and out, and so on. +Geomview lets you view and manipulate three-dimensional objects: +you use the mouse to rotate, translate, zoom in and out, and so on. Geomview can be used as a standalone viewer for static objects (it supports a variety of file formats) or as a display engine for other programs which produce dynamically changing geometry. -This slackBuild uses the configure option --with-opengl. +This SlackBuild uses the configure option --with-opengl. diff --git a/academic/geomview/geomview.SlackBuild b/academic/geomview/geomview.SlackBuild index b5205f067b..546d3fb357 100644 --- a/academic/geomview/geomview.SlackBuild +++ b/academic/geomview/geomview.SlackBuild @@ -2,28 +2,45 @@ # Slackware build script for geomview -# Written by (Jorge Barros de Abreu) -# (http://sites.google.com/site/ficmatinf) +# Copyright 2013 Jorge Barros de Abreu +# 2013-2022 Maintained by the SBo team +# 2023 Updated to 1.9.5 by Philip Lacroix <slackph at posteo dot de> +# +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. cd $(dirname $0) ; CWD=$(pwd) PRGNAM=geomview -VERSION=${VERSION:-1.9.4} +VERSION=${VERSION:-1.9.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -33,8 +50,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -62,10 +79,6 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; -# -#geomview compilation -# - CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -96,12 +109,24 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r gzip -c -9 $PRGNAM-2 > $PRGNAM.info-2.gz rm -fr dir figs $PRGNAM-* $PRGNAM ) -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +# Install documentation. +PRGDOC=$PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PRGDOC cp -a \ doc/figs doc/*.txt doc/*.c doc/*.tcl doc/README* doc/*.gvplot doc/oogltour* \ - $PKG/usr/doc/$PRGNAM-$VERSION -rm -f $PKG/usr/doc/$PRGNAM-$VERSION/*.pdf # We already have the html ones -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + $PRGDOC +# +# Move plain text files (no troff) to /usr/doc. +( cd $PKG/usr/man/man3 + zcat lisp.3gv.gz > $PRGDOC/lisp.txt + rm -rf lisp.3gv.gz ) +( cd $PKG/usr/man/man5 + zcat geomview.5gv.gz > $PRGDOC/geomview.txt + zcat oogl.5gv.gz > $PRGDOC/oogl.txt + rm -rf geomview.5gv.gz oogl.5gv.gz ) +cat $CWD/$PRGNAM.SlackBuild > $PRGDOC/$PRGNAM.SlackBuild + +rm -f $PKG/usr/lib*/*.la mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/geomview/geomview.info b/academic/geomview/geomview.info index 012d830954..c8601b3d2c 100644 --- a/academic/geomview/geomview.info +++ b/academic/geomview/geomview.info @@ -1,8 +1,8 @@ PRGNAM="geomview" -VERSION="1.9.4" +VERSION="1.9.5" HOMEPAGE="http://www.geomview.org" -DOWNLOAD="http://downloads.sourceforge.net/geomview/geomview-1.9.4.tar.gz" -MD5SUM="29c7e6d678af7b9968980f92954419bb" +DOWNLOAD="https://downloads.sourceforge.net/geomview/geomview-1.9.5.tar.gz" +MD5SUM="98ada147dfcbabca7c48137590e74a85" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/geomview/slack-desc b/academic/geomview/slack-desc index d3d3e38801..58bedec367 100644 --- a/academic/geomview/slack-desc +++ b/academic/geomview/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| geomview: geomview (3D geometrical package) geomview: -geomview: Geomview is an interactive 3D viewing program for Unix. -geomview: Geomview lets you view and manipulate three-dimensional objects: you -geomview: use the mouse to rotate, translate, zoom in and out, and so on. -geomview: Geomview can be used as a standalone viewer for static objects (it -geomview: supports a variety of file formats) or as a display engine for other -geomview: programs which produce dynamically changing geometry. +geomview: Geomview is an interactive 3D viewing program for Unix. It lets you +geomview: view and manipulate three-dimensional objects: you use the mouse to +geomview: rotate, translate, zoom in and out, etc. Geomview can be used as a +geomview: standalone viewer for static objects (it supports a variety of file +geomview: formats) or as a display engine for other programs which produce +geomview: dynamically changing geometry. geomview: -geomview: homepage: http://www.geomview.org +geomview: Homepage: http://www.geomview.org geomview: diff --git a/academic/gephi/README b/academic/gephi/README new file mode 100644 index 0000000000..1f997e187b --- /dev/null +++ b/academic/gephi/README @@ -0,0 +1,42 @@ +The Open Graph Viz Platform + +Gephi is the leading visualization and exploration software for all +kinds of graphs and networks. Gephi is open-source and free. + +Exploratory Data Analysis: intuition-oriented analysis by networks +manipulations in real time. + +Link Analysis: revealing the underlying structures of associations +between objects. + +Social Network Analysis: easy creation of social data connectors to +map community organizations and small-world networks. + +Biological Network analysis: representing patterns of biological data. + +Poster creation: scientific work promotion with hi-quality printable +maps. + +METRICS READY + +Centrality: used in sociology to indicate how well a node is +connected. Available: degree (power-law), betweenness, closeness. + +And more: density, path length, diameter, HITS, modularity, clustering +coefficient. + +TECHNOLOGY + +Ergonomic interface: no programming skills needed + +High-performance: built-in rendering engine. + +Native file formats: GDF (GUESS), GraphML (NodeXL), GML, NET (Pajek), +GEXF and more. + +Customizable by plugins: layouts, metrics, data sources, manipulation +tools, rendering presets and more. + +NOTE: Gephi's support for importing even non-trivial Graphviz dot is +totally broken, so do not rely on it. For dot, the graphviz package +is providing the gvedit tool. diff --git a/academic/flashqard/doinst.sh b/academic/gephi/doinst.sh index 4a25de5e6f..65c7e2eeb9 100644 --- a/academic/flashqard/doinst.sh +++ b/academic/gephi/doinst.sh @@ -7,4 +7,3 @@ if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 fi fi - diff --git a/academic/gephi/gephi.SlackBuild b/academic/gephi/gephi.SlackBuild new file mode 100644 index 0000000000..d9d650d503 --- /dev/null +++ b/academic/gephi/gephi.SlackBuild @@ -0,0 +1,88 @@ +#!/bin/bash + +# Slackware build script for gephi + +# Copyright 2023, Lockywolf +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gephi +VERSION=${VERSION:-0.10.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION-linux-x64.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} + -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + + +install -d -m 755 $PKG/usr/bin +install -d -m 755 $PKG/opt/$PRGNAM +cp -r . $PKG/opt/$PRGNAM +echo "#!/bin/bash +exec /opt/$PRGNAM/bin/gephi $@" > $PKG/usr/bin/$PRGNAM +chmod +x $PKG/usr/bin/$PRGNAM + +install -d -m0755 $PKG/usr/share/applications/ +install -m0644 $PKG/opt/$PRGNAM/flathub/org.gephi.Gephi.desktop $PKG/usr/share/applications/ +install -d -m0755 $PKG/usr/share/icons/hicolor/512x512/apps/ +install -m0644 $PKG/opt/$PRGNAM/flathub/gephi.png $PKG/usr/share/icons/hicolor/512x512/apps/ + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION + +cat $CWD/gephi-tutorial-quick_start.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/gephi-tutorial-quick_start.pdf + +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gephi/gephi.info b/academic/gephi/gephi.info new file mode 100644 index 0000000000..1d7443d07d --- /dev/null +++ b/academic/gephi/gephi.info @@ -0,0 +1,12 @@ +PRGNAM="gephi" +VERSION="0.10.1" +HOMEPAGE="https://gephi.org/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/gephi/gephi/releases/download/v0.10.1/gephi-0.10.1-linux-x64.tar.gz\ + https://gephi.org/tutorials/gephi-tutorial-quick_start.pdf" +MD5SUM_x86_64="b387916d8addb79935cff824b9973307\ + a5e956a201ac957a4acd09a3cdc06506" +REQUIRES="" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.gephi_2023-07-18@lockywolf.net" diff --git a/academic/gephi/slack-desc b/academic/gephi/slack-desc new file mode 100644 index 0000000000..881315966d --- /dev/null +++ b/academic/gephi/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gephi: gephi (The Open Graph Viz Platform) +gephi: +gephi: Gephi is the leading visualization and exploration software for all +gephi: kinds of graphs and networks. +gephi: +gephi: +gephi: +gephi: +gephi: +gephi: +gephi: diff --git a/academic/gerbv/doinst.sh b/academic/gerbv/doinst.sh index 4a25de5e6f..e924bab47c 100644 --- a/academic/gerbv/doinst.sh +++ b/academic/gerbv/doinst.sh @@ -8,3 +8,9 @@ if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then fi fi +if [ -e usr/share/glib-2.0/schemas ]; then + if [ -x /usr/bin/glib-compile-schemas ]; then + /usr/bin/glib-compile-schemas usr/share/glib-2.0/schemas >/dev/null 2>&1 + fi +fi + diff --git a/academic/gerbv/gerbv.SlackBuild b/academic/gerbv/gerbv.SlackBuild index c0dd769766..0b4d1094a2 100644 --- a/academic/gerbv/gerbv.SlackBuild +++ b/academic/gerbv/gerbv.SlackBuild @@ -2,27 +2,45 @@ # Slackware build script for gerbv -# Written by Felix Pfeifer (pfeifer [dot] felix [at] googlemail [dot] com) +# Copyright 2024 Juan M. Lasca juanmlasca@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +# Originally written by Felix Pfeifer (pfeifer.felix@googlemail.com) +# Thanks to Andrzej Telszewski for his suggestions cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gerbv -VERSION=${VERSION:-2.6.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-2.10.0} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -32,8 +50,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -61,7 +79,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; -CFLAGS="$SLKCFLAGS" \ +autoreconf -fi + +CFLAGS="$SLKCFLAGS -w -Wl,--allow-multiple-definition" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ @@ -71,21 +91,33 @@ CXXFLAGS="$SLKCFLAGS" \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --disable-update-desktop-database \ + --disable-static \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +# fix .desktop file: +sed -i '/^Encoding/d; s/^Categories.*/Categories=Science;Electronics;/' \ + $PKG/usr/share/applications/gerbv.desktop; + +gzip -9 ChangeLog COPYING + +rm -f */*.in */*.am + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - [ABCHINRT]*\ - $PKG/usr/doc/$PRGNAM-$VERSION + AUTHORS BUGS CONTRIBUTORS ChangeLog.gz COPYING.gz \ + HACKING NEWS README doc/ example/ \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install @@ -94,4 +126,3 @@ cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE - diff --git a/academic/gerbv/gerbv.info b/academic/gerbv/gerbv.info index 8e8e99d40d..2791874287 100644 --- a/academic/gerbv/gerbv.info +++ b/academic/gerbv/gerbv.info @@ -1,10 +1,10 @@ PRGNAM="gerbv" -VERSION="2.6.0" -HOMEPAGE="http://gerbv.gpleda.org/" -DOWNLOAD="http://downloads.sourceforge.net/gerbv/gerbv-2.6.0.tar.gz" -MD5SUM="44a37dd202bc60fab54cbc298a477572" +VERSION="2.10.0" +HOMEPAGE="https://gerbv.github.io/" +DOWNLOAD="https://github.com/gerbv/gerbv/archive/v2.10.0/gerbv-2.10.0.tar.gz" +MD5SUM="69c122c7fcba29ed9abae733419a913c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Felix Pfeifer" -EMAIL="pfeifer[dot]felix[at]googlemail[dot]com" +MAINTAINER="Juan M. Lasca" +EMAIL="juanmlasca@gmail.com" diff --git a/academic/getdp/Kernel_Operation__Broadcast.patch b/academic/getdp/Kernel_Operation__Broadcast.patch deleted file mode 100644 index 621e3e25aa..0000000000 --- a/academic/getdp/Kernel_Operation__Broadcast.patch +++ /dev/null @@ -1,11 +0,0 @@ -#diff a/Kernel/Operation_Broadcast.cpp b/Kernel/Operation_Broadcast.cpp -#--- a/Kernel/Operation_Broadcast.cpp -#+++ b/Kernel/Operation_Broadcast.cpp -@@ -5,6 +5,7 @@ - - #include <vector> - #include <string> -+#include <cstring> // for strncpy() - #include <sstream> - #include <stdio.h> - #include <stdlib.h> diff --git a/academic/getdp/README b/academic/getdp/README index 3dab37d132..4e131496bc 100644 --- a/academic/getdp/README +++ b/academic/getdp/README @@ -6,3 +6,13 @@ dimensions. The main feature of GetDP is the closeness between the input data defining discrete problems (written by the user in ASCII data files) and the symbolic mathematical expressions of these problems. + +Optional dependency: gmsh + +Note: +If you want to build Getdp with Gmsh support it is necessary to +install the Gmsh package first, but compiled with both static and +dynamic libraries. If you use the build script for Gmsh available at +SBo you just need to pass: +BUILDSTATICLIB=yes +prior to run gmsh.SlackBuild diff --git a/academic/getdp/getdp.SlackBuild b/academic/getdp/getdp.SlackBuild index edf57073d1..751b64a88c 100644 --- a/academic/getdp/getdp.SlackBuild +++ b/academic/getdp/getdp.SlackBuild @@ -1,7 +1,7 @@ #!/bin/bash # Slackware build script for getdp -# Copyright 2020 Fellype do Nascimento, Campinas, Brazil +# Copyright 2020-2022 Fellype do Nascimento, Guaratingueta, Brazil # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -23,7 +23,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=getdp -VERSION=${VERSION:-3.3.0} +VERSION=${VERSION:-3.5.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -77,9 +77,6 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Patch that allow compilation without a fail (credits to: DragonFlyBSD/DPorts) -patch -p1 < $CWD/Kernel_Operation__Broadcast.patch Kernel/Operation_Broadcast.cpp - mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr \ @@ -87,13 +84,14 @@ cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DENABLE_BUILD_SHARED=ON \ + -DENABLE_GMSH=ON \ -DENABLE_PETSC=OFF \ -DENABLE_SLEPC=OFF \ .. -# only demos/ and templates/ folders will be leaved in the /usr/share/getdp dir +# only demos/ and templates/ folders will be left in the /usr/share/getdp dir make -make install DESTDIR=$PKG +make -j1 install DESTDIR=$PKG cd - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ diff --git a/academic/getdp/getdp.info b/academic/getdp/getdp.info index 8b5b964589..bfacafe5f2 100644 --- a/academic/getdp/getdp.info +++ b/academic/getdp/getdp.info @@ -1,10 +1,10 @@ PRGNAM="getdp" -VERSION="3.3.0" +VERSION="3.5.0" HOMEPAGE="http://getdp.info/" -DOWNLOAD="http://getdp.info/src/getdp-3.3.0-source.tgz" -MD5SUM="0f3e4388bcecd454ff1a19fcfa5979ef" +DOWNLOAD="http://getdp.info/src/getdp-3.5.0-source.tgz" +MD5SUM="157d6604cc6a26ead0b0b4121216074a" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="arpack-ng OpenBLAS" +REQUIRES="arpack-ng OpenBLAS %README%" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/getfem/README b/academic/getfem/README new file mode 100644 index 0000000000..41f7a614a6 --- /dev/null +++ b/academic/getfem/README @@ -0,0 +1,22 @@ +GetFEM is an open source library based on collaborative development. +It aims to offer the most flexible framework for solving potentially +coupled systems of linear and nonlinear partial differential equations +with the finite element method. GetFEM is interfaced with some script +languages (Python, Octave, Scilab and Matlab) so that almost all of +the functionalities can be used just writing scripts. + +If you have matlab installed in your machine, you can also add support +to it by adding '--enable-matlab' to ./configure command + +Take a look at http://getfem.org/install/install_linux.html if you +build GetFEM with support to octave, scilab or matlab in order to make +those tools work properly. + +Optional dependencies are (if you add '--enable-FEATURE', e.g.: +--enable-octave, to ./configure command: + +- octave +- scilab +- qhull +- mumps +- metis diff --git a/academic/getfem/getfem.SlackBuild b/academic/getfem/getfem.SlackBuild new file mode 100644 index 0000000000..d4567aa2e7 --- /dev/null +++ b/academic/getfem/getfem.SlackBuild @@ -0,0 +1,114 @@ +#!/bin/bash + +# Slackware build script for GetFEM +# +# Copyright 2022, Fellype do Nascimento, Guaratingueta - Brazil +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=getfem +VERSION=${VERSION:-5.4.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +./configure \ + --prefix=/usr \ + --sysconfdir=/etc \ + --docdir=/usr/share/doc \ + --with-pic \ + --enable-python \ + --enable-shared \ + --enable-static=no \ + --mandir=/usr/man \ + --libdir=/usr/lib$LIBDIRSUFFIX + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS ChangeLog COPYING README $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# move getfem_toolbox dir to /usr/share/getfem +mkdir -p $PKG/usr/share/$PRGNAM +mv $PKG/usr/getfem_toolbox $PKG/usr/share/$PRGNAM/ + +# remove .la files +rm -f $PKG/usr/lib*/*.la + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/getfem/getfem.info b/academic/getfem/getfem.info new file mode 100644 index 0000000000..9a61fe097c --- /dev/null +++ b/academic/getfem/getfem.info @@ -0,0 +1,10 @@ +PRGNAM="getfem" +VERSION="5.4.2" +HOMEPAGE="https://getfem.org/" +DOWNLOAD="http://download-mirror.savannah.gnu.org/releases/getfem/stable/getfem-5.4.2.tar.gz" +MD5SUM="90ba2a270ec8c559796f2a7c90a79d32" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-scipy" +MAINTAINER="Fellype do Nascimento" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/getfem/slack-desc b/academic/getfem/slack-desc new file mode 100644 index 0000000000..275f3df7bf --- /dev/null +++ b/academic/getfem/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +getfem: getfem (finite element modeling software) +getfem: +getfem: GetFEM is an open source library based on collaborative development. +getfem: +getfem: It aims to offer the most flexible framework for solving potentially +getfem: coupled systems of linear and nonlinear partial differential +getfem: equations with the finite element method. +getfem: +getfem: For more information visit: http://getfem.org/ +getfem: +getfem: diff --git a/academic/ggobi/ggobi.SlackBuild b/academic/ggobi/ggobi.SlackBuild index f951fc056c..61f6523a37 100644 --- a/academic/ggobi/ggobi.SlackBuild +++ b/academic/ggobi/ggobi.SlackBuild @@ -4,10 +4,13 @@ # Written by Pedro Mendes pedro@gepasi.org # hereby put in the public domain +# 20220308 bkw: Modified by SlackBuilds.org: fix build on 15.0, +# by upgrading to v2.1.11. + cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ggobi -VERSION=${VERSION:-2.1.8} +VERSION=${VERSION:-2.1.11} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -20,9 +23,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -57,9 +57,9 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ CXXFLAGS="$SLKCFLAGS" \ CFLAGS="$SLKCFLAGS" \ @@ -74,9 +74,6 @@ CFLAGS="$SLKCFLAGS" \ --with-all-plugins \ --build=$ARCH-slackware-linux -# fix problem with graphviz plugin -patch -p1 < $CWD/ggobi-2.1.8-graphviz.patch - make make install-strip DESTDIR=$PKG make ggobirc @@ -86,10 +83,15 @@ cp ggobirc $PKG/etc/xdg/ggobi/ggobirc rm -f $PKG/usr/info/dir -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS COPYING CPLicense.txt ChangeLog INSTALL NEWS README \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +# 20220308 bkw: PDF docs go in the regular doc dir, we don't use /usr/share/doc +PKGDOC=$PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKGDOC +mv $PKG/usr/share/doc/$PRGNAM/* $PKGDOC +rm -rf $PKG/usr/share/doc +cp -a AUTHORS COPYING CPLicense.txt ChangeLog NEWS README $PKGDOC +cat $CWD/$PRGNAM.SlackBuild > $PKGDOC/$PRGNAM.SlackBuild + +rm -f $PKG/usr/lib*/*.la mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/ggobi/ggobi.info b/academic/ggobi/ggobi.info index 770af33fa2..b69169c2f4 100644 --- a/academic/ggobi/ggobi.info +++ b/academic/ggobi/ggobi.info @@ -1,8 +1,8 @@ PRGNAM="ggobi" -VERSION="2.1.8" +VERSION="2.1.11" HOMEPAGE="http://www.ggobi.org/" -DOWNLOAD="http://www.ggobi.org/downloads/ggobi-2.1.8.tar.bz2" -MD5SUM="0b07adffcf4379e819b1a26e4cd60d7b" +DOWNLOAD="http://ggobi.org/downloads/ggobi-2.1.11.tar.bz2" +MD5SUM="6e95e987f3a7b3f3d7ac4f4d0cd693e9" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/ghemical/fix_clang_ftbfs.patch b/academic/ghemical/fix_clang_ftbfs.patch new file mode 100644 index 0000000000..af3fd4f099 --- /dev/null +++ b/academic/ghemical/fix_clang_ftbfs.patch @@ -0,0 +1,37 @@ +Description: Fix FTBFS with clang instead of gcc +Bug-Debian: https://bugs.debian.org/756440 +Author: Alexander <sanek23994@gmail.com> +Last-Update: 2014-07-30 +--- a/src/project.h ++++ b/src/project.h +@@ -122,6 +122,14 @@ + graphical user interface. + */ + ++class project; ++ ++bool ReadGPR_OLD(project &, istream &, bool, bool = false); ///< this is for the very old version. ++bool ReadGPR_v100(project &, istream &, bool, bool = false); ///< this is for the version 1.00. ++bool ReadGPR_v110(project &, istream &, bool, bool = false); ///< this is for the version 1.10. ++/// This is an input function for the v1.11 ghemical file format. ++bool ReadGPR(project &, istream &, bool, bool = false); ++ + class project : + public custom_transformer_client, + public model +@@ -207,11 +215,11 @@ + + // methods for file I/O : ReadGPR and WriteGPR are friend functions so that it would be easier to "borrow" them elsewhere... + // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +- friend bool ReadGPR_OLD(project &, istream &, bool, bool = false); ///< this is for the very old version. +- friend bool ReadGPR_v100(project &, istream &, bool, bool = false); ///< this is for the version 1.00. +- friend bool ReadGPR_v110(project &, istream &, bool, bool = false); ///< this is for the version 1.10. ++ friend bool ReadGPR_OLD(project &, istream &, bool, bool); ///< this is for the very old version. ++ friend bool ReadGPR_v100(project &, istream &, bool, bool); ///< this is for the version 1.00. ++ friend bool ReadGPR_v110(project &, istream &, bool, bool); ///< this is for the version 1.10. + /// This is an input function for the v1.11 ghemical file format. +- friend bool ReadGPR(project &, istream &, bool, bool = false); ++ friend bool ReadGPR(project &, istream &, bool, bool); + + friend void WriteGPR_v100(project &, ostream &); ///< this is for the version 1.00. + /// This is an output function for the v1.11 ghemical file format. diff --git a/academic/ghemical/ghemical.SlackBuild b/academic/ghemical/ghemical.SlackBuild index 36ea7acff7..18c464ad65 100644 --- a/academic/ghemical/ghemical.SlackBuild +++ b/academic/ghemical/ghemical.SlackBuild @@ -61,6 +61,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +# Thanks Debian! +patch -p1 < $CWD/fix_clang_ftbfs.patch + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}" \ diff --git a/academic/glpk/glpk.SlackBuild b/academic/glpk/glpk.SlackBuild index 8d67f2a0d2..8c63ea3f9e 100644 --- a/academic/glpk/glpk.SlackBuild +++ b/academic/glpk/glpk.SlackBuild @@ -96,6 +96,9 @@ LDFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a AUTHORS COPYING ChangeLog INSTALL NEWS README THANKS doc examples \ $PKG/usr/doc/$PRGNAM-$VERSION @@ -106,6 +109,8 @@ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/glvis/README b/academic/glvis/README new file mode 100644 index 0000000000..acb344d7cb --- /dev/null +++ b/academic/glvis/README @@ -0,0 +1,2 @@ + GLVis is a lightweight tool for accurate and flexible finite element +visualization. diff --git a/academic/glvis/doinst.sh b/academic/glvis/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/glvis/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/glvis/glvis.SlackBuild b/academic/glvis/glvis.SlackBuild new file mode 100644 index 0000000000..62309cb23d --- /dev/null +++ b/academic/glvis/glvis.SlackBuild @@ -0,0 +1,128 @@ +#!/bin/bash + +# Slackware build script for GLVIs + +# Copyright 2022 William PC, Seattle (USA) +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=glvis +VERSION=${VERSION:-4.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# create a shared library +sed -i '270s/$/ -fPIC/' makefile +sed -i '278s/.a/.so/' makefile +sed -i '304i\\nlib/libglvis.so: $(OBJECT_FILES)\ +\t$(CCC) -shared -o $@ $^ $(GLVIS_FLAGS) $(LIBS)' makefile + +# fix install permissions +sed -i 's/-m 750/-m 755/' makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make CONFIG_MK=/usr/share/mfem-4.5/config.mk +make install \ + CONFIG_MK=/usr/share/mfem-4.5/config.mk \ + PREFIX=$PKG/usr/bin + +# install lib +install -d $PKG/usr/lib${LIBDIRSUFFIX} +install -m 755 lib/libglvis.so $PKG/usr/lib${LIBDIRSUFFIX} + +# install other files +install -d $PKG/usr/share/$PRGNAM +install -m 644 share/logo.ico $PKG/usr/share/$PRGNAM +install -d $PKG/usr/share/applications +install -m 644 $CWD/glvis.desktop $PKG/usr/share/applications + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CHANGELOG CONTRIBUTING.md LICENSE NOTICE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/glvis/glvis.desktop b/academic/glvis/glvis.desktop new file mode 100644 index 0000000000..0b65734a7e --- /dev/null +++ b/academic/glvis/glvis.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Name=GLVIs +Comment=Lightweight OpenGL finite element visualization +TryExec=/usr/bin/glvis +Exec=/usr/bin/glvis +Icon=/usr/share/glvis/logo.ico +Terminal=true +Type=Application +Categories=Education;Science;Math; +StartupNotify=false diff --git a/academic/glvis/glvis.info b/academic/glvis/glvis.info new file mode 100644 index 0000000000..0022d2c170 --- /dev/null +++ b/academic/glvis/glvis.info @@ -0,0 +1,10 @@ +PRGNAM="glvis" +VERSION="4.2" +HOMEPAGE="https://glvis.org" +DOWNLOAD="https://github.com/GLVis/glvis/archive/v4.2/glvis-4.2.tar.gz" +MD5SUM="a228c65c285e7a66e38b1ec2f2812842" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="glm mfem" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/glvis/slack-desc b/academic/glvis/slack-desc new file mode 100644 index 0000000000..3336f83588 --- /dev/null +++ b/academic/glvis/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +glvis: glvis (lightweight finite element visualization tool) +glvis: +glvis: +glvis: +glvis: GLVis is a lightweight tool for accurate and flexible finite +glvis: element visualization. +glvis: +glvis: +glvis: +glvis: +glvis: diff --git a/academic/gmsh/README b/academic/gmsh/README index e2980522f6..cbc93a7222 100644 --- a/academic/gmsh/README +++ b/academic/gmsh/README @@ -20,3 +20,11 @@ the documentation of the C++, C, Python and Julia API. The source code repository contains many examples written using both the built-in script language (see e.g. the tutorials and demos) and the API. + +Note: +If you want to build Getdp with Gmsh support is necessary to compile +also a static gmsh library (libgmsh.a). This can be done by passing +BUILDSTATICLIB=yes +prior to run gmsh.SlackBuild +In that case, you will also need to recompile Getdp when Gmsh is +updated. diff --git a/academic/gmsh/doinst.sh b/academic/gmsh/doinst.sh new file mode 100644 index 0000000000..8a5ffa8af5 --- /dev/null +++ b/academic/gmsh/doinst.sh @@ -0,0 +1,20 @@ + +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi + +if [ -e usr/share/glib-2.0/schemas ]; then + if [ -x /usr/bin/glib-compile-schemas ]; then + /usr/bin/glib-compile-schemas usr/share/glib-2.0/schemas >/dev/null 2>&1 + fi +fi diff --git a/academic/gmsh/gmsh.SlackBuild b/academic/gmsh/gmsh.SlackBuild index 32d8a75d81..e318452d91 100644 --- a/academic/gmsh/gmsh.SlackBuild +++ b/academic/gmsh/gmsh.SlackBuild @@ -1,7 +1,7 @@ #!/bin/bash # Slackware build script for gmsh -# Copyright 2020 Fellype do Nascimento, Campinas, Brazil +# Copyright 2020-2024 Fellype do Nascimento, Guaratingueta, Brazil # # Based on SlackBuild by Loris Vincenzi and PKGBUILD for gmsh at AUR # @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gmsh -VERSION=${VERSION:-4.5.4} +VERSION=${VERSION:-4.12.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -79,17 +79,53 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# In order build getdp with gmsh support it is needed to build +# a small static Gmsh library first +# do it using BUILDSTATICLIB=yes ./gmsh.SlackBuild +# default is BUILDSTATICLIB=no +if [ "${BUILDSTATICLIB:-no}" = "yes" ]; then + echo " " + echo "** building a static library for gmsh **" + echo " " + mkdir lib + cd lib + cmake -DDEFAULT=0 \ + -DENABLE_PARSER=1 \ + -DENABLE_POST=1 \ + -DENABLE_ANN=1 \ + -DENABLE_BLAS_LAPACK=1 \ + -DENABLE_BUILD_LIB=1 \ + -DENABLE_PRIVATE_API=1 \ + -DENABLE_MED=OFF \ + -DENABLE_CGNS=OFF \ + -DCMAKE_INSTALL_PREFIX:PATH=/usr \ + -DCMAKE_INSTALL_DOCDIR:PATH=/usr/share/gmsh \ + .. + make lib + make install/fast DESTDIR=$PKG/ + cd .. + echo " " + echo "** finished building the static library **" + echo " " +fi + mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DCMAKE_INSTALL_DOCDIR:PATH=/usr/share/gmsh \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ - -DENABLE_BUILD_SHARED=ON \ + -DENABLE_BLAS_LAPACK=1 \ + -DENABLE_BUILD_SHARED=1 \ + -DENABLE_PRIVATE_API=1 \ -DENABLE_PETSC=OFF \ -DENABLE_SLEPC=OFF \ + -DENABLE_MED=OFF \ + -DENABLE_CGNS=OFF \ .. -# only demos/ and tutorial/ folders will be leaved in the /usr/share/gmsh dir +# only demos/ and tutorial/ folders will be left in the /usr/share/gmsh dir +# TODO: Solve runtime issues with HDF5 - this is the reason for disabling +# MED and CGNS in gmsh 4.12.x make make install DESTDIR=$PKG @@ -100,7 +136,6 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr install -d "$PKG/usr/share/pixmaps/$PRGNAM" install -m644 utils/icons/*.png "$PKG/usr/share/pixmaps/$PRGNAM" -install -D -m644 utils/icons/solid_32x32.png "$PKG/usr/share/icons/$PRGNAM.png" install -D -m644 utils/icons/$PRGNAM.svg "$PKG/usr/share/icons/hicolor/scalable/apps/$PRGNAM.svg" desktop-file-install --dir="$PKG/usr/share/applications" "$CWD/$PRGNAM.desktop" @@ -116,10 +151,13 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a CHANGELOG.txt CREDITS.txt LICENSE.txt README.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild rm $PKG/usr/share/gmsh/*.txt -rm -Rf $PKG/tmp + +# Remove onelab.py launcher from /usr/bin, since we are not using it here +rm $PKG/usr/bin/onelab.py mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gmsh/gmsh.desktop b/academic/gmsh/gmsh.desktop index ad08eb309c..16f09b07af 100644 --- a/academic/gmsh/gmsh.desktop +++ b/academic/gmsh/gmsh.desktop @@ -4,7 +4,6 @@ Name=Gmsh Comment=Automatic 3D finite element mesh generator Icon=gmsh Exec=gmsh -Encoding=UTF-8 Terminal=false Type=Application -Categories=Education;Science;Math; +Categories=Science; diff --git a/academic/gmsh/gmsh.info b/academic/gmsh/gmsh.info index f628e2a4c5..f56d44b835 100644 --- a/academic/gmsh/gmsh.info +++ b/academic/gmsh/gmsh.info @@ -1,10 +1,10 @@ PRGNAM="gmsh" -VERSION="4.5.4" -HOMEPAGE="http://gmsh.info/" -DOWNLOAD="http://gmsh.info/src/gmsh-4.5.4-source.tgz" -MD5SUM="dc225d64508468107eda763915d9c959" +VERSION="4.12.2" +HOMEPAGE="https://gmsh.info/" +DOWNLOAD="https://gmsh.info/src/gmsh-4.12.2-source.tgz" +MD5SUM="2c99a1b94d1a4c597b8febb6e9b02f5b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="fltk lapack med OpenCASCADE" +REQUIRES="fltk lapack OpenCASCADE" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/gmsh/slack-desc b/academic/gmsh/slack-desc index 35305eed9d..3fe2e76a5d 100644 --- a/academic/gmsh/slack-desc +++ b/academic/gmsh/slack-desc @@ -11,7 +11,7 @@ gmsh: gmsh: Gmsh is an automatic three-dimensional finite element mesh generator gmsh: with built-in pre- and post-processing facilities. gmsh: -gmsh: Gmsh is copyright (C) 1997-2019 C. Geuzaine and J.-F. Remacle, +gmsh: Gmsh is copyright (C) 1997- C. Geuzaine and J.-F. Remacle, gmsh: and is distributed under the terms of the GNU General Public gmsh: License, Version 2 or later, with an exception to allow for gmsh: easier linking with external libraries. diff --git a/academic/gp2fasta/gp2fasta.SlackBuild b/academic/gp2fasta/gp2fasta.SlackBuild index d9e0168c2f..ce052827b0 100644 --- a/academic/gp2fasta/gp2fasta.SlackBuild +++ b/academic/gp2fasta/gp2fasta.SlackBuild @@ -36,7 +36,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -54,8 +54,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -86,6 +86,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh qmake -project qmake diff --git a/academic/gp2fasta/gp2fasta.info b/academic/gp2fasta/gp2fasta.info index 04cb8295c4..c4522ea239 100644 --- a/academic/gp2fasta/gp2fasta.info +++ b/academic/gp2fasta/gp2fasta.info @@ -5,6 +5,6 @@ DOWNLOAD="http://gp2fasta.netmark.pl/gp2fasta.zip" MD5SUM="f1124fb098c531154f4e6dcf7c9d174d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="qt4" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/gplates/README b/academic/gplates/README new file mode 100644 index 0000000000..8ba9347278 --- /dev/null +++ b/academic/gplates/README @@ -0,0 +1,45 @@ +GPlates is free and open source desktop software for the interactive +visualisation of plate tectonics for research, educational, +professional, and other purposes. It is developed by an international +team of researchers and software developers who refer to internal +divisions of the University of Sidney and Caltech (California +Institute of Technology). + +GPlates offers a novel combination of interactive plate tectonic +reconstructions, geographic information system (GIS) functionality and +raster data visualisation. GPlates enables both the visualisation and +the manipulation of plate tectonic reconstructions and associated data +through geological time. +GPlates can be used to handle and visualise data in a variety of +geometries and formats, including raster data, to link plate kinematics +to geodynamic models, to serve as an interactive client in a +grid-computing network, to facilitate the production of high-quality +paleo-geographic maps. + +GPlates requires in runtime pre-packed datasets provided by the project +or other datasets. By default, this slackbuild does not install any +dataset, since the download of project's data source is allowed only by +using a web browser. Standard procedure compliant with curl or wget is +not allowed. + +If you want to install the data source using this slackbuild follow the +download instructions reported in README.SBo file and save the archive +gplates_2.3.0_geodata.zip in the same directory of the slackbuild +script. The slackbuild autodetect this archive and if found will +include the datasets in the installation package. Datasets will be +installed in the directory /usr/share/gplates/GeoData + +Alternative datasets are not handled by this slackbuild. If you want +to use other datasets you have to add them in local or shared +directories and apply them using the tools of the application GUI. + +CGAL library is a required dependency, but the build can also use the +alternative header-only library CGAL5 if installed in your system. + +Published works powered with GPlates should include the following +citation: + +Müller, R. D., Cannon, J., Qin, X., Watson, R. J., Gurnis, M., +Williams, S., et al. 2018. GPlates: Building a virtual Earth through +deep time. Geochemistry, Geophysics, Geosystems, 19. +doi:10.1029/2018GC007584. diff --git a/academic/gplates/README.SBo b/academic/gplates/README.SBo new file mode 100644 index 0000000000..eb20e6214f --- /dev/null +++ b/academic/gplates/README.SBo @@ -0,0 +1,32 @@ +Although this is not strictly required for build GPlates, since +alternative datasets can be used, you would install the data source +provided by EarthByte, the official maintainer of GPlates project at +the same time of the build of GPlates package. +Unfortunately, this dataset is not released in the github repository +of GPlates and can be downloaded only using a Web browser, not with +other applications like curl or wget. + +If you want install this dataset (strongly recommended) please follow +these instructions: + +1. Connect to the webpage: + https://www.earthbyte.org/download-gplates-2-3/ + +2. In the section "Download file links" select the option from the + Download selection list: + gplates_2.3.0_geodata.zip + + (Warning: do not select the application source, because the + tarball will not handled by the slackbuild script. Use the tarball + downloaded from the github repository of GPlates) + +3. Fill the form notifying: + - your name (OPTIONAL: leave empty for anonymous download) + - your email address (OPTIONAL: leave empty for anonymous download) + - select your purposes (REQUIRED) + +4. Click the button "Get download link(s)" + +After the above steps, you will get at the bottom of the page the +hardlink to download the geodata archive. This must be saved in the +same directory of the slackbuild script. diff --git a/academic/gplates/boost-placeholders.patch b/academic/gplates/boost-placeholders.patch new file mode 100644 index 0000000000..aefc26e64f --- /dev/null +++ b/academic/gplates/boost-placeholders.patch @@ -0,0 +1,35 @@ +--- gplates_2.3.0_src/src/gui/TopologyTools.cc 2021-07-05 07:28:32.000000000 +0200 ++++ gplates_2.3.0_src-fixed/src/gui/TopologyTools.cc 2022-04-10 16:00:01.000000000 +0200 +@@ -39,4 +39,6 @@ + #include <boost/none.hpp> + #include <boost/numeric/conversion/cast.hpp> ++#include <boost/bind/placeholders.hpp> ++using namespace boost::placeholders; + + #include <QtDebug> +--- gplates_2.3.0_src/src/qt-widgets/ViewportWindow.cc 2021-08-05 07:40:35.000000000 +0200 ++++ gplates_2.3.0_src-fixed/src/qt-widgets/ViewportWindow.cc 2022-04-10 16:10:01.000000000 +0200 +@@ -37,4 +37,6 @@ + #include <boost/foreach.hpp> + #include <boost/bind/bind.hpp> ++#include <boost/bind/placeholders.hpp> ++using namespace boost::placeholders; + + #include <QActionGroup> +--- gplates_2.3.0_src/src/presentation/ReconstructionGeometryRenderer.cc 2021-08-05 07:40:35.000000000 +0200 ++++ gplates_2.3.0_src-fixed/src/presentation/ReconstructionGeometryRenderer.cc 2022-04-10 16:20:01.000000000 +0200 +@@ -30,4 +30,6 @@ + #include <boost/bind/bind.hpp> + #include <boost/foreach.hpp> ++#include <boost/bind/placeholders.hpp> ++using namespace boost::placeholders; + + #include "ReconstructionGeometryRenderer.h" +--- gplates_2.3.0_src/src/presentation/VisualLayerRegistry.cc 2021-08-05 07:40:35.000000000 +0200 ++++ gplates_2.3.0_src-fixed/src/presentation/VisualLayerRegistry.cc 2022-04-10 16:30:01.000000000 +0200 +@@ -27,4 +27,6 @@ + #include <boost/bind/bind.hpp> + #include <boost/foreach.hpp> ++#include <boost/bind/placeholders.hpp> ++using namespace boost::placeholders; + #include <QPixmap> diff --git a/academic/QtiPlot/doinst.sh b/academic/gplates/doinst.sh index 9a8ded3c60..aea0f894eb 100644 --- a/academic/QtiPlot/doinst.sh +++ b/academic/gplates/doinst.sh @@ -5,3 +5,9 @@ fi if [ -x /usr/bin/update-mime-database ]; then /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/gplates/gplates.SlackBuild b/academic/gplates/gplates.SlackBuild new file mode 100644 index 0000000000..e237b951ad --- /dev/null +++ b/academic/gplates/gplates.SlackBuild @@ -0,0 +1,156 @@ +#!/bin/bash + +# Slackware build script for gplates + +# Copyright 2022-2024 Giancarlo Dessi, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gplates +SRCNAM=GPlates-GPlates +VERSION=${VERSION:-2.3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +GEODATADIR=GeoData +GEODATAVERSION=$VERSION.0 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +rm -rf $GEODATADIR +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz + +# Detect if GeoData archive if present +if [ -f $CWD/gplates_${GEODATAVERSION}_geodata.zip ]; then + echo "*********************************************************" + echo "* GeoData source found! This slackbuild will include in *" + echo "* the install package the official datasets released by *" + echo "* the EarthByte project. *" + echo "* *" + echo "* Remember that you can also use other compatible *" + echo "* datasets. *" + echo "*********************************************************" + + withGeoData=" -DGPLATES_INSTALL_GEO_DATA=true \ + -DGPLATES_INSTALL_GEO_DATA_DIR=$TMP/$GEODATADIR " + unzip $CWD/gplates_${GEODATAVERSION}_geodata.zip -d $TMP + + +else + echo "*********************************************************" + echo "* WARNING! GeoData source released by EarthByte project *" + echo "* not found. This slackbuild will not include datasets *" + echo "* in the install package but only the application. *" + echo "* *" + echo "* Remember that GPlates requires compatible datasets *" + echo "* that you have to use in runtime. *" + echo "*********************************************************" + + withGeoData=" -DGPLATES_INSTALL_GEO_DATA=false " +fi + +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# This fix errors given by gcc 11 or earlier compilers +patch -p1 < $CWD/boost-placeholders.patch + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + $withGeoData \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +mv $PKG/usr/share/man $PKG/usr/man + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +# Include application icon and desktop entry +mkdir -p $PKG/usr/share/icons/hicolor/160x160/apps +cp -a src/qt-resources/GPlates-icon-160x160-opaque.png \ + $PKG/usr/share/icons/hicolor/160x160/apps/gplates.png + +mkdir -p $PKG/usr/share/applications +cp -a $CWD/gplates.desktop $PKG/usr/share/applications +chown root:root $PKG/usr/share/applications/gplates.desktop + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS CHANGELOG COPYING CREDITS README $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gplates/gplates.desktop b/academic/gplates/gplates.desktop new file mode 100644 index 0000000000..249b8af64b --- /dev/null +++ b/academic/gplates/gplates.desktop @@ -0,0 +1,21 @@ +[Desktop Entry] +Type=Application +Name=GPlates +GenericName=Plate tectonics program +GenericName[de]=Programm der Plattentektonik +GenericName[es]=Programa de placas tectónicas +GenericName[fr]=Programme des plaques tectoniques +GenericName[it]=Programma sulle placche tettoniche +GenericName[pt]=Programa de placas tectônicas +Comment=Interactive visualisation of plate tectonics +Comment[de]=Interaktive Visualisierung von tektonischen Platten +Comment[es]=Visualización interactiva de placas tectónicas +Comment[fr]=Visualisation interactive des plaques tectoniques +Comment[it]=Visualizzazione interattiva delle placche tettoniche +Comment[pt]=Visualização interativa de placas tectônicas +Exec=gplates %f +Icon=/usr/share/icons/hicolor/160x160/apps/gplates.png +Terminal=false +Categories=Qt;Education;Science;Geology; +StartupNotify=true +MimeType=application/x-gproj;text/gpml;text/grot; diff --git a/academic/gplates/gplates.info b/academic/gplates/gplates.info new file mode 100644 index 0000000000..c465138289 --- /dev/null +++ b/academic/gplates/gplates.info @@ -0,0 +1,10 @@ +PRGNAM="gplates" +VERSION="2.3" +HOMEPAGE="https://www.gplates.org" +DOWNLOAD="https://github.com/GPlates/GPlates/archive/GPlates-2.3/GPlates-GPlates-2.3.tar.gz" +MD5SUM="f6d3db99c7388615019f05a87d838e1f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="CGAL gdal python3-numpy qwt" +MAINTAINER="Giancarlo Dessi" +EMAIL="slack@giand.it" diff --git a/academic/gplates/slack-desc b/academic/gplates/slack-desc new file mode 100644 index 0000000000..ec6094b579 --- /dev/null +++ b/academic/gplates/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gplates: gplates (interactive visualisation of plate tectonics) +gplates: +gplates: GPlates is a desktop application for the interactive visualisation of +gplates: plate tectonics. It offers combination of interactive plate tectonic +gplates: reconstructions, geographic information system (GIS) functionality +gplates: and raster data visualisation. +gplates: +gplates: +gplates: Home page: https://www.gplates.org +gplates: +gplates: diff --git a/academic/gpredict/gpredict.SlackBuild b/academic/gpredict/gpredict.SlackBuild index bcef232014..4f6d1c7981 100644 --- a/academic/gpredict/gpredict.SlackBuild +++ b/academic/gpredict/gpredict.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gpredict -VERSION=${VERSION:-2.3} +VERSION=${VERSION:-2.2.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -60,6 +60,9 @@ elif [ "$ARCH" = "i686" ]; then elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" LIBDIRSUFFIX="" diff --git a/academic/gpredict/gpredict.info b/academic/gpredict/gpredict.info index dfafad0f3f..1b08c53140 100644 --- a/academic/gpredict/gpredict.info +++ b/academic/gpredict/gpredict.info @@ -1,8 +1,8 @@ PRGNAM="gpredict" -VERSION="2.3" +VERSION="2.2.1" HOMEPAGE="http://gpredict.oz9aec.net" -DOWNLOAD="https://github.com/csete/gpredict/archive/v2.3/gpredict-2.3.tar.gz" -MD5SUM="58081bc4d55298b941c1f30f334fa6ca" +DOWNLOAD="https://github.com/csete/gpredict/archive/v2.2.1/gpredict-2.2.1.tar.gz" +MD5SUM="1e947f195c7182a52a2984c35594fef8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="goocanvas2 hamlib" diff --git a/academic/grace/grace.info b/academic/grace/grace.info index 2ba34f78e3..1784546f10 100644 --- a/academic/grace/grace.info +++ b/academic/grace/grace.info @@ -1,7 +1,7 @@ PRGNAM="grace" VERSION="5.1.25" -HOMEPAGE="http://plasma-gate.weizmann.ac.il/Grace/" -DOWNLOAD="ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/grace-5.1.25.tar.gz" +HOMEPAGE="https://plasma-gate.weizmann.ac.il/Grace/" +DOWNLOAD="https://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/grace-5.1.25.tar.gz" MD5SUM="c0482b1f18b113192946a96f5ff35a4d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/gresistor/gresistor.SlackBuild b/academic/gresistor/gresistor.SlackBuild index 7271b8c13d..9aba26dce9 100644 --- a/academic/gresistor/gresistor.SlackBuild +++ b/academic/gresistor/gresistor.SlackBuild @@ -13,7 +13,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -28,18 +28,18 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README" -if [ $ARCH = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" -elif [ $ARCH = "i686" ]; then +elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" LIBDIRSUFFIX="" -elif [ $ARCH = "x86_64" ]; then +elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" else diff --git a/academic/gretl/gretl.SlackBuild b/academic/gretl/gretl.SlackBuild index 43cf7a8c8c..d6a8650813 100644 --- a/academic/gretl/gretl.SlackBuild +++ b/academic/gretl/gretl.SlackBuild @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gretl -VERSION=${VERSION:-2017c} -BUILD=${BUILD:-1} +VERSION=${VERSION:-2022a} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -90,7 +90,7 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --disable-static \ --build=$ARCH-slackware-linux -make -j1 +make make -j1 install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ @@ -98,14 +98,16 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr mv $PKG/usr/share/man $PKG/usr find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/share/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a README README.audio COPYING INSTALL README.win32 $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README COPYING INSTALL README.win32 $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cp $CWD/$PRGNAM.png $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.png cp $CWD/*.pdf $PKG/usr/doc/$PRGNAM-$VERSION/ +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/doinst.sh > $PKG/install/doinst.sh cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/gretl/gretl.info b/academic/gretl/gretl.info index 6e21f6923f..a46978b95e 100644 --- a/academic/gretl/gretl.info +++ b/academic/gretl/gretl.info @@ -1,14 +1,14 @@ PRGNAM="gretl" -VERSION="2017c" -HOMEPAGE="http://gretl.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/gretl/gretl-2017c.tar.xz \ - http://ponce.cc/slackware/sources/repo/gretl-ref.pdf \ - http://ponce.cc/slackware/sources/repo/gretl-guide.pdf" -MD5SUM="a785bbdbfce1306a2366235b5659e289 \ - d6adb54ba9247b049a5c3dc7e442b37a \ - f8f058a9b43db33bedefedee4bf461d4" +VERSION="2022a" +HOMEPAGE="https://gretl.sourceforge.net" +DOWNLOAD="https://downloads.sourceforge.net/gretl/gretl-2022a.tar.xz \ + https://ponce.cc/slackware/sources/repo/gretl/2022a/gretl-ref.pdf \ + https://ponce.cc/slackware/sources/repo/gretl/2022a/gretl-guide.pdf" +MD5SUM="21ca11178c3373222944daebdd5f1612 \ + faa9858bb8fb516a882aa28e365e99f8 \ + 2b995eeb8a82b7962e2e279c3a457625" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="lapack unixODBC" +REQUIRES="lapack" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/gromacs/README b/academic/gromacs/README new file mode 100644 index 0000000000..a49f531bd4 --- /dev/null +++ b/academic/gromacs/README @@ -0,0 +1,20 @@ +GROMACS is a versatile package to perform molecular dynamics, i.e. +simulate the Newtonian equations of motion for systems with hundreds +to millions of particles and is a community-driven project. + +It is primarily designed for biochemical molecules like proteins, +lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the +nonbonded interactions (that usually dominate simulations) many groups +are also using it for research on non-biological systems, e.g. +polymers and fluid dynamics. + + +Optional dependences: +For run-time detection of hardware capabilities set HWLOC=yes. This +requires hwloc. +To enable MPI set PARALLEL=yes. This requires a MPI implementation +either openmpi or mpich. +For enabling CUDA set CUDA=yes. This requires the CUDA SDK. +To enable OpenCL set OPENCL=yes. This requires a OpenCL +implementation. diff --git a/academic/gromacs/gromacs.SlackBuild b/academic/gromacs/gromacs.SlackBuild new file mode 100644 index 0000000000..aaa0ac7022 --- /dev/null +++ b/academic/gromacs/gromacs.SlackBuild @@ -0,0 +1,144 @@ +#!/bin/bash + +# Slackware build script for gromacs + +# Copyright 2022 William PC - Seattle (USA) +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gromacs +VERSION=${VERSION:-2021.6} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION-Source +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# Enable run-time detection of hardware capabilities +if [ "${HWLOC:-no}" == "yes" ]; then + OPT_DEPS="$OPT_DEPS -DGMX_HWLOC=ON" +fi + +# Use CUDA SDK. +if [ "${CUDA:-no}" == "yes" ]; then + OPT_DEPS="$OPT_DEPS -DGMX_GPU=CUDA" +fi + +# Use an OpenCL implementation. +if [ "${OPENCL:-no}" == "yes" ]; then + OPT_DEPS="$OPT_DEPS -DGMX_GPU=OpenCL" +fi + +CFGSERIAL="-DGMX_MPI=OFF" + +CFGPARALLEL="-DGMX_MPI=ON" + +CFGGROMACS=$CFGSERIAL +BUILDDIR=build-serial + +if [ "${PARALLEL:-no}" == "yes" ]; then + CFGGROMACS=$CFGPARALLEL + BUILDDIR=build-parallel +fi + + rm -fr $BUILDDIR + mkdir -p $BUILDDIR + cd $BUILDDIR + + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/opt/$PRGNAM \ + $CFGGROMACS \ + $OPT_DEPS \ + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_BUILD_TYPE=RELEASE .. + + make +# make check + make install DESTDIR=$PKG +cd .. + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -name perllocal.pod -o -name ".packlist" -o -name "*.bs" | xargs rm -f || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a {AUTHORS,COPYING,README} $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gromacs/gromacs.info b/academic/gromacs/gromacs.info new file mode 100644 index 0000000000..f800414e54 --- /dev/null +++ b/academic/gromacs/gromacs.info @@ -0,0 +1,10 @@ +PRGNAM="gromacs" +VERSION="2021.6" +HOMEPAGE="https://www.gromacs.org" +DOWNLOAD="https://ftp.gromacs.org/gromacs/gromacs-2021.6.tar.gz" +MD5SUM="ed1bdc2a634413dfdd5a7c0be82f6a9d" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/gromacs/slack-desc b/academic/gromacs/slack-desc new file mode 100644 index 0000000000..606601ed62 --- /dev/null +++ b/academic/gromacs/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gromacs: gromacs (gromacs project) +gromacs: +gromacs: GROMACS is a versatile package to perform molecular dynamics, i.e. +gromacs: simulate the Newtonian equations of motion for systems with hundreds +gromacs: to millions of particles and is a community-driven project. +gromacs: +gromacs: +gromacs: +gromacs: +gromacs: +gromacs: diff --git a/academic/grpn/grpn.SlackBuild b/academic/grpn/grpn.SlackBuild index 1c44619689..f0a9c04743 100644 --- a/academic/grpn/grpn.SlackBuild +++ b/academic/grpn/grpn.SlackBuild @@ -16,7 +16,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -34,8 +34,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/gspiceui/gspiceui.SlackBuild b/academic/gspiceui/gspiceui.SlackBuild index c00b034973..2b5f7956fb 100644 --- a/academic/gspiceui/gspiceui.SlackBuild +++ b/academic/gspiceui/gspiceui.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gspiceui -VERSION=${VERSION:-1.2.36} +VERSION=${VERSION:-1.2.87} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/gspiceui/gspiceui.info b/academic/gspiceui/gspiceui.info index d2d260e790..223171695c 100644 --- a/academic/gspiceui/gspiceui.info +++ b/academic/gspiceui/gspiceui.info @@ -1,8 +1,8 @@ PRGNAM="gspiceui" -VERSION="1.2.36" +VERSION="1.2.87" HOMEPAGE="http://users.tpg.com.au/micksw012/gspiceui.html" -DOWNLOAD="https://sourceforge.net/projects/gspiceui/files/gSpiceUI/gspiceui-v1.2.36/gspiceui-v1.2.36.tar.gz" -MD5SUM="a385028952ada5aa69acdb7298332c8c" +DOWNLOAD="https://sourceforge.net/projects/gspiceui/files/gSpiceUI/gspiceui-v1.2.87/gspiceui-v1.2.87.tar.gz" +MD5SUM="ae580ac1665674fda3b7029392695157" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="pangox-compat wxGTK3" diff --git a/academic/gtkwave/gtkwave.SlackBuild b/academic/gtkwave/gtkwave.SlackBuild index c6b008729b..1c4fbb4a14 100644 --- a/academic/gtkwave/gtkwave.SlackBuild +++ b/academic/gtkwave/gtkwave.SlackBuild @@ -6,14 +6,14 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gtkwave -VERSION=${VERSION:-3.3.51} +VERSION=${VERSION:-3.3.111} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -31,8 +31,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/gtkwave/gtkwave.info b/academic/gtkwave/gtkwave.info index c76491fcc6..b027e7ff05 100644 --- a/academic/gtkwave/gtkwave.info +++ b/academic/gtkwave/gtkwave.info @@ -1,8 +1,8 @@ PRGNAM="gtkwave" -VERSION="3.3.51" +VERSION="3.3.111" HOMEPAGE="http://gtkwave.sourceforge.net/" -DOWNLOAD="http://gtkwave.sourceforge.net/gtkwave-3.3.51.tar.gz" -MD5SUM="7214a0358bdeadbbe305dfd6eeced828" +DOWNLOAD="http://gtkwave.sourceforge.net/gtkwave-3.3.111.tar.gz" +MD5SUM="ec9978cc21582ccb89b844e0abfc9b94" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/gtypist/gtypist.SlackBuild b/academic/gtypist/gtypist.SlackBuild index 49e7087d86..b23279fa52 100644 --- a/academic/gtypist/gtypist.SlackBuild +++ b/academic/gtypist/gtypist.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for gtypist # Copyright 2007-2012 Grigorios Bouzakis <grbzks@imap.cc> -# Copyright 2014 Aaditya Bagga <aaditya_gnulinux@zoho.com> +# Copyright 2014 Aaditya <aaditya_gnulinux@zoho.com> # All rights reserved. # # Permission to use, copy, modify, and distribute this software for any purpose @@ -30,7 +30,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -48,8 +48,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/gtypist/gtypist.info b/academic/gtypist/gtypist.info index 5e318927d7..fbcdbb4e74 100644 --- a/academic/gtypist/gtypist.info +++ b/academic/gtypist/gtypist.info @@ -6,5 +6,5 @@ MD5SUM="010824327ebbc0e01626da2b50b0efaf" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Aaditya Bagga" +MAINTAINER="Aaditya" EMAIL="aaditya_gnulinux@zoho.com" diff --git a/academic/gwyddion/README b/academic/gwyddion/README index f54770136f..06564ec378 100644 --- a/academic/gwyddion/README +++ b/academic/gwyddion/README @@ -4,4 +4,4 @@ height fields obtained by means of scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM), however it can be generally used for any other height field and image analysis. -libminizip is an optional dependency. +libunique and hdf5 are the optional dependencies. diff --git a/academic/gwyddion/gwyddion.SlackBuild b/academic/gwyddion/gwyddion.SlackBuild index a5e2e2c36e..5f741433c1 100644 --- a/academic/gwyddion/gwyddion.SlackBuild +++ b/academic/gwyddion/gwyddion.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for gwyddion -# Copyright 2012-2017 Daniil Bratashov <dn2010@gmail.com> +# Copyright 2012-2022 Daniil Bratashov <dn2010@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gwyddion -VERSION=${VERSION:-2.58} +VERSION=${VERSION:-2.65} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -102,6 +102,8 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a AUTHORS ChangeLog README $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh diff --git a/academic/gwyddion/gwyddion.info b/academic/gwyddion/gwyddion.info index 13e0741611..6dc1a61df0 100644 --- a/academic/gwyddion/gwyddion.info +++ b/academic/gwyddion/gwyddion.info @@ -1,8 +1,8 @@ PRGNAM="gwyddion" -VERSION="2.58" +VERSION="2.65" HOMEPAGE="http://gwyddion.net" -DOWNLOAD="http://downloads.sourceforge.net/gwyddion/gwyddion-2.58.tar.xz" -MD5SUM="a1157cd107049fdc141aec268f9b0032" +DOWNLOAD="http://downloads.sourceforge.net/gwyddion/gwyddion-2.65.tar.xz" +MD5SUM="6c55a05fe3040d6e102bd34d46d3da7d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="gtkglext" diff --git a/academic/h5utils/README b/academic/h5utils/README index 3b0ed29af6..60dcde6366 100644 --- a/academic/h5utils/README +++ b/academic/h5utils/README @@ -1,9 +1,33 @@ -H5utils is is a set of utilities for visualization and -conversion of scientific data in the free, portable HDF5 -format. Besides providing a simple tool for batch -visualization as PNG images, h5utils also includes -programs to convert HDF5 datasets into the formats -required by other free visualization software (e.g. -plain text, Vis5d, and VTK). - -Optional dependencies: libmatheval, octave, hdf, and perhaps Vis5d. +h5utils (visualization and conversion of HDF5 data) + +H5utils is is a set of utilities for visualization and conversion of +scientific data in the free, portable HDF5 format. Besides providing +a simple tool for batch visualization as PNG images, h5utils also +includes programs to convert HDF5 datasets into the formats required +by other free visualization software (e.g. plain text, Vis5d, and +VTK). + +This package requires: hdf5 + +You probably want to preinstall: libmatheval + +You possibly want to install: octave, hdf; and perhaps Vis5d (not on +SBo). + + +Configuration: + +You can add additional options to the command line using the +environment variable SBOPTIONS_H5UTILS; e.g. to enable the hdf4 utils +and not rely on the conversion routines, use + +SBOPTIONS_H5UTILS="--with-hdf4" ./h5utils.Slackbuild + +Alternatively, if building non-interactively (e.g. if using slpkg), +use/create the file /etc/sbo_pkg_options.conf since this slackbuild +script will search it for options. Simply include a line starting +"h5utils:" followed by options, e.g.: + +h5utils: --with-hdf4 + + diff --git a/academic/h5utils/h5utils.SlackBuild b/academic/h5utils/h5utils.SlackBuild index 030abacf28..1bc4c3a5ef 100644 --- a/academic/h5utils/h5utils.SlackBuild +++ b/academic/h5utils/h5utils.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=h5utils -VERSION=${VERSION:-1.13.1} +VERSION=${VERSION:-1.13.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -64,13 +64,13 @@ else LIBDIRSUFFIX="" fi +set -e + # change annoying underscores into hyphens SVERSION=$(echo $VERSION | tr '_' '-') # make a custom list of doc files in advance DOCFILES="AUTHORS COPYING" -set -e - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP @@ -85,11 +85,20 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # if there is no configure script, try to build one! -if [ ! -f ./configure ] ; then +if [ ! -f ./configure ] ; then ./autogen.sh fi LOCALCONFIGS= +XDBFILE=/etc/sbo_pkg_options.conf +if [ -f ${XDBFILE} ] ; then + LOCALCONFIGS=${LOCALCONFIGS}" "$(grep "^${PRGNAM}:" ${XDBFILE} | grep -v '^#' | awk -F: '{print$2}') + echo Build options selected by file: LOCALCONFIGS=${LOCALCONFIGS} +fi +if [ -n "${SBOPTIONS_H5UTILS}" ] ; then + LOCALCONFIGS=${LOCALCONFIGS}" "${SBOPTIONS_H5UTILS} + echo Build options selected by environment: LOCALCONFIGS=${LOCALCONFIGS} +fi CFLAGS="$SLKCFLAGS" \ CPPFLAGS="$SLKCFLAGS" \ @@ -101,12 +110,6 @@ CPPFLAGS="$SLKCFLAGS" \ --build=$ARCH-slackware-linux \ $LOCALCONFIGS -# allow parallel makes if this variable is set; -# but always finish with a single make in case -# there is a problem with that -if [ "${JMULTIMAKE}" ] ; then - make -j ${JMULTIMAKE} -fi make make install DESTDIR=$PKG @@ -117,6 +120,9 @@ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/h5utils/h5utils.info b/academic/h5utils/h5utils.info index a600f211b9..08f261fe8b 100644 --- a/academic/h5utils/h5utils.info +++ b/academic/h5utils/h5utils.info @@ -1,8 +1,8 @@ PRGNAM="h5utils" -VERSION="1.13.1" +VERSION="1.13.2" HOMEPAGE="https://github.com/NanoComp/h5utils" -DOWNLOAD="https://github.com/NanoComp/h5utils/releases/download/1.13.1/h5utils-1.13.1.tar.gz" -MD5SUM="b116cbb79ea22bbd1640cd8a1290f6f8" +DOWNLOAD="https://github.com/NanoComp/h5utils/releases/download/1.13.2/h5utils-1.13.2.tar.gz" +MD5SUM="32949375c6bfbe5849b940e82a0464dd" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="hdf5" diff --git a/academic/h5utils/slack-desc b/academic/h5utils/slack-desc index 226340b323..2fecfe9c9a 100644 --- a/academic/h5utils/slack-desc +++ b/academic/h5utils/slack-desc @@ -8,7 +8,7 @@ |-----handy-ruler------------------------------------------------------| h5utils: h5utils (visualization and conversion of HDF5 data) h5utils: -h5utils: These utilities provide simple tools for batch visualization of +h5utils: These utilities provide simple tools for batch visualization of h5utils: hdf5 datafiles as PNG images. They also allow conversion from hdf5 h5utils: format into other formats used for visualization, such as plain text, h5utils: Vis5d, and VTK. diff --git a/academic/harminv/README b/academic/harminv/README index fc3c9c0bc7..f574c1996c 100644 --- a/academic/harminv/README +++ b/academic/harminv/README @@ -1,5 +1,14 @@ -Harminv is a program and library that solves the problem of -harmonic inversion. It takes a discrete-time, finite-length -signal, and decomposes it into a sum of finitely-many -sinusoids, determining the frequencies, decay constants, +harminv (harmonic inversion from a time series) + +Harminv is a program and library that solves the problem of +harmonic inversion. It takes a discrete-time, finite-length +signal, and decomposes it into a sum of finitely-many +sinusoids, determining the frequencies, decay constants, amplitudes, and phases of those sinusoids. + +This package requires: lapack + +If the build script can find the ATLAS libraries, it will +adapt the configure options to use them rather than the +default lapack. + diff --git a/academic/harminv/harminv.SlackBuild b/academic/harminv/harminv.SlackBuild index 2dbbcbc71d..7bbd8433bf 100644 --- a/academic/harminv/harminv.SlackBuild +++ b/academic/harminv/harminv.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=harminv -VERSION=${VERSION:-1.4.1} +VERSION=${VERSION:-1.4.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -64,13 +64,13 @@ else LIBDIRSUFFIX="" fi +set -e + # change annoying underscores into hyphens SVERSION=$(echo $VERSION | tr '_' '-') # make a custom list of doc files in advance DOCFILES="COPYING COPYRIGHT NEWS.md README.md doc/*.md " -set -e - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP @@ -89,7 +89,20 @@ if [ ! -f ./configure ] ; then ./autogen.sh fi -LOCALCONFIGS="--enable-shared --with-blas=atlas" + +LOCALCONFIGS="--enable-shared --enable-static=no " + + +# check for the Atlas replacement for blas; if the libraries are found, +# add the configure option accordingly + +if [ -f /usr/lib/libatlas.a ] ; then + if [ -f /usr/lib/libatlas.so ] ; then + echo "NOTICE: libatlas was found, configure --with-blas=atlas" + LOCALCONFIGS=${LOCALCONFIGS}" --with-blas=atlas" + fi +fi + CFLAGS="$SLKCFLAGS" \ CPPFLAGS="$SLKCFLAGS" \ @@ -99,12 +112,14 @@ CPPFLAGS="$SLKCFLAGS" \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux \ - --enable-static=no \ $LOCALCONFIGS make make install DESTDIR=$PKG +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/harminv/harminv.info b/academic/harminv/harminv.info index 4ba38e5070..298d496d12 100644 --- a/academic/harminv/harminv.info +++ b/academic/harminv/harminv.info @@ -1,8 +1,8 @@ PRGNAM="harminv" -VERSION="1.4.1" +VERSION="1.4.2" HOMEPAGE="https://github.com/NanoComp/harminv" -DOWNLOAD="https://github.com/NanoComp/harminv/releases/download/v1.4.1/harminv-1.4.1.tar.gz" -MD5SUM="a1ac921b1b97cd2c0354c35b2d8a77fc" +DOWNLOAD="https://github.com/NanoComp/harminv/releases/download/v1.4.2/harminv-1.4.2.tar.gz" +MD5SUM="0ad9ed9b2b345c2e8c2929f20bdf2492" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="lapack" diff --git a/academic/harminv/slack-desc b/academic/harminv/slack-desc index 63773e4878..7e7a2360d6 100644 --- a/academic/harminv/slack-desc +++ b/academic/harminv/slack-desc @@ -8,9 +8,9 @@ |-----handy-ruler------------------------------------------------------| harminv: harminv (harmonic inversion from a time series) harminv: -harminv: Harminv is a program and library that solves the problem of -harminv: harmonic inversion. It takes a discrete-time, finite-length -harminv: signal, and decomposes it into a sum of finitely-many +harminv: Harminv is a program and library that solves the problem of +harminv: harmonic inversion. It takes a discrete-time, finite-length +harminv: signal, and decomposes it into a sum of finitely-many harminv: sinusoids, dettermining the frequencies, decay constants, harminv: amplitudes, and phases of those sinusoids. harminv: diff --git a/academic/hdfview/README b/academic/hdfview/README new file mode 100644 index 0000000000..70371cc79a --- /dev/null +++ b/academic/hdfview/README @@ -0,0 +1,15 @@ +HDFView Software + +HDFView software consists of the HDFView utility and the Java HDF +Object Package. + +HDFView is a visual tool written in Java for browsing and editing HDF +(HDF5 and HDF4) files. Using HDFView, you can: + +View a file hierarchy in a tree structure +Create new files, add or delete groups and datasets +View and modify the content of a dataset +Add, delete and modify attributes + +HDFView uses the Java HDF Object Package, which implements HDF4 and +HDF5 data objects in an object-oriented form. diff --git a/academic/hdfview/hdfview.SlackBuild b/academic/hdfview/hdfview.SlackBuild new file mode 100644 index 0000000000..bb19668283 --- /dev/null +++ b/academic/hdfview/hdfview.SlackBuild @@ -0,0 +1,112 @@ +#!/bin/bash + +# Slackware build script for hdfview + +# Copyright 2023, Lockywolf +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=hdfview +VERSION=${VERSION:-3.3.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP + +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +#https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfview-3.1.3/bin/HDFView-3.1.3-fedora33_64.tar.gz" + +tar xvf $CWD/HDFView-$VERSION-centos8_64.tar.gz +rpm2cpio $PRGNAM-$VERSION-1.x86_64.rpm | cpio --extract --make-directories + +chown -R root:root . +# find -L . \ +# \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ +# -o -perm 511 \) -exec chmod 755 {} + -o \ +# \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ +# -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + +find -L . \ + -type d -exec chmod 755 {} + +find -L . \ + -type f -exec chmod 755 {} + + + +install -d -m 755 $PKG/usr/bin + +cp -r ./opt $PKG/ + +echo "#!/bin/bash +exec /opt/$PRGNAM/bin/HDFView \"$@\"" > $PKG/usr/bin/$PRGNAM +chmod +x $PKG/usr/bin/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION + +cat README.txt > $PKG/usr/doc/$PRGNAM-$VERSION/README.txt +cat COPYING > $PKG/usr/doc/$PRGNAM-$VERSION/COPYING + +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/hdfview/hdfview.info b/academic/hdfview/hdfview.info new file mode 100644 index 0000000000..ff596fab36 --- /dev/null +++ b/academic/hdfview/hdfview.info @@ -0,0 +1,10 @@ +PRGNAM="hdfview" +VERSION="3.3.1" +HOMEPAGE="https://gephi.org/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfview-3.3.1/bin/HDFView-3.3.1-centos8_64.tar.gz" +MD5SUM_x86_64="f54feb3dcd15be989d762320a57753f8" +REQUIRES="" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.gephi_2023-07-18@lockywolf.net" diff --git a/academic/hdfview/slack-desc b/academic/hdfview/slack-desc new file mode 100644 index 0000000000..28e9b7e7d0 --- /dev/null +++ b/academic/hdfview/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +hdfview: hdfview (visual tool written in Java for browsing and editing HDF) +hdfview: +hdfview: HDFView is a visual tool written in Java for browsing and editing HDF +hdfview: (HDF5 and HDF4) files. Using HDFView, you can: +hdfview: View a file hierarchy in a tree structure +hdfview: Create new files, add or delete groups and datasets +hdfview: View and modify the content of a dataset +hdfview: Add, delete and modify attributes +hdfview: HDFView uses the Java HDF Object Package, which implements HDF4 +hdfview: and HDF5 data objects in an object-oriented form. +hdfview: diff --git a/academic/hyphy/README b/academic/hyphy/README index 4405702da1..2aca901dff 100644 --- a/academic/hyphy/README +++ b/academic/hyphy/README @@ -51,6 +51,10 @@ NOTE! The script builds two executables: HYPHYMP, which uses pthreads to do multiprocessing and HYPHYMPI, which uses openmpi (hence the dependency). +HyPhy Vision +To visualise your results produced offline, you can use HyPhy Vision: +http://vision.hyphy.org/ + Citing Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse (2005) HyPhy: hypothesis testing using phylogenies. diff --git a/academic/hyphy/hyphy.SlackBuild b/academic/hyphy/hyphy.SlackBuild index 954ebd08dd..aa4484c239 100644 --- a/academic/hyphy/hyphy.SlackBuild +++ b/academic/hyphy/hyphy.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for hyphy -# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=hyphy -VERSION=${VERSION:-2.5.31} +VERSION=${VERSION:-2.5.50} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -100,10 +100,7 @@ cd build -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Release .. -# It is actually not necessary anymore to specify here MP and HYPHYMPI, -# as 'make' alone will attempt to build them both. However, let's leave -# them, just in case. - make MP HYPHYMPI + make HYPHYMPI make install DESTDIR=$PKG cd .. diff --git a/academic/hyphy/hyphy.info b/academic/hyphy/hyphy.info index 440a4e7e1d..b35f93b3bb 100644 --- a/academic/hyphy/hyphy.info +++ b/academic/hyphy/hyphy.info @@ -1,8 +1,8 @@ PRGNAM="hyphy" -VERSION="2.5.31" +VERSION="2.5.50" HOMEPAGE="https://veg.github.io/hyphy-site/" -DOWNLOAD="https://github.com/veg/hyphy/archive/2.5.31/hyphy-2.5.31.tar.gz" -MD5SUM="f4d6e48aa47b657810e29dacf183860b" +DOWNLOAD="https://github.com/veg/hyphy/archive/2.5.50/hyphy-2.5.50.tar.gz" +MD5SUM="c4e02d58025f4d1f129cc2b0c2dc97dd" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi" diff --git a/academic/iTest/iTest.SlackBuild b/academic/iTest/iTest.SlackBuild index a569a2df93..9ba531b79c 100644 --- a/academic/iTest/iTest.SlackBuild +++ b/academic/iTest/iTest.SlackBuild @@ -33,7 +33,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -51,8 +51,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -87,6 +87,8 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh + cd iTestServer lrelease iTestServer.pro cd .. diff --git a/academic/iTest/iTest.info b/academic/iTest/iTest.info index 093a59a20d..a4933c1590 100644 --- a/academic/iTest/iTest.info +++ b/academic/iTest/iTest.info @@ -5,6 +5,6 @@ DOWNLOAD="http://sourceforge.net/projects/itest/files/itest-prereleases/iTest-1. MD5SUM="8e4b055c42850ec740cccc18db681bd6" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="qt4" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/io_lib/io_lib.SlackBuild b/academic/io_lib/io_lib.SlackBuild index 6821bcde97..2f78cde485 100644 --- a/academic/io_lib/io_lib.SlackBuild +++ b/academic/io_lib/io_lib.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for io_lib -# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=io_lib -VERSION=${VERSION:-1.14.14} +VERSION=${VERSION:-1.15.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -105,6 +105,8 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/io_lib/io_lib.info b/academic/io_lib/io_lib.info index 9a1928285e..dc94f30b2b 100644 --- a/academic/io_lib/io_lib.info +++ b/academic/io_lib/io_lib.info @@ -1,8 +1,8 @@ PRGNAM="io_lib" -VERSION="1.14.14" +VERSION="1.15.0" HOMEPAGE="https://github.com/jkbonfield/io_lib" -DOWNLOAD="https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-14/io_lib-1.14.14.tar.gz" -MD5SUM="fb2d897709d567f257445306e0f5a781" +DOWNLOAD="https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-15-0/io_lib-1.15.0.tar.gz" +MD5SUM="5d0949836d6e235a69f59a9a3b2af022" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/iqtree/README b/academic/iqtree/README new file mode 100644 index 0000000000..00f5a25553 --- /dev/null +++ b/academic/iqtree/README @@ -0,0 +1,62 @@ +iqtree (IQ-TREE): Efficient and versatile phylogenomic software by +maximum likelihood (ML) + +The IQ-TREE software was created as the successor of IQPNNI and TREE- +PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid +accumulation of phylogenomic data, leading to a need for efficient +phylogenomic software that can handle a large amount of data and provide +more complex models of sequence evolution. To this end, IQ-TREE can +utilize multicore computers and distributed parallel computing to speed +up the analysis. IQ-TREE automatically performs checkpointing to resume +an interrupted analysis. + +As input IQ-TREE accepts all common sequence alignment formats including +PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a +self-readable report file (name suffix .iqtree), a NEWICK tree file +(.treefile) which can be visualized by tree viewer programs such as +FigTree, Dendroscope or iTOL. + +Key features +- Efficient search algorithm: Fast and effective stochastic algorithm to + reconstruct phylogenetic trees by maximum likelihood. IQ-TREE compares + favorably to RAxML and PhyML in terms of likelihood while requiring + similar amount of computing time. +- Ultrafast bootstrap: An ultrafast bootstrap approximation (UFBoot) to + assess branch supports. UFBoot is 10 to 40 times faster than RAxML + rapid bootstrap and obtains less biased support values. +- Ultrafast model selection: An ultrafast and automatic model selection + (ModelFinder) which is 10 to 100 times faster than jModelTest and + ProtTest. ModelFinder also finds best-fit partitioning scheme like + PartitionFinder. +- Big Data Analysis: Supporting huge datasets with thousands of + sequences or millions of alignment sites via checkpointing, safe + numerical and low memory mode. Multicore CPUs and parallel MPI system + are utilized to speedup analysis. +- Phylogenetic testing: Several fast branch tests like SH-aLRT and a + Bayes test and tree topology tests like the approximately unbiased + (AU) test. + +The strength of IQ-TREE is the availability of a wide variety of +phylogenetic models: +- Common models: All common substitution models for DNA, protein, codon, + binary and morphological data with rate heterogeneity among sites and + ascertainment bias correction for e.g. SNP data. +- Partition models: Allowing individual models for different genomic + loci (e.g. genes or codon positions), mixed data types, mixed rate + heterogeneity types, linked or unlinked branch lengths between + partitions. +- Mixture models: fully customizable mixture models and empirical + protein mixture models and. +- Polymorphism-aware models: Accounting for incomplete lineage sorting + to infer species tree from genome-wide population data. + +CITING: +To maintain IQ-TREE, support users and secure fundings, it is important +that you cite the papers, whenever the corresponding features were +applied for your analysis. Note that the paper of Nguyen et al. (2015) +only described the tree search algorithm. Thus, it is not enough to only +cite this paper if you, for example, use partition models, where +Chernomor et al. (2016) should be cited. + +Check the "References" file in the package doc folder, as well as, the +program's web-page. diff --git a/academic/iqtree/References b/academic/iqtree/References new file mode 100644 index 0000000000..37b6382d9c --- /dev/null +++ b/academic/iqtree/References @@ -0,0 +1,35 @@ +How to cite? +To maintain IQ-TREE, support users and secure fundings, it is important for us that you cite the following papers, whenever the corresponding features were applied for your analysis. Note that the paper of Nguyen et al. (2015) only described the tree search algorithm. Thus, it is not enough to only cite this paper if you, for example, use partition models, where Chernomor et al. (2016) should be cited. + +General citation for IQ-TREE 2: +B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37:1530-1534. https://doi.org/10.1093/molbev/msaa015 + +When using concordance factors please cite: +B.Q. Minh, M.W. Hahn, R. Lanfear (2020) New methods to calculate concordance factors for phylogenomic datasets. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msaa106 + +When using heterotachy models please cite: +S.M. Crotty, B.Q. Minh, N.G. Bean, B.R. Holland, J. Tuke, L.S. Jermiin, A. von Haeseler (2020) GHOST: Recovering historical signal from heterotachously-evolved sequence alignments. Syst. Biol., 69:249-264. https://doi.org/10.1093/sysbio/syz051 + +When using the tests of symmetry please cite: +S. Naser-Khdour, B.Q. Minh, W. Zhang, E.A. Stone, R. Lanfear (2019) The Prevalence and Impact of Model Violations in Phylogenetic Analysis. Genome Biol. Evol., 11:3341-3352. https://doi.org/10.1093/gbe/evz193 + +When using polymorphism-aware models please cite: +D. Schrempf, B.Q. Minh, A. von Haeseler, C. Kosiol (2019) Polymorphism-aware species trees with advanced mutation models, bootstrap, and rate heterogeneity. Mol. Biol. Evol., 36:1294–1301. https://doi.org/10.1093/molbev/msz043 + +When performing ultrafast bootstrap (UFBoot) please cite: +D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281 + +When using posterior mean site frequency model (PMSF) please cite: +H.C. Wang, B.Q. Minh, S. Susko, A.J. Roger (2018) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol., 67:216–235. https://doi.org/10.1093/sysbio/syx068 + +When using model selection (ModelFinder) please cite: +S. Kalyaanamoorthy, B.Q. Minh, T.K.F. Wong, A. von Haeseler, L.S. Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods, 14:587-589. https://doi.org/10.1038/nmeth.4285 + +When using partition models please cite: +O. Chernomor, A. von Haeseler, B.Q. Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol., 65:997-1008. https://doi.org/10.1093/sysbio/syw037 + +When using IQ-TREE web server please cite: +J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.. Nucleic Acids Res., 44:W232-W235. https://doi.org/10.1093/nar/gkw256 + +For IQ-TREE 1 please cite: +L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.. Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300 diff --git a/academic/iqtree/iqtree.SlackBuild b/academic/iqtree/iqtree.SlackBuild new file mode 100644 index 0000000000..83542b001d --- /dev/null +++ b/academic/iqtree/iqtree.SlackBuild @@ -0,0 +1,86 @@ +#!/bin/bash + +# Slackware build script for <iqtree> + +# Copyright 2022-2023 Petar Petrov slackalaxy at gmail dot com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=iqtree +VERSION=${VERSION:-2.2.2.7} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION-Linux +tar xvf $CWD/$PRGNAM-$VERSION-Linux.tar.gz +cd $PRGNAM-$VERSION-Linux +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +install -D -m755 bin/iqtree2 $PKG/usr/bin/iqtree2 + +cd $PKG/usr/bin/ +ln -s iqtree2 $PRGNAM +cd - + +mkdir -p $PKG/usr/share/$PRGNAM +cp -a example.* models.nex $PKG/usr/share/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/iqtree/iqtree.info b/academic/iqtree/iqtree.info new file mode 100644 index 0000000000..fed2f89662 --- /dev/null +++ b/academic/iqtree/iqtree.info @@ -0,0 +1,10 @@ +PRGNAM="iqtree" +VERSION="2.2.2.7" +HOMEPAGE="http://www.iqtree.org/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-Linux.tar.gz" +MD5SUM_x86_64="8159c4bb33dae900ccd513a19561fd01" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/iqtree/slack-desc b/academic/iqtree/slack-desc new file mode 100644 index 0000000000..cecc57ba48 --- /dev/null +++ b/academic/iqtree/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +iqtree: iqtree (Efficient and versatile phylogenomic software by ML) +iqtree: +iqtree: The IQ-TREE software was created as the successor of IQPNNI and +iqtree: TREE-PUZZLE. IQ-TREE can utilize multicore computers and +iqtree: distributed parallel computing to speed up the analysis. IQ-TREE +iqtree: automatically performs checkpointing to resume an interrupted +iqtree: analysis. +iqtree: +iqtree: http://www.iqtree.org/ +iqtree: https://github.com/Cibiv/IQ-TREE +iqtree: diff --git a/academic/isoelectric-point/isoelectric-point.SlackBuild b/academic/isoelectric-point/isoelectric-point.SlackBuild index 93c39e2074..3e9244579b 100644 --- a/academic/isoelectric-point/isoelectric-point.SlackBuild +++ b/academic/isoelectric-point/isoelectric-point.SlackBuild @@ -32,7 +32,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -50,8 +50,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -80,6 +80,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh cd ./sources qmake -project qmake diff --git a/academic/isoelectric-point/isoelectric-point.info b/academic/isoelectric-point/isoelectric-point.info index 40ae7acf7a..4d9e2d005d 100644 --- a/academic/isoelectric-point/isoelectric-point.info +++ b/academic/isoelectric-point/isoelectric-point.info @@ -5,6 +5,6 @@ DOWNLOAD="http://ipc.netmark.pl/files/isoelectric-point-linux.tar.gz" MD5SUM="7c2ab92babad116c586f9dc21659d306" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="qt4" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/jalview/README b/academic/jalview/README index ba6e70c2c7..a028e48bcd 100644 --- a/academic/jalview/README +++ b/academic/jalview/README @@ -11,4 +11,7 @@ Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191. NOTE: -The 'source' is hosted at SourceForge by the SlackBuild maintainer. +If you have several jdk-s/jre-s installed, the program may have trouble +starting. If that's the case check the instructions in the wrapper: + +/usr/bin/jalview diff --git a/academic/jalview/jalview b/academic/jalview/jalview index cfdcceef1f..21f9cff3d2 100644..100755 --- a/academic/jalview/jalview +++ b/academic/jalview/jalview @@ -1,2 +1,10 @@ -#!/bin/sh -java -jar /opt/jalview/jalview +#!/bin/bash + +# If you have several jdk-s/jre-s, zulu-openjdk8 may not be the "active" +# one. If that's the case, uncomment the three lines below: + +# export JAVA_HOME=/usr/lib64/zulu-openjdk8 +# export MANPATH="${MANPATH}:${JAVA_HOME}/man" +# export PATH="${JAVA_HOME}/bin:${JAVA_HOME}/jre/bin:${PATH}" + +java -jar /usr/share/jalview/jalview diff --git a/academic/jalview/jalview.SlackBuild b/academic/jalview/jalview.SlackBuild index 6bdf1a487d..879740e8fa 100644 --- a/academic/jalview/jalview.SlackBuild +++ b/academic/jalview/jalview.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for jalview -# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=jalview -VERSION=${VERSION:-2.11.1.4} +VERSION=${VERSION:-2.11.2.7} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -52,7 +52,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -install -D -m755 $CWD/$PRGNAM-all-$VERSION-$JAVA.jar $PKG/opt/$PRGNAM/$PRGNAM +install -D -m755 $CWD/$PRGNAM-all-$VERSION-$JAVA.jar $PKG/usr/share/$PRGNAM/$PRGNAM install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/jalview/jalview.info b/academic/jalview/jalview.info index cdcb70e3d9..90b4e3b971 100644 --- a/academic/jalview/jalview.info +++ b/academic/jalview/jalview.info @@ -1,10 +1,10 @@ PRGNAM="jalview" -VERSION="2.11.1.4" +VERSION="2.11.2.7" HOMEPAGE="http://www.jalview.org/" -DOWNLOAD="http://www.jalview.org/getdown/release/jalview-all-2.11.1.4-j1.8.jar" -MD5SUM="725915975f65ce4ae5570578e68d1b03" +DOWNLOAD="http://www.jalview.org/getdown/release/jalview-all-2.11.2.7-j1.8.jar" +MD5SUM="15b9f3e9ca81c56050efea28e530a4c1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk8" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/jalview/slack-desc b/academic/jalview/slack-desc index 3afaa82c61..fd372a3f3a 100644 --- a/academic/jalview/slack-desc +++ b/academic/jalview/slack-desc @@ -14,6 +14,6 @@ jalview: It can also work with sequence annotation, secondary structure jalview: information, phylogenetic trees and 3D molecular structures. jalview: jalview: Home: http://www.jalview.org/ -jalview: References: /usr/doc/jalview-2.10.0b1/References +jalview: jalview: jalview: diff --git a/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild b/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild index 67282200e2..2a13437dd8 100644 --- a/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild +++ b/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=jellyfish_k-mer VERSION=${VERSION:-1.1.12} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -107,6 +107,8 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/jpicedt/jpicedt.SlackBuild b/academic/jpicedt/jpicedt.SlackBuild index 0de293eb4b..799ef4a103 100644 --- a/academic/jpicedt/jpicedt.SlackBuild +++ b/academic/jpicedt/jpicedt.SlackBuild @@ -30,7 +30,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -48,8 +48,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/jpicedt/jpicedt.info b/academic/jpicedt/jpicedt.info index 584e475fdf..e67a6ff736 100644 --- a/academic/jpicedt/jpicedt.info +++ b/academic/jpicedt/jpicedt.info @@ -5,6 +5,6 @@ DOWNLOAD="http://downloads.sourceforge.net/jpicedt/jpicedt-install_1_4_1_03_2007 MD5SUM="bc1894efbe41c87e5767fb17c8a21d20" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk8" MAINTAINER="Robert Allen" EMAIL="slacker@slaphappygeeks.com" diff --git a/academic/jugglinglab/jugglinglab.info b/academic/jugglinglab/jugglinglab.info index 3f55b9112c..3a72ece5e5 100644 --- a/academic/jugglinglab/jugglinglab.info +++ b/academic/jugglinglab/jugglinglab.info @@ -5,6 +5,6 @@ DOWNLOAD="http://downloads.sourceforge.net/jugglinglab/JugglingLab-0.6.2_other.t MD5SUM="752a399833f0c78c2a2517ef6fffc46b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk8" MAINTAINER="Petr Kletecka" EMAIL="admin@zonglovani.info" diff --git a/academic/kalign/README b/academic/kalign/README new file mode 100644 index 0000000000..23331f54fe --- /dev/null +++ b/academic/kalign/README @@ -0,0 +1,9 @@ +Kalign is a fast multiple sequence alignment program for biological +sequences. + +Kalign expects the input to be a set of unaligned sequences in fasta +format or aligned sequences in aligned fasta, MSF or clustal format. If +the sequences are already aligned, kalign will remove all gap characters +and re-align the sequences. By default, Kalign automatically detects +whether the input sequences are protein or DNA and selects appropriate +alignment parameters. diff --git a/academic/kalign/kalign.SlackBuild b/academic/kalign/kalign.SlackBuild new file mode 100644 index 0000000000..a679082f32 --- /dev/null +++ b/academic/kalign/kalign.SlackBuild @@ -0,0 +1,107 @@ +#!/bin/bash + +# Slackware build script for kalign + +# Copyright 2023 Petar Petrov slackalaxy.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=kalign +VERSION=${VERSION:-3.3.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DMAN_INSTALL_DIR=/usr/man \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/kalign/kalign.info b/academic/kalign/kalign.info new file mode 100644 index 0000000000..431f1f7bd1 --- /dev/null +++ b/academic/kalign/kalign.info @@ -0,0 +1,10 @@ +PRGNAM="kalign" +VERSION="3.3.5" +HOMEPAGE="https://github.com/TimoLassmann/kalign/" +DOWNLOAD="https://github.com/TimoLassmann/kalign/archive/v3.3.5/kalign-3.3.5.tar.gz" +MD5SUM="4634d95e88ea3bacfbad856afab91685" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/kalign/slack-desc b/academic/kalign/slack-desc new file mode 100644 index 0000000000..1dac2dad23 --- /dev/null +++ b/academic/kalign/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +kalign: kalign (A fast multiple sequence alignment program) +kalign: +kalign: Kalign is a fast multiple sequence alignment program for +kalign: biological sequences. +kalign: +kalign: https://github.com/TimoLassmann/kalign +kalign: +kalign: +kalign: +kalign: +kalign: diff --git a/academic/karma/karma.SlackBuild b/academic/karma/karma.SlackBuild index 338f9117a5..ff42bd236d 100644 --- a/academic/karma/karma.SlackBuild +++ b/academic/karma/karma.SlackBuild @@ -22,6 +22,8 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220318 bkw: Modified by SlackBuilds.org: fix build when ARCH is +# set to i586 in the environment. cd $(dirname $0) ; CWD=$(pwd) @@ -39,9 +41,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -53,14 +52,11 @@ OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" = "x86_64" ]; then - ARCHDEP="amd64_Linux_libc6.3" -elif [ "$ARCH" = "i686" ]; then - ARCHDEP="i386_Linux_libc6" -else - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi +case "$ARCH" in + x86_64) ARCHDEP="amd64_Linux_libc6.3" ;; + i?86) ARCHDEP="i386_Linux_libc6" ;; + *) printf "\n\n$ARCH is not supported... \n"; exit 1 ;; +esac rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT @@ -79,10 +75,9 @@ rm -R $ARCHDEP chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ # Copy everything to package directory mkdir -p $PKG/opt/$PRGNAM diff --git a/academic/kissat/README b/academic/kissat/README new file mode 100644 index 0000000000..27b8882eb3 --- /dev/null +++ b/academic/kissat/README @@ -0,0 +1,16 @@ +Kissat is a "keep it simple and clean bare metal SAT solver" written +in C. It is a port of CaDiCaL back to C with improved data +structures, better scheduling of inprocessing and optimized +algorithms and implementation. + +Coincidentally "kissat" also means "cats" in Finnish. + +You can get more information about Kissat in the last solver +description for the SAT Competition 2022: + +Armin Biere and Mathias Fleury. Gimsatul, IsaSAT and Kissat entering +the SAT Competition 2022. In Proc. of SAT Competition 2022 - Solver +and Benchmark Descriptions, Tomas Balyo, Marijn Heule, Markus Iser, +Matti Järvisalo, Martin Suda (editors), vol. B-2022-1 of Department +of Computer Science Report Series B, pages 10-11, University of +Helsinki, 2022. diff --git a/academic/kissat/kissat.SlackBuild b/academic/kissat/kissat.SlackBuild new file mode 100644 index 0000000000..6fdda8acf6 --- /dev/null +++ b/academic/kissat/kissat.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/bash + +# Slackware build script for kissat + +# Copyright Caterino Tommaso, T.O.P. 2024 USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=kissat +VERSION=${VERSION:-3.1.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-rel-$VERSION +tar xvf $CWD/$PRGNAM-rel-$VERSION.tar.gz +cd $PRGNAM-rel-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure + +cd build +make +cd .. + +mkdir -p $PKG/usr/bin $PKG/usr/lib${LIBDIRSUFFIX} +cp -a build/kissat $PKG/usr/bin/ +cp -a build/libkissat.a $PKG/usr/lib${LIBDIRSUFFIX}/ + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +rm -f $PKG/usr/info/dir + +find $PKG -name perllocal.pod -o -name ".packlist" -o -name "*.bs" | xargs rm -f || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CONTRIBUTING LICENSE NEWS.md README.md VERSION \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/kissat/kissat.info b/academic/kissat/kissat.info new file mode 100644 index 0000000000..cefa036030 --- /dev/null +++ b/academic/kissat/kissat.info @@ -0,0 +1,10 @@ +PRGNAM="kissat" +VERSION="3.1.1" +HOMEPAGE="https://github.com/arminbiere/kissat" +DOWNLOAD="https://github.com/arminbiere/kissat/archive/refs/tags/rel-3.1.1.tar.gz" +MD5SUM="601d796884d5e9efe2af78dfe77d73ba" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Caterino Tommaso, T.O.P." +EMAIL="alan_NaverOsa@lavSaPbiAtM.com (remove capital letters)" diff --git a/academic/kissat/slack-desc b/academic/kissat/slack-desc new file mode 100644 index 0000000000..02a27e4e5d --- /dev/null +++ b/academic/kissat/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +kissat: kissat (International SAT Competition award-winning SAT solver) +kissat: Kissat is a "keep it simple and clean bare metal SAT solver" written +kissat: in C. It is a port of CaDiCaL back to C with improved data +kissat: structures, better scheduling of inprocessing and optimized +kissat: algorithms and implementation. +kissat: Armin Biere and Mathias Fleury. Gimsatul, IsaSAT and Kissat entering +kissat: the SAT Competition 2022. In Proc. of SAT Competition 2022 - Solver +kissat: and Benchmark Descriptions, Tomas Balyo, Marijn Heule, Markus Iser, +kissat: Matti Jarvisalo, Martin Suda (editors), vol. B-2022-1 of Department +kissat: of Computer Science Report Series B, pages 10-11, University of +kissat: Helsinki, 2022 diff --git a/academic/kiwisolver/README b/academic/kiwisolver/README deleted file mode 100644 index 96743769c0..0000000000 --- a/academic/kiwisolver/README +++ /dev/null @@ -1,7 +0,0 @@ -This is an efficient C++ implementation of the Cassowary constraint -solving algorithm. Kiwi(solver) is an implementation of the algorithm -based on the seminal Cassowary paper. It is not a refactoring of the -original C++ solver. Kiwi(solver) has been designed from the ground -up to be lightweight and fast. It ranges from 10x to 500x faster than -the original Cassowary solver with typical use cases gaining a 40x -improvement. Memory savings are consistently > 5x. diff --git a/academic/kiwisolver/kiwisolver.info b/academic/kiwisolver/kiwisolver.info deleted file mode 100644 index 41a6cb3771..0000000000 --- a/academic/kiwisolver/kiwisolver.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="kiwisolver" -VERSION="1.0.1" -HOMEPAGE="https://pypi.org/project/kiwisolver" -DOWNLOAD="https://files.pythonhosted.org/packages/31/60/494fcce70d60a598c32ee00e71542e52e27c978e5f8219fae0d4ac6e2864/kiwisolver-1.0.1.tar.gz" -MD5SUM="e2a1718b837e2cd001f7c06934616fcd" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Serban Udrea" -EMAIL="S.Udrea@gsi.de" diff --git a/academic/kiwisolver/slack-desc b/academic/kiwisolver/slack-desc deleted file mode 100644 index ccdb0a1776..0000000000 --- a/academic/kiwisolver/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -kiwisolver: kiwisolver (an implementation of the Cassowary algorithm) -kiwisolver: -kiwisolver: This is an efficient C++ implementation of the Cassowary constraint -kiwisolver: solving algorithm. Kiwi(solver) is an implementation of the algorithm -kiwisolver: based on the seminal Cassowary paper. It is not a refactoring of the -kiwisolver: original C++ solver. Kiwi(solver) has been designed from the ground -kiwisolver: up to be lightweight and fast. -kiwisolver: -kiwisolver: Homepage: https://pypi.org/project/kiwisolver -kiwisolver: -kiwisolver: diff --git a/academic/klavaro/klavaro.SlackBuild b/academic/klavaro/klavaro.SlackBuild index 1c841bc66c..926705cdc7 100644 --- a/academic/klavaro/klavaro.SlackBuild +++ b/academic/klavaro/klavaro.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for Klavaro # Copyright 2015 Thibaut Notteboom -# Copyright 2019 Johannes Schoepfer, Germany +# Copyright 2019-2022 Johannes Schoepfer, Germany # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=klavaro -VERSION=${VERSION:-3.03} +VERSION=${VERSION:-3.14} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -39,9 +39,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -92,8 +89,7 @@ CXXFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG -# Don't ship .la files: -#rm -f $PKG/usr/lib${LIBDIRSUFFIX}/*.la +rm -f $PKG/usr/lib${LIBDIRSUFFIX}/*.la find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -102,7 +98,7 @@ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a ABOUT-NLS AUTHORS ChangeLog COPYING INSTALL NEWS README TODO \ +cp -a ABOUT-NLS AUTHORS ChangeLog COPYING NEWS README TODO \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/klavaro/klavaro.info b/academic/klavaro/klavaro.info index a7b7be9946..eed8101207 100644 --- a/academic/klavaro/klavaro.info +++ b/academic/klavaro/klavaro.info @@ -1,10 +1,10 @@ PRGNAM="klavaro" -VERSION="3.03" +VERSION="3.14" HOMEPAGE="https://klavaro.sourceforge.io/" -DOWNLOAD="https://downloads.sourceforge.net/project/klavaro/klavaro-3.03.tar.bz2" -MD5SUM="0299f185ed8f9aac3441685fbf7177dc" +DOWNLOAD="https://downloads.sourceforge.net/project/klavaro/klavaro-3.14.tar.bz2" +MD5SUM="68ee70d964b23dc4db97aa066a12f8e2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="gtkdatabox" MAINTAINER="Johannes Schoepfer" EMAIL="slackbuilds@schoepfer.info" diff --git a/academic/klu/klu.SlackBuild b/academic/klu/klu.SlackBuild index be1af5591a..9cabf3f4c0 100644 --- a/academic/klu/klu.SlackBuild +++ b/academic/klu/klu.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/klu/klu.info b/academic/klu/klu.info index 2a2faab22f..44adddda01 100644 --- a/academic/klu/klu.info +++ b/academic/klu/klu.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/Suit MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="suitesparseconfig amd colamd btf" +REQUIRES="amd colamd btf" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/kurso/doinst.sh b/academic/kurso/doinst.sh index 65c7e2eeb9..4e8ba7071d 100644 --- a/academic/kurso/doinst.sh +++ b/academic/kurso/doinst.sh @@ -2,8 +2,3 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi -if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then - if [ -x /usr/bin/gtk-update-icon-cache ]; then - /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 - fi -fi diff --git a/academic/kurso/icons/kurso128.png b/academic/kurso/icons/kurso128.png Binary files differdeleted file mode 100644 index 86b72c8a21..0000000000 --- a/academic/kurso/icons/kurso128.png +++ /dev/null diff --git a/academic/kurso/icons/kurso16.png b/academic/kurso/icons/kurso16.png Binary files differdeleted file mode 100644 index 0ca94f4ca9..0000000000 --- a/academic/kurso/icons/kurso16.png +++ /dev/null diff --git a/academic/kurso/icons/kurso24.png b/academic/kurso/icons/kurso24.png Binary files differdeleted file mode 100644 index 0151c02f30..0000000000 --- a/academic/kurso/icons/kurso24.png +++ /dev/null diff --git a/academic/kurso/icons/kurso256.png b/academic/kurso/icons/kurso256.png Binary files differdeleted file mode 100644 index a62d795335..0000000000 --- a/academic/kurso/icons/kurso256.png +++ /dev/null diff --git a/academic/kurso/icons/kurso32.png b/academic/kurso/icons/kurso32.png Binary files differdeleted file mode 100644 index 5425b260a1..0000000000 --- a/academic/kurso/icons/kurso32.png +++ /dev/null diff --git a/academic/kurso/icons/kurso48.png b/academic/kurso/icons/kurso48.png Binary files differdeleted file mode 100644 index c3cf1f56b8..0000000000 --- a/academic/kurso/icons/kurso48.png +++ /dev/null diff --git a/academic/kurso/icons/kurso64.png b/academic/kurso/icons/kurso64.png Binary files differdeleted file mode 100644 index c63abae818..0000000000 --- a/academic/kurso/icons/kurso64.png +++ /dev/null diff --git a/academic/kurso/kurso b/academic/kurso/kurso index 21a08a19ce..335c8a3ea3 100644 --- a/academic/kurso/kurso +++ b/academic/kurso/kurso @@ -1,4 +1,3 @@ #!/bin/sh - -export QT_PLUGIN_PATH=/usr/lib64/kde4/plugins -/usr/bin/kurso4 +cd /opt/kurso +./kursokape diff --git a/academic/kurso/kurso.SlackBuild b/academic/kurso/kurso.SlackBuild index 5f762d4b83..227840e5a1 100644 --- a/academic/kurso/kurso.SlackBuild +++ b/academic/kurso/kurso.SlackBuild @@ -25,21 +25,15 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=kurso -VERSION=${VERSION:-4.1.2} -BUILD=${BUILD:-2} +VERSION=${VERSION:-5.2} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -SRCTARNAM=kurso4_source -SRCNAM=kurso4 -BINTARNAM=kurso.i386 -BINNAM="kurso-de-esperanto-4" +ARCH=$( uname -m ) -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac +if [ "${ARCH}" != "x86_64" ]; then + echo "Architecture ${ARCH} is not supported." + exit 1 fi # If the variable PRINT_PACKAGE_NAME is set, then this script will report what @@ -54,68 +48,14 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCTARNAM.tar.gz -cd $SRCNAM -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 -o -perm 700 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -sed -i -e '/.*Loko = QApplication.*/i \ /*\r' \ - -e '/Loko.append.*/a \ */\r\n Loko = "/usr/share/kurso/";\r' \ - main.cpp - -qmake \ - QMAKE_CFLAGS="$SLKCFLAGS" \ - QMAKE_CXXFLAGS="$SLKCFLAGS" - -make - -mkdir -p $PKG/usr/bin -install -m 755 -t $PKG/usr/bin kurso4 -mkdir -p $PKG/usr/share/kurso -# stiloj and tradukoj are embedded into the binary but they aren't -# being called properly, so it will look for them in the data dir. :( -# Patching this isn't worth the effort. -mv -f stiloj $PKG/usr/share/kurso/ -mv -f tradukoj $PKG/usr/share/kurso/ -cd $PKG/usr/share/kurso/tradukoj/kiel -for i in *.html -do - ln -s $i kiel_${i} -done -cd $PKG/usr/share/kurso/tradukoj/kio -for i in *.html -do - ln -s $i kio_${i} -done - -cd $TMP -rm -rf $BINNAM -tar xvf $CWD/$BINTARNAM.tar.gz -cd $BINNAM +rm -rf ${PRGNAM}_${ARCH} +tar xvf $CWD/${PRGNAM}_${ARCH}.tar.gz +cd ${PRGNAM}_${ARCH} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -123,20 +63,12 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -mv -f sonoj $PKG/usr/share/kurso/ -mv -f video $PKG/usr/share/kurso/ - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -install -m 755 -t $PKG/usr/bin $CWD/kurso -sed -i "s/64/${LIBDIRSUFFIX}/" $PKG/usr/bin/kurso +mkdir -p $PKG/opt/kurso +cp -a kursokape sonoj video $PKG/opt/kurso/ -for i in 16 24 32 48 64 128 256 -do - install -D -m 0644 $CWD/icons/kurso${i}.png $PKG/usr/share/icons/hicolor/${i}x${i}/apps/kurso.png -done +install -D -m 0644 kurso_256.png $PKG/usr/share/pixmaps/kurso.png install -D -m 0644 $CWD/kurso.desktop $PKG/usr/share/applications/kurso.desktop +install -D -m 0755 $CWD/kurso $PKG/usr/bin/kurso mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/kurso/kurso.desktop b/academic/kurso/kurso.desktop index bfdc44c3eb..2fed560086 100644 --- a/academic/kurso/kurso.desktop +++ b/academic/kurso/kurso.desktop @@ -6,4 +6,4 @@ Type=Application Exec=kurso Icon=kurso Terminal=false -Categories=Education;Languages;KDE;Qt; +Categories=Education;Languages;Qt; diff --git a/academic/kurso/kurso.info b/academic/kurso/kurso.info index e05c18b257..001428a797 100644 --- a/academic/kurso/kurso.info +++ b/academic/kurso/kurso.info @@ -1,12 +1,10 @@ PRGNAM="kurso" -VERSION="4.1.2" +VERSION="5.2" HOMEPAGE="http://www.kurso.com.br/index.php?en" -DOWNLOAD="http://kurso.com.br/kurso4_source.tar.gz \ - http://kurso.com.br/kurso.i386.tar.gz" -MD5SUM="a92fb13a1ec6734d0d254a8733b610b3 \ - fa580797b4fb2ee34b30dccc79fb4b8d" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://ponce.cc/slackware/sources/repo/kurso_x86_64.tar.gz" +MD5SUM_x86_64="ed6cc642b8c7b368516b871377b5af4d" REQUIRES="" MAINTAINER="T3slider" EMAIL="t3slider@gmail.com" diff --git a/academic/labplot2/README b/academic/labplot2/README index ae07007ac1..11b9ca7430 100644 --- a/academic/labplot2/README +++ b/academic/labplot2/README @@ -3,17 +3,21 @@ labplot2 (interactive graphing and analysis of scientific data) LabPlot is a KDE-application for interactive graphing and analysis of scientific data. -LabPlot provides an easy way to create, manage and edit plots. It allows -you to produce plots based on data from a spreadsheet or on data imported -from external files. Plots can be exported to several pixmap and vector -graphic formats. +LabPlot provides an easy way to create, manage and edit plots. It +allows you to produce plots based on data from a spreadsheet or on +data imported from external files. Plots can be exported to several +pixmap and vector graphic formats. -LabPlot2 is a complete rewrite of LabPlot1 and lacks in the first release -a lot of features available in the predecessor. On the other hand, the -GUI and the usability is more superior as compared to LabPlot1 and there -are several new features that were not available in LabPlot1. +LabPlot2 is a complete rewrite of LabPlot1 and lacks in the first +release a lot of features available in the predecessor. On the other +hand, the GUI and the usability is more superior as compared to +LabPlot1 and there are several new features that were not available +in LabPlot1. optional dependencies: - hdf5 - netcdf +- cfitsio +- matio +- discount diff --git a/academic/labplot2/doinst.sh b/academic/labplot2/doinst.sh new file mode 100644 index 0000000000..4f83cde390 --- /dev/null +++ b/academic/labplot2/doinst.sh @@ -0,0 +1,14 @@ + +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/labplot2/labplot2.SlackBuild b/academic/labplot2/labplot2.SlackBuild index c1da77ddf7..a4b4946d00 100644 --- a/academic/labplot2/labplot2.SlackBuild +++ b/academic/labplot2/labplot2.SlackBuild @@ -1,8 +1,10 @@ #!/bin/bash # # Slackware build script for LabPlot -# Based on the Slackware 14.1 SlackBuild and AUR PKGBUILD for labplot -# Written by Fellype do Nascimento <fellype(at)gmail.com> +# Based on the Slackware 15.0 SlackBuild and AUR PKGBUILD for labplot +# +# Copyright 2014-2023, Fellype do Nascimento, Guaratingueta - Brazil +# All rights reserved. # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -21,12 +23,12 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -NAME=labplot cd $(dirname $0) ; CWD=$(pwd) +NAME=labplot PRGNAM=labplot2 -VERSION=${VERSION:-2.4.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-2.10.1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -51,11 +53,17 @@ PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX=""; CHOST=i486 + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX=""; CHOST=i486 + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC"; SLKLDFLAGS="-L/usr/lib64"; LIBDIRSUFFIX="64" + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" fi set -e @@ -66,6 +74,7 @@ cd $TMP rm -rf $NAME-$VERSION tar -xJf $CWD/$NAME-$VERSION.tar.xz cd $NAME-$VERSION + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -73,31 +82,47 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -./compile - +mkdir build ( cd build/ -cmake ./ -DCMAKE_INSTALL_PREFIX=/usr -cmake ./ -DCMAKE_BUILD_TYPE=Release -make install DESTDIR=$PKG +cmake -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_BUILD_TYPE=Release \ + -DMAN_INSTALL_DIR=/usr/man \ + -DENABLE_READSTAT=OFF \ + -DENABLE_TESTS=OFF \ + -DLOCAL_DBC_PARSER=OFF \ + -DLOCAL_VECTOR_BLF=OFF \ + .. +make +make install/strip DESTDIR=$PKG ) -( cd $PKG -find -L . | xargs -O file | grep "executable" | grep ELF | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -find -L . | xargs -O file | grep "shared object" | grep ELF | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -find -L . | xargs -O file | grep "current ar archive" | cut -f 1 -d : | xargs strip -g 2> /dev/null || true -) +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +# no usr/share/doc dir +mkdir -p $PKG/usr/doc +mv $PKG/usr/share/doc/* $PKG/usr/doc +rmdir $PKG/usr/share/doc + +# Leave only one main category in key "Categories" for the .desktop file +sed -i "s:Qt;KDE;Education;Science;Physics;Math;:Science;:" $PKG/usr/share/applications/org.kde.labplot2.desktop + +# Fix permissions in .desktop file +chmod 0644 $PKG/usr/share/applications/org.kde.labplot2.desktop + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING INSTALL README \ +cp -a AUTHORS ChangeLog README.md LICENSES/* \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc - -if [ -e /usr/bin/requiredbuilder ]; then - requiredbuilder -v -y -s $CWD $PKG -fi +cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/labplot2/labplot2.info b/academic/labplot2/labplot2.info index cf80183dd6..fca8ba5bad 100644 --- a/academic/labplot2/labplot2.info +++ b/academic/labplot2/labplot2.info @@ -1,10 +1,10 @@ PRGNAM="labplot2" -VERSION="2.4.0" +VERSION="2.10.1" HOMEPAGE="https://labplot.kde.org/" -DOWNLOAD="http://kde.c3sl.ufpr.br/stable/labplot/2.4.0/labplot-2.4.0.tar.xz" -MD5SUM="ee59c0095190bb3dc100e29e1a00c654" +DOWNLOAD="https://download.kde.org/stable/labplot/labplot-2.10.1.tar.xz" +MD5SUM="b3cdfe029d64fa834e0990e9b5ab446f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Fellype do Nascimento" -EMAIL="fellype(at)gmail.com" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/ladr/README b/academic/ladr/README index 2bee5905d9..c2fd2fb0fc 100644 --- a/academic/ladr/README +++ b/academic/ladr/README @@ -1,3 +1,4 @@ -LADR includes some mathematical programs like - - prover 9 (automated theorem prover for first-order and equational logic) - - mace4 (search for finite models and counterexamples) +LADR includes some mathematical programs like: + +prover 9 (automated theorem prover for first-order and equational logic) +mace4 (search for finite models and counterexamples) diff --git a/academic/laghos/README b/academic/laghos/README new file mode 100644 index 0000000000..655cace20f --- /dev/null +++ b/academic/laghos/README @@ -0,0 +1,4 @@ + Laghos (LAGrangian High-Order Solver) is a miniapp that solves the +time-dependent Euler equations of compressible gas dynamics in a +moving Lagrangian frame using unstructured high-order finite element +spatial discretization and explicit high-order time-stepping. diff --git a/academic/laghos/laghos.SlackBuild b/academic/laghos/laghos.SlackBuild new file mode 100644 index 0000000000..c0ddd9ffc5 --- /dev/null +++ b/academic/laghos/laghos.SlackBuild @@ -0,0 +1,123 @@ +#!/bin/bash + +# Slackware build script for Laghos + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=laghos +VERSION=${VERSION:-3.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=Laghos + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +sed -i 's#config/config.mk#share/mfem-4.5/config.mk#' {.,amr,serial}/makefile +sed -i 's#config/test.mk#share/mfem-4.5/test.mk#' amr/makefile + +# not working keep it or later (do not tell about it at README) +if [ "${PARALLEL:-no}" == "yes" ]; then + make MFEM_DIR=/usr +else + cd serial + make MFEM_DIR=/usr + make MFEM_DIR=/usr checks + cd .. +fi + +install -d $PKG/usr/bin +install -m 0755 serial/laghos $PKG/usr/bin + +install -d $PKG/usr/share/$PRGNAM +cp -av data $PKG/usr/share/$PRGNAM + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a CHANGELOG LICENSE NOTICE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/laghos/laghos.info b/academic/laghos/laghos.info new file mode 100644 index 0000000000..e7f2ae8aed --- /dev/null +++ b/academic/laghos/laghos.info @@ -0,0 +1,10 @@ +PRGNAM="laghos" +VERSION="3.1" +HOMEPAGE="https://math-atlas.sourceforge.net" +DOWNLOAD="https://github.com/CEED/Laghos/archive/v3.1/Laghos-3.1.tar.gz" +MD5SUM="5c2cc3c9fb68985cd9d6fa2c36721f21" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="mfem hypre" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/laghos/slack-desc b/academic/laghos/slack-desc new file mode 100644 index 0000000000..c772f12ebf --- /dev/null +++ b/academic/laghos/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +laghos: laghos (LAGrangian High-Order Solver) +laghos: +laghos: +laghos: Laghos (LAGrangian High-Order Solver) is a miniapp that solves +laghos: the time-dependent Euler equations of compressible gas dynamics +laghos: in a moving Lagrangian frame using unstructured high-order finite +laghos: element spatial discretization and explicit high-order time-stepping. +laghos: +laghos: +laghos: +laghos: diff --git a/academic/lammps/README b/academic/lammps/README new file mode 100644 index 0000000000..2a2f19c3ee --- /dev/null +++ b/academic/lammps/README @@ -0,0 +1,48 @@ +LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel +Simulator. + +It is a classical molecular dynamics simulation code designed to +run efficiently on parallel computers. It was developed at Sandia +National Laboratories, a US Department of Energy facility. + +A basic installation of LAMMPS can be enhanced enabling the build of +internal or external extensions (packages) that add methods and/or +give support to third parts libraries or platforms. + +Dependencies strictly needed to build LAMMPS with most internal +packages enabled are already present in a full installation of +Slackware 15.0 and the slackbuild can be launched without any other +dependency not released with the official Slackware. Only openmpi is +highly recommended since LAMMPS takes advantage of the parallel +computation. Furthermore some packages require it as strictly +dependency. Instead of openmpi LAMMPS can be build with the support +of mpich, although the latter does not support the enabling of a +package (OPENMP). If any MPI platform is found in the system, LAMMPS +will be built anyway but with a reduced functionality. + +Other optional dependencies available in Slackbuilds.org are +autodetected and allow the enabling of some additional packages: HDF5, +OpenBLAS, python3-numpy, voro++, PLUMED, netcdf. Other packages need +third parts libraries given by downloaded extrafile and bundled in +the application during the compilation. The slackbuild prevent the +download during the build, so you have to download these extrafiles +listed in lammps.info. Optional dependencies and the download of +extrafiles are not needed if you do not require the respective +packages. + +Warning: except to GPU, all packages are enabled by default if no +dependencies are required (or they dependencies are found in the +system), but you have to disable the packages that require the +extrafiles listed in lammps.info if you do not download them, +otherwise the build fails during the check of cmake. +For GPU package you can try: + GPU=yes ./lammps.SlackBuild +or + GPU=yes STATIC_OCL=yes ./lammps.SlackBuild +The latter uses an internal static OpenCL loader. + +See README.SBo for a full list of available packages and their +dependencies. + +Some packages available in the source of LAMMPS cannot be enabled for +reasons reported in README.SBo. diff --git a/academic/lammps/README.SBo b/academic/lammps/README.SBo new file mode 100644 index 0000000000..b74f864a25 --- /dev/null +++ b/academic/lammps/README.SBo @@ -0,0 +1,211 @@ +Table of contents + +1. HOW TO DISABLE NOT REQUIRED PACKAGES +2. INTERDEPENDENT PACKAGES +3. EXTERNAL PACKAGES +4. LIST OF PACKAGES AND RELATED REQUIREMENTS +5. PACKAGES NOT AVAILABLE +6. NOTES + +1. HOW TO DISABLE NOT REQUIRED PACKAGES + +Almost all packages that are supported by your system and dependencies +installed (autodetected) are enabled by default. You can disable those +not required in three different ways: +A. edit the code of the slackbuild + for example, a package enabled by default has this condition: + atc="" [ "${ATC:-no}" = "yes" ] && atc="-DPKG_ATC=yes " + if you want to disable it you have to edit as following: + atc="" [ "${ATC:-no}" = "yes" ] && atc="-DPKG_ATC=yes " +B. remove the variables not required from the global $packages at line + 221. The script will not pass the related flags to cmake) + for example, if you want to disable AMOEBA and ATC you have to + remove the strings $amoeba and $atc from packages=$amoeba$asphere... +C. pass to the script the related environment variable as following + AMOEBA=no ATC=no ./lammps.SlackBuild + +2. INTERDEPENDENT PACKAGES + + The enabling of some packages require that also other packages are + enabled. For example, the ATC package require also MANYBODY enabled. + The script or cmake check if this condition is not respected, so all + required additional packages will be enabled automatically + +3. EXTERNAL PACKAGES + + Various packages are build as bundled features that interface LAMMPS + to third part software that it should already installed in your + system. These deps are released with the official Slackware (fftw + for example) or available in Slackbuilds.org. Some packages require + the download of additional sources (listed in lammps.info). Please + make sure to download all required extrafiles if the dependent + package is enable. If you do not do this, the process will fail or + starts the download during the compilation. + +4. LIST OF PACKAGES AND RELATED REQUIREMENTS + + For description of each package see the documentation on line at + https://docs.lammps.org/Packages_list.html + + Dependencies available in the official Slackware are not reported. +----------------------------------------------------------------------- +PACKAGE ; ENV. VARIABLE ; ENABLED ALSO ; EXTERNAL DEPENDENCIES +----------------------------------------------------------------------- +AMOEBA ; AMOEBA ; ; +ASPHERE ; ASPHERE ; ; +ATC ; ATC ; MANYBODY ; +AWPMD ; AWPMD ; ; +BOCS ; BOCS ; ; +BODY ; BODY ; ; +BPM ; BPM ; ; +BROWNIAN ; BROWNIAN ; ; +CG-DNA ; CGDNA ; ASPHERE \ + MOLECULE ; +CG-SPICA ; CGSPICA ; ; +CLASS2 ; CLASS2 ; ; +COLLOID ; COLLOID ; ; +COLVARS ; COLVARS ; ; +COMPRESS ; COMPRESS ; ; +CORESHELL ; CORESHELL ; ; +DIELECTRIC ; DIELECTRIC ; EXTRA-PAIR \ + KSPACE ; +DIFFRACTION ; DIFFRACTION ; ; +DIPOLE ; DIPOLE ; ; +DPD-BASIC ; DPDBASIC ; ; +DPD-MESO ; DPDMESO ; ; +DPD-REACT ; DPDREACT ; ; +DPD-SMOOTH ; DPDSMOOTH ; ; +DRUDE ; DRUDE ; ; +EFF ; EFF ; ; +ELECTRODE ; ELECTRODE ; KSPACE ; OpenBLAS (optional) +EXTRA-COMPUTE ; EXTRACOMPUTE ; ; +EXTRA-DUMP ; EXTRADUMP ; ; +EXTRA-FIX ; EXTRAFIX ; ; +EXTRA-MOLECULE ; EXTRAMOLECULE ; ; +EXTRA-PAIR ; EXTRAPAIR ; ; +FEP ; FEP ; ; +GPU ; GPU ; ; see NOTES +GRANULAR ; GRANULAR ; ; +H5MD ; H5MD ; ; hdf5 (needed) +INTEL ; INTEL ; OPENMP ; see NOTES +INTERLAYER ; INTERLAYER ; ; +KOKKOS ; KOKKOS ; ; see NOTES +KSPACE ; KSPACE ; ; +LATBOLTZ ; LATBOLTZ ; ; see NOTES +LEPTON ; LEPTON ; ; +MACHDYN ; MACHDYN ; ; +MANIFOLD ; MANIFOLD ; ; +MANYBODY ; MANYBODY ; ; +MC ; MC ; ; +MDI ; MDI ; ; download extrasource +MEAM ; MEAM ; ; +MESONT ; MESONT ; MOLECULE ; download data file +MGPT ; MGPT ; ; +MISC ; MISC ; ; +ML-HDNNP ; MLHDNNP ; ; download extrasource +ML-IAP ; MLIAP ; ML-SNAP \ + PYTHON ; python3-numpy (needed) +ML-PACE ; MLPACE ; ; download extrasource +ML-POD ; MLPOD ; ; +ML-RANN ; MLRANN ; ; +ML-SNAP ; MLSNAP ; ; +MOFFF ; MOFFF ; ; +MOLECULE ; MOLECULE ; ; +NETCDF ; NETCDF ; ; netcdf +OPENMP ; OPENMP ; ; openmpi (needed) \ + (mpich not supported) +OPT ; OPT ; ; +ORIENT ; ORIENT ; ; +PERI ; PERI ; ; +PHONON ; PHONON ; KSPACE ; +PLUMED ; PLUMED ; ; PLUMED +POEMS ; POEMS ; ; +PTM ; PTM ; ; +PYTHON ; PYTHON ; ; +QEQ ; QEQ ; ; +QTB ; QTB ; ; +REACTION ; REACTION ; ; +REAXFF ; REAXFF ; ; +REPLICA ; REPLICA ; ; +RIGID ; RIGID ; ; +SCAFACOS ; SCAFACOS ; ; scafacos +SHOCK ; SHOCK ; ; +SMTBQ ; SMTBQ ; ; +SPH ; SPH ; ; +SPIN ; SPIN ; ; +SRD ; SRD ; ; +TALLY ; TALLY ; ; +UEF ; UEF ; ; +YAFF ; YAFF ; ; +----------------------------------------------------------------------- + +5. PACKAGES NOT AVAILABLE + +Some packages, available in the source, are not supported in this +slackbuild for various reasons. These are: +- ADIOS: requires a library not available in Slackware or SBo. +- KIM: requires the download of extrasource during the compilation + which cannot be prevented by a predownload. +- ML-QUIP: the version for non-commercial uses can be downloaded only + during the compilation. A preventive download is allowed + only via git. +- MOLFILE: this package supports the VMD plugin that is must be built + and installed only by sources or packages downloaded after + registration +- MPIIO: this packages is unmantained and it should be enabled with + caution +- MSCG: requires the download of extrasource during the compilation or + the installation in the system. This library is free and open + source but the anonymous download is not permitted. +- QMMM: requires a library that can be built and installed from source + downloaded after registration +- VORONOI: since the required dependency available in this repository + can be build as static library, this package is not compatible + when lammps is built enabling shared libraries, so support to + it is disabled +- VTK: not available at the moment because the build fails. It is + possible that this is caused by the VTK built in my system: the + issue is a conflict with the support of VTK to openmpi in my + built. I have to make some tests to find the problem. + +6. NOTES + +The GPU package supports OpenCL, CUDA and HIP by setting the +appropriate build configuration. See the documentation on line if you +would extend the functionality of LAMMPS adapted to you hardware. This +slackbuild sets a basic configuration build the package with OpenCL. +LAMMPS can be build linking the system OpenCL or using a static +internal OpenCL loader. To enable the build with the internal OpenCL +you have to download the extrasource from the link indicated in +lammps.info and pass the variable STATIC_OCL=yes to the slackbuild. +The enabling of this package gives different results depending on the +hardware/software configurations, so it is disabled by default because +we have to apply additional settings to prevent the issues (build +failures and segmentation faults). With a basic configuration I enabled +it in a Slackware current with a an old Nvidia GPU and driver and +using the system OpenCL (the bundled OpenCL gives segmentation fault). +In other tests (Slackware 15 with older Nvidia GPU and driver, +Slackware 32-bit in virtual machine) the build not works. You could +passing GPU=yes (and eventually STATIC_OCL=yes) to the slackbuild to +try if it works in your system with a basic configuration, but it is no +guaranteed. + +The INTEL package takes advantage in build and runtime of an advanced +configuration using Intel compilers and hardware it should work also +with other with reduced performances. If detected, the build takes +advantage of the parallelism (MPI and tbb, for example). + +KOKKOS is another package that enhances the functionality of LAMMPS +taking advandage of the parallel computation. Since its build requires +resources and a build with a single core seems very long, I set the +enabling by default only for 64-bit architectures because I do not know +how it can be useful in 32-bit systems. + +The LATBOLTZ package must be enabled only if LAMMPS is built with the +support to MPI (openmpi or mpich). The script allows the enabling of +LATBOLTZ if one of these dependencies are found in the system. + +By default, LAMMPS will be built with Python anyway, even if packages +that require it will not be enabled. If you want disable the support +to Python, you have to launch the slackbuild with + PYTHON=no ./lammps.SlackBuild diff --git a/academic/lammps/lammps.SlackBuild b/academic/lammps/lammps.SlackBuild new file mode 100644 index 0000000000..2cf95b7453 --- /dev/null +++ b/academic/lammps/lammps.SlackBuild @@ -0,0 +1,389 @@ +#!/bin/bash + +# Slackware build script for lammps + +# Copyright 2023-2024 Giancarlo Dessi, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=lammps +VERSION=${VERSION:-2023.08.02_update3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +SRCNAM=lammps-stable +SRCVERSION=${SRCVERSION:-2Aug2023_update3} +PACEVERSION=v.2023.10.04 +MDIVERSION=1.4.26 +N2P2VERSION=2.2.0 +OCLLVERSION=2022.01.04 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +# First detect if openmpi or mpich are installed, so we can build LAMMPS with the +# parallel computing and enable some packages +MP="" +mpi="" +if pkg-config --exists ompi; then + MP="openmpi"; + mpi="-DBUILD_OMP=yes " +fi +if pkg-config --exists mpich; then + MP="mpich"; + mpi="-DBUILD_MPI=yes " +fi + +# Detect if some dependencies are installed or extrafile download. +# These are needed conditions to prevent the download of extrafiles +# during the build +scafacos="" +mdi="" +mlpace="" +# External ScaFaCos must be installed in the system +if pkg-config --exists scafacos; then + scafacos="-DPKG_SCAFACOS=yes -DDOWNLOAD_SCAFACOS=OFF " +fi +# lammps-user-pace must be downloaded in $CWD +PACETARBALL=$CWD/lammps-user-pace-$PACEVERSION.tar.gz +if [ -f $PACETARBALL ]; then + mlpace="" ; [ "${MLPACE:-yes}" = "yes" ] && mlpace="-DPKG_ML-PACE=yes " +fi +# MDI_Library must be downloaded in $CWD. Installation of this library +# in the system does not work +MDITARBALL=$CWD/MDI_Library-$MDIVERSION.tar.gz +if [ -f $MDITARBALL ]; then + mdi="" ; [ "${MDI:-yes}" = "yes" ] && mdi="-DPKG_MDI=yes -DDOWNLOAD_MDI=ON " +fi +# N2P2 must be downloaded in $CWD +N2P2=$CWD/n2p2-$N2P2VERSION.tar.gz +if [ -f $MDITARBALL ]; then + mlhdnnp="" ; [ "${MLHDNNP:-yes}" = "yes" ] && mlhdnnp="-DPKG_ML-HDNNP=yes " +fi + + +# These internal packages are enabled by default. +# If you do not require some of them you have to edit the conditions in this block +# otherwise pass the respective environment variables set to "no" to the script +# for each package not desired +# (for example: AMOEBA=no ASPHERE=no ./lammps.SlackBuild) + +amoeba="" [ "${AMOEBA:-yes}" = "yes" ] && amoeba="-DPKG_AMOEBA=yes " +asphere="" ; [ "${ASPHERE:-yes}" = "yes" ] && asphere="-DPKG_ASPHERE=yes " +atc="" ; [ "${ATC:-yes}" = "yes" ] && atc="-DPKG_ATC=yes " +awpmd="" ; [ "${AWPMD:-yes}" = "yes" ] && awpmd="-DPKG_AWPMD=yes " +bocs="" ; [ "${BOCS:-yes}" = "yes" ] && bocs="-DPKG_BOCS=yes " +body="" ; [ "${BODY:-yes}" = "yes" ] && body="-DPKG_BODY=yes " +bpm="" ; [ "${BPM:-yes}" = "yes" ] && bpm="-DPKG_BPM=yes " +brownian="" ; [ "${BROWNIAN:-yes}" = "yes" ] && brownian="-DPKG_BROWNIAN=yes " +cgdna="" ; [ "${CGDNA:-yes}" = "yes" ] && cgdna="-DPKG_CG-DNA=yes " +cgspica="" ; [ "${CGSPICA:-yes}" = "yes" ] && cgspica="-DPKG_CG-SPICA=yes " +class2="" ; [ "${CLASS2:-yes}" = "yes" ] && class2="-DPKG_CLASS2=yes " +colloid="" ; [ "${COLLOID:-yes}" = "yes" ] && colloid="-DPKG_COLLOID=yes " +colvars="" ; [ "${COLVARS:-yes}" = "yes" ] && colvars="-DPKG_COLVARS=yes " +compress="" ; [ "${COMPRESS:-yes}" = "yes" ] && compress="-DPKG_COMPRESS=yes " +coreshell="" ; [ "${CORESHELL:-yes}" = "yes" ] && coreshell="-DPKG_CORESHELL=yes " +dielectric="" ; [ "${DIELECTRIC:-yes}" = "yes" ] && dielectric="-DPKG_DIELECTRIC=yes " +diffraction="" ; [ "${DIFFRACTION:-yes}" = "yes" ] && diffraction="-DPKG_DIFFRACTION=yes " +dipole="" ; [ "${DIPOLE:-yes}" = "yes" ] && dipole="-DPKG_DIPOLE=yes " +dpdbasic="" ; [ "${DPDBASIC:-yes}" = "yes" ] && dpdbasic="-DPKG_DPD-BASIC=yes " +dpdmeso="" ; [ "${DPDMESO:-yes}" = "yes" ] && dpdmeso="-DPKG_DPD-MESO=yes " +dpdreact="" ; [ "${DPDREACT:-yes}" = "yes" ] && dpdreact="-DPKG_DPD-REACT=yes " +dpdsmooth="" ; [ "${DPDSMOOTH:-yes}" = "yes" ] && dpdsmooth="-DPKG_DPD-SMOOTH=yes " +drude="" ; [ "${DRUDE:-yes}" = "yes" ] && drude="-DPKG_DRUDE=yes " +eff="" ; [ "${EFF:-yes}" = "yes" ] && eff="-DPKG_EFF=yes " +electrode="" ; [ "${ELECTRODE:-yes}" = "yes" ] && electrode="-DPKG_ELECTRODE=yes " +extracompute="" ; [ "${EXTRACOMPUTE:-yes}" = "yes" ] && extracompute="-DPKG_EXTRA-COMPUTE=yes " +extradump="" ; [ "${EXTRADUMP:-yes}" = "yes" ] && extradump="-DPKG_EXTRA-DUMP=yes " +extrafix="" ; [ "${EXTRAFIX:-yes}" = "yes" ] && extrafix="-DPKG_EXTRA-FIX=yes " +extramolecule="" ; [ "${EXTRAMOLECULE:-yes}" = "yes" ] && extramolecule="-DPKG_EXTRA-MOLECULE=yes " +extrapair="" ; [ "${EXTRAPAIR:-yes}" = "yes" ] && extrapair="-DPKG_EXTRA-PAIR=yes " +fep="" ; [ "${FEP:-yes}" = "yes" ] && fep="-DPKG_FEP=yes " +granular="" ; [ "${GRANULAR:-yes}" = "yes" ] && granular="-DPKG_GRANULAR=yes " +intel="" ; [ "${INTEL:-yes}" = "yes" ] && intel="-DPKG_INTEL=yes " +interlayer="" ; [ "${INTERLAYER:-yes}" = "yes" ] && interlayer="-DPKG_INTERLAYER=yes " +kspace="" ; [ "${KSPACE:-yes}" = "yes" ] && kspace="-DPKG_KSPACE=yes " +lepton="" ; [ "${LEPTON:-yes}" = "yes" ] && lepton="-DPKG_LEPTON=yes " +machdyn="" ; [ "${MACHDYN:-yes}" = "yes" ] && machdyn="-DPKG_MACHDYN=yes " +manifold="" ; [ "${MANIFOLD:-yes}" = "yes" ] && manifold="-DPKG_MANIFOLD=yes " +manybody="" ; [ "${MANYBODY:-yes}" = "yes" ] && manybody="-DPKG_MANYBODY=yes " +mc="" ; [ "${MC:-yes}" = "yes" ] && mc="-DPKG_MC=yes " +meam="" ; [ "${MEAM:-yes}" = "yes" ] && meam="-DPKG_MEAM=yes " +mesont="" ; [ "${MESONT:-yes}" = "yes" ] && mesont="-DPKG_MESONT=yes " +mgpt="" ; [ "${MGPT:-yes}" = "yes" ] && mgpt="-DPKG_MGPT=yes " +misc="" ; [ "${MISC:-yes}" = "yes" ] && misc="-DPKG_MISC=yes " +mlpod="" ; [ "${MLPOD:-yes}" = "yes" ] && mlpod="-DPKG_ML-POD=yes " +mlrann="" ; [ "${MLRANN:-yes}" = "yes" ] && mlrann="-DPKG_ML-RANN=yes " +mlsnap="" ; [ "${MLSNAP:-yes}" = "yes" ] && mlsnap="-DPKG_ML-SNAP=yes " +mofff="" ; [ "${MOFFF:-yes}" = "yes" ] && mofff="-DPKG_MOFFF=yes " +molecule="" ; [ "${MOLECULE:-yes}" = "yes" ] && molecule="-DPKG_MOLECULE=yes " +opt="" ; [ "${OPT:-yes}" = "yes" ] && opt="-DPKG_OPT=yes " +orient="" ; [ "${ORIENT:-yes}" = "yes" ] && orient="-DPKG_ORIENT=yes " +peri="" ; [ "${PERI:-yes}" = "yes" ] && peri="-DPKG_PERI=yes " +phonon="" ; [ "${PHONON:-yes}" = "yes" ] && phonon="-DPKG_PHONON=yes " +plugin="" ; [ "${PLUGIN:-yes}" = "yes" ] && plugin="-DPKG_PLUGIN=yes " +poems="" ; [ "${POEMS:-yes}" = "yes" ] && poems="-DPKG_POEMS=yes " +ptm="" ; [ "${PTM:-yes}" = "yes" ] && ptm="-DPKG_PTM=yes " +qeq="" ; [ "${QEQ:-yes}" = "yes" ] && qeq="-DPKG_QEQ=yes " +qtb="" ; [ "${QTB:-yes}" = "yes" ] && qtb="-DPKG_QTB=yes " +reaction="" ; [ "${REACTION:-yes}" = "yes" ] && reaction="-DPKG_REACTION=yes " +reaxff="" ; [ "${REAXFF:-yes}" = "yes" ] && reaxff="-DPKG_REAXFF=yes " +replica="" ; [ "${REPLICA:-yes}" = "yes" ] && replica="-DPKG_REPLICA=yes " +rigid="" ; [ "${RIGID:-yes}" = "yes" ] && rigid="-DPKG_RIGID=yes " +shock="" ; [ "${SHOCK:-yes}" = "yes" ] && shock="-DPKG_SHOCK=yes " +smtbq="" ; [ "${SMTBQ:-yes}" = "yes" ] && smtbq="-DPKG_SMTBQ=yes " +sph="" ; [ "${SPH:-yes}" = "yes" ] && sph="-DPKG_SPH=yes " +spin="" ; [ "${SPIN:-yes}" = "yes" ] && spin="-DPKG_SPIN=yes " +srd="" ; [ "${SRD:-yes}" = "yes" ] && srd="-DPKG_SRD=yes " +tally="" ; [ "${TALLY:-yes}" = "yes" ] && tally="-DPKG_TALLY=yes " +uef="" ; [ "${UEF:-yes}" = "yes" ] && uef="-DPKG_UEF=yes " +yaff="" ; [ "${YAFF:-yes}" = "yes" ] && yaff="-DPKG_YAFF=yes " + +# If OpenBLAS is installed ELECTRODE will be enabled using the system LAPACK +# otherwise a bundled linear algebra is used. To force the use of internal +# linear algebra edit the CMake flag setting "-DUSE_INTERNAL_LINALG=yes " +if [ "$electrode" = "-DPKG_ELECTRODE=yes " ]; then + if pkg-config --exists openblas; then + electrode=$electrode"-DUSE_INTERNAL_LINALG=no " + fi +fi + +if [ "${PYTHON:-yes}" = "yes" ]; then + python="-DPKG_PYTHON=yes " + if [ -d /usr/doc/python3-numpy* ]; then + mliap="" ; [ "${MLIAP:-yes}" = "yes" ] && mliap="-DPKG_ML-IAP=yes -DMLIAP_ENABLE_PYTHON=autodetected " + else + mliap="" + fi +else + python="" + mliap="" +fi + +# The GPU package requires some basic settings that may be customized through environment +# variables. For advanced options requiring specific hardware configurations (GPU) see the +# documentation in lammps.org +# This package causes many issues depending on the hardware/software configuration (build +# failure or segmentation fault) that require additional settings to be solved, so it is +# disabled by default. +if [ "${GPU:-no}" = "yes" ]; then + # by default the GPU package is enabled using bundled OpenCL ICD loader library/headers + # but users may prefer the local opencl installed in the system + opencl_loader="yes" ; [ "${STATIC_OCL:-no}" = "no" ] && opencl_loader="no" + gpu="-DPKG_GPU=yes -DGPU_API=opencl -DUSE_STATIC_OPENCL_LOADER=${opencl_loader} " +else + opencl_loader="" + gpu="" +fi + +# Following conditions enable by default all packages that require dependencies if these +# are installed in the system + +latboltz="" +openmp="" +if [ "$MP" = "openmpi" ]; then + latboltz="" ; [ "${LATBOLTZ:-yes}" = "yes" ] && latboltz="-DPKG_LATBOLTZ=yes " + openmp="" ; [ "${OPENMP:-yes}" = "yes" ] && openmp="-DPKG_OPENMP=yes " +fi + +if [ "$MP" = "mpich" ]; then + latboltz="" ; [ "${LATBOLTZ:-yes}" = "yes" ] && latboltz="-DPKG_LATBOLTZ=yes " +fi + +if pkg-config --exists plumed; then + plumed="" ; [ "${PLUMED:-yes}" = "yes" ] && plumed="-DPKG_PLUMED=yes -DDOWNLOAD_PLUMED=no " +else + plumed="" +fi + +netcdf="" +if pkg-config --exists netcdf; then + netcdf="" ; [ "${NETCDF:-yes}" = "yes" ] && netcdf="-DPKG_NETCDF=yes " +fi + +h5md="" +if [ -f /usr/bin/h5cc ]; then + h5md="" ; [ "${H5MD:-yes}" = "yes" ] && h5md="-DPKG_H5MD=yes " +fi + +# This shouldn't need in 32-bit architectures, however it significantly extends the build times +# and absorbs many resources. Openmpi is strictly required. +kokkos="" +if [ "$ARCH" = "x86_64" ]; then + if [ "${KOKKOS:-yes}" = "yes" ] ; then + kokkos="-DPKG_KOKKOS=yes -DKokkos_ARCH_NATIVE=yes -DKokkos_ENABLE_OPENMP=yes " + fi + if [ "$MP" != "openmpi" ]; then + kokkos="" + fi +fi + +# All required cmake flags related to packages are included in a single global variable +packages=$amoeba$asphere$atc$awpmd$bocs$body$bpm$brownian$cgdna$cgspica$class2$colloid\ +$colvars$compress$coreshell$dielectric$diffraction$dipole$dpdbasic$dpdmeso$dpdreact\ +$dpdsmooth$drude$eff$electrode$extracompute$extradump$extrafix$extramolecule$extrapair\ +$fep$gpu$granular$h5md$intel$interlayer$kokkos$kspace$latboltz$lepton$machdyn$manifold\ +$manybody$mc$mdi$meam$mesont$mgpt$misc$mlhdnnp$mliap$mlpod$mlrann$mlsnap$mofff$molecule\ +$netcdf$openmp$opt$orient$peri$phonon$plugin$plumed$poems$ptm$qeq$qtb$reaction\ +$reaxff$replica$rigid$shock$smtbq$sph$spin$srd$tally$uef$yaff + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${SRCNAM}_${SRCVERSION} +tar xvf $CWD/${SRCNAM}_${SRCVERSION}.tar.gz +cd ${SRCNAM}_${SRCVERSION} + +if [ "$mesont" != "" ]; then + cp -a $CWD/C_10_10.mesocnt ./potentials + if [ "$molecule" = "" ]; then + echo -e "\n\033[33mYou have enabled the package MESONT. Since this package requires also " + echo -e "the package MOLECULE, the build of MOLECULE will be automatically enabled\033[0m\n" + packages=$packages" -DPKG_MOLECULE=yes " + fi +fi + +if [ "$MP" = "" ]; then + echo -e "\n\033[33m******************** WARNING ********************\n" + echo " no API supporting MPI (mpich or openmpi) are " + echo " installed on your system. This does not affect " + echo " the build and installation of LAMMPS, but some " + echo " packages cannot be enabled and other may work " + echo " not optimally. " + echo -e "\n*************************************************\n\033[0m" +fi + +# Prepare directories to move the extrafiles needed to build some packages +mkdir -p cmake/build + +if [ "$opencl_loader" = "yes" ]; then + mkdir -p cmake/build/_deps + cp -a $CWD/opencl-loader-$OCLLVERSION.tar.gz cmake/build/_deps +fi + +if [ "$mdi" != "" ]; then + mkdir -p cmake/build/mdi_build_ext/src/ + cp -a $CWD/MDI_Library-$MDIVERSION.tar.gz cmake/build/mdi_build_ext/src/v$MDIVERSION.tar.gz +fi + + +if [ "$mlhdnnp" != "" ]; then + mkdir -p cmake/build/n2p2_build-prefix/src/ + cp -a $CWD/n2p2-$N2P2VERSION.tar.gz cmake/build/n2p2_build-prefix/src/v$N2P2VERSION.tar.gz +fi + +if [ "$mlpace" != "" ]; then + cp -a $CWD/lammps-user-pace-$PACEVERSION.tar.gz cmake/build/libpace.tar.gz +fi + +echo -e "\nFLAGS FOR PACKAGES ENABLED:\n "$packages"\n" + +echo -e "FLAGS FOR PYTHON:\n "$python + +echo -e "\nFLAGS FOR MPI:\n "$mpi + +echo -e "\nFLAGS FOR SCAFACOS:\n "$scafacos + +echo -e "\nFLAGS FOR ML-PACE:\n "$mlpace + +echo "" + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# The Source has not a CMakeLists.txt file in the root directory we +# need to change in the cmake directory +cd cmake +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + -DBUILD_SHARED_LIBS=ON \ + $mpi \ + $scafacos \ + $mdi \ + $python \ + $mlpace \ + $packages \ + .. + make + make install DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +#Since the build installs man in /usr/share we move the directory in /usr +mv -v $PKG/usr/share/man $PKG/usr +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +#Since the build installs etc as subfolder of /usr (?), we move it in the root directory +mv -v $PKG/usr/etc $PKG + +cd $TMP/${SRCNAM}_${SRCVERSION} +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE README $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/lammps/lammps.info b/academic/lammps/lammps.info new file mode 100644 index 0000000000..8583388823 --- /dev/null +++ b/academic/lammps/lammps.info @@ -0,0 +1,20 @@ +PRGNAM="lammps" +VERSION="2023.08.02_update3" +HOMEPAGE="https://www.lammps.org" +DOWNLOAD="https://github.com/lammps/lammps/archive/stable_2Aug2023_update3/lammps-stable_2Aug2023_update3.tar.gz \ + https://download.lammps.org/potentials/C_10_10.mesocnt \ + https://download.lammps.org/thirdparty/opencl-loader-2022.01.04.tar.gz \ + https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26/MDI_Library-1.4.26.tar.gz \ + https://github.com/CompPhysVienna/n2p2/archive/v2.2.0/n2p2-2.2.0.tar.gz \ + https://github.com/ICAMS/lammps-user-pace/archive/v.2023.10.04.tar.gz" +MD5SUM="a68cd5d9f70822da73092457bc3ccede \ + 68b5ca26283968fd9889aa0a37f7b7fb \ + 8d3a801e87a2c6653bf0e27707063914 \ + 3124bb85259471e2a53a891f04bf697a \ + a2d9ab7f676b3a74a324fc1eda0a911d \ + 70ff79f4e59af175e55d24f3243ad1ff" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="openmpi scafacos" +MAINTAINER="Giancarlo Dessi" +EMAIL="slack@giand.it" diff --git a/academic/lammps/slack-desc b/academic/lammps/slack-desc new file mode 100644 index 0000000000..c082c858ab --- /dev/null +++ b/academic/lammps/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +lammps: lammps (LAMMPS Molecular Dynamics Simulator) +lammps: +lammps: LAMMPS stands for +lammps: Large-scale Atomic/Molecular Massively Parallel Simulator. +lammps: It was developed at Sandia National Laboratories (US Department of +lammps: Energy) and is designed to run efficiently on parallel computers. +lammps: +lammps: +lammps: Home page: https://www.lamps.org +lammps: +lammps: diff --git a/academic/lapacke/lapacke.SlackBuild b/academic/lapacke/lapacke.SlackBuild index 6c8b77bc67..61025be61b 100644 --- a/academic/lapacke/lapacke.SlackBuild +++ b/academic/lapacke/lapacke.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for LAPACKE -# Copyright 2016-2021 Kyle Guinn <elyk03@gmail.com> +# Copyright 2016-2024 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=lapacke SRCNAM=lapack -VERSION=${VERSION:-3.10.0} +VERSION=${VERSION:-3.12.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -39,22 +39,19 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="LAPACKE/LICENSE LAPACKE/README DOCS/lapacke.pdf" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then diff --git a/academic/lapacke/lapacke.info b/academic/lapacke/lapacke.info index 414042cc96..fe7070f8aa 100644 --- a/academic/lapacke/lapacke.info +++ b/academic/lapacke/lapacke.info @@ -1,8 +1,8 @@ PRGNAM="lapacke" -VERSION="3.10.0" +VERSION="3.12.0" HOMEPAGE="https://www.netlib.org/lapack/lapacke.html" -DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.10.0/lapack-3.10.0.tar.gz" -MD5SUM="d70fc27a8bdebe00481c97c728184f09" +DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.12.0/lapack-3.12.0.tar.gz" +MD5SUM="c1b38bef123584d86a1bd8000784a7b2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="lapack" diff --git a/academic/lapacke/patches/cmake-piecewise.diff b/academic/lapacke/patches/cmake-piecewise.diff index f8ee150b59..37cde2acaa 100644 --- a/academic/lapacke/patches/cmake-piecewise.diff +++ b/academic/lapacke/patches/cmake-piecewise.diff @@ -2,15 +2,15 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt --- a/CBLAS/CMakeLists.txt +++ b/CBLAS/CMakeLists.txt @@ -1,8 +1,6 @@ - message(STATUS "CBLAS enable") + message(STATUS "CBLAS enabled") enable_language(C) -set(LAPACK_INSTALL_EXPORT_NAME ${CBLASLIB}-targets) - # Create a header file cblas.h for the routines called in my C programs - include(FortranCInterface) - ## Ensure that the fortran compiler and c compiler specified are compatible -@@ -51,22 +49,3 @@ + include(CheckLanguage) + check_language(Fortran) +@@ -54,22 +52,3 @@ DESTINATION ${PKG_CONFIG_DIR} COMPONENT Development ) @@ -56,15 +56,12 @@ diff --git a/CBLAS/cmake/cblas-config-install.cmake.in b/CBLAS/cmake/cblas-confi deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-install.cmake.in +++ /dev/null -@@ -1,23 +0,0 @@ +@@ -1,19 +0,0 @@ -# Compute locations from <prefix>/@{LIBRARY_DIR@/cmake/lapacke-<v>/<self>.cmake -get_filename_component(_CBLAS_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_SELF_DIR}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_PREFIX}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_CBLAS_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") +-set(LAPACK_DIR "@CMAKE_INSTALL_FULL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. @@ -73,12 +70,11 @@ deleted file mode 100644 -endif() - -# Report lapacke header search locations. --set(CBLAS_INCLUDE_DIRS ${_CBLAS_PREFIX}/include) +-set(CBLAS_INCLUDE_DIRS @CMAKE_INSTALL_FULL_INCLUDEDIR@) - -# Report lapacke libraries. -set(CBLAS_LIBRARIES @CBLASLIB@) - --unset(_CBLAS_PREFIX) -unset(_CBLAS_SELF_DIR) diff --git a/CBLAS/cmake/cblas-config-version.cmake.in b/CBLAS/cmake/cblas-config-version.cmake.in deleted file mode 100644 @@ -96,15 +92,15 @@ deleted file mode 100644 diff --git a/CBLAS/src/CMakeLists.txt b/CBLAS/src/CMakeLists.txt --- a/CBLAS/src/CMakeLists.txt +++ b/CBLAS/src/CMakeLists.txt -@@ -123,9 +123,5 @@ +@@ -172,9 +172,5 @@ if(HAS_ATTRIBUTE_WEAK_SUPPORT) target_compile_definitions(${CBLASLIB} PRIVATE HAS_ATTRIBUTE_WEAK_SUPPORT) endif() -target_include_directories(${CBLASLIB} PUBLIC -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../include> +- $<BUILD_INTERFACE:${LAPACK_BINARY_DIR}/include> - $<INSTALL_INTERFACE:include> -) - target_link_libraries(${CBLASLIB} PRIVATE ${BLAS_LIBRARIES}) + target_link_libraries(${CBLASLIB} PUBLIC ${BLAS_LIBRARIES}) lapack_install_library(${CBLASLIB}) diff --git a/CMAKE/lapack-config-build.cmake.in b/CMAKE/lapack-config-build.cmake.in deleted file mode 100644 @@ -152,8 +148,8 @@ deleted file mode 100644 diff --git a/CMakeLists.txt b/CMakeLists.txt --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -157,11 +157,8 @@ - +@@ -155,11 +155,8 @@ + endif() # -------------------------------------------------- -set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKLIB}-targets) @@ -164,30 +160,8 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Development LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT RuntimeLibraries RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT RuntimeLibraries -@@ -201,21 +198,6 @@ - include(CheckLAPACKCompilerFlags) - CheckLAPACKCompilerFlags() +@@ -218,8 +215,9 @@ --# -------------------------------------------------- --# Check second function -- --include(CheckTimeFunction) --set(NONE ${TIME_FUNC}) --CHECK_TIME_FUNCTION(NONE TIME_FUNC) --CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) --CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) --CHECK_TIME_FUNCTION(EXT_ETIME_ TIME_FUNC) --CHECK_TIME_FUNCTION(INT_ETIME TIME_FUNC) --message(STATUS "--> Will use second_${TIME_FUNC}.f and dsecnd_${TIME_FUNC}.f as timing function.") -- --set(SECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/second_${TIME_FUNC}.f) --set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) -- - # deprecated LAPACK and LAPACKE routines - option(BUILD_DEPRECATED "Build deprecated routines" OFF) - message(STATUS "Build deprecated routines: ${BUILD_DEPRECATED}") -@@ -239,8 +221,9 @@ - endif() # -------------------------------------------------- -# Subdirectories that need to be processed @@ -197,7 +171,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided BLAS libraries if(BLAS_LIBRARIES) -@@ -251,131 +234,105 @@ +@@ -230,59 +228,41 @@ if(BLAS_FOUND) message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRARIES}.") else() @@ -268,21 +242,28 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided or automatically found LAPACK libraries if(LAPACK_LIBRARIES) - include(CheckFortranFunctionExists) - set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) - # Check if new routine of 3.4.0 is in LAPACK_LIBRARIES -- CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LATESTLAPACK_FOUND) -+ CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LAPACK_FOUND) - unset(CMAKE_REQUIRED_LIBRARIES) -- if(LATESTLAPACK_FOUND) -+ if(LAPACK_FOUND) - message(STATUS "--> LAPACK supplied by user is WORKING, will use ${LAPACK_LIBRARIES}.") +@@ -293,27 +273,28 @@ + include(CheckFortranFunctionExists) + set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) + # Check if new routine of 3.4.0 is in LAPACK_LIBRARIES +- CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LATESTLAPACK_FOUND) ++ CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LAPACK_FOUND) + unset(CMAKE_REQUIRED_LIBRARIES) +- if(LATESTLAPACK_FOUND) ++ if(LAPACK_FOUND) + message(STATUS "--> LAPACK supplied by user is WORKING, will use ${LAPACK_LIBRARIES}.") + else() +- message(ERROR "--> LAPACK supplied by user is not WORKING or is older than LAPACK 3.4.0, CANNOT USE ${LAPACK_LIBRARIES}.") +- message(ERROR "--> Will use REFERENCE LAPACK (by default)") +- message(ERROR "--> Or Correct your LAPACK_LIBRARIES entry ") +- message(ERROR "--> Or Consider checking USE_OPTIMIZED_LAPACK") ++ message(SEND_ERROR "--> LAPACK supplied by user is NOT WORKING or is older than LAPACK 3.4.0, cannot use ${LAPACK_LIBRARIES}.") + endif() else() -- message(ERROR "--> LAPACK supplied by user is not WORKING or is older than LAPACK 3.4.0, CANNOT USE ${LAPACK_LIBRARIES}.") -- message(ERROR "--> Will use REFERENCE LAPACK (by default)") -- message(ERROR "--> Or Correct your LAPACK_LIBRARIES entry ") -- message(ERROR "--> Or Consider checking USE_OPTIMIZED_LAPACK") -+ message(SEND_ERROR "--> LAPACK supplied by user is NOT WORKING or is older than LAPACK 3.4.0, cannot use ${LAPACK_LIBRARIES}.") + message(STATUS "--> LAPACK supplied by user is ${LAPACK_LIBRARIES}.") + message(STATUS "--> CMake couldn't find a Fortran compiler, so it cannot check if the provided LAPACK library works.") +- set(LATESTLAPACK_FOUND TRUE) ++ set(LAPACK_FOUND TRUE) endif() -endif() @@ -298,20 +279,12 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + set(LAPACK_FOUND TRUE) + + set(NEED_BLAS TRUE) -+ -+ # Check second function -+ include(CheckTimeFunction) -+ set(NONE ${TIME_FUNC}) -+ CHECK_TIME_FUNCTION(NONE TIME_FUNC) -+ CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) -+ CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) -+ CHECK_TIME_FUNCTION(EXT_ETIME_ TIME_FUNC) -+ CHECK_TIME_FUNCTION(INT_ETIME TIME_FUNC) -+ message(STATUS "--> Will use second_${TIME_FUNC}.f and dsecnd_${TIME_FUNC}.f as timing function.") -+ -+ set(SECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/second_${TIME_FUNC}.f) -+ set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) -+ + + enable_language(Fortran) + +@@ -336,67 +317,38 @@ + set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) + add_subdirectory(SRC) -else() - set(CMAKE_EXE_LINKER_FLAGS @@ -349,16 +322,17 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt option(LAPACKE_WITH_TMG "Build LAPACKE with tmglib routines" OFF) if(LAPACKE_WITH_TMG) - set(LAPACKE ON) -+ set(BUILD_LAPACKE ON) - endif() - +-endif() +- -# TMGLIB -# Cache export target -set(LAPACK_INSTALL_EXPORT_NAME_CACHE ${LAPACK_INSTALL_EXPORT_NAME}) -if(BUILD_TESTING OR LAPACKE_WITH_TMG) +- enable_language(Fortran) - if(LATESTLAPACK_FOUND AND LAPACKE_WITH_TMG) - set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) - # Check if dlatms (part of tmg) is found +- include(CheckFortranFunctionExists) - CHECK_FORTRAN_FUNCTION_EXISTS("dlatms" LAPACK_WITH_TMGLIB_FOUND) - unset(CMAKE_REQUIRED_LIBRARIES) - if(NOT LAPACK_WITH_TMGLIB_FOUND) @@ -368,18 +342,29 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt - endif() - endif() - add_subdirectory(TESTING/MATGEN) --endif() ++ set(BUILD_LAPACKE ON) + endif() -# Reset export target -set(LAPACK_INSTALL_EXPORT_NAME ${LAPACK_INSTALL_EXPORT_NAME_CACHE}) -unset(LAPACK_INSTALL_EXPORT_NAME_CACHE) - + +-#------------------------------------- +-# LAPACKE + # Include lapack.h and lapacke_mangling.h even if LAPACKE is not built + add_subdirectory(LAPACKE/include) + -if(LAPACKE) +if(BUILD_LAPACKE) + set(NEED_LAPACK TRUE) add_subdirectory(LAPACKE) endif() -@@ -428,111 +385,16 @@ +- + #------------------------------------- + # BLAS++ / LAPACK++ + option(BLAS++ "Build BLAS++" OFF) +@@ -446,111 +398,16 @@ ExternalProject_Add_StepDependencies(lapackpp build blaspp ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) endif() @@ -397,7 +382,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -set(CPACK_PACKAGE_INSTALL_DIRECTORY "LAPACK") -if(WIN32 AND NOT UNIX) - # There is a bug in NSI that does not handle full unix paths properly. Make -- # sure there is at least one set of four (4) backlasshes. +- # sure there is at least one set of four (4) backslashes. - set(CPACK_NSIS_HELP_LINK "http:\\\\\\\\http://icl.cs.utk.edu/lapack-forum") - set(CPACK_NSIS_URL_INFO_ABOUT "http:\\\\\\\\www.netlib.org/lapack") - set(CPACK_NSIS_CONTACT "lapack@eecs.utk.edu") @@ -501,20 +486,20 @@ diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt --- a/LAPACKE/CMakeLists.txt +++ b/LAPACKE/CMakeLists.txt @@ -1,8 +1,6 @@ - message(STATUS "LAPACKE enable") + message(STATUS "LAPACKE enabled") enable_language(C) -set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKELIB}-targets) - - # Create a header file lapacke_mangling.h for the routines called in my C programs - include(FortranCInterface) - ## Ensure that the fortran compiler and c compiler specified are compatible -@@ -79,14 +77,6 @@ + include_directories(include ${LAPACK_BINARY_DIR}/include) + add_subdirectory(src) + add_subdirectory(utils) +@@ -74,14 +72,6 @@ VERSION ${LAPACK_VERSION} SOVERSION ${LAPACK_MAJOR_VERSION} ) -target_include_directories(${LAPACKELIB} PUBLIC -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> +- $<BUILD_INTERFACE:${LAPACK_BINARY_DIR}/include> - $<INSTALL_INTERFACE:include> -) -if(WIN32 AND NOT UNIX) @@ -524,7 +509,7 @@ diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt if(LAPACKE_WITH_TMG) target_link_libraries(${LAPACKELIB} PRIVATE ${TMGLIB}) -@@ -111,22 +101,3 @@ +@@ -106,22 +96,3 @@ DESTINATION ${PKG_CONFIG_DIR} COMPONENT Development ) @@ -573,15 +558,12 @@ diff --git a/LAPACKE/cmake/lapacke-config-install.cmake.in b/LAPACKE/cmake/lapac deleted file mode 100644 --- a/LAPACKE/cmake/lapacke-config-install.cmake.in +++ /dev/null -@@ -1,26 +0,0 @@ +@@ -1,22 +0,0 @@ -# Compute locations from <prefix>/@{LIBRARY_DIR@/cmake/lapacke-<v>/<self>.cmake -get_filename_component(_LAPACKE_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_SELF_DIR}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_PREFIX}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_LAPACKE_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") +-set(LAPACK_DIR "@CMAKE_INSTALL_FULL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. @@ -593,12 +575,11 @@ deleted file mode 100644 -set(LAPACKE_Fortran_COMPILER_ID ${LAPACK_Fortran_COMPILER_ID}) - -# Report lapacke header search locations. --set(LAPACKE_INCLUDE_DIRS ${_LAPACKE_PREFIX}/include) +-set(LAPACKE_INCLUDE_DIRS @CMAKE_INSTALL_FULL_INCLUDEDIR@) - -# Report lapacke libraries. -set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) - --unset(_LAPACKE_PREFIX) -unset(_LAPACKE_SELF_DIR) diff --git a/LAPACKE/cmake/lapacke-config-version.cmake.in b/LAPACKE/cmake/lapacke-config-version.cmake.in deleted file mode 100644 @@ -613,3 +594,20 @@ deleted file mode 100644 - endif() -endif() - +diff --git a/LAPACKE/include/CMakeLists.txt b/LAPACKE/include/CMakeLists.txt +--- a/LAPACKE/include/CMakeLists.txt ++++ b/LAPACKE/include/CMakeLists.txt +@@ -1,5 +1,5 @@ + set(LAPACKE_INCLUDE lapack.h) +-IF(LAPACKE) ++IF(BUILD_LAPACKE) + list(APPEND LAPACKE_INCLUDE lapacke.h lapacke_config.h lapacke_utils.h) + endif() + +@@ -23,4 +23,4 @@ + message(WARNING "Reverting to pre-defined include/lapacke_mangling.h") + configure_file(lapacke_mangling_with_flags.h.in + ${LAPACK_BINARY_DIR}/include/lapacke_mangling.h) +-endif() +\ No newline at end of file ++endif() diff --git a/academic/ldl/ldl.SlackBuild b/academic/ldl/ldl.SlackBuild index 75e05912fe..d7b79fb194 100644 --- a/academic/ldl/ldl.SlackBuild +++ b/academic/ldl/ldl.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/libghemical/libghemical.SlackBuild b/academic/libghemical/libghemical.SlackBuild index 2e17949822..21465899c3 100644 --- a/academic/libghemical/libghemical.SlackBuild +++ b/academic/libghemical/libghemical.SlackBuild @@ -8,13 +8,13 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=libghemical VERSION=${VERSION:-3.0.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -32,8 +32,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -88,6 +88,8 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/link-grammar/link-grammar.SlackBuild b/academic/link-grammar/link-grammar.SlackBuild index f36e347907..a7686f7c7a 100644 --- a/academic/link-grammar/link-grammar.SlackBuild +++ b/academic/link-grammar/link-grammar.SlackBuild @@ -9,13 +9,13 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=link-grammar VERSION=${VERSION:-4.8.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -33,8 +33,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -88,6 +88,8 @@ find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/link-grammar/link-grammar.info b/academic/link-grammar/link-grammar.info index ce4fe11b19..5e493b4686 100644 --- a/academic/link-grammar/link-grammar.info +++ b/academic/link-grammar/link-grammar.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.abisource.com/downloads/link-grammar/4.8.0/link-grammar-4.8 MD5SUM="218a2ee5ffed258bc52a0718811ca66e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="apache-ant jdk" +REQUIRES="apache-ant zulu-openjdk8" MAINTAINER="Michael Gabilondo" EMAIL="mgabilo{at}gmail{dot}com" diff --git a/academic/locarna/locarna.SlackBuild b/academic/locarna/locarna.SlackBuild index 1834ccf8f8..1e84cfa434 100644 --- a/academic/locarna/locarna.SlackBuild +++ b/academic/locarna/locarna.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=locarna VERSION=${VERSION:-1.9.2.3} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -109,6 +109,8 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/louvain-community/README b/academic/louvain-community/README new file mode 100644 index 0000000000..8a989dc3f4 --- /dev/null +++ b/academic/louvain-community/README @@ -0,0 +1,98 @@ +[License: LGPL v3] [build] + +Multi-criteria community detection library + +This library makes the Louvain community detection system +significantly easier to use. Example code: + + #include "louvain_communities/louvain_communities.h" #include +<iostream> + + int main(int /*argc*/, char** /*argv*/) { LouvainC::Communities +graph; + + //First community graph.add_edge(1, 2, 2L); +graph.add_edge(1, 3, 2L); graph.add_edge(1, 4, 2L); +graph.add_edge(2, 3, 2L); graph.add_edge(2, 4, 2L); +graph.add_edge(3, 4, 2L); + + //Second community graph.add_edge(4, 5, 2L); +graph.add_edge(4, 6, 2L); graph.add_edge(4, 7, 2L); +graph.add_edge(5, 6, 2L); graph.add_edge(5, 7, 2L); +graph.add_edge(6, 7, 2L); + + //Weak connection between 1st and 2nd communities +graph.add_edge(1, 4, 0.1L); + + //Calculate communities gplain.calculate(true); + + //Get community mapping auto r = gplain.get_mapping(); +for(auto& vert_to_comm: r) { std::cout << "Vertext " << +vert_to_comm.first << " is in community " << vert_to_comm.second << +std::endl; } } + +How to build + +To build: + + git clone https://github.com/meelgroup/louvain-community cd +louvain-community mkdir build && cd build cmake .. make -j4 sudo +make install + +In case you are going to use the system in another cmake based +project, you don’t even need to install. In these cases, you can +look for the library in your CMakeLists.txt file via: + + find_package(louvain_communities CONFIG) if +(louvain_communities_FOUND) message(STATUS "Found Louvain +Communities library") message(STATUS "Louvain Communities dynamic +lib: ${LOUVAIN_COMMUNITIES_LIBRARIES}") message(STATUS "Louvain +Communities include dirs: ${LOUVAIN_COMMUNITIES_INCLUDE_DIRS}") +else() message(FATAL_ERROR "Cannot find Louvain Communities +libraries. Please install it! Exiting.") endif() + +To compile a static library simply do: + + git clone https://github.com/meelgroup/louvain-community cd +louvain-community mkdir build && cd build cmake -DSTATICCOMPILE=ON +.. make -j4 sudo make install + +Testing + +To test: + + pip install python-louvain + + git clone https://github.com/jlguillaume/louvain cd louvain make +-j4 + + git clone https://github.com/meelgroup/louvain-community cd +louvain-community mkdir build && cd build ln -s ../scritps/* . ln +-s ../../louvain/louvain . ./mytest.py 50-10-9-q.cnf.gz.no_w.cnf +awk '{print "gplain.add_edge(" $1 ", " $2 ", " $3 "L);"}' graph.txt +> ../src/mygraph.cpp cmake -DENABLE_TESTING=ON .. make -j4 +> ./test.sh 50-10-9-q.cnf.gz.no_w.cnf + +To check how well the communities fit a graph generated via VIG +(“Variable Incidence Graph”) graph-generation from a DIMACS CNF and +a layout engine using the spring method: + + pip install python-louvain git clone +https://github.com/meelgroup/louvain-community cd louvain-community +mkdir build && cd build ln -s ../scritps/* . ./mytest.py +50-10-9-q.cnf.gz.no_w.cnf --draw + +References + +Based on Community Detection “Louvain”, version 0.3, from +SourceForge + +Based on the article “Fast unfolding of community hierarchies in +large networks” Copyright (C) 2008 V. Blondel, J.-L. Guillaume, R. +Lambiotte, E. Lefebvre + +And based on the article Copyright (C) 2013 R. Campigotto, P. Conde +Céspedes, J.-L. Guillaume + +Authors: E. Lefebvre, adapted by J.-L. Guillaume and R. Campigotto, +Mate Soos diff --git a/academic/louvain-community/louvain-community.SlackBuild b/academic/louvain-community/louvain-community.SlackBuild new file mode 100644 index 0000000000..1afcd20183 --- /dev/null +++ b/academic/louvain-community/louvain-community.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/bash + +# Slackware build script for louvain-community + +# Copyright 2024 Caterino Tommaso, T.O.P. USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=louvain-community +VERSION=${VERSION:-681a711} +FULLHASH=${FULLHASH:-681a711a530ded0b25af72ee4881d453a80ac8ac} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$FULLHASH +tar xvf $CWD/$PRGNAM-$FULLHASH.tar.gz +cd $PRGNAM-$FULLHASH +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -name perllocal.pod -o -name ".packlist" -o -name "*.bs" | xargs rm -f || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE.txt README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/louvain-community/louvain-community.info b/academic/louvain-community/louvain-community.info new file mode 100644 index 0000000000..df40a89ce7 --- /dev/null +++ b/academic/louvain-community/louvain-community.info @@ -0,0 +1,10 @@ +PRGNAM="louvain-community" +VERSION="681a711" +HOMEPAGE="https://github.com/meelgroup/louvain-community" +DOWNLOAD="https://github.com/meelgroup/louvain-community/archive/681a711/louvain-community-681a711a530ded0b25af72ee4881d453a80ac8ac.tar.gz" +MD5SUM="f148a5a439ccf5c47a9795c31350b467" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Caterino Tommaso, T.O.P." +EMAIL="aNOlan_aversa@lavabiSPAMt.com (remove NO and SPAM)" diff --git a/academic/louvain-community/slack-desc b/academic/louvain-community/slack-desc new file mode 100644 index 0000000000..a4fd5d8f82 --- /dev/null +++ b/academic/louvain-community/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +louvain-community: louvain-community (Louvain Community Detection Library) +louvain-community: +louvain-community: This graph algorithms library finds communities in networks. +louvain-community: +louvain-community: It is a requirement for cryptominisat's advanced statistics option. +louvain-community: +louvain-community: +louvain-community: +louvain-community: +louvain-community: +louvain-community: diff --git a/academic/mafft/mafft.SlackBuild b/academic/mafft/mafft.SlackBuild index 4757e84b57..746a5978c3 100644 --- a/academic/mafft/mafft.SlackBuild +++ b/academic/mafft/mafft.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for mafft -# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=mafft -VERSION=${VERSION:-7.475} +VERSION=${VERSION:-7.520} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -69,9 +69,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION-with-extensions -tar xvf $CWD/$PRGNAM-$VERSION-with-extensions-src.tgz -cd $PRGNAM-$VERSION-with-extensions +rm -rf $PRGNAM-v${VERSION} +tar xvf $CWD/$PRGNAM-v${VERSION}.tar.gz +cd $PRGNAM-v${VERSION} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -134,7 +134,7 @@ cp -a test $PKG/usr/share/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - license readme \ + license license.extensions README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References diff --git a/academic/mafft/mafft.info b/academic/mafft/mafft.info index 5663f559f8..5b589bcf11 100644 --- a/academic/mafft/mafft.info +++ b/academic/mafft/mafft.info @@ -1,8 +1,8 @@ PRGNAM="mafft" -VERSION="7.475" +VERSION="7.520" HOMEPAGE="https://mafft.cbrc.jp/alignment/software/" -DOWNLOAD="https://mafft.cbrc.jp/alignment/software/mafft-7.475-with-extensions-src.tgz" -MD5SUM="7edeb0ff62260bba8bdf682e0bb604e4" +DOWNLOAD="https://gitlab.com/sysimm/mafft/-/archive/v7.520/mafft-v7.520.tar.gz" +MD5SUM="8d53ef6ecf6822d00c9d356f59f5aabe" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/mathics/README b/academic/mathics/README index 9cac17e266..59741fe499 100644 --- a/academic/mathics/README +++ b/academic/mathics/README @@ -1,4 +1,22 @@ -Mathics is a free, light-weight alternative to Mathematica. Mathics is -a general-purpose online computer algebra system featuring Mathematica- -compatible syntax and functions. It is backed by highly extensible -Python code, relying on SymPy for most mathematical tasks. +Mathics is a general-purpose computer algebra system (CAS). It is an +open-source alternative to Mathematica. It is free both as in "free +beer" and as in "freedom". + +The home page of Mathics is https://mathics.org. + +Installing and Running +See read the docs guide +https://mathics-development-guide.readthedocs.io/en/latest/ +for instructions on installing +https://mathics-development-guide.readthedocs.io/en/latest/ +and running +https://mathics-development-guide.readthedocs.io/en/latest/running.html + +Contributing +Please feel encouraged to contribute to Mathics! Create your own fork, +make the desired changes, commit, and make a pull request. + +License + +Mathics is released under the GNU General Public License Version 3 +(GPL3). diff --git a/academic/mathics/mathics.SlackBuild b/academic/mathics/mathics.SlackBuild index 6979a0b9ab..72870973ea 100644 --- a/academic/mathics/mathics.SlackBuild +++ b/academic/mathics/mathics.SlackBuild @@ -25,11 +25,13 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=mathics -VERSION=${VERSION:-1.0} +VERSION=${VERSION:-4.0.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +SRCNAM=Mathics3 + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -69,9 +71,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf Mathics-$VERSION -tar xvf $CWD/Mathics-$VERSION.tar.gz -cd Mathics-$VERSION +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -79,7 +81,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -python2 setup.py install --root=$PKG +python3 setup.py install --root=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/mathics/mathics.info b/academic/mathics/mathics.info index bfd80981e7..4f4c0e7aa2 100644 --- a/academic/mathics/mathics.info +++ b/academic/mathics/mathics.info @@ -1,10 +1,10 @@ PRGNAM="mathics" -VERSION="1.0" +VERSION="4.0.0" HOMEPAGE="http://www.mathics.org/" -DOWNLOAD="https://github.com/mathics/Mathics/archive/v1.0/Mathics-1.0.tar.gz" -MD5SUM="a0a161a1787093b90b21e73b0d44c0fc" +DOWNLOAD="https://files.pythonhosted.org/packages/35/68/72d4ec12fe91c3cf569fe95ba20ae324414e59f624ad3fb3eaf767cf2620/Mathics3-4.0.0.tar.gz" +MD5SUM="f221aaf0ef9a27e2953429a32fe94652" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="colorama mpmath python2-dateutil python2-django-legacy sympy" +REQUIRES="python2-numpy python2-sympy" MAINTAINER="David Melik" EMAIL="dchmelik@gmail.com" diff --git a/academic/mathics/slack-desc b/academic/mathics/slack-desc index 1578bda0e9..a351c60962 100644 --- a/academic/mathics/slack-desc +++ b/academic/mathics/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| mathics: mathics (A free, light-weight alternative to Mathematica) mathics: -mathics: Mathics is a free, general-purpose online computer algebra system -mathics: featuring Mathematica-compatible syntax and functions. It is backed -mathics: by highly extensible Python code, relying on SymPy for most -mathics: mathematical tasks. -mathics: -mathics: http://www.mathics.org/ -mathics: +mathics: Mathics is a general-purpose computer algebra system (CAS). It is an +mathics: open-source alternative to Mathematica. It is free both as in "free +mathics: beer" and as in "freedom". mathics: +mathics: The home page of Mathics is https://mathics.org. mathics: +mathics: Installing and Running +mathics: See https://mathics-development-guide.readthedocs.io/en/latest/ for +mathics: instructions on installing and running. diff --git a/academic/mathjax2/README b/academic/mathjax2/README new file mode 100644 index 0000000000..432f11787d --- /dev/null +++ b/academic/mathjax2/README @@ -0,0 +1,2 @@ +MathJax is an open-source JavaScript display engine for mathematics +that works in all modern browsers. diff --git a/academic/mathjax2/mathjax2.SlackBuild b/academic/mathjax2/mathjax2.SlackBuild new file mode 100644 index 0000000000..fb1d4ce3a2 --- /dev/null +++ b/academic/mathjax2/mathjax2.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/bash + +# Slackware build script for mathjax2 + +# Copyright 2022 Isaac Yu <isaacyu@protonmail.com> +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=mathjax2 +VERSION=${VERSION:-2.7.9} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=MathJax + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Remove unneeded stuff. Refer to the Arch Linux PKGBUILD: +# https://github.com/archlinux/svntogit-community/blob/packages/mathjax2/trunk/PKGBUILD +rm -r docs test unpacked +rm -r fonts/HTML-CSS/TeX/png +for _format in eot otf svg ; do + find . -type d -name "$_format" -prune -exec rm -rf {} \; +done + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/share/fonts +cp -a ../$SRCNAM-$VERSION $PKG/usr/share/mathjax2 +mv $PKG/usr/share/mathjax2/fonts $PKG/usr/share/fonts/mathjax2 +ln -s /usr/share/fonts/mathjax2 $PKG/usr/share/mathjax2/fonts + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CONTRIBUTING.md LICENSE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mathjax2/mathjax2.info b/academic/mathjax2/mathjax2.info new file mode 100644 index 0000000000..66b659c608 --- /dev/null +++ b/academic/mathjax2/mathjax2.info @@ -0,0 +1,10 @@ +PRGNAM="mathjax2" +VERSION="2.7.9" +HOMEPAGE="https://www.mathjax.org/" +DOWNLOAD="https://github.com/mathjax/MathJax/archive/2.7.9/MathJax-2.7.9.tar.gz" +MD5SUM="9032fe7c1c9dcae7f85c20c67435de23" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Isaac Yu" +EMAIL="isaacyu@protonmail.com" diff --git a/academic/avogadro/slack-desc b/academic/mathjax2/slack-desc index 50fba281d9..88b8b156bf 100644 --- a/academic/avogadro/slack-desc +++ b/academic/mathjax2/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -avogadro: avogadro (An advanced molecular editor based on Qt 4.) -avogadro: -avogadro: Avogadro is a molecular graphics and modelling system targetted at -avogadro: molecules and biomolecules. It can visualize properties like -avogadro: molecular orbitals or electrostatic potentials and features an -avogadro: intuitive molecular builder. -avogadro: -avogadro: Homepage: http://avogadro.cc/ -avogadro: -avogadro: -avogadro: +mathjax2: mathjax2 (Beautiful math in all browsers) +mathjax2: +mathjax2: MathJax is an open-source JavaScript display engine for mathematics +mathjax2: that works in all modern browsers. +mathjax2: +mathjax2: +mathjax2: +mathjax2: +mathjax2: +mathjax2: +mathjax2: diff --git a/academic/mathomatic/mathomatic.SlackBuild b/academic/mathomatic/mathomatic.SlackBuild index 498aab76d1..ec96c60228 100644 --- a/academic/mathomatic/mathomatic.SlackBuild +++ b/academic/mathomatic/mathomatic.SlackBuild @@ -34,7 +34,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -52,8 +52,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/matio/matio.SlackBuild b/academic/matio/matio.SlackBuild index 359465d8b9..9c12742701 100644 --- a/academic/matio/matio.SlackBuild +++ b/academic/matio/matio.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=matio -VERSION=${VERSION:-1.5.9} +VERSION=${VERSION:-1.5.23} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -105,6 +105,8 @@ rm -rf $PKG/usr/share/info/ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/matio/matio.info b/academic/matio/matio.info index a10b48a397..4ceeb67884 100644 --- a/academic/matio/matio.info +++ b/academic/matio/matio.info @@ -1,8 +1,8 @@ PRGNAM="matio" -VERSION="1.5.9" +VERSION="1.5.23" HOMEPAGE="https://sourceforge.net/projects/matio/" -DOWNLOAD="https://sourceforge.net/projects/matio/files/matio/1.5.9/matio-1.5.9.tar.gz" -MD5SUM="aab5b4219a3c0262afe7eeb7bdd2f463" +DOWNLOAD="https://downloads.sf.net/matio/matio-1.5.23.tar.gz" +MD5SUM="25dfaf33af030a170eb9d3814cac1fca" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="hdf5" diff --git a/academic/maxima/README b/academic/maxima/README index 35a04af3fa..d084e4cb04 100644 --- a/academic/maxima/README +++ b/academic/maxima/README @@ -1,7 +1,26 @@ -Maxima is a system for the manipulation of symbolic and numerical -expressions, including differentiation, integration, Taylor series, -Laplace transforms, ordinary differential equations, systems of linear -equations, polynomials, and sets, lists, vectors, matrices, and tensors. -Maxima yields high precision numeric results by using exact fractions, -arbitrary precision integers, and arbitrarily precision floating point -numbers. Maxima can plot functions and data in two and three dimensions. + +Maxima is a GPL computer algebra system based on DOE-MACSYMA. It +is comparable to commercial systems like Mathematica and Maple. It +emphasizes symbolic mathematical computation: algebra, trigonometry, +calculus, and much more. + +For example, Maxima solves x^2-r*x-s^2-r*s=0 giving the symbolic +results [x=r+s, x=-s]. + +Maxima can calculate with exact integers and fractions, native +floating-point and high-precision big floats. + +Maxima has user-friendly front-ends, an on-line manual, plotting +commands, and numerical libraries. Users can write programs in its +native programming language, and many have contributed useful packages +in a variety of areas over the decades. + +Maxima is GPL-licensed and largely written in Common Lisp. Executables +can be downloaded for Windows, Mac, Linux, and Android; source code +is also available. An active community maintains and extends the +system. Maxima is widely used. + +SBo Installation notes: +- The info files are not compressed. +- Two .lisp files install to /usr/info. +These are required for maxima's help facility. diff --git a/academic/maxima/doinst.sh b/academic/maxima/doinst.sh new file mode 100644 index 0000000000..7b028b1845 --- /dev/null +++ b/academic/maxima/doinst.sh @@ -0,0 +1,10 @@ + + +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q /usr/share/applications >/dev/null 2>&1 +fi + +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database /usr/share/mime >/dev/null 2>&1 +fi + diff --git a/academic/maxima/maxima.SlackBuild b/academic/maxima/maxima.SlackBuild index 6163ace6fa..15ba5bebbe 100644 --- a/academic/maxima/maxima.SlackBuild +++ b/academic/maxima/maxima.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for maxima -# Copyright 2021 Judah Milgram <milgram@cgpp.com> +# Copyright 2021-23 Judah Milgram <milgram@cgpp.com> # Copyright 2017 Dhaby Xiloj <slack.dhabyx@gmail.com> # All rights reserved. # Based on work of Robby and others slackers. @@ -32,11 +32,13 @@ # Modified by Glenn Becker to update to version 5.28.0 # Glenn Becker -> update to version 5.38.1 # JM -> update version 5.39 -> 5.44 +# JM -> update to version 5.46 +# JM -> update to version 5.47 cd $(dirname $0) ; CWD=$(pwd) PRGNAM=maxima -VERSION=${VERSION:-5.44.0} +VERSION=${VERSION:-5.47.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -111,15 +113,15 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r # NOTE: Do not compress the info pages; they are needed by Maxima's help facility. rm -rf $PKG/usr/info/dir -# gzip -9 $PKG/usr/info/*.info* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS COPYING ChangeLog* INSTALL* NEWS README* \ +cp -a AUTHORS COPYING ChangeLog* NEWS README* \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/maxima/maxima.info b/academic/maxima/maxima.info index 8235c0ba3c..4bc595b8bc 100644 --- a/academic/maxima/maxima.info +++ b/academic/maxima/maxima.info @@ -1,10 +1,10 @@ PRGNAM="maxima" -VERSION="5.44.0" +VERSION="5.47.0" HOMEPAGE="http://maxima.sourceforge.net/" -DOWNLOAD="https://sourceforge.net/projects/maxima/files/Maxima-source/5.44.0-source/maxima-5.44.0.tar.gz" -MD5SUM="75e040745161901968d9c99c7a258e5c" +DOWNLOAD="https://sourceforge.net/projects/maxima/files/Maxima-source/5.47.0-source/maxima-5.47.0.tar.gz" +MD5SUM="8ddf54f90fc36e8773fe47a5a9023106" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Judah Milgram" -EMAIL="milgram@cgpp.com" +EMAIL="milgram cgpp com" diff --git a/academic/maxima/slack-desc b/academic/maxima/slack-desc index 360e5737ae..0963a7bfea 100644 --- a/academic/maxima/slack-desc +++ b/academic/maxima/slack-desc @@ -8,11 +8,11 @@ |-----handy-ruler------------------------------------------------------| maxima: maxima (a computer algebra system) maxima: -maxima: Maxima is a system for the manipulation of symbolic and numerical -maxima: expressions, including differentiation, integration, Taylor series, -maxima: Laplace transforms, ordinary differential equations, systems of -maxima: linear equations, polynomials, and sets, lists, vectors, matrices, -maxima: and tensors. +maxima: Maxima is a GPL computer algebra system based on DOE-MACSYMA. +maxima: +maxima: It is comparable to commercial systems like Mathematica and Maple end +maxima: emphasizes symbolic mathematical computation in algebra, trigonometry, +maxima: calculus, and much more. maxima: maxima: Homepage: http://maxima.sourceforge.net/ maxima: diff --git a/academic/meep/README b/academic/meep/README index a0623df2cc..4bfc8b293b 100644 --- a/academic/meep/README +++ b/academic/meep/README @@ -1,8 +1,11 @@ meep (electromagnetic FDTD solver) Meep is a free and open-source software package for electromagnetics -simulation via the finite-difference time-domain (FDTD) method spanning -a broad range of applications. It saves results in hdf5 format. +simulation via the finite-difference time-domain (FDTD) method +spanning a broad range of applications. It saves results in hdf5 +format. + +This package requires: hdf5, libctl, lapack, mpb You probably will also want to preinstall: harminv, openmpi @@ -17,26 +20,27 @@ interface will not build without it. Configuration: -If the build script can find the ATLAS libraries, it will adapt the -configure options to use them, rather than the the default choice of -lapack. +If the build script can find the ATLAS libraries, it will adapt the +configure options to use them, rather than the the default choice of +lapack. -You can add additional options to the command line using -the environment variable SBOPTIONS_MEEP; e.g. to enable MPI -(multi-processor calculation) using openmp, use: +You can add additional options to the command line using the +environment variable SBOPTIONS_MEEP; e.g. to enable MPI (multi- +processor calculation) using openmp, use: SBOPTIONS_MEEP="--with-openmp" ./meep.Slackbuild -Alternatively, if building non-interactively (e.g. if using slpkg), -use/create the file /etc/sbo_pkg_options.conf since this slackbuild -script will search it for options. Simply include a line starting +Alternatively, if building non-interactively (e.g. if using slpkg), +use/create the file /etc/sbo_pkg_options.conf since this slackbuild +script will search it for options. Simply include a line starting "meep:" followed by options, e.g.: meep: --with-openmp -Currently, building the python support for meep can be problematic -unless the mpb package is also installed; if you do so, and (e.g.) use -openmp, it is best to build mpb with the same option. You may also -need to install mpi4py using pip. If you do not want python support, -specify "--without-python", and in this case installing mpb is not -necessary. +Currently, building the python support for meep can be problematic +unless the mpb package is also installed; if you do so, and (e.g.) +use openmp, it is best to build mpb with the same option. You may +also need to install mpi4py using pip. If you do not want python +support, specify "--without-python", and in this case installing mpb +is not necessary. + diff --git a/academic/meep/i386-fix.patch.gz b/academic/meep/i386-fix.patch.gz Binary files differnew file mode 100644 index 0000000000..c5572c316c --- /dev/null +++ b/academic/meep/i386-fix.patch.gz diff --git a/academic/meep/meep.SlackBuild b/academic/meep/meep.SlackBuild index 09b3411e22..629d20e14d 100644 --- a/academic/meep/meep.SlackBuild +++ b/academic/meep/meep.SlackBuild @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=meep -VERSION=${VERSION:-1.17.1} -BUILD=${BUILD:-1} +VERSION=${VERSION:-1.25.0} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -64,19 +64,23 @@ else LIBDIRSUFFIX="" fi +set -e + # change annoying underscores into hyphens SVERSION=$(echo $VERSION | tr '_' '-') # make a custom list of doc files in advance DOCFILES="AUTHORS COPYRIGHT LICENSE TODO NEWS.md" -set -e - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$SVERSION tar xvf $CWD/$PRGNAM-$SVERSION.tar.gz cd $PRGNAM-$SVERSION +# patch 32bit build - thanks debian devs +case "$ARCH" in + i?86) zcat $CWD/i386-fix.patch.gz | patch -p1 ;; +esac chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -112,6 +116,7 @@ fi CFLAGS="$SLKCFLAGS" \ CPPFLAGS="$SLKCFLAGS" \ +PYTHON=/usr/bin/python3 \ ./configure \ --prefix=/usr \ --mandir=/usr/man \ @@ -130,6 +135,8 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION install -m 0644 $DOCFILES $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/meep/meep.info b/academic/meep/meep.info index 8faea2fd0f..e999eb6ae0 100644 --- a/academic/meep/meep.info +++ b/academic/meep/meep.info @@ -1,10 +1,10 @@ PRGNAM="meep" -VERSION="1.17.1" +VERSION="1.25.0" HOMEPAGE="https://github.com/NanoComp/meep" -DOWNLOAD="https://github.com/NanoComp/meep/releases/download/v1.17.1/meep-1.17.1.tar.gz" -MD5SUM="657ecf1fa5459c73fdddd749dd81ec04" +DOWNLOAD="https://github.com/NanoComp/meep/releases/download/v1.25.0/meep-1.25.0.tar.gz" +MD5SUM="968b8da6c25aae3757457520d1520eb2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="lapack hdf5 libctl mpb" +REQUIRES="mpb" MAINTAINER="PaulKinsler" EMAIL="dr.paul@kinsler.org" diff --git a/academic/megax/megax.SlackBuild b/academic/megax/megax.SlackBuild index 165c9f4de6..4f20e38180 100644 --- a/academic/megax/megax.SlackBuild +++ b/academic/megax/megax.SlackBuild @@ -1,6 +1,6 @@ #!/bin/bash -# Slackware build script for megax (formerly 'megacc') +# Slackware build script for megax (formerly 'megacc', called now simply 'mega') # This takes the place of "megacc" in 2018, as it includes also the GUI # of the program (megax) in addition to megacc. @@ -27,21 +27,32 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=megax -VERSION=${VERSION:-10.2.5_1} +VERSION=${VERSION:-11.0.11_1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +SRCNAM=mega DEBVER=$(echo $VERSION | tr _ -) if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi +if [ "$ARCH" = "x86_64" ]; then + LIBDIRSUFFIX="64" + DEBARCH="amd64" +elif [[ $ARCH =~ i?86 ]]; then + LIBDIRSUFFIX="" + DEBARCH="i386" +else + printf "\n\n$ARCH is not supported... \n" >/dev/stderr + exit 1 +fi + # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information # could be useful to other scripts. @@ -54,17 +65,6 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i386" ] || [ "$ARCH" = "i486" ] || [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then - LIBDIRSUFFIX="" - DEBARCH="i386" -elif [ "$ARCH" = "x86_64" ]; then - LIBDIRSUFFIX="64" - DEBARCH="amd64" -else - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - set -e rm -rf $PKG @@ -73,7 +73,7 @@ cd $TMP rm -rf $PRGNAM-$VERSION mkdir $PRGNAM-$VERSION cd $PRGNAM-$VERSION -ar p $CWD/${PRGNAM}_${DEBVER}_${DEBARCH}.deb data.tar.xz | tar xJv +ar p $CWD/${SRCNAM}_${DEBVER}_${DEBARCH}.deb data.tar.xz | tar xJv chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -82,20 +82,23 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Fix path in runmega.sh for x86_64 -sed -i "s|/usr/lib/megax|/usr/lib${LIBDIRSUFFIX}/megax|g" usr/lib/$PRGNAM/runmega.sh +sed -i "s|/usr/lib/megax|/usr/lib${LIBDIRSUFFIX}/$PRGNAM|g" usr/lib/mega/runmega.sh # Place things in /usr/lib and just create symlinks later. # This is what Debian's and RedHat's packages do. mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} -cp -a usr/lib/$PRGNAM $PKG/usr/lib${LIBDIRSUFFIX} +cp -a usr/lib/mega $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM # Copy man pages to their proper place. cp -a usr/local/share/man $PKG/usr +sed -i "s:lib:lib${LIBDIRSUFFIX}:" $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/runmega.sh +sed -i "s:mega:$PRGNAM:" $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/runmega.sh + mkdir -p $PKG/usr/bin cd $PKG/usr/bin ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/megacc - ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/runmega.sh megax + ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/runmega.sh runmega cd - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ diff --git a/academic/megax/megax.desktop b/academic/megax/megax.desktop index 336d4eb395..4ec785dbf3 100644 --- a/academic/megax/megax.desktop +++ b/academic/megax/megax.desktop @@ -1,7 +1,7 @@ [Desktop Entry] Categories=Education; Comment=Molecular evolutionary genetics analysis -Exec=megax +Exec=runmega Icon=megax Name=MEGA X StartupNotify=false diff --git a/academic/megax/megax.info b/academic/megax/megax.info index 17a8b6a7ce..3d1c83a869 100644 --- a/academic/megax/megax.info +++ b/academic/megax/megax.info @@ -1,10 +1,10 @@ PRGNAM="megax" -VERSION="10.2.5_1" +VERSION="11.0.11_1" HOMEPAGE="http://www.megasoftware.net/" -DOWNLOAD="https://www.megasoftware.net/releases/megax_10.2.5-1_i386.deb" -MD5SUM="cda0edb08a1688e4b82d0f0f61722741" -DOWNLOAD_x86_64="https://www.megasoftware.net/releases/megax_10.2.5-1_amd64.deb" -MD5SUM_x86_64="98fbfb10289e24efaea7d525e3316726" +DOWNLOAD="https://www.megasoftware.net/releases/mega_11.0.11-1_i386.deb" +MD5SUM="087a4673f20aec8fd92f18e11683ebbd" +DOWNLOAD_x86_64="https://www.megasoftware.net/releases/mega_11.0.11-1_amd64.deb" +MD5SUM_x86_64="83a2aa21353eabeaf084f38bce496a23" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/meme-db-motif/meme-db-motif.SlackBuild b/academic/meme-db-motif/meme-db-motif.SlackBuild index 5221e6c98c..949df9e2be 100644 --- a/academic/meme-db-motif/meme-db-motif.SlackBuild +++ b/academic/meme-db-motif/meme-db-motif.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=meme-db-motif -VERSION=${VERSION:-12.21} +VERSION=${VERSION:-12.23} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/meme-db-motif/meme-db-motif.info b/academic/meme-db-motif/meme-db-motif.info index 4dc3827ebd..21a7543ae0 100644 --- a/academic/meme-db-motif/meme-db-motif.info +++ b/academic/meme-db-motif/meme-db-motif.info @@ -1,8 +1,8 @@ PRGNAM="meme-db-motif" -VERSION="12.21" +VERSION="12.23" HOMEPAGE="https://meme-suite.org/db/motifs" -DOWNLOAD="https://meme-suite.org/meme/meme-software/Databases/motifs/motif_databases.12.21.tgz" -MD5SUM="c37d53c3146f2e8cf6218c0251108d44" +DOWNLOAD="https://meme-suite.org/meme/meme-software/Databases/motifs/motif_databases.12.23.tgz" +MD5SUM="4a351edb28e456453c804f2da5889b23" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/meme-suite/meme-suite.SlackBuild b/academic/meme-suite/meme-suite.SlackBuild index ecf755c3c9..e8f7f9c521 100644 --- a/academic/meme-suite/meme-suite.SlackBuild +++ b/academic/meme-suite/meme-suite.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for meme-suite -# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=meme-suite -VERSION=${VERSION:-5.3.3} +VERSION=${VERSION:-5.5.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/meme-suite/meme-suite.info b/academic/meme-suite/meme-suite.info index a459321ac4..f0d7634d52 100644 --- a/academic/meme-suite/meme-suite.info +++ b/academic/meme-suite/meme-suite.info @@ -1,10 +1,10 @@ PRGNAM="meme-suite" -VERSION="5.3.3" +VERSION="5.5.4" HOMEPAGE="https://meme-suite.org/" -DOWNLOAD="https://meme-suite.org/meme-software/5.3.3/meme-5.3.3.tar.gz" -MD5SUM="97b258e6a6627ada02404a2224b13e92" +DOWNLOAD="https://meme-suite.org/meme-software/5.5.4/meme-5.5.4.tar.gz" +MD5SUM="eed938a859b551209af3c4adf7e41fa1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="openmpi perl-HTML-Template perl-JSON python3 meme-db-gomo meme-db-motif meme-db-tgene" +REQUIRES="openmpi perl-HTML-Template perl-JSON meme-db-gomo meme-db-motif meme-db-tgene" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/mendeleydesktop/mendeleydesktop.SlackBuild b/academic/mendeleydesktop/mendeleydesktop.SlackBuild index e9b7410cc2..bdc072f10d 100644 --- a/academic/mendeleydesktop/mendeleydesktop.SlackBuild +++ b/academic/mendeleydesktop/mendeleydesktop.SlackBuild @@ -35,15 +35,12 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -53,10 +50,9 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then - ARCH="i486" # mendeleydesktop doesn't have i586/i686 pre-builds. +SRCARCH="$ARCH" +if [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then + SRCARCH="i486" # mendeleydesktop doesn't have i586/i686 pre-builds. LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then LIBDIRSUFFIX="64" @@ -70,15 +66,15 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION-linux-$ARCH -tar xvf $CWD/$PRGNAM-$VERSION-linux-${ARCH}.tar.bz2 -cd $PRGNAM-$VERSION-linux-$ARCH +rm -rf $PRGNAM-$VERSION-linux-$SRCARCH +tar xvf $CWD/$PRGNAM-$VERSION-linux-${SRCARCH}.tar.bz2 +cd $PRGNAM-$VERSION-linux-$SRCARCH chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} + -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + # removing QT5 bundled libraries if [ "${SYSTEM_QT5:-yes}" != "no" ]; then @@ -108,7 +104,7 @@ MENDELEY_LIB=lib LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}:\${MENDELEY_BASE}/\${MENDELEY_LIB} export LD_LIBRARY_PATH cd /opt/mendeleydesktop/lib/mendeleydesktop/libexec -./mendeleydesktop.$ARCH \$@ +./mendeleydesktop.$SRCARCH \$@ EOF chmod 755 $PKG/usr/bin/$PRGNAM else diff --git a/academic/metalwalls/README b/academic/metalwalls/README new file mode 100644 index 0000000000..586416382a --- /dev/null +++ b/academic/metalwalls/README @@ -0,0 +1,9 @@ + MetalWalls (MW) is a molecular dynamics code dedicated to the +modelling of electrochemical systems. Its main originality is the +inclusion of a series of methods allowing to apply a constant +potential within the electrode materials. + + For building the MPI version set the environment variable MPI=yes +this requires a MPI implementation either openmpi or mpich. + + The final executable is metalwalls diff --git a/academic/metalwalls/metalwalls.SlackBuild b/academic/metalwalls/metalwalls.SlackBuild new file mode 100644 index 0000000000..8aaaf8a2ed --- /dev/null +++ b/academic/metalwalls/metalwalls.SlackBuild @@ -0,0 +1,123 @@ +#!/bin/bash + +# Slackware build script for MetalWalls + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=metalwalls +VERSION=${VERSION:-21.06.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +cp computers/laptop/config-gnu-linux.mk config.mk +sed -i '4s/$/ -std=legacy/' config.mk + +# the laptop config file requires MPI by default +# here we forces a serial build +if [ ! "${MPI:-no}" == "yes" ]; then + sed -i 's#mpif90#gfortran#' config.mk + sed -i '5s#$# -DMW_SERIAL#' config.mk + # fix double setting for error "Sumbol comm already has basic type" + sed -i '42s/^/!/' src/parallel.F90 +fi + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make +#make install DESTDIR=$PKG + +mkdir -p $PKG/usr/bin +cp mw $PKG/usr/bin/metalwalls + +# install some examples and tools +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/tools +cp -a example $PKG/usr/share/$PRGNAM-$VERSION +cp -a tools $PKG/usr/share/$PRGNAM-$VERSION/tools + + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CONTRIBUTORS LICENSE doc \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/metalwalls/metalwalls.info b/academic/metalwalls/metalwalls.info new file mode 100644 index 0000000000..126a022fc5 --- /dev/null +++ b/academic/metalwalls/metalwalls.info @@ -0,0 +1,10 @@ +PRGNAM="metalwalls" +VERSION="21.06.1" +HOMEPAGE="https://gitlab.com/ampere2/metalwalls" +DOWNLOAD="https://gitlab.com/ampere2/metalwalls/-/archive/21.06.1/metalwalls-21.06.1.tar.gz" +MD5SUM="24e8549490d9d9e5c24659fe50d8276e" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="lapack" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/metalwalls/slack-desc b/academic/metalwalls/slack-desc new file mode 100644 index 0000000000..1e47821fe9 --- /dev/null +++ b/academic/metalwalls/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +metalwalls: metalwalls (A molecular code for modelling electrochemical systems) +metalwalls: +metalwalls: +metalwalls: +metalwalls: metalwalls (MW) is a molecular dynamics code dedicated to the +metalwalls: modelling of electrochemical systems. Its main originality is the +metalwalls: inclusion of a series of methods allowing to apply a constant +metalwalls: potential within the electrode materials. +metalwalls: +metalwalls: +metalwalls: diff --git a/academic/metis/metis.SlackBuild b/academic/metis/metis.SlackBuild index 665e144a8e..a7f2a4926e 100644 --- a/academic/metis/metis.SlackBuild +++ b/academic/metis/metis.SlackBuild @@ -47,13 +47,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="Changelog LICENSE.txt manual/manual.pdf" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/mfem/README b/academic/mfem/README new file mode 100644 index 0000000000..96f8496889 --- /dev/null +++ b/academic/mfem/README @@ -0,0 +1,16 @@ + MFEM is a free, lightweight, scalable C++ library for finite element +methods. + + + Building options that can be set using the environment variable: + - OMP=yes, use OpenMP. + - MPI=yes, use MPI (requires a MPI implementation either mpich or + openmpi and the hypre and metis package. + - CUDA=yes, requires the CUDA toolkit. + - TESTS=yes, to run the tests. + + Compiling the examples: + # mkdir mfem-examples; cd mfem-examples + # cp -av /usr/share/mfem-4.5/{data,examples} . + # make -C examples + # make diff --git a/academic/mfem/mfem.SlackBuild b/academic/mfem/mfem.SlackBuild new file mode 100644 index 0000000000..f85c2c679d --- /dev/null +++ b/academic/mfem/mfem.SlackBuild @@ -0,0 +1,188 @@ +#!/bin/bash + +# Slackware build script for mfem + +# Copyright 2022 William PC, Seattle (USA) +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=mfem +VERSION=${VERSION:-4.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +if [ "${OMP:-no}" == "yes" ]; then + OPT_BUILD="MFEM_USE_OPENMP=YES" +fi + +# this can't be null even without using MPI it has to be set +# to don't throw an error at make +MFEM_MPIEXEC="MFEM_MPIEXEC=mpirun" +if [ "${MPI:-no}" == "yes" ]; then + OPT_BUILD="$OPT_BUILD MFEM_USE_MPI=YES" + OPT_BUILD="$OPT_BUILD MFEM_USE_METIS_5=YES" + # fix hypre location + sed -i 's#^HYPRE_DIR = .*#HYPRE_DIR = /usr#' config/defaults.mk + sed -i 's#$(HYPRE_DIR)/include#&/hypre#' config/defaults.mk + sed -i 's#$(HYPRE_DIR)/lib#&'${LIBDIRSUFFIX}'#' config/defaults.mk + # fix metis location + sed -i 's#METIS_DIR = @MFEM_DIR@/../metis-5.0#METIS_DIR = /usr#' config/defaults.mk + sed -i 's#$(METIS_DIR)/include#&/metis#' config/defaults.mk + sed -i 's#-L$(METIS_DIR)/lib#&'${LIBDIRSUFFIX}'#' config/defaults.mk + # fix for running check with MPI + if pkg-config --exists mpich; then + echo "Using mpich" + MFEM_MPIEXEC="MFEM_MPIEXEC=\"mpirun -host localhost\"" + else + echo "Using openmpi" + export OMPI_ALLOW_RUN_AS_ROOT=1 + export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 + + fi +fi + + +if [ "${CUDA:-no}" == "yes" ]; then + OPT_BUILD="$OPT_BUILD MFEM_USE_CUDA=YES" +fi + +# fix lib and share install location +sed -i 's#$(PREFIX)/lib#&'${LIBDIRSUFFIX}'#' makefile +sed -i 's#$(PREFIX)/share/mfem#&-'${VERSION}'#' makefile + +# "$MFEM_MPIEXEC" \ +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make config \ + MFEM_STATIC=NO \ + MFEM_SHARED=YES \ + $OPT_BUILD \ + "$MFEM_MPIEXEC" \ + BUILD_DIR=build +cd build +make +make check +if [ "${TESTS:-no}" == "yes" ]; then + make test +fi +make install \ + MFEM_PREFIX=/usr \ + MFEM_INC_DIR="@MFEM_PREFIX@/include" \ + MFEM_LIB_DIR="@MFEM_PREFIX@/lib${LIBDIRSUFFIX}" \ + MFEM_TEST_MK="@MFEM_PREFIX@/share/$PRGNAM-$VERSION/test.mk" \ + PREFIX=$PKG/usr +cd .. + +# fix permissions +find -L $PKG/usr/{include,share} \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# install data files, examples and miniapps +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a {data,examples,miniapps} $PKG/usr/share/$PRGNAM-$VERSION +cp -a config/defaults.mk $PKG/usr/share/$PRGNAM-$VERSION + +# fix examples +sed -i -e 's$# MFEM_INSTALL_DIR = ../mfem$MFEM_INSTALL_DIR = /usr$' \ + -e 's$# CONFIG_MK$CONFIG_MK$' \ + -e 's#share/mfem#&-'$VERSION'#' \ + -e 's/^MFEM_LIB_FILE/#&/' \ + $PKG/usr/share/$PRGNAM-$VERSION/examples/makefile + +# fix miniapps +for file in $(find $PKG/usr/share/$PRGNAM-$VERSION/miniapps -iname makefile); do + sed -i 's$# MFEM_INSTALL_DIR = ../../mfem$MFEM_INSTALL_DIR = /usr$' $file + sed -i 's$# CONFIG_MK$CONFIG_MK$' $file + sed -i 's#share/mfem#&-'$VERSION'#' $file + sed -i 's#^DEFAULTS_MK.*#DEFAULTS_MK = /usr/share/'$PRGNAM-$VERSION'/defaults.mk#' $file +done +sed -i 's#../../general#mfem/general#' $PKG/usr/share/$PRGNAM-$VERSION/miniapps/meshing/{minimal-surface,pminimal-surface}.cpp +sed -i 's#../../general#mfem/general#' $PKG/usr/share/$PRGNAM-$VERSION/miniapps/navier/navier_solver.cpp +sed -i 's#../../linalg#mfem/linalg#' $PKG/usr/share/$PRGNAM-$VERSION/miniapps/autodiff/admfem.hpp + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CHANGELOG CITATION.cff {CODE_OF_CONDUCT,CONTRIBUTING}.md LICENSE doc \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mfem/mfem.info b/academic/mfem/mfem.info new file mode 100644 index 0000000000..d39a1518f5 --- /dev/null +++ b/academic/mfem/mfem.info @@ -0,0 +1,10 @@ +PRGNAM="mfem" +VERSION="4.5" +HOMEPAGE="https://mfem.org" +DOWNLOAD="https://github.com/mfem/mfem/archive/v4.5/mfem-4.5.tar.gz" +MD5SUM="1a93d4d9982612f52b9434b93265b979" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/mfem/slack-desc b/academic/mfem/slack-desc new file mode 100644 index 0000000000..118db0fce4 --- /dev/null +++ b/academic/mfem/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +mfem: mfem (library for finite element methods) +mfem: +mfem: +mfem: +mfem: MFEM is a free, lightweight, scalable C++ library for finite +mfem: element methods. +mfem: +mfem: +mfem: +mfem: +mfem: diff --git a/academic/minorminer/README b/academic/minorminer/README new file mode 100644 index 0000000000..c1d4ef7222 --- /dev/null +++ b/academic/minorminer/README @@ -0,0 +1,12 @@ + minorminer is a heuristic tool for minor embedding: given a minor +and target graph, it tries to find a mapping that embeds the minor +into the target. + minorminer is a tool for finding graph minors, developed to embed +Ising problems onto quantum annealers (QA). Where it can be used to +find minors in arbitrary graphs, it is particularly geared towards +the state of the art in QA: problem graphs of a few to a few hundred +variables, and hardware graphs of a few thousand qubits. + + + Optional building mode set with environment variables: + - TESTS=yes (performs tests, requires gtest) diff --git a/academic/minorminer/minorminer.SlackBuild b/academic/minorminer/minorminer.SlackBuild new file mode 100644 index 0000000000..caa9a029d1 --- /dev/null +++ b/academic/minorminer/minorminer.SlackBuild @@ -0,0 +1,140 @@ +#!/bin/bash + +# Slackware build script for minorminer + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="minorminer" +VERSION=${VERSION:-0.2.9} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# fix util.hpp +sed -i '19a#include <memory>' include/find_embedding/util.hpp + +# fix examples and tests CMakeLists.txt +sed -i '11s/ minorminer//' examples/CMakeLists.txt +sed -i '11s/ minorminer//' tests/CMakeLists.txt + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + cd tests + cmake \ + -DCMAKE_CXX_FLAGS="-I../include" . + make + ./run_tests + cd .. +fi + +# run tests (requires homebase, networkx and several other pkgs) +#for file in $(ls test_*.py); do +# PYTHONPATH=../build/lib.linux-x86_64-3.9 \ +# python3 -c "print ('$file'); exec(open('$file').read())" ; +#done + +# install includes +install -d $PKG/usr/include/minorminer +cp -av include/* $PKG/usr/include/minorminer + +# install examples +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a examples $PKG/usr/share/$PRGNAM-$VERSION + +# fix example +sed -i 's#\(../include\)/\(find_embedding\).hpp#/usr/include/minorminer/\2/\2.hpp#' $PKG/usr/share/$PRGNAM-$VERSION/examples/example.cpp + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +# fix broken symlink and copy real file +rm $PKG/usr/doc/$PRGNAM-$VERSION/docs/source/parameter_checklist.txt +cp -av parameter_checklist.txt $PKG/usr/doc/$PRGNAM-$VERSION/docs/source/ + +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/minorminer/minorminer.info b/academic/minorminer/minorminer.info new file mode 100644 index 0000000000..a9ea741a1e --- /dev/null +++ b/academic/minorminer/minorminer.info @@ -0,0 +1,10 @@ +PRGNAM="minorminer" +VERSION="0.2.9" +HOMEPAGE="https://github.com/dwavesystems/minorminer" +DOWNLOAD="https://github.com/dwavesystems/minorminer/archive/0.2.9/minorminer-0.2.9.tar.gz" +MD5SUM="de59a2d16a94ee5853938cbf19d61a6f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/minorminer/slack-desc b/academic/minorminer/slack-desc new file mode 100644 index 0000000000..125054455f --- /dev/null +++ b/academic/minorminer/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +minorminer: minorminer (heuristic tool for minor embedding) +minorminer: +minorminer: +minorminer: +minorminer: minorminer is a heuristic tool for minor embedding: given a minor +minorminer: and target graph, it tries to find a mapping that embeds the minor +minorminer: into the target. +minorminer: +minorminer: +minorminer: +minorminer: diff --git a/academic/mkDSSP/mkDSSP.SlackBuild b/academic/mkDSSP/mkDSSP.SlackBuild index 66793c86d7..d5461df266 100644 --- a/academic/mkDSSP/mkDSSP.SlackBuild +++ b/academic/mkDSSP/mkDSSP.SlackBuild @@ -25,13 +25,12 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=mkDSSP -VERSION=${VERSION:-4.0_git6338c83} +VERSION=${VERSION:-4.0.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} SRCNAM=dssp -COMMIT="6338c836b631e87fc03bd147ec67d27ea72f6f70" if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -72,9 +71,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM-$COMMIT -tar xvf $CWD/$SRCNAM-$COMMIT.tar.gz -cd $SRCNAM-$COMMIT +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -82,20 +81,20 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --disable-revision \ - --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux - -make -make install DESTDIR=$PKG mandir=$PKG/usr/man +sed -i "s|CMAKE_INSTALL_DATADIR}/man|CMAKE_INSTALL_PREFIX}/man|" CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$PKG +cd .. # Some programs (like aline) expect the binary to be called just "dssp" cd $PKG/usr/bin @@ -105,6 +104,9 @@ cd - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ LICENSE README.md \ diff --git a/academic/mkDSSP/mkDSSP.info b/academic/mkDSSP/mkDSSP.info index 43a6d3a224..494233066f 100644 --- a/academic/mkDSSP/mkDSSP.info +++ b/academic/mkDSSP/mkDSSP.info @@ -1,8 +1,8 @@ PRGNAM="mkDSSP" -VERSION="4.0_git6338c83" +VERSION="4.0.3" HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/DSSP_3.html" -DOWNLOAD="https://github.com/PDB-REDO/dssp/archive/6338c83/dssp-6338c836b631e87fc03bd147ec67d27ea72f6f70.tar.gz" -MD5SUM="c4616197bb510c36f1c4dcce018e870d" +DOWNLOAD="https://github.com/PDB-REDO/dssp/archive/v4.0.3/dssp-4.0.3.tar.gz" +MD5SUM="fac80f6b2ca0120c414510b420dc5b6a" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="libcifpp" diff --git a/academic/molequeue/README b/academic/molequeue/README new file mode 100644 index 0000000000..62e5ed704e --- /dev/null +++ b/academic/molequeue/README @@ -0,0 +1,20 @@ +MoleQueue is an open-source, cross-platform, system-tray resident +desktop application for abstracting, managing, and coordinating the +execution of tasks both locally and on remote computational resources. + +Users can set up local and remote queues that describe where the task +will be executed. Each queue can have programs, with templates to +facilitate the execution of the program. Input files can be staged, +and output files collected using a standard interface. + +It is a subproject of OpenChemistry needed by Avogadro 2. + +By default MoleQueue should be started as a resident service and +launched from a script or a shell command line. If you want to lauch +the Graphic Interface User using a desktop entry pass the variable +DESKTOP=yes to the slackbuild script: + +DESKTOP=yes ./molequeue.SlackBuild + +This may be useful if you want to launch the service only when you +are going to start Avogadro 2. diff --git a/academic/molequeue/doinst.sh b/academic/molequeue/doinst.sh new file mode 100644 index 0000000000..65c7e2eeb9 --- /dev/null +++ b/academic/molequeue/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/molequeue/molequeue.SlackBuild b/academic/molequeue/molequeue.SlackBuild new file mode 100644 index 0000000000..b1ac314514 --- /dev/null +++ b/academic/molequeue/molequeue.SlackBuild @@ -0,0 +1,136 @@ +#!/bin/bash + +# Slackware build script for molequeue. + +# Copyright 2020-2022 Giancarlo Dessì, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=molequeue +VERSION=${VERSION:-0.9.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + -DENABLE_TESTING=OFF \ + -Wno-dev \ + .. + make + make install/strip DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +# Remove redundant files installed by make install in /usr/share/doc/Molequeue +rm -rf $PKG/usr/share/doc +mkdir -p $PKG/install + +if [ "${DESKTOP:-no}" = "yes" ]; then + + #Copy application icon and create a desktop entry + + mkdir -p $PKG/usr/share/icons/hicolor/32x32/apps + cp -a $TMP/$PRGNAM-$VERSION/molequeue/app/icons/molequeue.png \ + $PKG/usr/share/icons/hicolor/32x32/apps + + mkdir -p $PKG/usr/share/applications + cat << EOF > $PKG/usr/share/applications/molequeue.desktop +[Desktop Entry] +Type=Application +Name=MoleQueue +GenericName=MoleQueue Server for Avogadro 2 +Comment=Desktop integration of high performance computing resources. +Exec=molequeue +Icon=/usr/share/icons/hicolor/32x32/apps/molequeue.png +Terminal=false +Categories=Qt;Science;Chemistry;Physics;Education; +X-KDE-StartupNotify=false +StartupNotify=false +EOF + cat $CWD/doinst.sh > $PKG/install/doinst.sh +else + rm -rf $PKG/usr/share +fi + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a *.md LICENSE $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/molequeue/molequeue.info b/academic/molequeue/molequeue.info new file mode 100644 index 0000000000..3b3945ec12 --- /dev/null +++ b/academic/molequeue/molequeue.info @@ -0,0 +1,10 @@ +PRGNAM="molequeue" +VERSION="0.9.0" +HOMEPAGE="https://www.openchemistry.org/projects/molequeue/" +DOWNLOAD="https://github.com/OpenChemistry/molequeue/archive/0.9.0/molequeue-0.9.0.tar.gz" +MD5SUM="28e707668bfaf2ebc615da54fc98002f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Giancarlo Dessì" +EMAIL="slack@giand.it" diff --git a/academic/molequeue/slack-desc b/academic/molequeue/slack-desc new file mode 100644 index 0000000000..dbb89964a6 --- /dev/null +++ b/academic/molequeue/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +molequeue: molequeue (Desktop integration of high quality computing resources) +molequeue: +molequeue: This is an open-source, cross-platform, system-tray resident +molequeue: desktop application for abstracting, managing, and coordinating +molequeue: the execution of tasks both locally and on remote computational +molequeue: resources. +molequeue: MoleQueue is a project of OpenChemistry. +molequeue: +molequeue: https://www.openchemistry.org/projects/molequeue/ +molequeue: +molequeue: diff --git a/academic/mpb/mpb.SlackBuild b/academic/mpb/mpb.SlackBuild index a1f22544ce..b1d7ff0ec8 100644 --- a/academic/mpb/mpb.SlackBuild +++ b/academic/mpb/mpb.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=mpb VERSION=${VERSION:-1.11.1} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -153,6 +153,8 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION install -m 0644 $DOCFILES $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/mumsa/README b/academic/mumsa/README new file mode 100644 index 0000000000..3fad0cf560 --- /dev/null +++ b/academic/mumsa/README @@ -0,0 +1,17 @@ +Mumsa is a tool for automatic assessment of alignment quality. A number +of alternate (to be compared) multiple alignments have to be generated +and submitted. + +Mumsa computes: +- the average overlap score (AOS), reflecting the difficulty of aligning + the sequences +- multiple overlap score (MOS) indicating the quality of each individual + alignment. + +Both scores range between one and zero. + +CITING +Lassmann T, Sonnhammer EL. Kalign, Kalignvu and Mumsa: web servers for +multiple sequence alignment. Nucleic Acids Res. 2006 Jul 1;34(Web Server +issue): W596-9. doi: 10.1093/nar/gkl191. +PMID: 16845078; PMCID: PMC1538774 diff --git a/academic/mumsa/References.txt b/academic/mumsa/References.txt new file mode 100644 index 0000000000..5dd7f95313 --- /dev/null +++ b/academic/mumsa/References.txt @@ -0,0 +1,4 @@ +Lassmann T, Sonnhammer EL. Kalign, Kalignvu and Mumsa: web servers for +multiple sequence alignment. Nucleic Acids Res. 2006 Jul 1;34(Web Server +issue): W596-9. doi: 10.1093/nar/gkl191. +PMID: 16845078; PMCID: PMC1538774 diff --git a/academic/mumsa/mumsa.SlackBuild b/academic/mumsa/mumsa.SlackBuild new file mode 100644 index 0000000000..6d9d8cf01e --- /dev/null +++ b/academic/mumsa/mumsa.SlackBuild @@ -0,0 +1,102 @@ +#!/bin/bash + +# Slackware build script for <mumsa> + +# Copyright 2022 Petar Petrov slackalaxy at gmail dot com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=mumsa +VERSION=${VERSION:-1.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tgz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +sed -i "/^CFLAGS/s/=/+=/" Makefile +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +PREFIX=/usr make +make + +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + COPYING \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References.txt > $PKG/usr/doc/$PRGNAM-$VERSION/References.txt + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mumsa/mumsa.info b/academic/mumsa/mumsa.info new file mode 100644 index 0000000000..86eb69b883 --- /dev/null +++ b/academic/mumsa/mumsa.info @@ -0,0 +1,10 @@ +PRGNAM="mumsa" +VERSION="1.0" +HOMEPAGE="https://msa.sbc.su.se/cgi-bin/msa.cgi" +DOWNLOAD="https://msa.sbc.su.se/downloads/mumsa-1.0.tgz" +MD5SUM="80ad4dbd2dc2e5402ad9753c25cc896b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/mumsa/slack-desc b/academic/mumsa/slack-desc new file mode 100644 index 0000000000..2f487a6eba --- /dev/null +++ b/academic/mumsa/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +mumsa: mumsa (A tool to assess MSA quality) +mumsa: +mumsa: Mumsa is a tool for automatic assessment of alignment quality. +mumsa: +mumsa: https://msa.sbc.su.se/cgi-bin/msa.cgi +mumsa: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538774/ +mumsa: +mumsa: +mumsa: +mumsa: +mumsa: diff --git a/academic/muscle5/README b/academic/muscle5/README new file mode 100644 index 0000000000..bdea0f68e6 --- /dev/null +++ b/academic/muscle5/README @@ -0,0 +1,28 @@ +MUSCLE 5: Next-generation MUSCLE + +Muscle v5 is a major re-write of MUSCLE based on new algorithms. + +* Highest accuracy, scalable to thousands of sequences: +Compared to previous versions, Muscle v5 is much more accurate, is often +faster, and scales to much larger datasets. At the time of writing (late +2021), Muscle v5 has the highest scores on multiple alignment benchmarks +including Balibase, Bralibase, Prefab and Balifam. It can align tens of +thousands of sequences with high accuracy on a low-cost commodity +computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets, +Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega. + +* Alignment ensembles: +Muscle v5 can generate ensembles of high-accuracy alternative +alignments. All replicates have equal average accuracy on benchmark +test, including the MSA made with default parameters. By comparing +results of downstream analysis (trees, structure prediction...) on +different replicates, you can assess the effects of alignment errors on +your study. + +* Manual: +https://drive5.com/muscle5/manual/ + +* Reference (included in the package) +R.C. Edgar (2021) "MUSCLE v5 enables improved estimates of phylogenetic +tree confidence by ensemble bootstrapping" +https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf diff --git a/academic/muscle5/References b/academic/muscle5/References new file mode 100644 index 0000000000..e11f73531f --- /dev/null +++ b/academic/muscle5/References @@ -0,0 +1,5 @@ +References + +R.C. Edgar (2021) "MUSCLE v5 enables improved estimates of phylogenetic +tree confidence by ensemble bootstrapping" +https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf diff --git a/academic/muscle5/muscle5.1 b/academic/muscle5/muscle5.1 new file mode 100644 index 0000000000..d1c2661ec2 --- /dev/null +++ b/academic/muscle5/muscle5.1 @@ -0,0 +1,93 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5. +.TH MUSCLE "1" "January 2022" "muscle 5.1" "User Commands" +.SH NAME +muscle \- Multiple alignment program of protein sequences +.SH DESCRIPTION +MUSCLE is a multiple alignment program for protein sequences. MUSCLE +stands for multiple sequence comparison by log-expectation. In the +authors tests, MUSCLE achieved the highest scores of all tested +programs on several alignment accuracy benchmarks, and is also one of +the fastest programs out there. +.SH USAGE +.SS "Align FASTA input, write aligned FASTA (AFA) output:" +.IP +muscle \fB\-align\fR input.fa \fB\-output\fR aln.afa +.PP +Align large input using Super5 algorithm if \fB\-align\fR is too expensive, +typically needed with more than a few hundred sequences: +.IP +muscle \fB\-super5\fR input.fa \fB\-output\fR aln.afa +.SS "Single replicate alignment:" +.IP +muscle \fB\-align\fR input.fa \fB\-perm\fR PERM \fB\-perturb\fR SEED \fB\-output\fR aln.afa +muscle \fB\-super5\fR input.fa \fB\-perm\fR PERM \fB\-perturb\fR SEED \fB\-output\fR aln.afa +.IP +PERM is guide tree permutation none, abc, acb, bca (default none). +SEED is perturbation seed 0, 1, 2... (default 0 = don't perturb). +.PP +Ensemble of replicate alignments, output in Ensemble FASTA (EFA) format, +EFA has one aligned FASTA for each replicate with header line "<PERM.SEED": +.IP +muscle \fB\-align\fR input.fa \fB\-stratified\fR \fB\-output\fR stratified_ensemble.efa +muscle \fB\-align\fR input.fa \fB\-diversified\fR \fB\-output\fR diversified_ensemble.afa +.HP +\fB\-replicates\fR N +.IP +Number of replicates, defaults 4, 100, 100 for stratified, +.IP +diversified, resampled. With \fB\-stratified\fR there is one +replicate per guide tree permutation, total is 4 x N. +.PP +Generate resampled ensemble from existing ensemble by sampling columns +with replacement: +.IP +muscle \fB\-resample\fR ensemble.efa \fB\-output\fR resampled.efa +.HP +\fB\-maxgapfract\fR F +.IP +Maximum fraction of gaps in a column (F=0..1, default 0.5). +.HP +\fB\-minconf\fR CC +.IP +Minimum column confidence (CC=0..1, default 0.5). +.PP +If ensemble output filename has @, then one FASTA file is generated +for each replicate where @ is replaced by perm.s, otherwise all replicates +are written to one EFA file. +.SS "Calculate disperson of an ensemble:" +.IP +muscle \fB\-disperse\fR ensemble.efa +.SS "Extract replicate with highest total CC (diversified input recommended):" +.IP +muscle \fB\-maxcc\fR ensemble.efa \fB\-output\fR maxcc.afa +.SS "Extract aligned FASTA files from EFA file:" +.IP +muscle \fB\-efa_explode\fR ensemble.efa +.SS "Convert FASTA to EFA, input has one filename per line:" +.IP +muscle \fB\-fa2efa\fR filenames.txt \fB\-output\fR ensemble.efa +.PP +Update ensemble by adding two sequences of digits to each replicate, digits +are column confidence (CC) values, e.g. "73" means CC=0.73, "++" is CC=1.0: +.IP +muscle \fB\-addconfseqs\fR ensemble.efa \fB\-output\fR ensemble_cc.efa +.PP +Calculate letter confidence (LC) values, \fB\-ref\fR specifies the alignment to +compare against the ensemble (e.g. from \fB\-maxcc\fR), output is in aligned +FASTA format with LC values 0, 1 ... 9 instead of letters: +.IP +muscle \fB\-letterconf\fR ensemble.efa \fB\-ref\fR aln.afa \fB\-output\fR letterconf.afa +.HP +\fB\-html\fR aln.html +.IP +Alignment colored by LC in HTML format. +.HP +\fB\-jalview\fR aln.features +.IP +Jalview feature file with LC values and colors. +.SS "More documentation at:" +.IP +https://drive5.com/muscle +.SH AUTHOR + This manpage was written by Andreas Tille for the Debian distribution and + can be used for any other usage of the program. diff --git a/academic/muscle5/muscle5.SlackBuild b/academic/muscle5/muscle5.SlackBuild new file mode 100644 index 0000000000..541a2182a3 --- /dev/null +++ b/academic/muscle5/muscle5.SlackBuild @@ -0,0 +1,118 @@ +#!/bin/bash + +# Slackware build script for muscle5 + +# Copyright 2022 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=muscle5 +VERSION=${VERSION:-5.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=muscle + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +cd src + +# do not create static executable +sed -i "s:LDFLAGS += -static:#LDFLAGS += -static:" Makefile +make CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" + +install -D -m755 Linux/$SRCNAM $PKG/usr/bin/$PRGNAM +cd .. + +# Thanks to Debian for the man page +mkdir -p $PKG/usr/man/man1 +cp $CWD/$PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1 + +# The Makefile strips the binary... +#find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ +# | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CONTRIBUTING.md LICENSE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION + +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/muscle5/muscle5.info b/academic/muscle5/muscle5.info new file mode 100644 index 0000000000..1749642b98 --- /dev/null +++ b/academic/muscle5/muscle5.info @@ -0,0 +1,10 @@ +PRGNAM="muscle5" +VERSION="5.1" +HOMEPAGE="https://github.com/rcedgar/muscle" +DOWNLOAD="https://github.com/rcedgar/muscle/archive/v5.1/muscle-5.1.tar.gz" +MD5SUM="99b5ef38a119994e7a8f0ea7a12b5987" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/muscle5/slack-desc b/academic/muscle5/slack-desc new file mode 100644 index 0000000000..bc8ca32705 --- /dev/null +++ b/academic/muscle5/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +muscle5: muscle5 (MUSCLE 5: Next-generation MUSCLE) +muscle5: +muscle5: Muscle v5 is a major re-write of MUSCLE based on new algorithms. +muscle5: Compared to previous versions, Muscle v5 is much more accurate, +muscle5: faster, and scales to much larger datasets. +muscle5: +muscle5: https://drive5.com/muscle5/ +muscle5: https://drive5.com/muscle5/manual/ +muscle5: +muscle5: +muscle5: diff --git a/academic/ncbi-blast+/ncbi-blast+.SlackBuild b/academic/ncbi-blast+/ncbi-blast+.SlackBuild index 5958727d3f..26a8981142 100644 --- a/academic/ncbi-blast+/ncbi-blast+.SlackBuild +++ b/academic/ncbi-blast+/ncbi-blast+.SlackBuild @@ -4,7 +4,7 @@ # This takes the place of ncbi-blast-plus (2013-2019), which just # repackaged the binaries provided by upstream. -# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -27,7 +27,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ncbi-blast+ -VERSION=${VERSION:-2.11.0} +VERSION=${VERSION:-2.14.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -42,9 +42,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -95,7 +92,7 @@ cd c++ # Do not specify the libraries dir by the default way (--libdir=/lib${LIBDIRSUFFIX}), # because the libs will not be included in the package. CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS -Wno-narrowing" \ ./configure \ --prefix=/usr \ --libdir='${exec_prefix}'/lib${LIBDIRSUFFIX} \ @@ -121,6 +118,16 @@ make prefix=$PKG/usr install find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +# fix a few permissions +chmod 0644 $PKG/usr/include/ncbi-tools++/algo/dustmask/*.tex +chmod 0644 $PKG/usr/include/ncbi-tools++/objects/gbproj/*.{hpp,h} +chmod 0644 $PKG/usr/include/ncbi-tools++/objects/taxon3/*.hpp +chmod 0644 $PKG/usr/include/ncbi-tools++/objtools/edit/*.hpp +chmod 0755 $PKG/usr/lib${LIBDIRSUFFIX}/*.so + +# remove static libs +rm -rf $PKG/usr/lib${LIBDIRSUFFIX}/*.a + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/ncbi-blast+/ncbi-blast+.info b/academic/ncbi-blast+/ncbi-blast+.info index b688877e0b..135aa023f6 100644 --- a/academic/ncbi-blast+/ncbi-blast+.info +++ b/academic/ncbi-blast+/ncbi-blast+.info @@ -1,8 +1,8 @@ PRGNAM="ncbi-blast+" -VERSION="2.11.0" +VERSION="2.14.1" HOMEPAGE="https://blast.ncbi.nlm.nih.gov/" -DOWNLOAD="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.11.0/ncbi-blast-2.11.0+-src.tar.gz" -MD5SUM="13f93eea6741af2bbcc07f59941dc77b" +DOWNLOAD="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.14.1/ncbi-blast-2.14.1+-src.tar.gz" +MD5SUM="e931f0821d26326b7493882f135f8f60" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/ncbi-blast/ncbi-blast.SlackBuild b/academic/ncbi-blast/ncbi-blast.SlackBuild index 5004bcd266..0adf5cbdae 100644 --- a/academic/ncbi-blast/ncbi-blast.SlackBuild +++ b/academic/ncbi-blast/ncbi-blast.SlackBuild @@ -34,12 +34,16 @@ SRCNAM=blast if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi +if ! [ "$ARCH" = "x86_64" ] && ! [[ $ARCH =~ i?86 ]]; then + printf "\n\n$ARCH is not supported... \n" >/dev/stderr + exit 1 +fi + # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information # could be useful to other scripts. @@ -54,11 +58,6 @@ OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - # Determine the source arch if [ "$ARCH" = "x86_64" ]; then SRCARCH="x64" diff --git a/academic/ncbi-edirect/README b/academic/ncbi-edirect/README new file mode 100644 index 0000000000..f318903e06 --- /dev/null +++ b/academic/ncbi-edirect/README @@ -0,0 +1,8 @@ +Entrez Direct: E-utilities on the Unix Command Line + +Entrez Direct (EDirect) provides access to the NCBI's suite of inter- +connected databases (publication, sequence, structure, gene, variation, +expression, etc.) from a Unix terminal window. Search terms are entered +as command-line arguments. Individual operations are connected with Unix +pipes to construct multi-step queries. Selected records can then be +retrieved in a variety of formats. diff --git a/academic/ncbi-edirect/ncbi-edirect.SlackBuild b/academic/ncbi-edirect/ncbi-edirect.SlackBuild new file mode 100644 index 0000000000..19ea8fed86 --- /dev/null +++ b/academic/ncbi-edirect/ncbi-edirect.SlackBuild @@ -0,0 +1,114 @@ +#!/bin/bash + +# Slackware build script for ncbi-edirect + +# Copyright 2023 Petar Petrov, slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=ncbi-edirect +VERSION=${VERSION:-20.5.20231007} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +MANPG=ncbi-entrez-direct_19.0.20230216+dfsg-2.debian.tar.xz + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +if [ "$ARCH" != "x86_64" ]; then + printf "\n$ARCH is not supported... \n" + exit 1 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION + +tar xvf $CWD/edirect-$VERSION.tar.gz +cd edirect +tar xvf $CWD/$MANPG +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Move these to their proper place +mkdir -p $PKG/usr/share/$PRGNAM +mv ./{cmd,eutils} $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +mv ./{help,readme.pdf,README} $PKG/usr/doc/$PRGNAM-$VERSION + +# remove these +rm -rf ./{CA.pm,cacert.pem,Mozilla-CA.tar.gz} + +# include the binaries +mkdir -p $PKG/usr/bin +gunzip -c $CWD/rchive.Linux.gz > $PKG/usr/bin/rchive.Linux +gunzip -c $CWD/transmute.Linux.gz > $PKG/usr/bin/transmute.Linux +gunzip -c $CWD/xtract.Linux.gz > $PKG/usr/bin/xtract.Linux +chmod 755 $PKG/usr/bin/* + +# thanks Debian for the man pages +mkdir -p $PKG/usr/man/man1 +cp -a debian/man/* $PKG/usr/man/man1 +rm -rf debian + +# move what's left +cp -a * $PKG/usr/bin + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ncbi-edirect/ncbi-edirect.info b/academic/ncbi-edirect/ncbi-edirect.info new file mode 100644 index 0000000000..6124a85041 --- /dev/null +++ b/academic/ncbi-edirect/ncbi-edirect.info @@ -0,0 +1,18 @@ +PRGNAM="ncbi-edirect" +VERSION="20.5.20231007" +HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/NBK179288/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.5.20231007/edirect-20.5.20231007.tar.gz \ +https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.5.20231007/rchive.Linux.gz \ +https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.5.20231007/transmute.Linux.gz \ +https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.5.20231007/xtract.Linux.gz \ +http://deb.debian.org/debian/pool/main/n/ncbi-entrez-direct/ncbi-entrez-direct_19.0.20230216+dfsg-2.debian.tar.xz" +MD5SUM_x86_64="c86b7a39bf08d4fdcfd4894c2810f35b \ +81d15957b38f37c8896836fffe68cf6d \ +ef7f2ca1ad37685c3adffff5b2b15bce \ +67cdff6edaeef6fa6e3b104126538c55 \ +f640a8d59b75655b411c984c984efef0" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/ncbi-edirect/slack-desc b/academic/ncbi-edirect/slack-desc new file mode 100644 index 0000000000..8cbe8e8cd5 --- /dev/null +++ b/academic/ncbi-edirect/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +ncbi-edirect: ncbi-edirect (E-utilities on the Unix Command Line) +ncbi-edirect: +ncbi-edirect: Entrez Direct (EDirect) provides access to the NCBI's suite of +ncbi-edirect: interconnected databases from a Unix terminal window. +ncbi-edirect: +ncbi-edirect: https://www.ncbi.nlm.nih.gov/books/NBK179288/ +ncbi-edirect: +ncbi-edirect: +ncbi-edirect: +ncbi-edirect: +ncbi-edirect: diff --git a/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild b/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild index 7e196c6153..451486417c 100644 --- a/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild +++ b/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild @@ -32,15 +32,12 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -53,11 +50,11 @@ OUTPUT=${OUTPUT:-/tmp} set -e # Determine the binary arch -if [ "$ARCH" = "x86_64" ]; then - BINARCH="x64" -else - BINARCH="ia32" -fi +case "$ARCH" in + x86_64) BINARCH="x64" ;; + i?86) BINARCH="ia32" ;; + *) echo "Unsupported ARCH '$ARCH'"; exit 1 ;; +esac rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT @@ -68,17 +65,14 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ cd bin -install -D -m755 rmblastn $PKG/usr/bin/rmblastn +install -s -D -m755 rmblastn $PKG/usr/bin/rmblastn cd .. -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a LICENSE README $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/nco/doinst.sh b/academic/nco/doinst.sh new file mode 100644 index 0000000000..849153dbfd --- /dev/null +++ b/academic/nco/doinst.sh @@ -0,0 +1,7 @@ +if [ -x /usr/bin/install-info ]; then + /usr/bin/install-info --info-dir=usr/info usr/info/nco.info.gz 1> /dev/null 2>&1 + /usr/bin/install-info --info-dir=usr/info usr/info/nco.info-1.gz 1> /dev/null 2>&1 + /usr/bin/install-info --info-dir=usr/info usr/info/nco.info-1.gz 1> /dev/null 2>&1 + /usr/bin/install-info --info-dir=usr/info usr/info/nco.info-3.gz 1> /dev/null 2>&1 + /usr/bin/install-info --info-dir=usr/info usr/info/nco.info-4.gz 1> /dev/null 2>&1 +fi diff --git a/academic/nco/douninst.sh b/academic/nco/douninst.sh new file mode 100644 index 0000000000..6a6fb6c07b --- /dev/null +++ b/academic/nco/douninst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/install-info -a -d usr/info ]; then + ( + cd usr/info + rm -f dir + for i in *.info*; do + /usr/bin/install-info $i dir 1>/dev/null 2>&1 + done + ) +fi diff --git a/academic/nco/nco.SlackBuild b/academic/nco/nco.SlackBuild index 72da777f42..202f45a72e 100644 --- a/academic/nco/nco.SlackBuild +++ b/academic/nco/nco.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for nco -# Copyright 2020-2021 Gregory J. L. Tourte <artourter@gmail.com> +# Copyright 2020-2024 Gregory J. L. Tourte <artourter@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=nco -VERSION=${VERSION:-5.0.3} +VERSION=${VERSION:-5.2.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -75,10 +75,8 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -perm /111 -a \! -perm 755 -a -exec chmod 755 {} + -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -107,12 +105,16 @@ gzip -9 $PKG/usr/info/*.info* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -aL \ - AUTHORS CITATION COPYING COPYRIGHT ChangeLog INSTALL LICENSE README.md \ + AUTHORS CITATION COPYING COPYRIGHT ChangeLog LICENSE README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/douninst.sh > $PKG/install/douninst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/nco/nco.info b/academic/nco/nco.info index f724e3b258..a532879aeb 100644 --- a/academic/nco/nco.info +++ b/academic/nco/nco.info @@ -1,8 +1,8 @@ PRGNAM="nco" -VERSION="5.0.3" +VERSION="5.2.2" HOMEPAGE="http://nco.sf.net" -DOWNLOAD="https://github.com/nco/nco/archive/5.0.3/nco-5.0.3.tar.gz" -MD5SUM="33fa1a4175456a39292beb4c14022f9c" +DOWNLOAD="https://github.com/nco/nco/archive/5.2.2/nco-5.2.2.tar.gz" +MD5SUM="5baea71f85e0344cc1d74244ac8441b6" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="netcdf udunits antlr2" diff --git a/academic/ngspice/ngspice.SlackBuild b/academic/ngspice/ngspice.SlackBuild index 471f9d9241..db12c3aab6 100644 --- a/academic/ngspice/ngspice.SlackBuild +++ b/academic/ngspice/ngspice.SlackBuild @@ -9,8 +9,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ngspice -VERSION=${VERSION:-34} -BUILD=${BUILD:-5} +VERSION=${VERSION:-42} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -22,9 +22,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -117,7 +114,7 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/examples cp -a \ ANALYSES AUTHORS BUGS COPYING ChangeLog DEVICES FAQ \ - INSTALL NEWS README* examples/ \ + NEWS README* examples/ \ $PKG/usr/doc/$PRGNAM-$VERSION/ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -125,16 +122,19 @@ cat $CWD/$PRGNAM-$VERSION-manual.pdf \ > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM-$VERSION-manual.pdf # The shared library enabled by "--with-ngshared" -install -Dm755 ./release/src/.libs/libngspice.so.0.0.0 \ - "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0.0.0" +install -Dm755 ./release/src/.libs/libngspice.so.0.0.9 \ + "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0.0.9" -ln -s "libngspice.so.0.0.0" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0" -ln -s "libngspice.so.0.0.0" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so" +strip -s $PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0.0.9 + +ln -s "libngspice.so.0.0.9" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0" +ln -s "libngspice.so.0.0.9" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so" # The include file needed to use the shared library enabled by "--with-ngshared" install -Dm644 ./src/include/ngspice/sharedspice.h $PKG/usr/include/ngspice/sharedspice.h # Move the configure output file. -mv $PKG/usr/include/config.h $PKG/usr/include/ngspice/ +mv $TMP/$PRGNAM-$VERSION/release/src/include/ngspice/config.h $PKG/usr/include/ngspice/ +chmod 644 $PKG/usr/doc/ngspice-42/examples/klu/Circuits/libraries/*.lib install -Dm644 $CWD/$PRGNAM.png $PKG/usr/share/icons/hicolor/48x48/apps/$PRGNAM.png diff --git a/academic/ngspice/ngspice.info b/academic/ngspice/ngspice.info index 23f93fdba1..d7fa1f2449 100644 --- a/academic/ngspice/ngspice.info +++ b/academic/ngspice/ngspice.info @@ -1,12 +1,12 @@ PRGNAM="ngspice" -VERSION="34" +VERSION="42" HOMEPAGE="http://ngspice.sourceforge.net/" -DOWNLOAD="https://sourceforge.net/projects/ngspice/files/ng-spice-rework/34/ngspice-34.tar.gz \ - https://sourceforge.net/projects/ngspice/files/ng-spice-rework/34/ngspice-34-manual.pdf" -MD5SUM="e88377ff1e5a466dcd240fa235de7551 \ - ea1bfad9fccd20d58007898bc5f5a15d" +DOWNLOAD="https://sourceforge.net/projects/ngspice/files/ng-spice-rework/42/ngspice-42.tar.gz \ + https://sourceforge.net/projects/ngspice/files/ng-spice-rework/42/ngspice-42-manual.pdf" +MD5SUM="84ab9e67127f9732639195dd63b98a5e \ + f1b1bf8a0bd18af216cbe0ccdbacb47f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="openmpi" +REQUIRES="" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/octave/README b/academic/octave/README index 46429c6687..a0f531e127 100644 --- a/academic/octave/README +++ b/academic/octave/README @@ -1,32 +1,36 @@ GNU Octave is a high-level language, primarily intended for numerical -computations. It provides a convenient command line interface for solving -linear and nonlinear problems numerically, and for performing other numerical -experiments using a language that is mostly compatible with Matlab. It may -also be used as a batch-oriented language. +computations. It provides a convenient command line interface for +solving linear and nonlinear problems numerically, and for performing +other numerical experiments using a language that is mostly compatible +with Matlab. It may also be used as a batch-oriented language. + +This requires a BLAS/LAPACK implementation. Choose one of these package +sets: -This requires a BLAS/LAPACK implementation. Choose one of these package sets: * OpenBLAS (includes both a BLAS and a LAPACK implementation) * atlas (includes both a BLAS and a LAPACK implementation) * blas, lapack (the Netlib reference implementations) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. -These optional dependencies will be used if found (see INSTALL.OCTAVE, in the -Octave source, for a description of what each dependency offers): -amd, camd, colamd, ccolamd, cholmod, umfpack, cxsparse, glpk, arpack-ng, -qrupdate, sundials, qhull, hdf5, fltk, ftgl, gl2ps, jdk, GraphicsMagick, -portaudio. +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib +reference implementations; other packages that require a BLAS or +LAPACK implementation may not build if they are not configured to +detect/use alternate implementations. + +These optional dependencies will be used if found (see INSTALL.OCTAVE, +in the Octave source, for a description of what each dependency +offers): amd, camd, colamd, ccolamd, cholmod, umfpack, spqr, cxsparse, +glpk, arpack-ng, qrupdate, sundials, qhull, hdf5, fltk, ftgl, gl2ps, +jdk, GraphicsMagick, portaudio, rapidjson. -Octave can use ImageMagick (part of Slackware) or GraphicsMagick (available -from SBo) for image-reading functionality. If both are installed, -GraphicsMagick will be selected by default, since ImageMagick is not -well-supported by the Octave developers. If you have problems with -ImageMagick, try rebuilding Octave with GraphicsMagick, or pass MAGICK="" to -the script. +Octave can use ImageMagick (part of Slackware) or GraphicsMagick +(available from SBo) for image-reading functionality. If both +are installed, GraphicsMagick will be selected by default, +since ImageMagick is not well-supported by the Octave developers. +If you have problems with ImageMagick, try rebuilding Octave with +GraphicsMagick, or pass MAGICK="" to the script. -If you have arpack installed and the configure script segfaults when trying to -detect arpack, try switching to arpack-ng (which is partly maintained by -Octave developers). +If you have arpack installed and the configure script segfaults when +trying to detect arpack, try switching to arpack-ng (which is partly +maintained by Octave developers). diff --git a/academic/octave/octave.SlackBuild b/academic/octave/octave.SlackBuild index 79068a6c4b..7fba88f533 100644 --- a/academic/octave/octave.SlackBuild +++ b/academic/octave/octave.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for octave -# Copyright 2012-2021 Kyle Guinn <elyk03@gmail.com> +# Copyright 2012-2024 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=octave -VERSION=${VERSION:-6.3.0} +VERSION=${VERSION:-8.4.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,24 +38,18 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="AUTHORS BUGS CITATION COPYING ChangeLog INSTALL* NEWS README" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i586" ]; then +if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then @@ -70,13 +64,17 @@ else fi # Use GraphicsMagick by default. Fall back on ImageMagick from the full -# Slackware install if it's not present. Requires a patch for this bug: -# https://savannah.gnu.org/bugs/?49653 +# Slackware install if it's not present. # # GraphicsMagick is default due to the fact that the Octave devs mainly test # with that, and went several releases before noticing ImageMagick was broken. # If ImageMagick doesn't work, install GraphicsMagick, or set MAGICK="". -MAGICK=${MAGICK-GraphicsMagick} +# +# TODO: ImageMagick may no longer be compatible. The --with-magick argument +# should be the name of a pkg-config file. Documentation suggests +# "ImageMagick++" which does not exist. "ImageMagick" and "Magick++" exist; +# the former does not pass configure checks, the latter fails at compile time. +MAGICK=${MAGICK-GraphicsMagick++} if [ -n "$MAGICK" ] && ! pkg-config --exists $MAGICK; then MAGICK=ImageMagick fi @@ -95,7 +93,6 @@ cd $PRGNAM-$VERSION chown -R root:root . chmod -R u+w,go-w,a+rX-st . -patch -p1 < $CWD/patches/imagemagick.diff # https://savannah.gnu.org/bugs/?49653 patch -p1 < $CWD/patches/atlas-lib-rename.diff autoreconf -vif @@ -104,19 +101,16 @@ autoreconf -vif # If you live far enough east or west that the date contained in version.texi # does not match that file's timestamp when printed accounting for your # timezone, then the docs get rebuilt with your local date. -# -# The TeX environment in Slackware 14.1 fails to build the DVI and PDF -# targets in Octave 3.8.1. Maybe it works with a recent version of TeXLive? find . -name stamp-vti -exec touch {} + ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=\${exec_prefix}/lib${LIBDIRSUFFIX} \ --sysconfdir=/etc \ --localstatedir=/var \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ + --mandir=\${prefix}/man \ + --infodir=\${prefix}/info \ + --docdir=\${prefix}/doc/$PRGNAM-$VERSION \ --disable-dependency-tracking \ --with-openssl=auto \ ${MAGICK} \ @@ -126,7 +120,8 @@ find . -name stamp-vti -exec touch {} + FFLAGS="$SLKCFLAGS" \ make -make check +# TODO: May fail if not all optional deps are installed (gl2ps in particular). +#make check make install-strip DESTDIR=$PKG find $PKG/usr/lib${LIBDIRSUFFIX} -name '*.la' -delete diff --git a/academic/octave/octave.info b/academic/octave/octave.info index 4d22788614..13eccf569d 100644 --- a/academic/octave/octave.info +++ b/academic/octave/octave.info @@ -1,8 +1,8 @@ PRGNAM="octave" -VERSION="6.3.0" +VERSION="8.4.0" HOMEPAGE="https://www.gnu.org/software/octave/" -DOWNLOAD="https://ftpmirror.gnu.org/gnu/octave/octave-6.3.0.tar.lz" -MD5SUM="3b6db5db59a7f4eaaa2a6095131c890f" +DOWNLOAD="https://ftpmirror.gnu.org/gnu/octave/octave-8.4.0.tar.lz" +MD5SUM="c7146cef6666200c5c835ecacf950804" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="%README% lapack" diff --git a/academic/octave/patches/imagemagick.diff b/academic/octave/patches/imagemagick.diff deleted file mode 100644 index 7a15122a18..0000000000 --- a/academic/octave/patches/imagemagick.diff +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/libinterp/corefcn/__magick_read__.cc b/libinterp/corefcn/__magick_read__.cc ---- a/libinterp/corefcn/__magick_read__.cc -+++ b/libinterp/corefcn/__magick_read__.cc -@@ -42,6 +42,8 @@ - #include <Magick++.h> - #include <clocale> - -+using Magick::Quantum; // https://savannah.gnu.org/bugs/?49653 -+ - // In theory, it should be enough to check the class: - // Magick::ClassType - // PseudoClass: diff --git a/academic/openboard/README b/academic/openboard/README index 22095c5feb..75711418bc 100644 --- a/academic/openboard/README +++ b/academic/openboard/README @@ -2,3 +2,6 @@ OpenBoard is an open source cross-platform teaching software for interactive whiteboard designed primarily for use in schools and universities. It can be used both with interactive whiteboards or in a dual-screen setup with a pen-tablet display and a beamer. + +NOTE: Support for Qt6 is available upstream but not yet tested +by maintainer. diff --git a/academic/openboard/openboard.SlackBuild b/academic/openboard/openboard.SlackBuild index fed1c282dc..d244896916 100644 --- a/academic/openboard/openboard.SlackBuild +++ b/academic/openboard/openboard.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for openboard -# Copyright 2021 Willy Sudiarto Raharjo <willysr@slackbuilds.org> +# Copyright 2021-2023 Willy Sudiarto Raharjo <willysr@slackbuilds.org> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=openboard SRCNAM=OpenBoard -VERSION=${VERSION:-1.6.1} +VERSION=${VERSION:-1.7.0} SRCVER=$(echo $VERSION | tr _ -) BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -39,9 +39,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -53,16 +50,12 @@ OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2" - LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" - LIBDIRSUFFIX="" fi set -e @@ -83,9 +76,12 @@ find -L . \ # Thanks to ArchLinux for these patches patch -p1 < $CWD/quazip.patch +sed -i "s|lquazip5|lquazip1-qt5|g" OpenBoard.pro -# Patch to run in a window -patch -p1 < $CWD/run-in-a-window.patch +# Add changes for current +# Thanks to Robby Workman for the idea +QUAZIPVER=`pkg-config --modversion quazip1-qt5` +sed -i "s|QuaZip-Qt5-1.1|QuaZip-Qt5-$QUAZIPVER|g" OpenBoard.pro plugins/cffadaptor/UBCFFAdaptor.pro qmake-qt5 OpenBoard.pro -spec linux-g++ make @@ -103,6 +99,7 @@ install -D -m 644 $CWD/openboard.desktop $PKG/usr/share/applications/openboard.d cd $PKG/usr/bin ln -s /opt/openboard/OpenBoard $PKG/usr/bin/openboard ) +strip --strip-unneeded /$PKG/opt/openboard/OpenBoard mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/openboard/openboard.info b/academic/openboard/openboard.info index 96743ec67a..20a8614784 100644 --- a/academic/openboard/openboard.info +++ b/academic/openboard/openboard.info @@ -1,10 +1,10 @@ PRGNAM="openboard" -VERSION="1.6.1" +VERSION="1.7.0" HOMEPAGE="https://github.com/OpenBoard-org/OpenBoard/" -DOWNLOAD="https://github.com/OpenBoard-org/OpenBoard/archive/v1.6.1/OpenBoard-1.6.1.tar.gz" -MD5SUM="e99a4d32bd85bd15bcd6d6e3f2820733" +DOWNLOAD="https://github.com/OpenBoard-org/OpenBoard/archive/v1.7.0/OpenBoard-1.7.0.tar.gz" +MD5SUM="8e4b9780efffbd1adca5582fa161fd7e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="libpaper libass x264 libfdk-aac quazip-qt5" +REQUIRES="libpaper libass x264 libfdk-aac" MAINTAINER="Willy Sudiarto Raharjo" EMAIL="willysr@slackbuilds.org" diff --git a/academic/openboard/quazip.patch b/academic/openboard/quazip.patch index a5b121549d..6a5cb79865 100644 --- a/academic/openboard/quazip.patch +++ b/academic/openboard/quazip.patch @@ -5,7 +5,7 @@ } -LIBS += "-L$$THIRD_PARTY_PATH/quazip/lib/$$SUB_DIR" "-lquazip" -+LIBS += "-lquazip5" ++LIBS += "-lquazip1-qt5" QT += xml xmlpatterns core QT += gui @@ -17,7 +17,7 @@ -INCLUDEPATH += $$THIRD_PARTY_PATH/quazip/ -include($$THIRD_PARTY_PATH/quazip/quazip.pri) - -+INCLUDEPATH += /usr/include/quazip5/ ++INCLUDEPATH += /usr/include/QuaZip-Qt5-1.1/quazip/ SOURCES += \ src/UBCFFAdaptor.cpp @@ -28,14 +28,14 @@ - resources/resources.qrc \ No newline at end of file + resources/resources.qrc ---- OpenBoard-1.6.0a3/OpenBoard.pro.orig 2020-07-20 08:23:09.859918480 +0700 -+++ OpenBoard-1.6.0a3/OpenBoard.pro 2020-07-20 08:23:17.762002419 +0700 -@@ -434,7 +434,7 @@ - #LIBS += -lprofiler - LIBS += -lX11 - LIBS += -lquazip5 -- INCLUDEPATH += "/usr/include/quazip" -+ INCLUDEPATH += "/usr/include/quazip5" +--- OpenBoard-1.7.0/OpenBoard.pro.orig 2023-12-10 12:06:17.808153181 +0700 ++++ OpenBoard-1.7.0/OpenBoard.pro 2023-12-10 12:10:09.448432404 +0700 +@@ -470,7 +470,7 @@ + INCLUDEPATH += "/usr/include/quazip6" + } else { + LIBS += -lquazip5 +- INCLUDEPATH += "/usr/include/quazip5" ++ INCLUDEPATH += "/usr/include/QuaZip-Qt5-1.1/quazip" + } LIBS += -lpoppler - INCLUDEPATH += "/usr/include/poppler" diff --git a/academic/openboard/run-in-a-window.patch b/academic/openboard/run-in-a-window.patch deleted file mode 100644 index 84c9cca3eb..0000000000 --- a/academic/openboard/run-in-a-window.patch +++ /dev/null @@ -1,154 +0,0 @@ -Patch for OpenBoard v. 1.6.0a3 by Roberto Puzzanghera roberto.puzzanghera at sagredo.eu -based on this patch http://webdiis.unizar.es/~spd/openboard/index.html.en - -OpenBoard runs in fullscreen mode. This seems to prevent the possibility to be recognized -by Google meet as an application to share. This patch gets OpenBoard to optionally run in -a window and solves the issue. - -With this patch OB runs in fullscreen mode by default. To run it in a window simply -adjust this option to true in the config file: - -RunInWindow=true - -On linux the location of the config file is /opt/openboard/etc/OpenBoard.config. A user -can override this file acting in local config file ~/.local/share/OpenBoard/OpenBoardUser.config - -============================================================================================= - -diff -ruN OpenBoard-1.6.0a3-original/OpenBoard.pro OpenBoard-1.6.0a3/OpenBoard.pro ---- OpenBoard-1.6.0a3-original/OpenBoard.pro 2020-05-22 18:40:49.000000000 +0200 -+++ OpenBoard-1.6.0a3/OpenBoard.pro 2020-10-24 10:58:50.421254271 +0200 -@@ -442,6 +442,10 @@ - QMAKE_CFLAGS += -fopenmp - QMAKE_CXXFLAGS += -fopenmp - QMAKE_LFLAGS += -fopenmp -+# RunInWindow patch -+ # Necessary for CentOS/RHEL and won't harm in other distributions -+ INCLUDEPATH += /usr/include/ffmpeg -+# end patch - UB_LIBRARY.path = $$DESTDIR - UB_I18N.path = $$DESTDIR/i18n - UB_ETC.path = $$DESTDIR -diff -ruN OpenBoard-1.6.0a3-original/resources/etc/OpenBoard.config OpenBoard-1.6.0a3/resources/etc/OpenBoard.config ---- OpenBoard-1.6.0a3-original/resources/etc/OpenBoard.config 2020-05-22 18:40:49.000000000 +0200 -+++ OpenBoard-1.6.0a3/resources/etc/OpenBoard.config 2020-10-24 10:59:50.005263852 +0200 -@@ -14,6 +14,7 @@ - PageCacheSize=20 - PreferredLanguage=fr_CH - ProductWebAddress=http://www.openboard.ch -+RunInWindow=false - SoftwareUpdateURL=http://www.openboard.ch/update.json - StartMode= - SwapControlAndDisplayScreens=false -diff -ruN OpenBoard-1.6.0a3-original/src/core/UBApplication.cpp OpenBoard-1.6.0a3/src/core/UBApplication.cpp ---- OpenBoard-1.6.0a3-original/src/core/UBApplication.cpp 2020-05-22 18:40:49.000000000 +0200 -+++ OpenBoard-1.6.0a3/src/core/UBApplication.cpp 2020-10-24 11:03:09.881941449 +0200 -@@ -277,8 +277,21 @@ - gs->setAttribute(QWebSettings::JavascriptCanAccessClipboard, true); - gs->setAttribute(QWebSettings::DnsPrefetchEnabled, true); - -+ /* RunInWindow patch */ -+ if (UBSettings::settings()->appRunInWindow->get().toBool()) { -+ mainWindow = new UBMainWindow(0, -+ Qt::Window | -+ Qt::WindowCloseButtonHint | -+ Qt::WindowMinimizeButtonHint | -+ Qt::WindowMaximizeButtonHint | -+ Qt::WindowShadeButtonHint -+ ); // deleted by application destructor -+ } else { -+ mainWindow = new UBMainWindow(0, Qt::FramelessWindowHint); // deleted by application destructor -+ } -+ /* mainWindow = new UBMainWindow(0, Qt::FramelessWindowHint); // deleted by application destructor */ -+ /* end patch */ - -- mainWindow = new UBMainWindow(0, Qt::FramelessWindowHint); // deleted by application destructor - mainWindow->setAttribute(Qt::WA_NativeWindow, true); - - mainWindow->actionCopy->setShortcuts(QKeySequence::Copy); -diff -ruN OpenBoard-1.6.0a3-original/src/core/UBSettings.cpp OpenBoard-1.6.0a3/src/core/UBSettings.cpp ---- OpenBoard-1.6.0a3-original/src/core/UBSettings.cpp 2020-05-22 18:40:49.000000000 +0200 -+++ OpenBoard-1.6.0a3/src/core/UBSettings.cpp 2020-10-24 11:02:43.074387051 +0200 -@@ -265,6 +265,9 @@ - appLookForOpenSankoreInstall = new UBSetting(this, "App", "LookForOpenSankoreInstall", true); - - appStartMode = new UBSetting(this, "App", "StartMode", ""); -+ /* RunInWindow patch */ -+ appRunInWindow = new UBSetting(this, "App", "RunInWindow", false); -+ /* end patch */ - - featureSliderPosition = new UBSetting(this, "Board", "FeatureSliderPosition", 40); - -diff -ruN OpenBoard-1.6.0a3-original/src/core/UBSettings.h OpenBoard-1.6.0a3/src/core/UBSettings.h ---- OpenBoard-1.6.0a3-original/src/core/UBSettings.h 2020-05-22 18:40:49.000000000 +0200 -+++ OpenBoard-1.6.0a3/src/core/UBSettings.h 2020-10-24 11:06:13.206894166 +0200 -@@ -260,7 +260,9 @@ - UBSetting* appHideSwapDisplayScreens; - UBSetting* appToolBarOrientationVertical; - UBSetting* appPreferredLanguage; -- -+ /* RunInWindow patch */ -+ UBSetting* appRunInWindow; -+ /* end patch */ - UBSetting* appIsInSoftwareUpdateProcess; - - UBSetting* appLastSessionDocumentUUID; -diff -ruN OpenBoard-1.6.0a3-original/src/frameworks/UBPlatformUtils_linux.cpp OpenBoard-1.6.0a3/src/frameworks/UBPlatformUtils_linux.cpp ---- OpenBoard-1.6.0a3-original/src/frameworks/UBPlatformUtils_linux.cpp 2020-05-22 18:40:49.000000000 +0200 -+++ OpenBoard-1.6.0a3/src/frameworks/UBPlatformUtils_linux.cpp 2020-10-24 11:00:43.708371185 +0200 -@@ -36,7 +36,9 @@ - #include <X11/keysym.h> - - #include "frameworks/UBFileSystemUtils.h" -- -+/* RunInWindow patch */ -+#include "core/UBSettings.h" -+/* end patch */ - - void UBPlatformUtils::init() - { -@@ -439,7 +441,14 @@ - - void UBPlatformUtils::showFullScreen(QWidget *pWidget) - { -- pWidget->showFullScreen(); -+ /* RunInWindow patch */ -+ /* pWidget->showFullScreen(); */ -+ if (UBSettings::settings()->appRunInWindow->get().toBool()) { -+ pWidget->showNormal(); -+ } else { -+ pWidget->showFullScreen(); -+ } -+ /* end patch */ - } - - void UBPlatformUtils::showOSK(bool show) -diff -ruN OpenBoard-1.6.0a3-original/src/frameworks/UBPlatformUtils_win.cpp OpenBoard-1.6.0a3/src/frameworks/UBPlatformUtils_win.cpp ---- OpenBoard-1.6.0a3-original/src/frameworks/UBPlatformUtils_win.cpp 2020-05-22 18:40:49.000000000 +0200 -+++ OpenBoard-1.6.0a3/src/frameworks/UBPlatformUtils_win.cpp 2020-10-24 11:01:26.170665369 +0200 -@@ -36,6 +36,9 @@ - - #include "frameworks/UBFileSystemUtils.h" - #include "core/memcheck.h" -+/* RunInWindow patch */ -+#include "core/UBSettings.h" -+/* end patch */ - - void UBPlatformUtils::init() - { -@@ -436,7 +439,14 @@ - - void UBPlatformUtils::showFullScreen(QWidget *pWidget) - { -- pWidget->showFullScreen(); -+ /* RunInWindow patch */ -+ /* pWidget->showFullScreen(); */ -+ if (UBSettings::settings()->appRunInWindow->get().toBool()) { -+ pWidget->showNormal(); -+ } else { -+ pWidget->showFullScreen(); -+ } -+ /* end patch */ - } - - void UBPlatformUtils::showOSK(bool show) diff --git a/academic/openboard/slack-desc b/academic/openboard/slack-desc index af65381fdc..a3a20c653a 100644 --- a/academic/openboard/slack-desc +++ b/academic/openboard/slack-desc @@ -5,7 +5,7 @@ # You must make exactly 11 lines for the formatting to be correct. It's also # customary to leave one space after the ':' except on otherwise blank lines. - |-----handy-ruler------------------------------------------------------| + |-----handy-ruler------------------------------------------------------| openboard: openboard (Interactive whiteboard) openboard: openboard: OpenBoard is an open source cross-platform teaching software for diff --git a/academic/paml/LICENSE b/academic/paml/LICENSE deleted file mode 100644 index b58e250862..0000000000 --- a/academic/paml/LICENSE +++ /dev/null @@ -1,3 +0,0 @@ -PAML is maintained and distributed for academic use free of charge by -Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac -OSX, and executables are provided for MS Windows. diff --git a/academic/paml/paml.SlackBuild b/academic/paml/paml.SlackBuild index 1445b81259..d27df64db3 100644 --- a/academic/paml/paml.SlackBuild +++ b/academic/paml/paml.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for paml -# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=paml -VERSION=${VERSION:-4.9j} +VERSION=${VERSION:-4.10.6} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -69,9 +69,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf ${PRGNAM}${VERSION} -tar xvf $CWD/${PRGNAM}${VERSION}.tgz -cd ${PRGNAM}${VERSION} +rm -rf ${PRGNAM}-${VERSION} +tar xvf $CWD/${PRGNAM}-${VERSION}.tar.gz +cd ${PRGNAM}-${VERSION} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -112,9 +112,6 @@ install -D -m755 evolverNSsites $PKG/usr/libexec/$PRGNAM/evolverNSsites # cc $SLKCFLAGS -o TreeTimeJeff TreeTimeJeff.c tools.c -lm # install -D -m755 TreeTimeJeff $PKG/usr/libexec/$PRGNAM/TreeTimeJeff -# Rename the local README, so we include it in the package. -mv README.txt README-compiling.txt - # Compile and install NEB, BEB and BranchSite cd ../Technical/Simulation/Codon cc $SLKCFLAGS -DNEB -o PositiveSitesNEB PositiveSites.c -lm @@ -125,38 +122,29 @@ install -D -m755 PositiveSitesBEB $PKG/usr/libexec/$PRGNAM/PositiveSitesBEB install -D -m755 PositiveSitesBS $PKG/usr/libexec/$PRGNAM/PositiveSitesBS install -D -m755 PositiveSitesNEB $PKG/usr/libexec/$PRGNAM/PositiveSitesNEB -# Rename this README too so we include it in the package. -mv README.txt README-codon.txt - # Compile and install Multiruns cd .. cc -o multiruns $SLKCFLAGS multiruns.c -lm install -D -m755 multiruns $PKG/usr/libexec/$PRGNAM/multiruns -cd $TMP/${PRGNAM}${VERSION} +cd $TMP/${PRGNAM}-${VERSION} # Include sample system files and example experimental data. -mkdir -p $PKG/usr/share/$PRGNAM/{aa,codon,ctl,dat,nuc,paup,trees} -cp -a *.dat dat/* $PKG/usr/share/$PRGNAM/dat -cp -a Technical/Simulation/Codon/{codeml.ctl,*.dat} \ - $PKG/usr/share/$PRGNAM/codon +mkdir -p $PKG/usr/share/$PRGNAM/Simulation/Codon +cp -a src/*.ctl dat $PKG/usr/share/$PRGNAM +cp -a Technical/Simulation/Codon/{codeml.ctl,*.dat,README.txt} \ + $PKG/usr/share/$PRGNAM/Simulation/Codon cp -a examples $PKG/usr/share/$PRGNAM -cp -a *.aa $PKG/usr/share/$PRGNAM/aa -cp -a *.ctl $PKG/usr/share/$PRGNAM/ctl -cp -a *.nuc $PKG/usr/share/$PRGNAM/nuc -cp -a paup* $PKG/usr/share/$PRGNAM/paup -cp -a *.trees $PKG/usr/share/$PRGNAM/trees find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a README.txt GeneticCode.txt doc/* src/README-compiling.txt \ - Technical/{Pt/eigenQREV.pdf,Simulation/{multiruns.txt,Codon/README-codon.txt}}\ +cp -a README.md LICENSE doc/* \ $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/MCMCtree.Tutorials.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/MCMCtree.Tutorial.pdf +cp Technical/Pt/eigenQREV.pdf $PKG/usr/doc/$PRGNAM-$VERSION +cp $CWD/MCMCtreeDOC.pdf $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE # Fix permissions. find $PKG/usr/{doc,share} -type d -exec chmod 755 {} \; -o \ diff --git a/academic/paml/paml.info b/academic/paml/paml.info index 7c31ba8a04..38bdd3d6ee 100644 --- a/academic/paml/paml.info +++ b/academic/paml/paml.info @@ -1,10 +1,10 @@ PRGNAM="paml" -VERSION="4.9j" -HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" -DOWNLOAD="http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz \ - http://ponce.cc/slackware/sources/repo/MCMCtree.Tutorials.pdf" -MD5SUM="50c1760512b7a5df50305e5fd26d0ca5 \ - 29c851d887eea56b949c01ab42cc48fb" +VERSION="4.10.6" +HOMEPAGE="https://github.com/abacus-gene/paml/" +DOWNLOAD="https://github.com/abacus-gene/paml/archive/v4.10.6/paml-4.10.6.tar.gz \ + https://raw.githubusercontent.com/slackalaxy/sources/main/MCMCtreeDOC.pdf" +MD5SUM="4a9b10fd6326f8ec51f1e0e9b6cc0352 \ + 99de7c0241b7152d619d899d72775410" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/pamlX/pamlX.SlackBuild b/academic/pamlX/pamlX.SlackBuild index cbefd5a500..c1a5f1e1cc 100644 --- a/academic/pamlX/pamlX.SlackBuild +++ b/academic/pamlX/pamlX.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for pamlX -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=pamlX VERSION=${VERSION:-1.3.1} -BUILD=${BUILD:-6} +BUILD=${BUILD:-8} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -79,13 +79,15 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh + # Fix the path where pamlX looks for the paml executables, its config # file (if necessary it should be in your home directory) and the # manuals installed by paml. sed -i 's|QApplication::applicationDirPath()|"/usr"|g' mainwindow.cpp sed -i 's|+= "/pamlx.conf"|= "~/.pamlX/pamlx.conf"|g' mainwindow.cpp -sed -i 's|/doc/|/doc/paml-4.9j/|g' mainwindow.cpp -sed -i 's|/doc/|/doc/paml-4.9j/|g' pamlhistorydialog.cpp +sed -i 's|/doc/|/doc/paml-4.10.6/|g' mainwindow.cpp +sed -i 's|/doc/|/doc/paml-4.10.6/|g' pamlhistorydialog.cpp # If you want the "Help" menu to use something else than Okular for # viewing the PDF documentation, uncomment the appropriate line below diff --git a/academic/pamlX/pamlX.info b/academic/pamlX/pamlX.info index 7e9ac1b1af..0fc74669f4 100644 --- a/academic/pamlX/pamlX.info +++ b/academic/pamlX/pamlX.info @@ -5,6 +5,6 @@ DOWNLOAD="http://abacus.gene.ucl.ac.uk/software/pamlX1.3.1-src.tgz" MD5SUM="55cd96e17d94a30232fc0cdd1eaeccf4" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="paml" +REQUIRES="paml qt4" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/papi/papi.SlackBuild b/academic/papi/papi.SlackBuild index a81de3bf55..d3f215c777 100644 --- a/academic/papi/papi.SlackBuild +++ b/academic/papi/papi.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=papi -VERSION=${VERSION:-5.5.1} +VERSION=${VERSION:-6.0.0.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -89,7 +89,7 @@ CXXFLAGS="$SLKCFLAGS" \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --with-static-lib=no \ + --with-static-lib=yes \ --with-shared-lib=yes \ --build=$ARCH-slackware-linux diff --git a/academic/papi/papi.info b/academic/papi/papi.info index 42d8c1de7b..04a6552694 100644 --- a/academic/papi/papi.info +++ b/academic/papi/papi.info @@ -1,8 +1,8 @@ PRGNAM="papi" -VERSION="5.5.1" +VERSION="6.0.0.1" HOMEPAGE="http://icl.utk.edu/papi/" -DOWNLOAD="http://icl.utk.edu/projects/papi/downloads/papi-5.5.1.tar.gz" -MD5SUM="86a8a6f3d0f34cd83251da3514aae15d" +DOWNLOAD="http://icl.cs.utk.edu/projects/papi/downloads/papi-6.0.0.1.tar.gz" +MD5SUM="34c536f3c4a6ad4b5615de23018503ad" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/parmetis/parmetis.SlackBuild b/academic/parmetis/parmetis.SlackBuild index c106737a06..6511e58083 100644 --- a/academic/parmetis/parmetis.SlackBuild +++ b/academic/parmetis/parmetis.SlackBuild @@ -34,7 +34,7 @@ SRCNAM="$(printf $PRGNAM | cut -d- -f2-)" if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -52,8 +52,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/patsy/patsy.SlackBuild b/academic/patsy/patsy.SlackBuild index f72b7d0d41..43c4ef9040 100644 --- a/academic/patsy/patsy.SlackBuild +++ b/academic/patsy/patsy.SlackBuild @@ -32,7 +32,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -50,8 +50,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/patsy/patsy.info b/academic/patsy/patsy.info index 60ef30f273..f7e632560f 100644 --- a/academic/patsy/patsy.info +++ b/academic/patsy/patsy.info @@ -5,6 +5,6 @@ DOWNLOAD="https://pypi.python.org/packages/source/p/patsy/patsy-0.3.0.zip" MD5SUM="7545518b413136ba8343dcebea07e5e2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="numpy" +REQUIRES="python2-numpy" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/penaltymodel/README b/academic/penaltymodel/README new file mode 100644 index 0000000000..be84eea915 --- /dev/null +++ b/academic/penaltymodel/README @@ -0,0 +1,14 @@ + One approach to solve a constraint satisfaction problem (CSP) using +an Ising model or a QUBO, is to map each individual constraint in +the CSP to a "small" Ising model or QUBO. This mapping is called +a penalty model. + + Imagine that we want to map an AND clause to a QUBO. In other words, +we want the solutions to the QUBO (the solutions that minimize the +energy) to be exactly the valid configurations of an AND gate. Let z = +AND(x_1, x_2). + + + Optional building mode set with environment variables: + - TESTS=yes, performs tests. Requires: dimod, python3-numpy, + networkx, python3-scipy, homebase, lapack. diff --git a/academic/penaltymodel/penaltymodel.SlackBuild b/academic/penaltymodel/penaltymodel.SlackBuild new file mode 100644 index 0000000000..c29dee1453 --- /dev/null +++ b/academic/penaltymodel/penaltymodel.SlackBuild @@ -0,0 +1,117 @@ +#!/bin/bash + +# Slackware build script for penaltymodel + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="penaltymodel" +VERSION=${VERSION:-1.0.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + cd tests + for file in $(ls test_*.py); do + echo -n "$file " + PYTHONPATH=../ python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/penaltymodel/penaltymodel.info b/academic/penaltymodel/penaltymodel.info new file mode 100644 index 0000000000..c04f042084 --- /dev/null +++ b/academic/penaltymodel/penaltymodel.info @@ -0,0 +1,10 @@ +PRGNAM="penaltymodel" +VERSION="1.0.2" +HOMEPAGE="https://github.com/dwavesystems" +DOWNLOAD="https://github.com/dwavesystems/penaltymodel/archive/1.0.2/penaltymodel-1.0.2.tar.gz" +MD5SUM="26c6d33ac5a17620c4d6de76985cc552" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/penaltymodel/slack-desc b/academic/penaltymodel/slack-desc new file mode 100644 index 0000000000..1e20efbea8 --- /dev/null +++ b/academic/penaltymodel/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +penaltymodel: penaltymodel (penalty model solver for Ising model or a QUBO) +penaltymodel: +penaltymodel: +penaltymodel: +penaltymodel: One approach to solve a constraint satisfaction problem (CSP) using +penaltymodel: an Ising model or a QUBO, is to map each individual constraint in +penaltymodel: the CSP to a "small" Ising model or QUBO. This mapping is called +penaltymodel: a penalty model. +penaltymodel: +penaltymodel: +penaltymodel: diff --git a/academic/pianobooster/pianobooster.SlackBuild b/academic/pianobooster/pianobooster.SlackBuild index bf44f6ef37..5850531d06 100644 --- a/academic/pianobooster/pianobooster.SlackBuild +++ b/academic/pianobooster/pianobooster.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for pianobooster -# Written by B. Watson (yalhcru@gmail.com) +# Written by B. Watson (urchlay@slackware.uk) # Modified by Willy Sudiarto Raharjo <willysr@slackware-id.org> # Licensed under the WTFPL. See http://www.wtfpl.net/txt/copying/ for details. diff --git a/academic/pianobooster/pianobooster.info b/academic/pianobooster/pianobooster.info index b0fdb7ddee..5ce9f314c9 100644 --- a/academic/pianobooster/pianobooster.info +++ b/academic/pianobooster/pianobooster.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/pianobooster/PianoBooster/archive/v1.0.0/PianoBoost MD5SUM="2a4701c18a9e3fb7a1185657d51f1dba" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="ftgl" MAINTAINER="B. Watson" -EMAIL="yalhcru@gmail.com" +EMAIL="urchlay@slackware.uk" diff --git a/academic/plus42/README b/academic/plus42/README new file mode 100644 index 0000000000..b23684de4c --- /dev/null +++ b/academic/plus42/README @@ -0,0 +1,19 @@ +Plus42 is an advanced scientific programmable calculator, based on +Free42 (a complete re-implementation of the HP-42S scientific +programmable RPN calculator) and adds: + +- A Larger Display, with 8 rows and 22 columns (131x64 pixels) by + default, which the user may resize at will. + +- Algebraic Expressions modeled after those used on the HP-27S and + HP-17B/19B. + +- Attached Units and unit conversions modeled after those used on the + HP-48/49/50 series. + +- Directories for more organized storage of programs and variables. + +- TVM and amortization tables. + +- Two-dimensional Plotting of functions, with ability to zoom and pan, + and find integrals and roots from points in the plot. diff --git a/academic/avogadro/doinst.sh b/academic/plus42/doinst.sh index 4e8ba7071d..4e8ba7071d 100644 --- a/academic/avogadro/doinst.sh +++ b/academic/plus42/doinst.sh diff --git a/academic/plus42/plus42.SlackBuild b/academic/plus42/plus42.SlackBuild new file mode 100644 index 0000000000..c89279a774 --- /dev/null +++ b/academic/plus42/plus42.SlackBuild @@ -0,0 +1,104 @@ +#!/bin/bash + +# Slackware build script for plus42 + +# Copyright 2023-2024 Antonio Leal, Porto Salvo, Oeiras, Portugal +# Copyright 2022-2023 Juan M. Lasca juanmlasca@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=plus42 +VERSION=${VERSION:-1.1.9} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz || + tar xvf $CWD/${PRGNAM}desktop-$VERSION.tar.gz +mv ${PRGNAM}desktop-$VERSION $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +cd gtk +sed -i "s|-g\ |$SLKCFLAGS|" Makefile +make -e BCD_MATH=1 AUDIO_ALSA=1 +cd .. +mkdir -p $PKG/usr/bin $PKG/usr/share/applications $PKG/usr/share/pixmaps + +cp gtk/plus42dec $PKG/usr/bin +cp gtk/icon-128x128.xpm $PKG/usr/share/pixmaps/plus42icon-128x128.xpm +cp $CWD/plus42.desktop $PKG/usr/share/applications +(cd $PKG/usr/bin; ln -s plus42dec plus42) + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README COPYING HISTORY CREDITS \ + $PKG/usr/doc/$PRGNAM-$VERSION +cp -a gtk/README $PKG/usr/doc/$PRGNAM-$VERSION/README-GTK +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/plus42/plus42.desktop b/academic/plus42/plus42.desktop new file mode 100644 index 0000000000..dfcf2b2c11 --- /dev/null +++ b/academic/plus42/plus42.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Comment= +Terminal=false +Name=Plus42 +Exec=/usr/bin/plus42dec +Type=Application +Categories=Utility;Calculator; +Icon=/usr/share/pixmaps/plus42icon-128x128.xpm diff --git a/academic/plus42/plus42.info b/academic/plus42/plus42.info new file mode 100644 index 0000000000..45e08e71d5 --- /dev/null +++ b/academic/plus42/plus42.info @@ -0,0 +1,10 @@ +PRGNAM="plus42" +VERSION="1.1.9" +HOMEPAGE="https://www.thomasokken.com/plus42" +DOWNLOAD="https://github.com/thomasokken/plus42desktop/archive/v1.1.9/plus42-1.1.9.tar.gz" +MD5SUM="a06f497124bc6b0e03d2f46c15097faa" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Antonio Leal" +EMAIL="antonioleal@yahoo.com" diff --git a/academic/plus42/slack-desc b/academic/plus42/slack-desc new file mode 100644 index 0000000000..f4de09afd9 --- /dev/null +++ b/academic/plus42/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +plus42: plus42 (An Enhanced HP-42S Calculator Simulator) +plus42: +plus42: Plus42 is an advanced scientific programmable calculator, based on +plus42: Free42 (a complete re-implementation of the HP-42S scientific +plus42: programmable RPN calculator) +plus42: +plus42: Plus42 builds on Free42 and adds: A Larger Display, with 8 rows and 22 +plus42: columns (131x64 pixels) by default, which the user may resize at will; +plus42: Algebraic Expressions; attached Units and unit conversions; +plus42: Directories; TVM and amortization tables; and two-dimensional Plotting +plus42: of functions. Homepage at https://www.thomasokken.com/plus42 diff --git a/academic/pomoxis/README b/academic/pomoxis/README new file mode 100644 index 0000000000..5214c86dc4 --- /dev/null +++ b/academic/pomoxis/README @@ -0,0 +1,4 @@ + Pomoxis comprises a set of basic bioinformatic tools tailored to +nanopore sequencing. Notably tools are included for generating and +analysing draft assemblies. Many of these tools are used by the +research data analysis group at Oxford Nanopore Technologies. diff --git a/academic/pomoxis/pomoxis.SlackBuild b/academic/pomoxis/pomoxis.SlackBuild new file mode 100644 index 0000000000..6c43667b34 --- /dev/null +++ b/academic/pomoxis/pomoxis.SlackBuild @@ -0,0 +1,102 @@ +#!/bin/bash + +# Slackware build script for pomoxis + +# Copyright 2023 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=pomoxis +VERSION=${VERSION:-0.3.12} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CHANGELOG.md LICENSE.md docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pomoxis/pomoxis.info b/academic/pomoxis/pomoxis.info new file mode 100644 index 0000000000..e78d77e751 --- /dev/null +++ b/academic/pomoxis/pomoxis.info @@ -0,0 +1,10 @@ +PRGNAM="pomoxis" +VERSION="0.3.12" +HOMEPAGE="https://github.com/nanoporetech/pomoxis" +DOWNLOAD="https://github.com/nanoporetech/pomoxis/archive/v0.3.12/pomoxis-0.3.12.tar.gz" +MD5SUM="a2c01f36a87982962143f8d99648a7f1" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="blas" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/pomoxis/slack-desc b/academic/pomoxis/slack-desc new file mode 100644 index 0000000000..8d2494de50 --- /dev/null +++ b/academic/pomoxis/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +pomoxis: pomoxis (bioinformatics tools for nanopore research) +pomoxis: +pomoxis: +pomoxis: Pomoxis comprises a set of basic bioinformatic tools tailored to +pomoxis: nanopore sequencing. Notably tools are included for generating and +pomoxis: analysing draft assemblies. Many of these tools are used by the +pomoxis: research data analysis group at Oxford Nanopore Technologies. +pomoxis: +pomoxis: +pomoxis: +pomoxis: diff --git a/academic/prank-msa/prank-msa.SlackBuild b/academic/prank-msa/prank-msa.SlackBuild index 0806584320..a3c6791cdd 100644 --- a/academic/prank-msa/prank-msa.SlackBuild +++ b/academic/prank-msa/prank-msa.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for prank-msa -# Copyright 2017-2021 Petar petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -39,9 +39,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 diff --git a/academic/primer3/README b/academic/primer3/README index 51977f2f12..3b57af159d 100644 --- a/academic/primer3/README +++ b/academic/primer3/README @@ -1,14 +1,24 @@ Primer3 is a widely used program for designing PCR primers (PCR = -"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool -in genetics and molecular biology. Primer3 can design hybridization -probes and sequencing primers. +"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in +genetics and molecular biology. Primer3 can design hybridization probes +and sequencing primers. PCR is used for many different goals. Consequently, primer3 has many different input parameters that you control and that tell primer3 exactly what characteristics make good primers for your goals. -For details and citation: -Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for -general users and for biologist programmers. In: Krawetz S, Misener S -(eds) Bioinformatics Methods and Protocols: Methods in Molecular -Biology. Humana Press, Totowa, NJ, pp 365-386 +Primer3 picks primers for PCR reactions, considering as criteria: +* oligonucleotide melting temperature, size, GC content and primer-dimer + possibilities, +* PCR product size +* positional constraints within the source (template) sequence +* possibilities for ectopic priming (amplifying the wrong sequence) +* many other constraints. + +All of these criteria are user-specifiable as constraints, and some are +specifiable as terms in an objective function that characterizes an +optimal primer pair. + +manual online: https://primer3.org/manual.html + +For details and citation see "References" in the package's doc folder. diff --git a/academic/primer3/References b/academic/primer3/References index 5009a52a1b..f951635a4d 100644 --- a/academic/primer3/References +++ b/academic/primer3/References @@ -1,4 +1,21 @@ -Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general -users and for biologist programmers. In: Krawetz S, Misener S (eds) -Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana -Press, Totowa, NJ, pp 365-386 +We request but do not require that use of this software be cited in publications as + +* Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M and Rozen SG. +Primer3--new capabilities and interfaces. +Nucleic Acids Res. 2012 Aug 1;40(15):e115. +The paper is available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424584/ + +and + +* Koressaar T and Remm M. +Enhancements and modifications of primer design program Primer3. +Bioinformatics 2007;23(10):1289-1291. +The paper is available at https://www.ncbi.nlm.nih.gov/pubmed/17379693 + +If you use masker function, please cite: +* Koressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R and Remm M. +Primer3_masker: integrating masking of template sequence with primer design software. +Bioinformatics 2018;34(11):1937-1938. +The paper is available at https://www.ncbi.nlm.nih.gov/pubmed/29360956 + +Source code available at https://github.com/primer3-org/primer3. diff --git a/academic/primer3/gcc-7.patch b/academic/primer3/gcc-7.patch deleted file mode 100644 index a92d0e77b7..0000000000 --- a/academic/primer3/gcc-7.patch +++ /dev/null @@ -1,22 +0,0 @@ -Author: Andreas Tille <tille@debian.org> -Last-Update: Sat, 26 Aug 2017 00:32:40 +0200 -Bug-Debian: https://bugs.debian.org/853621 -Description: Fix build with gcc-7 - ---- a/src/thal.c -+++ b/src/thal.c -@@ -426,12 +426,12 @@ thal(const unsigned char *oligo_f, - "Illegal type"); - o->align_end_1 = -1; - o->align_end_2 = -1; -- if ('\0' == oligo_f) { -+ if ('\0' == oligo_f[0]) { - strcpy(o->msg, "Empty first sequence"); - o->temp = 0.0; - return; - } -- if ('\0' == oligo_r) { -+ if ('\0' == oligo_r[0]) { - strcpy(o->msg, "Empty second sequence"); - o->temp = 0.0; - return; diff --git a/academic/primer3/primer3.SlackBuild b/academic/primer3/primer3.SlackBuild index 5281f13889..9a4bd6b511 100644 --- a/academic/primer3/primer3.SlackBuild +++ b/academic/primer3/primer3.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for primer3 -# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=primer3 -VERSION=${VERSION:-2.4.0} +VERSION=${VERSION:-2.6.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -79,13 +76,10 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Thanks to Debian for the patch -patch -p1 -i $CWD/gcc-7.patch - cd ./src # Use our CFLAGS -sed -i -e "s|-O2|$SLKCFLAGS|" -e "s|-g -Wall|-fpermissive|" Makefile +sed -i -e "s|-O2|$SLKCFLAGS|" Makefile # Look for configuration files in /usr/share instead of /opt sed -i "s:/opt/primer3_config:/usr/share/$PRGNAM/primer3_config:g" thal_main.c primer3_boulder_main.c @@ -94,7 +88,7 @@ make # This is recommended, but the tests take a really long time. Be patient # if you uncomment the line below. -# make test +#make test install -D -m755 primer3_core $PKG/usr/bin/primer3_core install -D -m755 ntdpal $PKG/usr/bin/ntdpal @@ -108,7 +102,9 @@ ln -s primer3_core primer32_core # Copy configuration files and settings to /usr/share cd $TMP/$PRGNAM-$VERSION mkdir -p $PKG/usr/share/$PRGNAM -cp -a settings_files src/primer3_config $PKG/usr/share/$PRGNAM +cp -a \ + kmer_lists/readme.txt settings_files example src/primer3_config \ + $PKG/usr/share/$PRGNAM # Copy the man pages from Debian mkdir -p $PKG/usr/man/man1 @@ -122,7 +118,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - src/{release_notes.txt,primer3_manual.htm} LICENSE example README.md \ + src/{release_notes.txt,primer3_manual.htm} LICENSE README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References diff --git a/academic/primer3/primer3.info b/academic/primer3/primer3.info index 861eb56e58..5a9c2ffe17 100644 --- a/academic/primer3/primer3.info +++ b/academic/primer3/primer3.info @@ -1,8 +1,8 @@ PRGNAM="primer3" -VERSION="2.4.0" -HOMEPAGE="http://primer3.sourceforge.net/" -DOWNLOAD="http://sourceforge.net/projects/primer3/files/primer3/2.4.0/primer3-2.4.0.tar.gz" -MD5SUM="aed6546bdfb60652cd7eba8d51eae8cc" +VERSION="2.6.1" +HOMEPAGE="https://primer3.org/" +DOWNLOAD="https://github.com/primer3-org/primer3/archive/v2.6.1/primer3-2.6.1.tar.gz" +MD5SUM="d18c095694b586c300c88fab4b116c8c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/primer3/slack-desc b/academic/primer3/slack-desc index 9e871a4b8c..4e4ce377e2 100644 --- a/academic/primer3/slack-desc +++ b/academic/primer3/slack-desc @@ -13,7 +13,7 @@ primer3: "Polymerase Chain Reaction"). PCR is an essential and primer3: ubiquitous tool in genetics and molecular biology. Primer3 can also primer3: design hybridization probes and sequencing primers. primer3: -primer3: Home: http://primer3.sourceforge.net/ -primer3: References: /usr/doc/primer3-2.3.7/References +primer3: https://primer3.org/manual.html +primer3: primer3: primer3: diff --git a/academic/pspp/pspp.SlackBuild b/academic/pspp/pspp.SlackBuild index 47443177fe..17b31eb664 100644 --- a/academic/pspp/pspp.SlackBuild +++ b/academic/pspp/pspp.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=pspp -VERSION=${VERSION:-1.2.0} +VERSION=${VERSION:-2.0.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -79,7 +76,6 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -LIBS="-ltermcap -lgmp" \ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -107,7 +103,7 @@ rm -f $PKG/usr/info/dir gzip -9 $PKG/usr/info/*.info* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING README AUTHORS ABOUT-NLS INSTALL NEWS ONEWS THANKS $PKG/usr/doc/$PRGNAM-$VERSION +cp -a COPYING README AUTHORS ABOUT-NLS NEWS ONEWS THANKS $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/pspp/pspp.info b/academic/pspp/pspp.info index 348b0649f4..702e496e28 100644 --- a/academic/pspp/pspp.info +++ b/academic/pspp/pspp.info @@ -1,10 +1,10 @@ PRGNAM="pspp" -VERSION="1.2.0" +VERSION="2.0.0" HOMEPAGE="http://www.gnu.org/software/pspp/" -DOWNLOAD="https://mirrors.up.pt/pub/gnu/pspp/pspp-1.2.0.tar.gz" -MD5SUM="e940d666b586f5bd2f17a2b305fac71f" +DOWNLOAD="http://mirrors.nav.ro/gnu/pspp/pspp-2.0.0.tar.gz" +MD5SUM="11f5949311bfe66a44999b9d7db6c99b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="spread-sheet-widget" MAINTAINER="Vitor Borrego" -EMAIL="vitor@bitarus.allowed.org" +EMAIL="vitor@bitarus.mooo.com" diff --git a/academic/pulseview/pulseview.SlackBuild b/academic/pulseview/pulseview.SlackBuild index 4c03296628..9b3885487e 100644 --- a/academic/pulseview/pulseview.SlackBuild +++ b/academic/pulseview/pulseview.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=pulseview -VERSION=${VERSION:-20210103_d023660} +VERSION=${VERSION:-20220225_4efbe9b} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/pulseview/pulseview.info b/academic/pulseview/pulseview.info index 50c6886414..534e4f0210 100644 --- a/academic/pulseview/pulseview.info +++ b/academic/pulseview/pulseview.info @@ -1,8 +1,8 @@ PRGNAM="pulseview" -VERSION="20210103_d023660" +VERSION="20220225_4efbe9b" HOMEPAGE="https://sigrok.org/wiki/PulseView" -DOWNLOAD="http://ponce.cc/slackware/sources/repo/pulseview-20210103_d023660.tar.xz" -MD5SUM="b9160d5d5777d723db68b5139a4b4ea6" +DOWNLOAD="http://ponce.cc/slackware/sources/repo/pulseview-20220225_4efbe9b.tar.xz" +MD5SUM="eec6859a8bb32d61c9d5f7eb14fda625" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="libsigrok libsigrokdecode" diff --git a/academic/pyCRAC/README b/academic/pyCRAC/README index 9eb56fc043..b9b74fd37b 100644 --- a/academic/pyCRAC/README +++ b/academic/pyCRAC/README @@ -5,8 +5,10 @@ data generated by CLIP or CRAC protocols). It can be used to remove duplicate reads,tackles directional libraries and reports sense and anti-sense hits. -Included is the pipeline used for the analysis of a group of CRAC data -sets. +A pipeline that streamlines the analysis of a group of CRAC datasets +is available at https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines and +depends on the python package 'ruffus', also at slackbuilds.org. + References @@ -23,21 +25,3 @@ A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G, Granneman S. If you want to run the test suite after installation, see README.tests. - - -Note on the Crac pipelines: - -Use the -h flag to get a detailed help menu. - -The CRAC_pipeline_PE.py script needs to be run from the folder that -contains the fastq files - -The barcode list file should contain two tab-separated columns in which -the first column is the barcode sequence and the second column is the -name of the experiment - -The file containing the adapter sequences should be in the fasta format. - -The chromosome_lengths file should contain two tab-separated columns in -which the first column has the chromosome name and the second the -chromosome length. diff --git a/academic/pyCRAC/pyCRAC.SlackBuild b/academic/pyCRAC/pyCRAC.SlackBuild index 51f54e1913..038db738b1 100644 --- a/academic/pyCRAC/pyCRAC.SlackBuild +++ b/academic/pyCRAC/pyCRAC.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for pyCRAC -# Copyright 2017-2021 Rob van Nues +# Copyright 2017-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,15 +25,11 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=pyCRAC -VERSION=${VERSION:-1.5.1} +VERSION=${VERSION:-1.5.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -PIPENAM=crac_pipelines -PIPEVER=master -#PIPETAG=sgrann - if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -74,18 +70,9 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -#rm -rf $PIPETAG-$PIPENAM-$PIPEVER -rm -rf $PIPENAM-$PIPEVER tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION -mkdir $PRGNAM/$PIPENAM - -if [[ -f $CWD/$PIPENAM-$PIPEVER.tar.gz ]]; then - tar xvf $CWD/$PIPENAM-$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 -else - echo "$PIPENAM-$PIPEVER.tar.gz not found" -fi #replace setup.py; test.sh mv setup.py setup.py.ORIG @@ -114,7 +101,6 @@ cp -a \ $CWD/README.tests $CWD/setup_slack.py \ $CWD/README \ $PKG/usr/doc/$PRGNAM-$VERSION -cp -a $PRGNAM/$PIPENAM/README.md $PKG/usr/doc/$PRGNAM-$VERSION/$PIPENAM-README.md cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/pyCRAC/pyCRAC.info b/academic/pyCRAC/pyCRAC.info index 32f9269715..8fcdeffd60 100644 --- a/academic/pyCRAC/pyCRAC.info +++ b/academic/pyCRAC/pyCRAC.info @@ -1,12 +1,10 @@ PRGNAM="pyCRAC" -VERSION="1.5.1" -HOMEPAGE="http://sandergranneman.bio.ed.ac.uk/pycrac-software" -DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.5.1.tar.gz \ - https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines/-/archive/master/crac_pipelines-master.tar.gz" -MD5SUM="f634167e03ef26213efb4400671dbc9c \ - 119c67d318a03ed29471e4caeb2690a4" +VERSION="1.5.2" +HOMEPAGE="https://git.ecdf.ed.ac.uk/sgrannem/pycrac" +DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.5.2.tar.gz" +MD5SUM="f2bbb5dbcbe2b17051b8843a7e4d519f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="flexbar novocraft numpy3 pysam scipy3 pandas ruffus" +REQUIRES="flexbar novocraft pysam python3-scipy python3-pandas" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/pyCRAC/setup_slack.py b/academic/pyCRAC/setup_slack.py index 0340228e84..db5c30751f 100644 --- a/academic/pyCRAC/setup_slack.py +++ b/academic/pyCRAC/setup_slack.py @@ -2,7 +2,7 @@ __author__ = "Sander Granneman" __copyright__ = "Copyright 2021" -__version__ = "1.5.1" +__version__ = "1.5.2" __credits__ = ["Sander Granneman","Grzegorz Kudla","Hywell Dunn Davies"] __maintainer__ = ["Sander Granneman","Rob van Nues for SlackBuilds.org"] __email__ = ["sgrannem@staffmail.ed.ac.uk", "sborg63@disroot.org"] @@ -25,7 +25,7 @@ setup(name='pyCRAC', description='Python NextGen sequencing data processing software', author='Sander Granneman', author_email='sgrannem@staffmail.ed.ac.uk', - url='http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html', + url='https://git.ecdf.ed.ac.uk/sgrannem/pycrac', packages=['pyCRAC','pyCRAC.Parsers','pyCRAC.Classes','pyCRAC.Methods'], install_requires=['numpy >= 1.5.1', 'cython >=0.19', 'pysam >= 0.6','six >= 1.9.0'], scripts=[ @@ -55,8 +55,6 @@ setup(name='pyCRAC', 'pyCRAC/scripts/pyGTF2bedGraph.py', 'pyCRAC/scripts/pyFilterGTF.py', 'pyCRAC/scripts/pyNormalizeIntervalLengths.py', - 'pyCRAC/crac_pipelines/CRAC_pipeline_PE.py', - 'pyCRAC/crac_pipelines/CRAC_pipeline_SE.py', ], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Environment :: Console', diff --git a/academic/pyfits/README b/academic/pyfits/README deleted file mode 100644 index 89eac1e478..0000000000 --- a/academic/pyfits/README +++ /dev/null @@ -1,3 +0,0 @@ -PyFITS provides an interface to FITS formatted files in the Python -scripting language. PyFITS is a development project of the Science -Software Branch at the Space Telescope Science Institute. diff --git a/academic/pyfits/pyfits.SlackBuild b/academic/pyfits/pyfits.SlackBuild deleted file mode 100644 index 100379b00e..0000000000 --- a/academic/pyfits/pyfits.SlackBuild +++ /dev/null @@ -1,66 +0,0 @@ -#!/bin/bash - -# Slackware build script for PyFITS. - -# Written by Nicky Chorley <nick.chorley@gmail.com>, but heavily -# based on the NumPy SlackBuild by Aleksandar Samardzic. - -cd $(dirname $0) ; CWD=$(pwd) - -PRGNAM=pyfits -VERSION=${VERSION:-3.1.2} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} -PKGTYPE=${PKGTYPE:-tgz} - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i486 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. -if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then - echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" - exit 0 -fi - -TMP=${TMP:-/tmp/SBo} -PKG=${PKG:-$TMP/package-$PRGNAM} -OUTPUT=${OUTPUT:-/tmp} - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -python setup.py install --root $PKG - -find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a CHANGES.txt LICENSE.txt README.txt\ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -find $PKG/usr/doc -type f -exec chmod 0644 {} \; - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pyfits/pyfits.info b/academic/pyfits/pyfits.info deleted file mode 100644 index 501d73913c..0000000000 --- a/academic/pyfits/pyfits.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="pyfits" -VERSION="3.1.2" -HOMEPAGE="https://github.com/spacetelescope/PyFITS" -DOWNLOAD="https://pypi.python.org/packages/source/p/pyfits/pyfits-3.1.2.tar.gz" -MD5SUM="d0f1dce1719170b0c9777bbb15bbd8b3" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="python-stsci.distutils numpy" -MAINTAINER="Nicky Chorley" -EMAIL="nick.chorley@gmail.com" diff --git a/academic/pysam/pysam.SlackBuild b/academic/pysam/pysam.SlackBuild index 7e991b8f38..17d0db3198 100644 --- a/academic/pysam/pysam.SlackBuild +++ b/academic/pysam/pysam.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for pysam -# Copyright 2017-2021 Rob van Nues +# Copyright 2017-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=pysam -VERSION=${VERSION:-0.17.0} -BUILD=${BUILD:-3} +VERSION=${VERSION:-0.21.0} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -80,10 +80,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -### pysam linked to htslib-1.13; SBo-htslib is at 1.14: -### for use system htslib: -#export HTSLIB_LIBRARY_DIR=/usr/lib$LIBDIRSUFFIX -#export HTSLIB_INCLUDE_DIR=/usr/include +# pysam linked to htslib-1.17; SBo-htslib is at 1.18 #the source does not allow 'read' to 'other', which could cause a problem on reloading a Jupyter-notebook chmod 644 pysam.egg-info/* diff --git a/academic/pysam/pysam.info b/academic/pysam/pysam.info index f49bd25d6c..d71c4d96bd 100644 --- a/academic/pysam/pysam.info +++ b/academic/pysam/pysam.info @@ -1,10 +1,10 @@ PRGNAM="pysam" -VERSION="0.17.0" +VERSION="0.21.0" HOMEPAGE="https://github.com/pysam-developers/pysam" -DOWNLOAD="https://pypi.python.org/packages/source/p/pysam/pysam-0.17.0.tar.gz" -MD5SUM="cddcf9bad79158fb2e2f9859c5188206" +DOWNLOAD="https://pypi.python.org/packages/source/p/pysam/pysam-0.21.0.tar.gz" +MD5SUM="dca7fb36d2cf69ef887fe05ddd726998" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="htslib" +REQUIRES="" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/python2-kiwisolver/README b/academic/python2-kiwisolver/README new file mode 100644 index 0000000000..5a37c5dfc8 --- /dev/null +++ b/academic/python2-kiwisolver/README @@ -0,0 +1,8 @@ +This is an efficient C++ implementation of the Cassowary constraint +solving algorithm. Kiwi(solver) is based on the seminal Cassowary +paper. It is not a refactoring of the original C++ solver, but has been +designed from the ground up to be lightweight and fast. It ranges from +10x to 500x faster than the original Cassowary solver with typical use +cases gaining a 40x improvement. Memory savings are consistently > 5x. + +Version 1.1.0 is the last one with support for python2. diff --git a/academic/kiwisolver/kiwisolver.SlackBuild b/academic/python2-kiwisolver/python2-kiwisolver.SlackBuild index a8642e3de6..01e961c82e 100644 --- a/academic/kiwisolver/kiwisolver.SlackBuild +++ b/academic/python2-kiwisolver/python2-kiwisolver.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for kiwisolver -# Copyright 2018 Serban Udrea <s.udrea@gsi.de> +# Copyright 2018-2022 Serban Udrea <s.udrea@gsi.de> # All rights reserved. # # Redistribution and use of this script, with or without modification, @@ -25,8 +25,9 @@ cd $(dirname $0) ; CWD=$(pwd) -PRGNAM=kiwisolver -VERSION=${VERSION:-1.0.1} +PRGNAM=python2-kiwisolver +SRCNAM=kiwisolver +VERSION=${VERSION:-1.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -48,7 +49,7 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=${PKG:-$TMP/package-$PRGNAM} +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e @@ -56,9 +57,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -66,13 +67,13 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -python setup.py install --root $PKG +python2 setup.py install --root $PKG find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING.txt PKG-INFO README.rst $PKG/usr/doc/$PRGNAM-$VERSION +cp -a releasenotes.rst PKG-INFO README.rst $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/python2-kiwisolver/python2-kiwisolver.info b/academic/python2-kiwisolver/python2-kiwisolver.info new file mode 100644 index 0000000000..875281ea80 --- /dev/null +++ b/academic/python2-kiwisolver/python2-kiwisolver.info @@ -0,0 +1,10 @@ +PRGNAM="python2-kiwisolver" +VERSION="1.1.0" +HOMEPAGE="https://pypi.org/project/kiwisolver" +DOWNLOAD="https://files.pythonhosted.org/packages/16/e7/df58eb8868d183223692d2a62529a594f6414964a3ae93548467b146a24d/kiwisolver-1.1.0.tar.gz" +MD5SUM="fc8a614367f7ba0d34a02fd08c535afc" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Serban Udrea" +EMAIL="S.Udrea@gsi.de" diff --git a/academic/python2-kiwisolver/slack-desc b/academic/python2-kiwisolver/slack-desc new file mode 100644 index 0000000000..ecf6335078 --- /dev/null +++ b/academic/python2-kiwisolver/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +python2-kiwisolver: python2-kiwisolver (an implementation of the Cassowary algorithm) +python2-kiwisolver: +python2-kiwisolver: This is an efficient C++ implementation of the Cassowary constraint +python2-kiwisolver: solving algorithm. Kiwi(solver) is based on the seminal Cassowary +python2-kiwisolver: paper. It is not a refactoring of the original C++ solver, but has +python2-kiwisolver: been designed from the ground up to be lightweight and fast. +python2-kiwisolver: +python2-kiwisolver: Homepage: https://pypi.org/project/kiwisolver +python2-kiwisolver: +python2-kiwisolver: Version 1.1.0 is the last one with support for python2. +python2-kiwisolver: diff --git a/academic/scipy/README b/academic/python2-scipy/README index 81198ddbe7..aa007f4f7d 100644 --- a/academic/scipy/README +++ b/academic/python2-scipy/README @@ -9,18 +9,17 @@ charge. NumPy and SciPy are easy to use, but powerful enough to be depended upon by some of the world's leading scientists and engineers. matplotlib and ipython are nice to have in connection with scipy, but -scipy does not depend on them. +scipy does not depend on them. Be aware that ipython gets installed just +for python3. Since ver. 0.14.0 scipy uses SuperLU instead of UMFPACK for solving unsymmetric sparse linear systems. If you want to use UMFPACK you must install it in advance of numpy and build numpy accordingly (see the README to numpy's SlackBuild). Moreover, after installing scipy, -you have to install scikit-umfpack, which presently is not available on -SlackBuilds.org. +you have to install scikit-umfpack. If you need to build scipy for debugging, set DEBUG=y. -NOTE: If you use this SlackBuild scipy will run with the python version - provided by Slackware Linux, which is presently 2.7.xx. If you'd - like to use python 3.x then you have to install scipy with the - scipy3 SlackBuild. +NOTE: Version 1.2.3 is the last one with python2 support. If you'd like + to use a newer scipy version you have to switch to using python3 + and install scipy with the scipy3 SlackBuild. diff --git a/academic/scipy3/scipy3.SlackBuild b/academic/python2-scipy/python2-scipy.SlackBuild index 68db3dcfd1..683c91db3d 100644 --- a/academic/scipy3/scipy3.SlackBuild +++ b/academic/python2-scipy/python2-scipy.SlackBuild @@ -1,8 +1,8 @@ #!/bin/bash -# Build script for the Python SciPy package to be used with python 3 +# Build script for the Python SciPy package -# Copyright 2016-2019 Serban Udrea <s.udrea@gsi.de> +# Copyright 2011-2022 Serban Udrea <s.udrea@gsi.de> # All rights reserved. # # Redistribution and use of this script, with or without modification, @@ -25,14 +25,15 @@ # Written by Eugene Suter <easuter@gmail.com> # Updated to 0.7.2 by João Felipe Santos <joao.eel@gmail.com> -# Updated up to 1.1.0 by Serban Udrea <S.Udrea@gsi.de> +# Updated to 1.2.2 by Matteo Bernardini <ponce@slackbuilds.org> +# Updated up to 1.1.0 and to 1.2.3 by Serban Udrea <S.Udrea@gsi.de> # Added support for building with debugging symbols (S. Udrea) cd $(dirname $0) ; CWD=$(pwd) -PRGNAM="scipy3" -SRCNAM="scipy" -VERSION=${VERSION:-1.5.4} +PRGNAM=python2-scipy +SRCNAM=scipy +VERSION=${VERSION:-1.2.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -54,7 +55,7 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=${PKG:-$TMP/package-$PRGNAM} +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e @@ -62,9 +63,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf "$SRCNAM-$VERSION" +rm -rf $SRCNAM-$VERSION tar xvf $CWD/$SRCNAM-$VERSION.tar.gz -cd "$SRCNAM-$VERSION" +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ @@ -73,17 +74,19 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +export FFLAGS="-fallow-argument-mismatch -fPIC" + DEBUG=${DEBUG:-no} DEBUG=$(echo "$DEBUG"|cut -b 1|tr a-z A-Z) if [ "$DEBUG" = "N" ] then - python3 setup.py install --root $PKG + python2 setup.py install --root $PKG find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true else - python3 setup.py build --debug - python3 setup.py install --root $PKG + python2 setup.py build --debug + python2 setup.py install --root $PKG fi mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/python2-scipy/python2-scipy.info b/academic/python2-scipy/python2-scipy.info new file mode 100644 index 0000000000..801dab6c3c --- /dev/null +++ b/academic/python2-scipy/python2-scipy.info @@ -0,0 +1,10 @@ +PRGNAM="python2-scipy" +VERSION="1.2.3" +HOMEPAGE="https://www.scipy.org/" +DOWNLOAD="https://files.pythonhosted.org/packages/62/4f/7e95c5000c411164d5ca6f55ac54cda5d200a3b6719dafd215ee0bd61578/scipy-1.2.3.tar.gz" +MD5SUM="43b42a507472dfa1dff4c91d58a6543f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python2-numpy lapack" +MAINTAINER="Serban Udrea" +EMAIL="S.Udrea@gsi.de" diff --git a/academic/python2-scipy/slack-desc b/academic/python2-scipy/slack-desc new file mode 100644 index 0000000000..040202c817 --- /dev/null +++ b/academic/python2-scipy/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +python2-scipy: python2-scipy (python library for math, science, and engineering) +python2-scipy: +python2-scipy: The SciPy library is built to work with NumPy arrays, and provides +python2-scipy: many user-friendly and efficient numerical routines such as routines +python2-scipy: for numerical integration and optimization. NumPy and SciPy are easy +python2-scipy: to use, but powerful enough to be depended upon by some of the world's +python2-scipy: leading scientists and engineers. +python2-scipy: Version 1.2.3 is the last with support for python2. +python2-scipy: +python2-scipy: https://www.scipy.org/ +python2-scipy: diff --git a/academic/python3-ase/README b/academic/python3-ase/README new file mode 100644 index 0000000000..b37a13ecf8 --- /dev/null +++ b/academic/python3-ase/README @@ -0,0 +1,7 @@ + The Atomic Simulation Environment (ASE) is a set of tools and Python +modules for setting up, manipulating, running, visualizing and +analyzing atomistic simulations. The code is freely available under +the GNU LGPL license. + + + Optional dependence autodetected, matplotlib diff --git a/academic/python3-ase/python3-ase.SlackBuild b/academic/python3-ase/python3-ase.SlackBuild new file mode 100644 index 0000000000..d8f092e024 --- /dev/null +++ b/academic/python3-ase/python3-ase.SlackBuild @@ -0,0 +1,111 @@ +#!/bin/bash + +# Slackware build script for ASE (Atomic Simulation Environment) + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=python3-ase +VERSION=${VERSION:-3.22.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM="ase" + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py build +[ "${TEST:-no}" == "yes" ] && PYTHONPATH=$PYTHONPATH:. ./bin/ase test +PYTHONPATH=$PYTHONPATH:. ./bin/ase info; sleep 2 +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + {CHANGELOG,CONTRIBUTING,README}.rst \ + COPYING COPYING.LESSER LICENSE PKG-INFO doc \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/python3-ase/python3-ase.info b/academic/python3-ase/python3-ase.info new file mode 100644 index 0000000000..c23706b96f --- /dev/null +++ b/academic/python3-ase/python3-ase.info @@ -0,0 +1,10 @@ +PRGNAM="python3-ase" +VERSION="3.22.1" +HOMEPAGE="https://wiki.fysik.dtu.dk/ase" +DOWNLOAD="https://pypi.org/packages/source/a/ase/ase-3.22.1.tar.gz" +MD5SUM="8173c8b598faf995ff11cbceafacedc1" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-scipy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/python3-ase/slack-desc b/academic/python3-ase/slack-desc new file mode 100644 index 0000000000..59d1cf5415 --- /dev/null +++ b/academic/python3-ase/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +python3-ase: python3-ase (Atomic Simulation Environment (ASE)) +python3-ase: +python3-ase: +python3-ase: +python3-ase: The Atomic Simulation Environment (ASE) is a set of tools and +python3-ase: Python modules for setting up, manipulating, running, visualizing +python3-ase: and analyzing atomistic simulations. The code is freely available +python3-ase: under the GNU LGPL license. +python3-ase: +python3-ase: +python3-ase: diff --git a/academic/python3-scipy/README b/academic/python3-scipy/README new file mode 100644 index 0000000000..c4b1d1d862 --- /dev/null +++ b/academic/python3-scipy/README @@ -0,0 +1,26 @@ +SciPy (pronounced "Sigh Pie") is open-source software for mathematics, +science, and engineering. + +The SciPy library is built to work with NumPy arrays, and provides +many user-friendly and efficient numerical routines such as routines +for numerical integration and optimization. Together, they run on +all popular operating systems, are quick to install, and are free of +charge. NumPy and SciPy are easy to use, but powerful enough to be +depended upon by some of the world's leading scientists and engineers. + +matplotlib and ipython are nice to have in connection with scipy, but +scipy does not depend on them. + +Since ver. 0.14.0 scipy uses SuperLU instead of UMFPACK for solving +unsymmetric sparse linear systems. If you want to use UMFPACK you +must install it in advance of numpy and build numpy accordingly (see +the README to numpy's SlackBuild). Moreover, after installing scipy, +you have to install scikit-umfpack. + +If you need to build scipy for debugging, set DEBUG=YES. + +NOTE: this is for Python 3. If you need Python 2 support, install +python2-scipy. + +ADDITIONAL NOTE: Unable to support newer versions than 1.12.0 due to +requiring a newer Cython than included in Slackware (needs 3.0.8). diff --git a/academic/scipy/scipy.SlackBuild b/academic/python3-scipy/python3-scipy.SlackBuild index 15c1957424..7586beabdc 100644 --- a/academic/scipy/scipy.SlackBuild +++ b/academic/python3-scipy/python3-scipy.SlackBuild @@ -1,8 +1,10 @@ #!/bin/bash -# Build script for the Python SciPy package +# Build script for the Python SciPy package to be used with python 3 -# Copyright 2011-2018 Serban Udrea <s.udrea@gsi.de> +# Copyright 2016-2019 Serban Udrea <s.udrea@gsi.de> +# Copyright 2022 Isaac Yu <isaacyu@protonmail.com> +# Copyright 2023-2024 Jeremy Hansen <jebrhansen+SBo@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, @@ -30,9 +32,10 @@ cd $(dirname $0) ; CWD=$(pwd) -PRGNAM=scipy -VERSION=${VERSION:-1.1.0} -BUILD=${BUILD:-2} +PRGNAM="python3-scipy" +SRCNAM="scipy" +VERSION=${VERSION:-1.12.0} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -44,16 +47,13 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 fi TMP=${TMP:-/tmp/SBo} -PKG=${PKG:-$TMP/package-$PRGNAM} +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e @@ -61,35 +61,39 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf "$PRGNAM-$VERSION" -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd "$PRGNAM-$VERSION" +rm -rf "$SRCNAM-$VERSION" +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd "$SRCNAM-$VERSION" chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -DEBUG=${DEBUG:-no} -DEBUG=$(echo "$DEBUG"|cut -b 1|tr a-z A-Z) - -if [ "$DEBUG" = "N" ] -then - python setup.py install --root $PKG - find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -else - python setup.py build --debug - python setup.py install --root $PKG + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ + +# Allow our version of numpy and pythran to work +sed -i 's|numpy==1.22.4|numpy>=1.22.4|' pyproject.toml +sed -i 's|numpy==1.23.2|numpy>=1.23.2|' pyproject.toml +sed -i 's|pythran>=0.15.0,<0.16.0|pythran|' pyproject.toml + +# needs newer meson +PYVER=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') +export PYTHONPATH=/opt/python$PYVER/site-packages/ + +python3 -m build --wheel --no-isolation +python3 -m installer --destdir "$PKG" dist/*.whl + +# Skip stripping symbols if DEBUG is YES +if [ "${DEBUG:-NO}" == "NO" ]; then + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true fi mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a LICENSE.txt THANKS.txt INSTALL.rst.txt HACKING.rst.txt PKG-INFO \ +cp -a CONTRIBUTING.rst LICENSE.txt LICENSES_bundled.txt README.rst PKG-INFO \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -find $PKG/usr/doc -type f -exec chmod 0644 {} \; mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/python3-scipy/python3-scipy.info b/academic/python3-scipy/python3-scipy.info new file mode 100644 index 0000000000..b2043cced7 --- /dev/null +++ b/academic/python3-scipy/python3-scipy.info @@ -0,0 +1,10 @@ +PRGNAM="python3-scipy" +VERSION="1.12.0" +HOMEPAGE="https://www.scipy.org/" +DOWNLOAD="https://github.com/scipy/scipy/releases/download/v1.12.0/scipy-1.12.0.tar.gz" +MD5SUM="22683fcf9a411f0a5254b7509bea0a6b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="pybind11 python3-pythran OpenBLAS" +MAINTAINER="Jeremy Hansen" +EMAIL="jebrhansen+SBo@gmail.com" diff --git a/academic/python3-scipy/slack-desc b/academic/python3-scipy/slack-desc new file mode 100644 index 0000000000..92ab6f1d7a --- /dev/null +++ b/academic/python3-scipy/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +python3-scipy: python3-scipy (python library for math, science, and engineering) +python3-scipy: +python3-scipy: The SciPy library is built to work with NumPy arrays, and provides +python3-scipy: many user-friendly and efficient numerical routines such as routines +python3-scipy: for numerical integration and optimization. Together, they run on all +python3-scipy: popular operating systems, are quick to install, and are free of +python3-scipy: charge. NumPy and SciPy are easy to use, but powerful enough to be +python3-scipy: depended upon by some of the world's leading scientists and engineers. +python3-scipy: +python3-scipy: https://www.scipy.org/ +python3-scipy: diff --git a/academic/qhull/qhull.SlackBuild b/academic/qhull/qhull.SlackBuild index 03e63ba985..feabf1cb97 100644 --- a/academic/qhull/qhull.SlackBuild +++ b/academic/qhull/qhull.SlackBuild @@ -4,6 +4,9 @@ # Copyright 2012 Chris Abela, Malta # Copyright 2014 Ryan P.C. McQuen, ryanpcmcquen@member.fsf.org, WA +# Copyright 2023, Lockywolf +# Contributed 2024, Kyle Guinn + # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,9 +29,12 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=qhull -VERSION=${VERSION:-2015.2} -BUILD_VERSION=${BUILD_VERSION:-7.2.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-8.0.2} +BUILD_VERSION=${BUILD_VERSION:-2020} +BUILD_VERSION_PATCH=${BUILD_VERSION_PATCH:-2} + +BUILD=${BUILD:-2} + TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -71,9 +77,11 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-${VERSION%.*}-src-${BUILD_VERSION}.tgz -cd $PRGNAM-$VERSION + +rm -rf $PRGNAM-$BUILD_VERSION.$BUILD_VERSION_PATCH +tar xvf $CWD/$PRGNAM-${BUILD_VERSION}-src-${VERSION}.tgz +cd $PRGNAM-$BUILD_VERSION.$BUILD_VERSION_PATCH + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -81,26 +89,28 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +sed -i \ + -e '/ConfigPackageLocation/s/lib/${LIB_INSTALL_DIR}/' \ + -e '/PkgConfigLocation/s/lib/${LIB_INSTALL_DIR}/' \ + CMakeLists.txt + mkdir -p build cd build cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ - -DBIN_INSTALL_DIR=/usr/bin \ - -DLIB_INSTALL_DIR=/usr/lib${LIBDIRSUFFIX} \ - -DINCLUDE_INSTALL_DIR=/usr/include \ - -DMAN_INSTALL_DIR=/usr/man/man1 \ - -DDOC_INSTALL_DIR=/usr/doc/$PRGNAM-$VERSION \ + -DLIB_INSTALL_DIR=lib${LIBDIRSUFFIX} \ + -DMAN_INSTALL_DIR=man/man1 \ + -DDOC_INSTALL_DIR=doc/$PRGNAM-$VERSION \ + -DCMAKE_SKIP_RPATH=YES \ + -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ + -DCMAKE_C_COMPILER_LAUNCHER=ccache \ -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG cd .. -# Let octave find us -ln -s libqhull $PKG/usr/include/qhull -ln -s libqhull.h $PKG/usr/include/libqhull/qhull.h - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/qhull/qhull.info b/academic/qhull/qhull.info index 2124edbf51..f296e70bab 100644 --- a/academic/qhull/qhull.info +++ b/academic/qhull/qhull.info @@ -1,10 +1,10 @@ PRGNAM="qhull" -VERSION="2015.2" +VERSION="8.0.2" HOMEPAGE="http://www.qhull.org/" -DOWNLOAD="http://www.qhull.org/download/qhull-2015-src-7.2.0.tgz" -MD5SUM="e6270733a826a6a7c32b796e005ec3dc" +DOWNLOAD="http://www.qhull.org/download/qhull-2020-src-8.0.2.tgz" +MD5SUM="295f7332269a38279478f555cc185296" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Jason Graham" -EMAIL="jgraha8@gmail.com" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.qhull2020_2023-11-19@lockywolf.net" diff --git a/academic/qrupdate/README b/academic/qrupdate/README index e5979003d8..ec5b475e39 100644 --- a/academic/qrupdate/README +++ b/academic/qrupdate/README @@ -1,12 +1,16 @@ qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. -This requires a BLAS/LAPACK implementation. Choose one of these package sets: +This requires a BLAS/LAPACK implementation. Choose one of these package +sets: + * OpenBLAS (includes both a BLAS and a LAPACK implementation) * atlas (includes both a BLAS and a LAPACK implementation) * blas, lapack (the Netlib reference implementations) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. + +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib reference +implementations; other packages that require a BLAS or LAPACK +implementation may not build if they are not configured to detect/use +alternate implementations. diff --git a/academic/qrupdate/qrupdate.SlackBuild b/academic/qrupdate/qrupdate.SlackBuild index e98a100038..859089ed67 100644 --- a/academic/qrupdate/qrupdate.SlackBuild +++ b/academic/qrupdate/qrupdate.SlackBuild @@ -47,13 +47,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="COPYING ChangeLog README" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/qrupdate/qrupdate.info b/academic/qrupdate/qrupdate.info index 22d6ccbd7f..b61013c4db 100644 --- a/academic/qrupdate/qrupdate.info +++ b/academic/qrupdate/qrupdate.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/qrupdate/files/qrupdate/1.2/qrupdate- MD5SUM="6d073887c6e858c24aeda5b54c57a8c4" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas lapack" +REQUIRES="lapack" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/qucs-s/README b/academic/qucs-s/README new file mode 100644 index 0000000000..c6b002c25d --- /dev/null +++ b/academic/qucs-s/README @@ -0,0 +1,8 @@ +Qucs-S is a spin-off of the Qucs circuit simulator. The "S" letter +indicates SPICE. It merges the power of SPICE and the simplicity of +the Qucs GUI. Qucs-S is not a simulator by itself, but it requires +to use a simulation backend with it. The schematic document format of +Qucs and Qucs-S are fully compatible. Qucs-S allows to use the following +simulation kernels: + +Ngspice(recommended optional dependency), XYCE and SpiceOpus. diff --git a/academic/qucs-s/doinst.sh b/academic/qucs-s/doinst.sh new file mode 100644 index 0000000000..65c7e2eeb9 --- /dev/null +++ b/academic/qucs-s/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/qucs-s/qucs-s.SlackBuild b/academic/qucs-s/qucs-s.SlackBuild new file mode 100644 index 0000000000..75d71ab548 --- /dev/null +++ b/academic/qucs-s/qucs-s.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/bash + +# Slackware build script for qucs-s + +# Copyright 2023-2024 Johannes Schoepfer, Germany +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=qucs-s +VERSION=${VERSION:-24.2.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} + -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + + +# Avoid dependency on dos2unix +sed -i qucsator_rf/src/CMakeLists.txt \ + -e "s/COMMAND \${gperfappgen_exe}.*/COMMAND \${gperfappgen_exe} | fromdos > \${CMAKE_CURRENT_BINARY_DIR}\/gperfapphash.gph/" + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -Wno-dev \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +sed \ + -e "/^Encoding/d" \ + -e "/^$/d" \ + -i $PKG/usr/share/applications/qucs-s.desktop + +mv $PKG/usr/share/man $PKG/usr +find $PKG/usr/man -type f -exec gzip -9 {} + +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS README* COPYING RELEASE ChangeLog THANKS TODO NEWS* VERSION \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/qucs-s/qucs-s.info b/academic/qucs-s/qucs-s.info new file mode 100644 index 0000000000..1feeb476ca --- /dev/null +++ b/academic/qucs-s/qucs-s.info @@ -0,0 +1,10 @@ +PRGNAM="qucs-s" +VERSION="24.2.1" +HOMEPAGE="https://ra3xdh.github.io" +DOWNLOAD="https://github.com/ra3xdh/qucs_s/releases/download/24.2.1/qucs-s-24.2.1.tar.gz" +MD5SUM="6af848a8184e13d3aa9f0c61c7b18845" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Johannes Schoepfer" +EMAIL="slackbuilds@schoepfer.info" diff --git a/academic/qucs-s/slack-desc b/academic/qucs-s/slack-desc new file mode 100644 index 0000000000..85d183826f --- /dev/null +++ b/academic/qucs-s/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +qucs-s: qucs-s (circuit simulator) +qucs-s: +qucs-s: Qucs-S is a spin-off of the Qucs circuit simulator. The "S" letter +qucs-s: indicates SPICE. It merges the power of SPICE and the simplicity of +qucs-s: the Qucs GUI. Qucs-S is not a simulator by itself, but it requires to +qucs-s: use a simulation backend with it. The schematic document format of +qucs-s: Qucs and Qucs-S are fully compatible. These backends are supported: +qucs-s: +qucs-s: Ngspice(recommended, available on SBo), XYCE and SpiceOpus. +qucs-s: +qucs-s: https://ra3xdh.github.io diff --git a/academic/qucs/doinst.sh b/academic/qucs/doinst.sh index 5fb28930db..65c7e2eeb9 100644 --- a/academic/qucs/doinst.sh +++ b/academic/qucs/doinst.sh @@ -1,3 +1,9 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/qucs/qucs.SlackBuild b/academic/qucs/qucs.SlackBuild index c619b6fd11..1cf3b6d6ca 100644 --- a/academic/qucs/qucs.SlackBuild +++ b/academic/qucs/qucs.SlackBuild @@ -13,22 +13,22 @@ # 1. Redistributions of this script must retain the above copyright # notice, this list of conditions and the following disclaimer. # -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. cd $(dirname $0) ; CWD=$(pwd) PRGNAM=qucs VERSION=${VERSION:-0.0.19} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -54,16 +54,24 @@ OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" SPEC="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" SPEC="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" SPEC="-spec linux-g++-64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" + SPEC="" fi set -e +source /etc/profile.d/qt4.sh rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT @@ -74,22 +82,26 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ --mandir=/usr/man \ --disable-doc \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done diff --git a/academic/qucs/qucs.info b/academic/qucs/qucs.info index fd2e34b3ab..2d17c1db1f 100644 --- a/academic/qucs/qucs.info +++ b/academic/qucs/qucs.info @@ -5,6 +5,6 @@ DOWNLOAD="http://downloads.sourceforge.net/qucs/qucs-0.0.19.tar.gz" MD5SUM="321b22b88099c6c8ac42ee8b7ab637a8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adms" +REQUIRES="adms qt4" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/ramulator/README b/academic/ramulator/README new file mode 100644 index 0000000000..fbc6c1077a --- /dev/null +++ b/academic/ramulator/README @@ -0,0 +1,6 @@ +Ramulator is a fast and cycle-accurate DRAM simulator that supports a +wide array of commercial, as well as academic, DRAM standards. + + +Support files are installed at: /usr/share/ramulator-VERSION +Test files are at: /usr/libexec/ramulator diff --git a/academic/ramulator/ramulator.SlackBuild b/academic/ramulator/ramulator.SlackBuild new file mode 100644 index 0000000000..1f1d5112e8 --- /dev/null +++ b/academic/ramulator/ramulator.SlackBuild @@ -0,0 +1,139 @@ +#!/bin/bash + +# Slackware build script for ramulator + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=ramulator +VERSION=${VERSION:-20220503} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +COMMIT=743b940b70a8e18bcffb14eec22d2ed731059540 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$COMMIT +tar xvf $CWD/$PRGNAM-$COMMIT.tar.gz +cd $PRGNAM-$COMMIT +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# make rule for libramulator.so +sed -i '39alibramulator.so: $(SRCS) $(SRCDIR)/*.h' Makefile +sed -i '40a\\t$(CXX) -c $(CXXFLAGS) -fpic -DRAMULATOR -o libramulator.o $<' Makefile +sed -i '41a\\t$(CXX) -shared -o libramulator.so libramulator.o' Makefile + +# update other files +sed -i '19,20s#./#/usr/share/'$PRGNAM-$VERSION'/#' test_ramulator.py +sed -i '26s/^/#/' test_ramulator.py +sed -i '27s#./#/usr/share/'$PRGNAM-$VERSION'/#' test_ramulator.py +sed -i '32s#./##' test_ramulator.py +sed -i '24s#./##' test_ddr3.py +sed -i '24s#configs/#/usr/share/'$PRGNAM-$VERSION'/&#' test_ddr3.py + + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make ramulator libramulator.so + +# installing +install -d $PKG/usr/{bin,include/ramulator,lib${LIBDIRSUFFIX}} +install -m 755 ramulator $PKG/usr/bin +install -m 644 src/*.h $PKG/usr/include/ramulator +install -m 755 libramulator.so $PKG/usr/lib${LIBDIRSUFFIX} + +# install other files +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -av configs mappings $PKG/usr/share/$PRGNAM-$VERSION +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/cputraces +find cputraces/ -type f \ + -size -2M -exec cp -av '{}' $PKG/usr/share/$PRGNAM-$VERSION/cputraces \; + +mkdir -p $PKG/usr/libexec/$PRGNAM +cp -av test_ramulator.py $PKG/usr/libexec/$PRGNAM +cp -av test_ddr3.py $PKG/usr/libexec/$PRGNAM +cp -av plot.py $PKG/usr/libexec/$PRGNAM + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ramulator/ramulator.info b/academic/ramulator/ramulator.info new file mode 100644 index 0000000000..1be349e32f --- /dev/null +++ b/academic/ramulator/ramulator.info @@ -0,0 +1,10 @@ +PRGNAM="ramulator" +VERSION="20220503" +HOMEPAGE="https://github.com/CMU-SAFARI/ramulator" +DOWNLOAD="https://github.com/CMU-SAFARI/ramulator/archive/743b940b70a8e18bcffb14eec22d2ed731059540/ramulator-743b940b70a8e18bcffb14eec22d2ed731059540.tar.gz" +MD5SUM="c8eb022ef2465831704bc8551bfa1a36" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/Mnemosyne/slack-desc b/academic/ramulator/slack-desc index eaef720461..ab7d81704f 100644 --- a/academic/Mnemosyne/slack-desc +++ b/academic/ramulator/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -Mnemosyne: Mnemosyne (A free flash-card tool) -Mnemosyne: -Mnemosyne: It's a free flash-card tool which optimizes your learning process. -Mnemosyne: uses a sophisticated algorithm to schedule the best time for -Mnemosyne: a card to come up for review. Difficult cards that you tend to forget -Mnemosyne: quickly will be scheduled more often, while Mnemosyne won't -Mnemosyne: waste your time on things you remember well. -Mnemosyne: -Mnemosyne: -Mnemosyne: -Mnemosyne: +ramulator: ramulator (a fast and cycle-accurate DRAM simulator) +ramulator: +ramulator: +ramulator: +ramulator: Ramulator is a fast and cycle-accurate DRAM simulator that +ramulator: supports a wide array of commercial, as well as academic, +ramulator: DRAM standards. +ramulator: +ramulator: +ramulator: +ramulator: diff --git a/academic/rbio/rbio.SlackBuild b/academic/rbio/rbio.SlackBuild index d5595a7d6d..ba45380aac 100644 --- a/academic/rbio/rbio.SlackBuild +++ b/academic/rbio/rbio.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/root/README b/academic/root/README index c8beb68da7..3f7a5201e2 100644 --- a/academic/root/README +++ b/academic/root/README @@ -1,20 +1,36 @@ ROOT - A data analysis framework. -ROOT is a data analysis framework used mostly, but not limited to, -high energy physics. It was written in C++ by the techs at CERN to -explore the benefits of object oriented programming in physics data -analysis. It consists of libraries, CINT or cling interpreter for -C/C++, plotting interface and powerful parellel processing support. -It is the preferred choice in many laboratories. - -It comes with A LOT of different options for compilation. And it +ROOT provides a set of frameworks with the functionality needed to +handle and analyze large amounts of data in an efficient way. It +includes specialized storage methods such as histograms, curve +fitting, function evaluation, minimization, graphics, visualization +classes; the C++ interpreter cling for fast prototyping; and powerful +parallel processing support. + +It comes with a lot of different options for compilation. And it seems impossible to stress all of them in this one script. Therefore -the potential user is strongly advised to check the configure -script. +the potential user is strongly advised to check the cmake command +arguments. + +Compilation takes quite a while, thus consider to build ROOT like that: +# MAKEFLAGS=-j5 ./root.SlackBuild + +REQUIREMENTS: gl2ps libAfterImage python3-numpy tbb ftgl + +NOTES: + - ROOT's python TMVA requires python3-numpy being built over blas. -For mathmore support, run the SlackBuild script with MATHMORE=yes, and -for QT support, run the SlackBuild script with QT=yes, for example + - This SlackBuild sets the root7 build option to ON in order to + prepare the migration to the new ROOT 7 release. More on the ROOT 7 + features you can find here: + https://root.cern/for_developers/root7 - MATHMORE=yes ./root.SlackBuild + - Starting from ROOT version 6.26/00 it uses the web-based version for + the TBrowser if it is build with the root7 option being ON. You can + switch back to the Win95-looking TBrowser by adding the following + line to your $HOME/.rootrc file: + Browser.Name: TRootBrowser -Compilation takes quite a while. + - Starting from ROOT 6.28/00 version, one can use rootssh script for + automatic configuration of ssh tunnel, necessary for web widgets: + rootssh username@remotenode diff --git a/academic/root/root.SlackBuild b/academic/root/root.SlackBuild index 88fd4250ea..1dc6bb4194 100644 --- a/academic/root/root.SlackBuild +++ b/academic/root/root.SlackBuild @@ -20,22 +20,19 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=root -VERSION=${VERSION:-6.10.02} +VERSION=${VERSION:-6.28.08} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -45,129 +42,219 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" + SLKCFLAGS="-march=i686 -mtune=i686" elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" + SLKCFLAGS="-fPIC" else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" + SLKCFLAGS="" fi -set -e +CXXSTD=${CXXSTD:-17} -if [ ${GSL:-yes} = "no" ]; then - GSL_FLAGS="--disable-gsl-shared" -else - GSL_FLAGS="--enable-gsl-shared \ - --with-gsl-incdir=/usr/include \ - --with-gsl-libdir=/usr/lib${LIBDIRSUFFIX}" - if [ "$MATHMORE" = "yes" ]; then - GSL_FLAGS="$GSL_FLAGS --enable-mathmore" - fi -fi - -if [ ${FFTW:-yes} = "no" ]; then - FFTW_FLAGS="--disable-fftw3" -else - FFTW_FLAGS="--enable-fftw3 \ - --with-fftw3-incdir=/usr/include \ - --with-fftw3-libdir=/usr/lib${LIBDIRSUFFIX}" -fi - -if [ ${QT:-no} = "no" ]; then - QT_FLAGS="--disable-qt" -else - QT_FLAGS="--enable-qt" -fi +set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM\_v$VERSION.source.tar.gz +mv root-$VERSION src +mkdir -p $PRGNAM-$VERSION +mv src $PRGNAM-$VERSION cd $PRGNAM-$VERSION + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -# Make sure we use system libs and headers -rm -r graf3d/ftgl/{inc,src} -rm -r graf2d/freetype/src -rm -r graf3d/glew/{inc,src} -rm -r core/pcre/src -LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | xargs -0 rm -f -rm -r core/lzma/src/*.tar.gz + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ # prefix where to install stuff -PREFIX=/opt/ROOT - -# Use --with-clang to avoid gcc-5.3 internal compiler error on i586 +PREFIX=/opt/ROOT-${VERSION} +mkdir -p build +cd build CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --with-clang \ - --prefix=$PREFIX \ - --libdir=$PREFIX/lib${LIBDIRSUFFIX} \ - --incdir=$PREFIX/include \ - --mandir=$PREFIX/man/man1 \ - --etcdir=$PREFIX/etc/root \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --enable-roofit \ - --enable-unuran \ - --disable-builtin-freetype \ - --disable-builtin-ftgl \ - --disable-builtin-glew \ - --disable-builtin-pcre \ - --disable-builtin-zlib \ - --disable-builtin-lzma \ - $GSL_FLAGS \ - $FFTW_FLAGS \ - $QT_FLAGS \ - --enable-shared \ - --build=$ARCH-slackware-linux - +cmake ../src \ + -DCMAKE_INSTALL_PREFIX=$PREFIX \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_STANDARD=${CXXSTD} \ + -DCMAKE_INSTALL_PYTHONDIR=lib \ + -DMAN_INSTALL_DIR=$PREFIX/man \ + -Dbuiltin_cfitsio=OFF \ + -Dbuiltin_davix=OFF \ + -Dbuiltin_fftw3=OFF \ + -Dbuiltin_gsl=OFF \ + -Dbuiltin_gtest=OFF \ + -Dbuiltin_openssl=OFF \ + -Dbuiltin_tbb=OFF \ + -Dbuiltin_vc=OFF \ + -Dbuiltin_vdt=OFF \ + -Dbuiltin_veccore=OFF \ + -Dclad=OFF \ + -Dalien=OFF \ + -Dall=OFF \ + -Darrow=OFF \ + -Dassan=OFF \ + -Dasserts=OFF \ + -Dbuiltin_freetype=OFF \ + -Dfftw3=ON \ + -Dbuiltin_glew=OFF \ + -Dbuiltin_clang=ON \ + -Dbuiltin_cling=ON \ + -Dbuiltin_llvm=ON \ + -Dbuiltin_lz4=OFF \ + -Dbuiltin_lzma=OFF \ + -Dbuiltin_nlohmannjson=ON \ + -Dbuiltin_openui5=ON \ + -Dbuiltin_pcre=OFF \ + -Dbuiltin_unuran=OFF \ + -Dbuiltin_xrootd=OFF \ + -Dbuiltin_xxhash=OFF \ + -Dbuiltin_zlib=OFF \ + -Dbuiltin_zstd=OFF \ + -Dccache=OFF \ + -Dcefweb=OFF \ + -Dclingtest=OFF \ + -Dcocoa=OFF \ + -Dcompression_default=zlib \ + -Dcoverage=OFF \ + -Dcuda=OFF \ + -Dcudnn=OFF \ + -Dcxx_modules=OFF \ + -Ddataframe=ON \ + -Ddavix=OFF \ + -Ddcache=OFF \ + -Ddev=OFF \ + -Ddistcc=OFF \ + -Dexceptions=ON \ + -Dfail-on-missing=ON \ + -Dfcgi=OFF \ + -Dfitsio=ON \ + -Dfortran=ON \ + -Dgdml=ON \ + -Dgfal=OFF \ + -Dgminimal=OFF \ + -Dgnuinstall=OFF \ + -Dgsl_shared=ON \ + -Dmathmore=ON \ + -Dgviz=OFF \ + -Dhttp=ON \ + -Djemalloc=OFF \ + -Dlibcxx=OFF \ + -Dmacos_native=OFF \ + -Dmemory_termination=OFF \ + -Dminimal=OFF \ + -Dminuit2=ON \ + -Dmlp=ON \ + -Dmonalisa=OFF \ + -Dmpi=OFF \ + -Dmysql=OFF \ + -Dodbc=OFF \ + -Dopengl=ON \ + -Doracle=OFF \ + -Dpgsql=OFF \ + -Dpyroot=ON \ + -Dpyroot_legacy=OFF \ + -Dpythia6=OFF \ + -Dpythia6_nolink=OFF \ + -Dpythia8=OFF \ + -Dqt5web=OFF \ + -Dr=OFF \ + -Droofit=ON \ + -Droot7=ON \ + -Drootbench=OFF \ + -Droottest=OFF \ + -Drpath=OFF \ + -Druntime_cxxmodules=ON \ + -Dshadowpw=OFF \ + -Dshared=ON \ + -Dsoversion=ON \ + -Dspectrum=ON \ + -Dsqlite=OFF \ + -Dssl=ON \ + -Dtcmalloc=OFF \ + -Dtest_distrdf_pyspark=OFF \ + -Dtesting=OFF \ + -Dtmva=ON \ + -Dtmva-cpu=ON \ + -Dtmva-gpu=OFF \ + -Dtmva-pymva=ON \ + -Dtmva-rmva=OFF \ + -Dunuran=OFF \ + -During=OFF \ + -Dvc=OFF \ + -Dvdt=OFF \ + -Dveccore=OFF \ + -Dvmc=OFF \ + -Dwebgui=ON \ + -Dwin_broken_tests=OFF \ + -Dwinrtdebug=OFF \ + -Dx11=ON \ + -Dxml=ON \ + -Dxproofd=OFF \ + -Dxrootd=OFF \ + -DCMAKE_BUILD_TYPE=Release ../src make -make install DESTDIR=$PKG - -# Move some python stuff in the proper place -PYTHONDIR=$(python -c "import sys, os; print os.path.join('/usr/lib${LIBDIRSUFFIX}', 'python%s' % sys.version[:3], 'site-packages')")/ -mkdir -p $PKG$PYTHONDIR -mv \ - $PKG$PREFIX/lib$LIBDIRSUFFIX/*.py \ - $PKG$PREFIX/lib$LIBDIRSUFFIX/*.pyc \ - $PKG$PREFIX/lib$LIBDIRSUFFIX/*.pyo \ - $PKG$PYTHONDIR +make install/strip DESTDIR=$PKG find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneded 2> /dev/null || true find $PKG$PREFIX/man -type f -exec gzip -9 {} \; +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +# We are still in build directory +# Copy documentation to system; also to ROOTSYS (ROOT expects it there) +cp -a README/ README.md LICENSE LGPL2_1.txt ../src/CONTRIBUTING.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +find $PKG/usr/doc/$PRGNAM-$VERSION -type f -exec chmod 644 {} \; +cp -a README/ LICENSE \ + $PKG$PREFIX +# README is a directory +find $PKG$PREFIX/README -type d -exec chmod 755 {} \; +find $PKG$PREFIX/README -type f -exec chmod 644 {} \; +chmod -R 644 $PKG$PREFIX/LICENSE +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + # Install some profile.d scripts to use the right paths mkdir -p $PKG/etc/profile.d -echo "set path = ( \$path $PREFIX/bin )" > $PKG/etc/profile.d/root.csh -echo "setenv MANPATH \${MANPATH}:$PREFIX/man" >> $PKG/etc/profile.d/root.csh -echo "PATH=\$PATH:$PREFIX/bin" > $PKG/etc/profile.d/root.sh -echo "MANPATH=\$MANPATH:$PREFIX/man" >> $PKG/etc/profile.d/root.sh +# Start with tcsh +echo "setenv ROOTSYS $PREFIX" > $PKG/etc/profile.d/root.csh +echo "set path = ( \$path $PREFIX/bin )" >> $PKG/etc/profile.d/root.csh +echo "setenv MANPATH \${MANPATH}:$PREFIX/man" >> $PKG/etc/profile.d/root.csh +echo "if ( ! \$?PYTHONPATH ) then" >> $PKG/etc/profile.d/root.csh +echo "setenv PYTHONPATH $PREFIX/lib" >> $PKG/etc/profile.d/root.csh +echo "else" >> $PKG/etc/profile.d/root.csh +echo "if ( \"\$PYTHONPATH\" != \"\") then" >> $PKG/etc/profile.d/root.csh +echo "setenv PYTHONPATH \$PYTHONPATH:$PREFIX/lib">> $PKG/etc/profile.d/root.csh +echo "else" >> $PKG/etc/profile.d/root.csh +echo "setenv PYTHONPATH $PREFIX/lib" >> $PKG/etc/profile.d/root.csh +echo "endif" >> $PKG/etc/profile.d/root.csh +echo "endif" >> $PKG/etc/profile.d/root.csh +# And bash +echo "ROOTSYS=$PREFIX" > $PKG/etc/profile.d/root.sh +echo "PATH=\$PATH:$PREFIX/bin" >> $PKG/etc/profile.d/root.sh +echo "MANPATH=\$MANPATH:$PREFIX/man" >> $PKG/etc/profile.d/root.sh +echo "if [ -z \"\${PYTHONPATH}\" ]; then" >> $PKG/etc/profile.d/root.sh +echo " export PYTHONPATH=$PREFIX/lib" >> $PKG/etc/profile.d/root.sh +echo "else" >> $PKG/etc/profile.d/root.sh +echo " export PYTHONPATH=\$PYTHONPATH:$PREFIX/lib" \ + >> $PKG/etc/profile.d/root.sh +echo "fi" >> $PKG/etc/profile.d/root.sh chmod +x $PKG/etc/profile.d/root.* -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +mkdir -p $PKG/etc/ld.so.conf.d +echo "$PREFIX/lib" > $PKG/etc/ld.so.conf.d/root.conf mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -sed \ - -e "s|@LIBDIRSUFFIX@|$LIBDIRSUFFIX|" \ - -e "s|@PREFIX@|$PREFIX|" \ - $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/root/root.info b/academic/root/root.info index 7df5c81738..9343758408 100644 --- a/academic/root/root.info +++ b/academic/root/root.info @@ -1,10 +1,10 @@ PRGNAM="root" -VERSION="6.10.02" -HOMEPAGE="http://root.cern.ch/drupal/" -DOWNLOAD="https://root.cern.ch/download/root_v6.10.02.source.tar.gz" -MD5SUM="19f2285c845a48355db779938fb4db99" +VERSION="6.28.08" +HOMEPAGE="https://root.cern" +DOWNLOAD="https://root.cern/download/root_v6.28.08.source.tar.gz" +MD5SUM="3eca7fadb7867232fa74a7262644b05d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="ftgl unixODBC" -MAINTAINER="Jože Zobec" -EMAIL="jozze.zepl@gmail.com" +REQUIRES="gl2ps libAfterImage python3-numpy tbb ftgl" +MAINTAINER="Andrei Rabusov" +EMAIL="arabusov@gmail.com" diff --git a/academic/root/slack-desc b/academic/root/slack-desc index 50c68b3ed0..8dfe3a9ded 100644 --- a/academic/root/slack-desc +++ b/academic/root/slack-desc @@ -1,5 +1,5 @@ # HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. +# The handy ruler below makes it easier to edit a package description. # Line up the first '|' above the ':' following the base package name, and # the '|' on the right side marks the last column you can put a character in. # You must make exactly 11 lines for the formatting to be correct. It's also @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| root: root (data analysis framework) root: -root: ROOT is a data analysis framework used mostly, but not limited to, -root: high energy physics. It was written in C++ by the techs at CERN to -root: explore the benefits of object oriented programming in physics data -root: analysis. It consists of libraries, CINT or cling interpreter for -root: C/C++, plotting interface and powerful parellel processing support. -root: It is the preferred choice in many laboratories. +root: ROOT provides a set of frameworks with the functionality needed to +root: handle and analyze large amounts of data in an efficient way. It +root: includes specialized storage methods such as histograms, curve +root: fitting, function evaluation, minimization, graphics, visualization +root: classes; the C++ interpreter cling for fast prototyping; and powerful +root: parallel processing support. root: -root: Homepage: http://root.cern.ch/drupal/ +root: Homepage: https://root.cern root: diff --git a/academic/rpy2/README b/academic/rpy2/README index 702373878f..3685736766 100644 --- a/academic/rpy2/README +++ b/academic/rpy2/README @@ -15,8 +15,10 @@ jupyter notebooks or ipython. NOTE: R needs to be compiled with the shared library flag, thus: build R on SBo with R_SHLIB=yes and BLAS_SHLIB=yes - (See also the notes in the rpy2.Slackbuild) +Remove installed rpy2 before building and upgrading to a new version. + + home:https://rpy2.github.io/ documentation:https://rpy2.github.io/doc/latest/html/index.html diff --git a/academic/rpy2/rpy2.SlackBuild b/academic/rpy2/rpy2.SlackBuild index 3ea8722097..ea640b1291 100644 --- a/academic/rpy2/rpy2.SlackBuild +++ b/academic/rpy2/rpy2.SlackBuild @@ -2,7 +2,7 @@ # # SlackBuild for rpy2 # -# Copyright 2020-2021 Rob van Nues (sborg63@disroot.org) +# Copyright 2020-2024 Rob van Nues (sborg63@disroot.org) # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -24,7 +24,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=rpy2 -VERSION=${VERSION:-3.4.5} +VERSION=${VERSION:-3.5.16} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -37,9 +37,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -98,10 +95,16 @@ fi ## this removes an error message from setup.py ## https://github.com/rpy2/rpy2/issues/675 -export LD_LIBRARY_PATH="${RHOMLIB}:${LD_LIBRARY_PATH}" +export LD_LIBRARY_PATH="${RHOMLIB}/lib:${LD_LIBRARY_PATH}" echo "LD_LIBRARY_PATH set to ${LD_LIBRARY_PATH}" -python3 setup.py build install --root=$PKG +# replace deprecated `python3 setup.py build install --root=$PKG` +# thanks to fourtysixandtwo +PYVER=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') +export PYTHONPATH=/opt/python$PYVER/site-packages/ + +python3 -m build --no-isolation +python3 -m installer -d "$PKG" dist/*.whl mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a AUTHORS gpl-2.0.txt NEWS README* $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/rpy2/rpy2.info b/academic/rpy2/rpy2.info index 3d174b0e13..2c3adced95 100644 --- a/academic/rpy2/rpy2.info +++ b/academic/rpy2/rpy2.info @@ -1,10 +1,10 @@ PRGNAM="rpy2" -VERSION="3.4.5" +VERSION="3.5.16" HOMEPAGE="https://rpy2.github.io/" -DOWNLOAD="https://pypi.python.org/packages/source/r/rpy2/rpy2-3.4.5.tar.gz" -MD5SUM="8842b153925a2eca21e2552e964facbb" +DOWNLOAD="https://pypi.python.org/packages/source/r/rpy2/rpy2-3.5.16.tar.gz" +MD5SUM="be5385a5547673f5b1b64e245dcd7f13" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="R cffi python3-pytest tzlocal" +REQUIRES="R cffi python3-pytest tzlocal python3-setuptools-scm-opt" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/sage-bin/9.4.patch b/academic/sage-bin/9.4.patch new file mode 100644 index 0000000000..307a558acb --- /dev/null +++ b/academic/sage-bin/9.4.patch @@ -0,0 +1,258 @@ +--- opt/SageMath/local/lib/python3.9/site-packages/sage/combinat/posets/poset_examples.py.bu 2021-08-22 19:12:42.000000000 +1000 ++++ opt/SageMath/local/lib/python3.9/site-packages/sage/combinat/posets/poset_examples.py 2022-01-02 13:10:42.447658457 +1100 +@@ -155,7 +155,7 @@ + + @staticmethod + def BooleanLattice(n, facade=None, use_subsets=False): +- """ ++ r""" + Return the Boolean lattice containing `2^n` elements. + + - ``n`` -- integer; number of elements will be `2^n` +--- opt/SageMath/local/lib/python3.9/site-packages/traitlets/config/loader.py.bu 2021-08-22 22:00:01.000000000 +1000 ++++ opt/SageMath/local/lib/python3.9/site-packages/traitlets/config/loader.py 2022-01-11 11:39:00.600018177 +1100 +@@ -792,7 +792,7 @@ + nargs = '?' + else: + nargs = None +- if len(key) is 1: ++ if len(key) == 1: + paa('-'+key, '--'+key, type=text_type, dest=value, nargs=nargs) + else: + paa('--'+key, type=text_type, dest=value, nargs=nargs) +@@ -801,7 +801,7 @@ + # + self.alias_flags[self.aliases[key]] = value + continue +- if len(key) is 1: ++ if len(key) == 1: + paa('-'+key, '--'+key, action='append_const', dest='_flags', const=value) + else: + paa('--'+key, action='append_const', dest='_flags', const=value) +--- opt/SageMath/local/lib/python3.9/site-packages/psutil/_pslinux.py.bu 2021-08-22 21:58:18.000000000 +1000 ++++ opt/SageMath/local/lib/python3.9/site-packages/psutil/_pslinux.py 2022-01-11 12:14:46.007349527 +1100 +@@ -548,7 +548,7 @@ + # https://github.com/giampaolo/psutil/issues/200 + # try to parse /proc/stat as a last resort + if num == 0: +- search = re.compile('cpu\d') ++ search = re.compile(r'cpu\d') + with open_text('%s/stat' % get_procfs_path()) as f: + for line in f: + line = line.split(' ')[0] +@@ -1465,9 +1465,9 @@ + @wrap_exceptions + def memory_full_info( + self, +- _private_re=re.compile(b"Private.*:\s+(\d+)"), +- _pss_re=re.compile(b"Pss.*:\s+(\d+)"), +- _swap_re=re.compile(b"Swap.*:\s+(\d+)")): ++ _private_re=re.compile(br"Private.*:\s+(\d+)"), ++ _pss_re=re.compile(br"Pss.*:\s+(\d+)"), ++ _swap_re=re.compile(br"Swap.*:\s+(\d+)")): + basic_mem = self.memory_info() + # Note: using 3 regexes is faster than reading the file + # line by line. +@@ -1580,7 +1580,7 @@ + raise + + @wrap_exceptions +- def num_ctx_switches(self, _ctxsw_re=re.compile(b'ctxt_switches:\t(\d+)')): ++ def num_ctx_switches(self, _ctxsw_re=re.compile(br'ctxt_switches:\t(\d+)')): + data = self._read_status_file() + ctxsw = _ctxsw_re.findall(data) + if not ctxsw: +@@ -1593,7 +1593,7 @@ + return _common.pctxsw(int(ctxsw[0]), int(ctxsw[1])) + + @wrap_exceptions +- def num_threads(self, _num_threads_re=re.compile(b'Threads:\t(\d+)')): ++ def num_threads(self, _num_threads_re=re.compile(br'Threads:\t(\d+)')): + # Note: on Python 3 using a re is faster than iterating over file + # line by line. On Python 2 is the exact opposite, and iterating + # over a file on Python 3 is slower than on Python 2. +@@ -1649,7 +1649,7 @@ + return cext.proc_cpu_affinity_get(self.pid) + + def _get_eligible_cpus( +- self, _re=re.compile(b"Cpus_allowed_list:\t(\d+)-(\d+)")): ++ self, _re=re.compile(br"Cpus_allowed_list:\t(\d+)-(\d+)")): + # See: https://github.com/giampaolo/psutil/issues/956 + data = self._read_status_file() + match = _re.findall(data) +@@ -1811,13 +1811,13 @@ + return int(self._parse_stat_file()[2]) + + @wrap_exceptions +- def uids(self, _uids_re=re.compile(b'Uid:\t(\d+)\t(\d+)\t(\d+)')): ++ def uids(self, _uids_re=re.compile(br'Uid:\t(\d+)\t(\d+)\t(\d+)')): + data = self._read_status_file() + real, effective, saved = _uids_re.findall(data)[0] + return _common.puids(int(real), int(effective), int(saved)) + + @wrap_exceptions +- def gids(self, _gids_re=re.compile(b'Gid:\t(\d+)\t(\d+)\t(\d+)')): ++ def gids(self, _gids_re=re.compile(br'Gid:\t(\d+)\t(\d+)\t(\d+)')): + data = self._read_status_file() + real, effective, saved = _gids_re.findall(data)[0] + return _common.pgids(int(real), int(effective), int(saved)) +./opt/SageMath/local/lib/python3.9/site-packages/sage/symbolic/RCS +diff -u -r1.1 expression_conversions.py +--- opt/SageMath/local/lib/python3.9/site-packages/sage/symbolic/expression_conversions.py 2021/08/22 09:12:43 1.1 ++++ opt/SageMath/local/lib/python3.9/site-packages/sage/symbolic/expression_conversions.py 2022/01/28 02:07:09 +@@ -969,7 +969,7 @@ + super(FriCASConverter, self).__init__(sage.interfaces.fricas.fricas) + + def pyobject(self, ex, obj): +- """ ++ r""" + Return a string which, when evaluated by FriCAS, returns the + object as an expression. + +./opt/SageMath/local/lib/python3.9/site-packages/IPython/core/RCS +diff -u -r1.1 oinspect.py +./opt/SageMath/local/lib/python3.9/site-packages/requests/RCS +diff -u -r1.1 api.py +--- opt/SageMath/local/lib/python3.9/site-packages/requests/api.py 2021/08/22 11:52:24 1.1 ++++ opt/SageMath/local/lib/python3.9/site-packages/requests/api.py 2022/01/28 00:49:42 +@@ -57,7 +57,7 @@ + + + def get(url, params=None, **kwargs): +- """Sends a GET request. ++ r"""Sends a GET request. + + :param url: URL for the new :class:`Request` object. + :param params: (optional) Dictionary or bytes to be sent in the query string for the :class:`Request`. +@@ -71,7 +71,7 @@ + + + def options(url, **kwargs): +- """Sends a OPTIONS request. ++ r"""Sends a OPTIONS request. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +@@ -84,7 +84,7 @@ + + + def head(url, **kwargs): +- """Sends a HEAD request. ++ r"""Sends a HEAD request. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +@@ -97,7 +97,7 @@ + + + def post(url, data=None, json=None, **kwargs): +- """Sends a POST request. ++ r"""Sends a POST request. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -111,7 +111,7 @@ + + + def put(url, data=None, **kwargs): +- """Sends a PUT request. ++ r"""Sends a PUT request. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -125,7 +125,7 @@ + + + def patch(url, data=None, **kwargs): +- """Sends a PATCH request. ++ r"""Sends a PATCH request. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -139,7 +139,7 @@ + + + def delete(url, **kwargs): +- """Sends a DELETE request. ++ r"""Sends a DELETE request. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +diff -u -r1.1 models.py +--- opt/SageMath/local/lib/python3.9/site-packages/requests/models.py 2021/08/22 11:52:24 1.1 ++++ opt/SageMath/local/lib/python3.9/site-packages/requests/models.py 2022/01/28 00:45:51 +@@ -840,7 +840,7 @@ + return content + + def json(self, **kwargs): +- """Returns the json-encoded content of a response, if any. ++ r"""Returns the json-encoded content of a response, if any. + + :param \*\*kwargs: Optional arguments that ``json.loads`` takes. + :raises ValueError: If the response body does not contain valid json. +diff -u -r1.1 sessions.py +--- opt/SageMath/local/lib/python3.9/site-packages/requests/sessions.py 2021/08/22 11:52:24 1.1 ++++ opt/SageMath/local/lib/python3.9/site-packages/requests/sessions.py 2022/01/28 01:00:24 +@@ -490,7 +490,7 @@ + return resp + + def get(self, url, **kwargs): +- """Sends a GET request. Returns :class:`Response` object. ++ r"""Sends a GET request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +@@ -501,7 +501,7 @@ + return self.request('GET', url, **kwargs) + + def options(self, url, **kwargs): +- """Sends a OPTIONS request. Returns :class:`Response` object. ++ r"""Sends a OPTIONS request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +@@ -512,7 +512,7 @@ + return self.request('OPTIONS', url, **kwargs) + + def head(self, url, **kwargs): +- """Sends a HEAD request. Returns :class:`Response` object. ++ r"""Sends a HEAD request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +@@ -523,7 +523,7 @@ + return self.request('HEAD', url, **kwargs) + + def post(self, url, data=None, json=None, **kwargs): +- """Sends a POST request. Returns :class:`Response` object. ++ r"""Sends a POST request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -535,7 +535,7 @@ + return self.request('POST', url, data=data, json=json, **kwargs) + + def put(self, url, data=None, **kwargs): +- """Sends a PUT request. Returns :class:`Response` object. ++ r"""Sends a PUT request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -546,7 +546,7 @@ + return self.request('PUT', url, data=data, **kwargs) + + def patch(self, url, data=None, **kwargs): +- """Sends a PATCH request. Returns :class:`Response` object. ++ r"""Sends a PATCH request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -557,7 +557,7 @@ + return self.request('PATCH', url, data=data, **kwargs) + + def delete(self, url, **kwargs): +- """Sends a DELETE request. Returns :class:`Response` object. ++ r"""Sends a DELETE request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. diff --git a/academic/sage-bin/9.4_sh b/academic/sage-bin/9.4_sh new file mode 100644 index 0000000000..7e29552a0d --- /dev/null +++ b/academic/sage-bin/9.4_sh @@ -0,0 +1,6 @@ +cp -a opt/SageMath/local/lib/python3.9/site-packages/sage/combinat/posets/poset_examples.py opt/SageMath/src/sage/combinat/posets +cp -a opt/SageMath/local/lib/python3.9/site-packages/sage/combinat/posets/poset_examples.py opt/SageMath/pkgs/sagemath-standard/build/lib.linux-x86_64-3.9/sage/combinat/posets +tar xf $CWD/debian_binaries-11.2.tar.xz -U -C opt/SageMath/local/lib64/gcc/x86_64-pc-linux-gnu/10.3.0 +tar xf $CWD/debian_libraries-11.2.tar.xz -U -C opt/SageMath/local/lib +mkdir -p usr/lib64 +mv opt/SageMath/local/lib/libbrotlicommon.so* usr/lib64/ diff --git a/academic/sage-bin/sage-bin.SlackBuild b/academic/sage-bin/sage-bin.SlackBuild index a81b408c5e..2ff263c6dd 100644 --- a/academic/sage-bin/sage-bin.SlackBuild +++ b/academic/sage-bin/sage-bin.SlackBuild @@ -25,11 +25,13 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=sage-bin -VERSION=${VERSION:-8.3} -DEBVERSION=${DEBVERSION:-9} +VERSION=${VERSION:-9.4} +DEBVERSION=${DEBVERSION:-11} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +SLK_VERSION=${SLK_VERSION:-$(cat /etc/slackware-version|cut -d' ' -f2)} +[ $SLK_VERSION = 14.2 ] && PYTHON=python || PYTHON=python2 if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -63,6 +65,8 @@ mkdir -p $TMP $PKG $OUTPUT cd $PKG mkdir root proc opt tar xvf $CWD/sage-$VERSION-Debian_GNU_Linux_$DEBVERSION-$ARCH.tar.bz2 -C $PKG/opt +[ ! -r $CWD/$VERSION.patch ] || patch -p0 < $CWD/$VERSION.patch +[ ! -r $CWD/${VERSION}_sh ] || . $CWD/${VERSION}_sh chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -71,8 +75,9 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; mkchroot . -addchroot . python sed util-linux +addchroot . $PYTHON sed util-linux chroot . <<//// +export SAGE_BANNER=bare mount -t proc proc proc opt/SageMath/sage < /dev/null # Run sage patch system umount proc @@ -84,6 +89,7 @@ rm -rf Tools bin dev etc lib64 proc root sbin usr # and other junk rm -rf $PKG/opt/SageMath/.git +mkdir -p $PKG/etc/profile.d install -D -m0755 $CWD/profile.d/sage.sh $PKG/etc/profile.d install -D -m0755 $CWD/profile.d/sage.csh $PKG/etc/profile.d @@ -103,8 +109,9 @@ for res in 16x16 32x32 64x64 128x128 ; do $PKG/usr/share/icons/hicolor/$res/mimetypes done -find $PKG/opt/SageMath/local/share/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/opt/SageMath/local/share/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +# Some man pages and their symlinks are already gzipped +find $PKG/opt/SageMath/local/share/man -type f ! -name '*.gz' -exec gzip -9 {} \; +for i in $( find $PKG/opt/SageMath/local/share/man -type l ! -name '*.gz' ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a opt/SageMath/*.{md,txt} $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/sage-bin/sage-bin.info b/academic/sage-bin/sage-bin.info index eddc8fbee5..9d85b66d3b 100644 --- a/academic/sage-bin/sage-bin.info +++ b/academic/sage-bin/sage-bin.info @@ -1,10 +1,14 @@ PRGNAM="sage-bin" -VERSION="8.3" -HOMEPAGE="http://www.sagemath.org" +VERSION="9.4" +HOMEPAGE="https://www.sagemath.org" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="http://mirrors.mit.edu/sage/linux/64bit/sage-8.3-Debian_GNU_Linux_9-x86_64.tar.bz2" -MD5SUM_x86_64="a97ff237de39d74faedc06b9f4e1fbcc" +DOWNLOAD_x86_64="https://mirrors.mit.edu/sage/linux/64bit/sage-9.4-Debian_GNU_Linux_11-x86_64.tar.bz2 \ + https://sourceforge.net/projects/slackbuildsdirectlinks/files/sage-bin/debian_binaries-11.2.tar.xz \ + https://sourceforge.net/projects/slackbuildsdirectlinks/files/sage-bin/debian_libraries-11.2.tar.xz" +MD5SUM_x86_64="3128ef3530f514932cabcaf62b78030a \ + dc0f1b19c9b73821865599e1cefe66b6 \ + 9380db91d6afbbc4e5a23ba13553d616" REQUIRES="mkchroot" MAINTAINER="Duncan Roe" EMAIL="duncan_roe@optusnet.com.au" diff --git a/academic/sage/sage.SlackBuild b/academic/sage/sage.SlackBuild index eb9bd0cc95..d70c643c99 100644 --- a/academic/sage/sage.SlackBuild +++ b/academic/sage/sage.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for sage # Written by Jack Maddox <jack@auburn.edu> # Currently maintained by Christopher L Duston <christopher.duston@protonmail.com> -# Last update May 2021. +# Last update June 2023. # # All rights reserved. # @@ -27,7 +27,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=sage -VERSION=${VERSION:-9.3} +VERSION=${VERSION:-10.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -41,12 +41,12 @@ if [ -z "$ARCH" ]; then fi #### These lines are to ensure the build can happen on multilib systems. -if [ "$ARCH" = "i586" ]; then -LIBDIRSUFFIX="" +if [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then + LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then -LIBDIRSUFFIX="64" + LIBDIRSUFFIX="64" else -LIBDIRSUFFIX="" + LIBDIRSUFFIX="" fi #### @@ -79,9 +79,9 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; mkdir -p $PKG/$SAGEROOT $PKG/usr/share/{applications,pixmaps} \ $PKG/usr/doc/$PRGNAM-$VERSION $PKG/etc/profile.d @@ -132,12 +132,15 @@ if [ "${INSTALLSCRIPTS:-no}" = "yes" ]; then fi sed "s%SAGEROOT%${SAGEROOT}%" $CWD/$PRGNAM-notebook.desktop > $PKG/usr/share/applications/$PRGNAM-notebook.desktop -cp src/doc/common/themes/sage/static/sageicon.png $PKG/usr/share/pixmaps/ +#cp src/doc/common/themes/sage/static/sageicon.png $PKG/usr/share/pixmaps/ # Put a line here which *actually* adds sage to the path +# Gotta source that .sh script, that works fine (see README) + # install sagetex to a location that is accessible to the system TeX installation -cp -a local/share/texmf $PKG/usr/share +cp -a local/var/lib/sage/venv-python3.9/share/texmf $PKG/usr/share + cp -a COPYING.txt README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/sage/sage.info b/academic/sage/sage.info index 81aec051bf..70070f617e 100644 --- a/academic/sage/sage.info +++ b/academic/sage/sage.info @@ -1,8 +1,8 @@ PRGNAM="sage" -VERSION="9.3" +VERSION="10.1" HOMEPAGE="http://www.sagemath.org" -DOWNLOAD="http://mirrors.mit.edu/sage/src/sage-9.3.tar.gz" -MD5SUM="e826c848c6bb972a188d5ddd4dc48308" +DOWNLOAD="http://mirrors.mit.edu/sage/src/sage-10.1.tar.gz" +MD5SUM="53a3ea057086eca87102eedb4efa9722" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/samtools/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild index 781cc8b6d4..7efbaf3288 100644 --- a/academic/samtools/samtools.SlackBuild +++ b/academic/samtools/samtools.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for samtools # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com -# Copyright 2017-2021 Rob van Nues # All rights reserved. +# Copyright 2017-2024 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -25,13 +25,14 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=samtools -VERSION=${VERSION:-1.14} +VERSION=${VERSION:-1.19.2} +HTSLIBV=${HTSLIBV:-1.19.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -# Some applications still rely on the legacy samtools API instead of using htslib -# exclusively, in that case, install the headers in /usr/include/bam and the static +# Some applications still rely on the legacy samtools API instead of using htslib +# exclusively, in that case, install the headers in /usr/include/bam and the static # libbam library as well by declaring (uncommenting): #SAMLIB="yes" # and commenting out: @@ -50,9 +51,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -91,7 +89,7 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # force linking to installed htslib -rm -r htslib-$VERSION +rm -r htslib-$HTSLIBV CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -125,7 +123,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS LICENSE README INSTALL NEWS examples \ + AUTHORS LICENSE README NEWS.md examples \ $PKG/usr/doc/$PRGNAM-$VERSION cp $CWD/README $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/samtools/samtools.info b/academic/samtools/samtools.info index b260a4aeed..eef9473b1e 100644 --- a/academic/samtools/samtools.info +++ b/academic/samtools/samtools.info @@ -1,8 +1,8 @@ PRGNAM="samtools" -VERSION="1.14" +VERSION="1.19.2" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz2" -MD5SUM="7bf6a6134e468608a716296dd12095a7" +DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.19.2/samtools-1.19.2.tar.bz2" +MD5SUM="318492d95f5d8cef697442d1be996b77" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="htslib" diff --git a/academic/scidavis/README b/academic/scidavis/README index 2591367f84..3f0de3cf1c 100644 --- a/academic/scidavis/README +++ b/academic/scidavis/README @@ -7,9 +7,5 @@ features such as scriptability and extensibility. SciDAVis started as a fork of QtiPlot. -Optional dependencies, after installation, are scipy and pygsl (to -improve python scripting). - -Note: -I have a #TODO in scidavis.SlackBuild: to avoid using qwtplot3d (qt5 -version) installed in the system +Optional dependencies at runtime are scipy and pygsl (to improve +python scripting) diff --git a/academic/scidavis/scidavis.SlackBuild b/academic/scidavis/scidavis.SlackBuild index 3b6b354d2f..6ebdd91a51 100644 --- a/academic/scidavis/scidavis.SlackBuild +++ b/academic/scidavis/scidavis.SlackBuild @@ -1,9 +1,9 @@ #!/bin/bash # Slackware build script for SciDAVis -# Based on the Slackware 14.2 SlackBuild +# Based on the Slackware 15.0 SlackBuild # -# Copyright 2017-2021, Fellype do Nascimento, Guaratingueta - Brazil +# Copyright 2017-2022, Fellype do Nascimento, Guaratingueta - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=scidavis -VERSION=${VERSION:-2.4.0} +VERSION=${VERSION:-2.9.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -53,13 +53,16 @@ OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" - SPEC="" + LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" - SPEC="" + LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" - SPEC="-spec linux-g++-64" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" fi rm -rf $PKG @@ -68,6 +71,18 @@ cd $TMP rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION + +rmdir 3rdparty/qwt5-qt5/ +rmdir 3rdparty/qwtplot3d/ +rmdir 3rdparty/liborigin/ + +tar xvf $CWD/qwt5-qt5-f7519200f102676fb04fb7bd0be555e0a419d378.tar.gz -C 3rdparty/ +mv 3rdparty/qwt5-qt5-f7519200f102676fb04fb7bd0be555e0a419d378 3rdparty/qwt5-qt5 +tar xvf $CWD/qwtplot3d-b2655743d30ed3185f3c0e2626b33a1d29655216.tar.gz -C 3rdparty/ +mv 3rdparty/qwtplot3d-b2655743d30ed3185f3c0e2626b33a1d29655216 3rdparty/qwtplot3d +tar xvf $CWD/liborigin-a92f26f28e531f64684b66a2731dd617bea3cb45.tar.gz -C 3rdparty/ +mv 3rdparty/liborigin-a92f26f28e531f64684b66a2731dd617bea3cb45 3rdparty/liborigin + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -75,6 +90,16 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +PYVER=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') + +# Set the correct python paths - code based on scidavis.spec for Fedora by Alexander Ploumistos +sed -i "s:set(PYTHON_SCRIPTDIR etc:set(PYTHON_SCRIPTDIR lib$LIBDIRSUFFIX/python$PYVER/site-packages/scidavis:" scidavis/CMakeLists.txt +sed -i "s:FILES scidavisrc.py \${CMAKE_CURRENT_BINARY_DIR}/\$<CONFIG>/scidavisrc.pyc DESTINATION:FILES scidavisrc.py DESTINATION:" scidavis/CMakeLists.txt +sed -i "s:FILES scidavisrc.py \${CMAKE_CURRENT_BINARY_DIR}/scidavisrc.pyc DESTINATION:FILES scidavisrc.py DESTINATION:" scidavis/CMakeLists.txt +sed -i "s:FILES scidavisUtil.py DESTINATION share/scidavis:FILES scidavisUtil.py DESTINATION \${PYTHON_SCRIPTDIR}:" scidavis/CMakeLists.txt +sed -i "s:PYTHON_CONFIG_PATH=\"\${CMAKE_INSTALL_PREFIX}/etc\":PYTHON_CONFIG_PATH=\"/usr/lib$LIBDIRSUFFIX/python$PYVER/site-packages/scidavis\":" libscidavis/CMakeLists.txt +sed -i "s:PYTHON_UTIL_PATH=\"\${CMAKE_INSTALL_PREFIX}/share/scidavis\":PYTHON_UTIL_PATH=\"/usr/lib$LIBDIRSUFFIX/python$PYVER/site-packages/scidavis\":" libscidavis/CMakeLists.txt + export PYTHON=python3 mkdir build && cd build @@ -91,10 +116,6 @@ make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -## Sometimes 'make install' fails to install the translation files -mkdir -p $PKG/usr/share/scidavis/translations -install -m 0644 scidavis/translations/*.qm $PKG/usr/share/scidavis/translations - # Move manpage to a more appropriated dir mkdir -p $PKG/usr/man/man1/ mv $PKG/usr/share/man/man1/scidavis.1 $PKG/usr/man/man1/scidavis.1 @@ -104,7 +125,6 @@ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a README.md LICENSE $PKG/usr/doc/$PRGNAM-$VERSION cp -a $PKG/usr/share/doc/scidavis/*.* $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild rm -rf $PKG/usr/share/doc diff --git a/academic/scidavis/scidavis.info b/academic/scidavis/scidavis.info index 2e015a53c9..7904927c3f 100644 --- a/academic/scidavis/scidavis.info +++ b/academic/scidavis/scidavis.info @@ -1,10 +1,16 @@ PRGNAM="scidavis" -VERSION="2.4.0" +VERSION="2.9.0" HOMEPAGE="http://scidavis.sourceforge.net/" -DOWNLOAD="https://ufpr.dl.sourceforge.net/project/scidavis/SciDAVis/2/2.4/scidavis-2.4.0.tar.gz" -MD5SUM="8846e90fb8b75d28c76ba9af2523c189" +DOWNLOAD="https://github.com/SciDAVis/scidavis/archive/2.9.0/scidavis-2.9.0.tar.gz \ + https://github.com/SciDAVis/qwt5-qt5/archive/f751920/qwt5-qt5-f7519200f102676fb04fb7bd0be555e0a419d378.tar.gz \ + https://github.com/SciDAVis/qwtplot3d/archive/b265574/qwtplot3d-b2655743d30ed3185f3c0e2626b33a1d29655216.tar.gz \ + https://github.com/SciDAVis/liborigin/archive/a92f26f/liborigin-a92f26f28e531f64684b66a2731dd617bea3cb45.tar.gz" +MD5SUM="fc80267e26c4ba75490d7baa9dfdf93f \ + da7c360266e318948919ab2ddc8a2c4b \ + aefa1c98e1a0df67418304b66d810b3d \ + 8baa9dffeacc1fedeb94ffa8d35eae2c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="muParser qwt5 qwtplot3d" +REQUIRES="muParser" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/scilab/README b/academic/scilab/README index 66d62a3753..9c9b1b0fd5 100644 --- a/academic/scilab/README +++ b/academic/scilab/README @@ -12,5 +12,9 @@ to run the updated profile scripts. If you have issues on upgrading/reinstalling or changing desktop environments, try delete/rename $HOME/.Scilab to resolve. -Openjdk8 or jdk are optional. Scilab will use the system-wide installed -java if found. Otherwise, scilab will use its own internal jre. +zulu-openjdk8, openjdk8 or jdk are optional. Scilab will use the +system-wide installed java if found. Otherwise, scilab will use +its own internal jre. + +*NOTE* the tarball url is not wget-friendly: you might need a browser +to download it. diff --git a/academic/scilab/scilab.SlackBuild b/academic/scilab/scilab.SlackBuild index 1f6c43cca0..5d3927f85c 100644 --- a/academic/scilab/scilab.SlackBuild +++ b/academic/scilab/scilab.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for Scilab # Copyright 2011-2015 Fridrich von Stauffenberg <cancellor2@gmail.com> -# Copyright 2018-2019 Edward W. Koenig ,kingbeowulf@gmail.com> +# Copyright 2018-2022 Edward W. Koenig ,kingbeowulf@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=scilab -VERSION=${VERSION:-6.1.0} +VERSION=${VERSION:-6.1.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/scilab/scilab.info b/academic/scilab/scilab.info index 16c72a868c..470c724c40 100644 --- a/academic/scilab/scilab.info +++ b/academic/scilab/scilab.info @@ -1,10 +1,10 @@ PRGNAM="scilab" -VERSION="6.1.0" +VERSION="6.1.1" HOMEPAGE="http://www.scilab.org" -DOWNLOAD="http://www.scilab.org/download/6.1.0/scilab-6.1.0.bin.linux-i686.tar.gz" -MD5SUM="dd249770ff4e4c8ef7c7395b1efb713b" -DOWNLOAD_x86_64="http://www.scilab.org/download/6.1.0/scilab-6.1.0.bin.linux-x86_64.tar.gz" -MD5SUM_x86_64="e52f9a66d5a015bd03be86b77fd0d7a0" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="http://www.scilab.org/download/6.1.1/scilab-6.1.1.bin.linux-x86_64.tar.gz" +MD5SUM_x86_64="406a6346866a4decdaea8127c27ea936" REQUIRES="" MAINTAINER="Edward W. Koenig" -EMAIL="kingbeowulf@gmail.com" +EMAIL="kingbeowulf@lnuxgalaxy.org" diff --git a/academic/scipy/scipy.info b/academic/scipy/scipy.info deleted file mode 100644 index 0dfd4507f6..0000000000 --- a/academic/scipy/scipy.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="scipy" -VERSION="1.1.0" -HOMEPAGE="https://www.scipy.org/" -DOWNLOAD="https://github.com/scipy/scipy/releases/download/v1.1.0/scipy-1.1.0.tar.gz" -MD5SUM="aa6bcc85276b6f25e17bcfc4dede8718" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="numpy lapack" -MAINTAINER="Serban Udrea" -EMAIL="S.Udrea@gsi.de" diff --git a/academic/scipy/slack-desc b/academic/scipy/slack-desc deleted file mode 100644 index 9dd00a3d2c..0000000000 --- a/academic/scipy/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -scipy: scipy (python library for math, science, and engineering) -scipy: -scipy: The SciPy library is built to work with NumPy arrays, and provides -scipy: many user-friendly and efficient numerical routines such as routines -scipy: for numerical integration and optimization. Together, they run on all -scipy: popular operating systems, are quick to install, and are free of -scipy: charge. NumPy and SciPy are easy to use, but powerful enough to be -scipy: depended upon by some of the world's leading scientists and engineers. -scipy: -scipy: https://www.scipy.org/ -scipy: diff --git a/academic/scipy3/README b/academic/scipy3/README deleted file mode 100644 index 5a72b73476..0000000000 --- a/academic/scipy3/README +++ /dev/null @@ -1,25 +0,0 @@ -SciPy (pronounced "Sigh Pie") is open-source software for mathematics, -science, and engineering. - -The SciPy library is built to work with NumPy arrays, and provides many -user-friendly and efficient numerical routines such as routines for -numerical integration and optimization. Together, they run on all popular -operating systems, are quick to install, and are free of charge. NumPy -and SciPy are easy to use, but powerful enough to be depended upon by -some of the world's leading scientists and engineers. - -matplotlib and ipython are nice to have in connection with scipy, but scipy -does not depend on them. - -Since ver. 0.14.0 scipy uses SuperLU instead of UMFPACK for solving unsymmetric -sparse linear systems. If you want to use UMFPACK you must install it in advance -of numpy and build numpy accordingly (see the README to numpy's SlackBuild). -Moreover, after installing scipy, you have to install scikit-umfpack, which -presently is not available on SlackBuilds.org. - -If you need to build scipy for debugging, set DEBUG=y. - -NOTE: If you use this SlackBuild scipy will run with the python 3 version - installed on your system. If you'd like to use python 2.7.xx as - provided by Slackware Linux then you have to install it with the scipy - SlackBuild. diff --git a/academic/scipy3/scipy3.info b/academic/scipy3/scipy3.info deleted file mode 100644 index bf76db0783..0000000000 --- a/academic/scipy3/scipy3.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="scipy3" -VERSION="1.5.4" -HOMEPAGE="https://www.scipy.org/" -DOWNLOAD="https://github.com/scipy/scipy/releases/download/v1.5.4/scipy-1.5.4.tar.gz" -MD5SUM="293401ee7ac354a2f2313373b497f40e" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="numpy3 lapack pybind11" -MAINTAINER="Serban Udrea" -EMAIL="S.Udrea@gsi.de" diff --git a/academic/scipy3/slack-desc b/academic/scipy3/slack-desc deleted file mode 100644 index 2e586787e1..0000000000 --- a/academic/scipy3/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -scipy3: scipy3 (python library for math, science, and engineering) -scipy3: -scipy3: The SciPy library is built to work with NumPy arrays, and provides -scipy3: many user-friendly and efficient numerical routines such as routines -scipy3: for numerical integration and optimization. Together, they run on all -scipy3: popular operating systems, are quick to install, and are free of -scipy3: charge. NumPy and SciPy are easy to use, but powerful enough to be -scipy3: depended upon by some of the world's leading scientists and engineers. -scipy3: -scipy3: https://www.scipy.org/ -scipy3: diff --git a/academic/scmutils/README b/academic/scmutils/README new file mode 100644 index 0000000000..1b97071fd6 --- /dev/null +++ b/academic/scmutils/README @@ -0,0 +1,4 @@ +scmutils is a mit-scheme library for classical mechanics. + +It is used as part of the course 6946 in MIT, +"Classical Mechanics: A Computational Approach". diff --git a/academic/scmutils/scmutils.SlackBuild b/academic/scmutils/scmutils.SlackBuild new file mode 100644 index 0000000000..ec734392d0 --- /dev/null +++ b/academic/scmutils/scmutils.SlackBuild @@ -0,0 +1,82 @@ +#!/bin/bash + +# Slackware build script for scmutils + +# Copyright 2023, Lockywolf +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=scmutils +VERSION=${VERSION:-20230902} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +target="$PKG/$(mit-scheme --batch-mode --no-init-file --eval "(write-string (->namestring (system-library-directory-pathname)))" "(exit)")" +install -Dm644 mechanics.com "$target/mechanics.com" +for src in $(find * -type f -name '*.bci'); do + install -Dm644 $src "$target/$src" +done +install -Dm755 mechanics.sh "$PKG/usr/bin/mechanics" + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README COPYING \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/scmutils/scmutils.info b/academic/scmutils/scmutils.info new file mode 100644 index 0000000000..fad299a360 --- /dev/null +++ b/academic/scmutils/scmutils.info @@ -0,0 +1,10 @@ +PRGNAM="scmutils" +VERSION="20230902" +HOMEPAGE="http://mitpress.mit.edu/sicm/" +DOWNLOAD="https://groups.csail.mit.edu/mac/users/gjs/6946/mechanics-system-installation/native-code/scmutils-20230902.tar.gz" +MD5SUM="12b7723c14219f7a3677cc88ec7b8429" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="mit-scheme" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.scmutils_2023-11-27@lockywolf.net" diff --git a/academic/scmutils/slack-desc b/academic/scmutils/slack-desc new file mode 100644 index 0000000000..6ce8862d2d --- /dev/null +++ b/academic/scmutils/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +scmutils: scmutils (numerical and algebraic packages, written in Scheme) +scmutils: +scmutils: Scmutils is a set of mathematical subroutines used for the course +scmutils: in Classical Mechanics in MIT. +scmutils: +scmutils: +scmutils: +scmutils: +scmutils: +scmutils: +scmutils: diff --git a/academic/seaview/README b/academic/seaview/README index e72249f563..2fd0c66479 100644 --- a/academic/seaview/README +++ b/academic/seaview/README @@ -14,7 +14,6 @@ sequence alignment and molecular phylogeny. Features: of evolutionary distances, maximum likelihood, driving program PhyML - Can use the Transfer Bootstrap Expectation method to compute the bootstrap support of PhyML and distance trees. -- Uses the Treerecs method to reconcile gene and species trees. - Prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files. - Allows to download sequences from EMBL / GenBank / UniProt. diff --git a/academic/seaview/seaview.SlackBuild b/academic/seaview/seaview.SlackBuild index 602b87f332..327d7df737 100644 --- a/academic/seaview/seaview.SlackBuild +++ b/academic/seaview/seaview.SlackBuild @@ -28,8 +28,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=seaview -VERSION=${VERSION:-5.0.4} -BUILD=${BUILD:-1} +VERSION=${VERSION:-5.0.5} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/seaview/seaview.info b/academic/seaview/seaview.info index 8a1ff60d21..d1968b049b 100644 --- a/academic/seaview/seaview.info +++ b/academic/seaview/seaview.info @@ -1,8 +1,8 @@ PRGNAM="seaview" -VERSION="5.0.4" +VERSION="5.0.5" HOMEPAGE="http://doua.prabi.fr/software/seaview/" -DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_5.0.4.tar.gz" -MD5SUM="8b36176fb98a508e483285966ad7100c" +DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_5.0.5.tar.gz" +MD5SUM="09f6800973308a91316bb820c4331cb0" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="fltk PDFlib-Lite Gblocks PhyML clustalo muscle treerecs" diff --git a/academic/seqkit/seqkit.SlackBuild b/academic/seqkit/seqkit.SlackBuild index 9ba611e7e1..d460717784 100644 --- a/academic/seqkit/seqkit.SlackBuild +++ b/academic/seqkit/seqkit.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for seqkit -# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,24 +25,27 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=seqkit -VERSION=${VERSION:-0.16.0} +VERSION=${VERSION:-2.5.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then - ARCH=$( uname -m ) + case "$( uname -m )" in + i?86) ARCH=i586 ;; + *) ARCH=$( uname -m ) ;; + esac fi case "$ARCH" in - i?86) ARCH=i386 + i?86) BINARCH="386" ;; x86_64) BINARCH="amd64" ;; *) - printf "\n\n%s\n" "$ARCH is not supported." + printf "\n\n%s\n" "$ARCH is not supported." >/dev/stderr exit 1 ;; esac diff --git a/academic/seqkit/seqkit.info b/academic/seqkit/seqkit.info index f1cd1d7bdd..8888b7bef9 100644 --- a/academic/seqkit/seqkit.info +++ b/academic/seqkit/seqkit.info @@ -1,10 +1,10 @@ PRGNAM="seqkit" -VERSION="0.16.0" +VERSION="2.5.1" HOMEPAGE="https://bioinf.shenwei.me/seqkit/" -DOWNLOAD="https://github.com/shenwei356/seqkit/releases/download/v0.16.0/seqkit_linux_386.tar.gz" -MD5SUM="74362686623a0cc96f43f47640129c90" -DOWNLOAD_x86_64="https://github.com/shenwei356/seqkit/releases/download/v0.16.0/seqkit_linux_amd64.tar.gz" -MD5SUM_x86_64="dfed8dc3cdd5ec2d2b739f04a68d7c91" +DOWNLOAD="https://github.com/shenwei356/seqkit/releases/download/v2.5.1/seqkit_linux_386.tar.gz" +MD5SUM="0357a5347d5c86677c542b3c6e6cf88f" +DOWNLOAD_x86_64="https://github.com/shenwei356/seqkit/releases/download/v2.5.1/seqkit_linux_amd64.tar.gz" +MD5SUM_x86_64="b90ee92597254007b93b57980528b2b4" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/sequence-analysis/sequence-analysis.info b/academic/sequence-analysis/sequence-analysis.info index 33c0fa06eb..b022257ddb 100644 --- a/academic/sequence-analysis/sequence-analysis.info +++ b/academic/sequence-analysis/sequence-analysis.info @@ -5,6 +5,6 @@ DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/sequence-analysis/1.7 MD5SUM="815c7e6a8717a9e2a7fedc9ed94fbd0e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/sigrok-cli/sigrok-cli.SlackBuild b/academic/sigrok-cli/sigrok-cli.SlackBuild index 248dd5813f..acf3296360 100644 --- a/academic/sigrok-cli/sigrok-cli.SlackBuild +++ b/academic/sigrok-cli/sigrok-cli.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=sigrok-cli -VERSION=${VERSION:-0.7.1} +VERSION=${VERSION:-20220222_525f481} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -70,7 +70,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +tar xvf $CWD/$PRGNAM-$VERSION.tar.?z cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -79,6 +79,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +./autogen.sh CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -99,7 +100,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr gzip -9 $PKG/usr/man/man1/sigrok-cli.1 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING INSTALL NEWS README $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS COPYING HACKING NEWS README $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/sigrok-cli/sigrok-cli.info b/academic/sigrok-cli/sigrok-cli.info index 513cb7e46c..afb44f0e69 100644 --- a/academic/sigrok-cli/sigrok-cli.info +++ b/academic/sigrok-cli/sigrok-cli.info @@ -1,8 +1,8 @@ PRGNAM="sigrok-cli" -VERSION="0.7.1" +VERSION="20220222_525f481" HOMEPAGE="https://sigrok.org/wiki/Sigrok-cli" -DOWNLOAD="https://sigrok.org/download/source/sigrok-cli/sigrok-cli-0.7.1.tar.gz" -MD5SUM="3f45ce664bad529d8b3f78a61b017d75" +DOWNLOAD="https://ponce.cc/slackware/sources/repo/sigrok-cli-20220222_525f481.tar.xz" +MD5SUM="047f3b75b01a17b94e736601f169f022" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="libsigrok" diff --git a/academic/sim/README b/academic/sim/README new file mode 100644 index 0000000000..b8dec9d5ba --- /dev/null +++ b/academic/sim/README @@ -0,0 +1,9 @@ +SIM - Local similarity program + +SIM finds k best non-intersecting alignments between two sequences or +within a sequence using dynamic programming techniques. The alignments +are reported in order of decreasing similarity score and share no +aligned pairs. + +Once the alignment is computed, you can view it using "lalnview", a +graphical viewer program for pairwise alignments, available at SBo. diff --git a/academic/sim/References b/academic/sim/References new file mode 100644 index 0000000000..6e829c7445 --- /dev/null +++ b/academic/sim/References @@ -0,0 +1,3 @@ +Xiaoquin Huang and Webb Miller: +"A Time-Efficient, Linear-Space Local Similarity Algorithm" +Advances in Applied Mathematics, vol. 12 (1991), pp. 337-357. diff --git a/academic/sim/sim.SlackBuild b/academic/sim/sim.SlackBuild new file mode 100644 index 0000000000..6fb9c1b34e --- /dev/null +++ b/academic/sim/sim.SlackBuild @@ -0,0 +1,91 @@ +#!/bin/bash + +# Slackware build script for sim + +# Copyright 2023 Petar Petrov, slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=sim +VERSION=${VERSION:-204} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +cp $CWD/${PRGNAM}* . +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +cc $SLKCFLAGS -o $PRGNAM ${PRGNAM}${VERSION}.c -lm +install -D -m 755 $PRGNAM $PKG/usr/bin/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a $PRGNAM.doc $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/sim/sim.info b/academic/sim/sim.info new file mode 100644 index 0000000000..c1026b3e92 --- /dev/null +++ b/academic/sim/sim.info @@ -0,0 +1,12 @@ +PRGNAM="sim" +VERSION="204" +HOMEPAGE="https://web.expasy.org/sim/" +DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/logiciel/lalnview/sim/sim204.c \ +ftp://pbil.univ-lyon1.fr/pub/logiciel/lalnview/sim/sim.doc" +MD5SUM="69edf7f5aa1c58bb3ad37ad761a289c2 \ +70f4bf9be3b16369dc21467d15cc7b48" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/coq/slack-desc b/academic/sim/slack-desc index a5c16bf092..c38253a06f 100644 --- a/academic/coq/slack-desc +++ b/academic/sim/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -coq: coq (The Coq Proof Assistant) -coq: -coq: coq is a formal proof management system. It provides a formal language -coq: to write mathematical definitions, executable algorithms and theorems -coq: together with an environment for semi-interactive development of -coq: machine-checked proofs. -coq: -coq: Homepage: https://coq.inria.fr/ -coq: -coq: -coq: +sim: sim (Local similarity program) +sim: +sim: SIM finds k best non-intersecting alignments between two sequences +sim: or within a sequence using dynamic programming techniques. The +sim: alignments are reported in order of decreasing similarity score and +sim: share no aligned pairs. Once the alignment is computed, you can view +sim: it using "lalnview" +sim: +sim: +sim: +sim: diff --git a/academic/siril/README b/academic/siril/README index 9d75056201..bdd99c4b52 100644 --- a/academic/siril/README +++ b/academic/siril/README @@ -5,3 +5,5 @@ reduction and improving the signal/noise ratio of an image from multiple captures as required in astronomy. SIRIL can align automatically or manually, stack and enhance pictures from various file formats, even images sequences (movies and SER files). + +libheif is an optional dependency. diff --git a/academic/siril/siril.SlackBuild b/academic/siril/siril.SlackBuild index 342d2be169..2da99a2d8e 100644 --- a/academic/siril/siril.SlackBuild +++ b/academic/siril/siril.SlackBuild @@ -25,7 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=siril -VERSION=${VERSION:-0.9.6} +VERSION=${VERSION:-1.0.0_rc2} +SRCVER=$(echo $VERSION | tr _ - ) BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -69,9 +70,10 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 -cd $PRGNAM-$VERSION +rm -rf $PRGNAM-$SRCVER +mkdir -p $PRGNAM-$SRCVER +cd $PRGNAM-$SRCVER +tar xvf $CWD/$PRGNAM-$SRCVER.tar.bz2 chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -79,21 +81,21 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -sh ./autogen.sh - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux - -make -make DESTDIR=$PKG install +mkdir compile +cd compile + CFLAGS="$SLKCFLAGS" \ + CXXFLAGS="$SLKCFLAGS" \ + meson .. \ + --buildtype=release \ + --infodir=/usr/info \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --localstatedir=/var \ + --mandir=/usr/man \ + --prefix=/usr \ + --sysconfdir=/etc \ + -Dstrip=true + DESTDIR=$PKG "${NINJA:=ninja}" install +cd .. find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -101,8 +103,9 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +rm -fR $PKG/usr/share/doc mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS README.md ChangeLog NEWS LICENSE COPYING $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS README.md ChangeLog NEWS LICENSE* $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/siril/siril.info b/academic/siril/siril.info index 68b04e4792..743f994968 100644 --- a/academic/siril/siril.info +++ b/academic/siril/siril.info @@ -1,8 +1,8 @@ PRGNAM="siril" -VERSION="0.9.6" -HOMEPAGE="https://free-astro.org/index.php?title=Main_Page" -DOWNLOAD="https://free-astro.org/download/siril-0.9.6.tar.bz2" -MD5SUM="aaa649ba5a57738ab8fb8c4223ed83dd" +VERSION="1.0.0_rc2" +HOMEPAGE="https://siril.org" +DOWNLOAD="https://free-astro.org/download/siril-1.0.0-rc2.tar.bz2" +MD5SUM="764767e35ea835fe2206d2dadf79dee6" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="libconfig" diff --git a/academic/smath-studio/README b/academic/smath-studio/README index 8871582bea..55547a2d61 100644 --- a/academic/smath-studio/README +++ b/academic/smath-studio/README @@ -12,3 +12,8 @@ Among its capabilities are: - Numeric integration - Simple multiline looped programs - User defined functions + + To download, you may need to go to the website URL + https://en.smath.com/view/SMathStudio/download + or try + wget --referer=https://en.smath.com/view/SMathStudio/download ... diff --git a/academic/smath-studio/smath-studio.SlackBuild b/academic/smath-studio/smath-studio.SlackBuild index ce018f0e4e..4b26c719c3 100644 --- a/academic/smath-studio/smath-studio.SlackBuild +++ b/academic/smath-studio/smath-studio.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=smath-studio -VERSION=${VERSION:-0.97.5346} +VERSION=${VERSION:-1.0.8348} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/smath-studio/smath-studio.info b/academic/smath-studio/smath-studio.info index d8e41f4084..bc40d92965 100644 --- a/academic/smath-studio/smath-studio.info +++ b/academic/smath-studio/smath-studio.info @@ -1,12 +1,12 @@ PRGNAM="smath-studio" -VERSION="0.97.5346" -HOMEPAGE="http://smath.info" -DOWNLOAD="http://ponce.cc/slackware/sources/repo/SMathStudioDesktop.0_97_5346.Mono.tar.gz \ +VERSION="1.0.8348" +HOMEPAGE="https://smath.info" +DOWNLOAD="https://smath.com/file/Lw2xA/SMathStudioDesktop.1_0_8348.Mono.tar.gz \ http://ponce.cc/slackware/sources/repo/SMathStudio.Icons.zip" -MD5SUM="cb922fa31fca89d347df6468d421eb52 \ +MD5SUM="4ae9109f910c0085eeb8c193f3ad1c10 \ 1dd3ff0477b5c3c57fb815320a387643" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="mono" MAINTAINER="Edward W. Koenig" -EMAIL="kingbeowulf@gmail.com" +EMAIL="kingbeowulf@linuxgalaxy.org" diff --git a/academic/snpEff/snpEff.SlackBuild b/academic/snpEff/snpEff.SlackBuild index 83261322fd..ec1346b235 100644 --- a/academic/snpEff/snpEff.SlackBuild +++ b/academic/snpEff/snpEff.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for snpEff -# Copyright 2015-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2015-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -27,7 +27,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=snpEff VERSION=${VERSION:-4.3t} SRCVER=${SRCVER:-v4_3t} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -50,7 +50,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM +rm -rf $PRGNAM-$VERSION +mkdir -p $PRGNAM-$VERSION +cd $PRGNAM-$VERSION unzip $CWD/${PRGNAM}_${SRCVER}_core.zip cd $PRGNAM chown -R root:root . @@ -60,8 +62,10 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -mkdir -p $PKG/usr/share/java/$PRGNAM -cp -a examples galaxy scripts $PRGNAM.config $PRGNAM.jar SnpSift.jar \ +install -D -m755 $PRGNAM.jar $PKG/usr/share/java/$PRGNAM/$PRGNAM.jar +install -D -m755 SnpSift.jar $PKG/usr/share/java/$PRGNAM/SnpSift.jar + +cp -a examples galaxy scripts $PRGNAM.config \ $PKG/usr/share/java/$PRGNAM mkdir -p $PKG/usr/bin diff --git a/academic/snpEff/snpEff.info b/academic/snpEff/snpEff.info index d7b9699c76..deace26fa8 100644 --- a/academic/snpEff/snpEff.info +++ b/academic/snpEff/snpEff.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/snpeff/files/snpEff_v4_3t_core.zip" MD5SUM="1fa84a703580a423e27f1e14a945901c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/solfege/solfege.SlackBuild b/academic/solfege/solfege.SlackBuild index 7dd3799cf8..4b69490ae4 100644 --- a/academic/solfege/solfege.SlackBuild +++ b/academic/solfege/solfege.SlackBuild @@ -13,7 +13,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -31,8 +31,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/spades/spades.SlackBuild b/academic/spades/spades.SlackBuild index 05b6960dcd..c6e75b0411 100644 --- a/academic/spades/spades.SlackBuild +++ b/academic/spades/spades.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for spades -# Copyright 2015-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2015-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=spades -VERSION=${VERSION:-3.15.2} +VERSION=${VERSION:-3.15.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -99,6 +99,8 @@ cd build make install DESTDIR=$PKG cd .. +chmod 755 $PKG/usr/bin/spades_init.py + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/spades/spades.info b/academic/spades/spades.info index 0ed0cadeca..3c72751ee4 100644 --- a/academic/spades/spades.info +++ b/academic/spades/spades.info @@ -1,10 +1,10 @@ PRGNAM="spades" -VERSION="3.15.2" +VERSION="3.15.5" HOMEPAGE="http://cab.spbu.ru/software/spades/" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="http://cab.spbu.ru/files/release3.15.2/SPAdes-3.15.2.tar.gz" -MD5SUM_x86_64="599a6bc98605cc25a739ee3f49794769" +DOWNLOAD_x86_64="http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5.tar.gz" +MD5SUM_x86_64="e181bf668ee96971458fb50cbfdaf604" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/spiceopus/spiceopus.SlackBuild b/academic/spiceopus/spiceopus.SlackBuild index 1c2be28533..74e9e2517e 100644 --- a/academic/spiceopus/spiceopus.SlackBuild +++ b/academic/spiceopus/spiceopus.SlackBuild @@ -34,7 +34,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -52,8 +52,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/spidey/spidey.SlackBuild b/academic/spidey/spidey.SlackBuild index 8010b54af8..09928e95bb 100644 --- a/academic/spidey/spidey.SlackBuild +++ b/academic/spidey/spidey.SlackBuild @@ -30,12 +30,16 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi +if ! [[ $ARCH =~ i?86 ]] && ! [ "$ARCH" = "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information # could be useful to other scripts. @@ -48,12 +52,6 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - # Determine the source arch. Many thanks to the Ugene project for the # 64bit executable! if [ "$ARCH" = "x86_64" ]; then @@ -73,7 +71,7 @@ cd $PRGNAM-$VERSION gunzip -c $CWD/$PRGNAM.linux${SRCARCH}.gz > spidey -install -D -m755 spidey $PKG/usr/bin/spidey +install -D -m 755 spidey $PKG/usr/bin/spidey mkdir -p $PKG/usr/man/man1 cp $CWD/$PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1 diff --git a/academic/spqr/README b/academic/spqr/README index 051977e0e6..8bb80aef4f 100644 --- a/academic/spqr/README +++ b/academic/spqr/README @@ -1,18 +1,22 @@ SuiteSparseQR is an implementation of the multifrontal sparse QR -factorization method. Parallelism is exploited both in the BLAS and -across different frontal matrices using Intel's Threading Building Blocks, -a shared-memory programming model for modern multicore +factorization method. Parallelism is exploited both in the BLAS and +across different frontal matrices using Intel's Threading Building +Blocks, a shared-memory programming model for modern multicore architectures. It can obtain a substantial fraction of the theoretical peak performance of a multicore computer. This package is part of SuiteSparse. -This requires a BLAS/LAPACK implementation. Choose one of these package sets: +This requires a BLAS/LAPACK implementation. Choose one of these package +sets: + * OpenBLAS (includes both a BLAS and a LAPACK implementation) * atlas (includes both a BLAS and a LAPACK implementation) * blas, lapack (the Netlib reference implementations) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. + +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib reference +implementations; other packages that require a BLAS or LAPACK +implementation may not build if they are not configured to detect/use +alternate implementations. diff --git a/academic/spqr/spqr.SlackBuild b/academic/spqr/spqr.SlackBuild index bb7d381e61..a99c21b3d7 100644 --- a/academic/spqr/spqr.SlackBuild +++ b/academic/spqr/spqr.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for SPQR -# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2023 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -29,7 +29,7 @@ SRCNAM=SuiteSparse SUBDIR=SPQR VERSION=${VERSION:-2.0.9} SRCVER=${SRCVER:-5.8.1} -BUILD=${BUILD:-3} +BUILD=${BUILD:-4} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -41,24 +41,18 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i586" ]; then +if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then @@ -102,6 +96,7 @@ touch Doc/spqr_user_guide.pdf --infodir=/usr/info \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --disable-dependency-tracking \ + --without-tbb \ --build=$ARCH-slackware-linux \ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ diff --git a/academic/spqr/spqr.info b/academic/spqr/spqr.info index daa36cb95e..eff7ce4d4d 100644 --- a/academic/spqr/spqr.info +++ b/academic/spqr/spqr.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/Suit MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas lapack suitesparseconfig cholmod tbb" +REQUIRES="cholmod" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/squizz/squizz.SlackBuild b/academic/squizz/squizz.SlackBuild index 0f0140812e..dfe2237f5c 100644 --- a/academic/squizz/squizz.SlackBuild +++ b/academic/squizz/squizz.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=squizz VERSION=${VERSION:-0.99d} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -105,6 +105,8 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/staden/README b/academic/staden/README index 0d8a67c590..aa36fdbcd8 100644 --- a/academic/staden/README +++ b/academic/staden/README @@ -1,20 +1,40 @@ The programs part of the Staden package provide an excellent and fully developed set of DNA sequence assembly, editing, analysis and more. - Some of its features include: -GAP4 - Performs assembly, contig joining, assembly checking, repeat - search, experiment suggestion, read pair analysis and contig - editing. -GAP5 - The new development version of Gap4, designed to work with the - large volumes of data attainable through the newer sequencing - technologies. -PREGAP4 - Provides a graphical user interface to set up the processing - required to prepare trace data for assembly or analysis. -SPIN - Compares pairs of sequences in many ways, often presenting its - results graphically and has a sliding sequence window linked to - the plots. -TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF - trace files. +* GAP4: Performs assembly, contig joining, assembly checking, repeat + search, experiment suggestion, read pair analysis and contig editing. + +* GAP5: The new development version of Gap4, designed to work with large + volumes of data attainable through the newer sequencing technologies. + +* PREGAP4: Provides a graphical user interface to set up the processing + required to prepare trace data for assembly or analysis. + +* SPIN: Compares pairs of sequences in many ways, often presenting its + results graphically and has a sliding sequence window linked to the + plots. + +* TREV: A rapid and flexible viewer and editor for ABI, ALF or SCF trace + files. + +NOTE: Xfce submenus +For XFCE, if you want to have the menu entries grouped in a submenu +folder (multilevel menu entry), do: + + SUBMENU="YES" ./staden.SlackBuild + +NOTE: Staden and EMBOSS: +Staden used to provide a GUI for (at least part of) the programs from +EMBOSS. To give it a try, run this after install (of course you need to +have installed EMBOSS, too): + + create_emboss_files + +This will create some files in: + + /usr/share/staden/tcl/spin_emboss/acdtcl/ + +CITING For more information and citing, visit Staden's web page and check the "References" file in the documentation. diff --git a/academic/staden/desktop/staden.directory b/academic/staden/desktop/staden.directory new file mode 100644 index 0000000000..2623e56005 --- /dev/null +++ b/academic/staden/desktop/staden.directory @@ -0,0 +1,4 @@ +[Desktop Entry] +Type=Directory +Name=Staden Package +Icon=folder diff --git a/academic/staden/desktop/staden.menu b/academic/staden/desktop/staden.menu new file mode 100644 index 0000000000..3f5ba10187 --- /dev/null +++ b/academic/staden/desktop/staden.menu @@ -0,0 +1,20 @@ +<!DOCTYPE Menu PUBLIC "-//freedesktop//DTD Menu 1.0//EN" +"http://www.freedesktop.org/standards/menu-spec/menu-1.0.dtd"> +<Menu> + <Name>Applications</Name> + <Menu> + <Name>Education</Name> + <Directory>xfce4-education.directory</Directory> + <Menu> + <Name>Staden Package</Name> + <Directory>staden.directory</Directory> + <Include> + <Filename>gap4.desktop</Filename> + <Filename>gap5.desktop</Filename> + <Filename>pregap4.desktop</Filename> + <Filename>trev.desktop</Filename> + <Filename>spin.desktop</Filename> + </Include> + </Menu> + </Menu> +</Menu> diff --git a/academic/staden/staden.SlackBuild b/academic/staden/staden.SlackBuild index 2c2bea2c39..4c16f47019 100644 --- a/academic/staden/staden.SlackBuild +++ b/academic/staden/staden.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for staden -# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=staden VERSION=${VERSION:-2.0.0b11} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -97,6 +97,11 @@ CXXFLAGS="$SLKCFLAGS" \ --with-tklib=/usr/lib${LIBDIRSUFFIX}/$TKLIB \ --build=$ARCH-slackware-linux +# Point to the right place of the EMBOSS .acd and data files. This is +# needed if the "create_emboss_files" script is run after install. +sed -i "133 c set acd_dir /usr/share/EMBOSS/acd" spin_emboss/create_emboss_files.tcl +sed -i "73 a EMBOSS_DATA=/usr/share/EMBOSS/data; export EMBOSS_DATA" spin/spin + make make install DESTDIR=$PKG @@ -111,6 +116,21 @@ mkdir -p $PKG/usr/share/{applications,pixmaps} cp $CWD/desktop/*.desktop $PKG/usr/share/applications cp $CWD/desktop/*.png $PKG/usr/share/pixmaps +# Do we want a submenu? For more info: +# https://slackalaxy.com/2021/08/08/xfce-multilevel-menu/ +if [ $SUBMENU = "YES" ]; then + # Use a separate "Staden Package" menu entry within "Education" + mkdir -p $PKG/etc/xdg/menus/applications-merged + cp $CWD/desktop/$PRGNAM.menu $PKG/etc/xdg/menus/applications-merged + + # Menu directory structure + mkdir -p $PKG/usr/share/desktop-directories + cp $CWD/desktop/$PRGNAM.directory $PKG/usr/share/desktop-directories + + # The category in the .desktop files is commented out to avoid duplication in menus + sed -i "s:Categories:#Categories:" $PKG/usr/share/applications/*.desktop +fi + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a ChangeLog LICENCE.txt NEWS README.build \ $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/stellarium/stellarium.SlackBuild b/academic/stellarium/stellarium.SlackBuild index 6bb00fb4d9..fa3ce9900c 100644 --- a/academic/stellarium/stellarium.SlackBuild +++ b/academic/stellarium/stellarium.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=stellarium -VERSION=${VERSION:-0.21.0} +VERSION=${VERSION:-23.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -70,7 +70,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar -xzvf $CWD/$PRGNAM-$VERSION.tar.gz +tar xvf $CWD/$PRGNAM-$VERSION.tar.xz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -79,25 +79,69 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -mkdir build && cd build - cmake -DCMAKE_INSTALL_PREFIX=/usr \ - -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ +# CPM dependency retrieval lifting: prepare a cache dir in the format +# expected by CPM with pre-downloaded sources. + +# CPM normally puts downloaded deps under this dir +CPM_CACHE_DIR=$TMP/$PRGNAM-$VERSION/build/_deps + +CPM_SHOWMYSKY_VERSION=v0.3.1 +CPM_QXSLX_VERSION=1.4.6 +CPM_INDI_VERSION=1.8.5 +CPM_GLM_VERSION=0.9.9.8 +CPM_NLOPT_VERSION=v2.7.1 + +# We need to match dependencies names used in cmake files with the +# actual dependency tarball names +declare -A CPM_SOURCE CPM_DEST +CPM_SOURCE["SHOWMYSKY"]="$CWD/CalcMySky-$CPM_SHOWMYSKY_VERSION.tar.gz" +CPM_SOURCE["QXLSX"]="$CWD/QXlsx-v$CPM_QXSLX_VERSION.tar.gz" +CPM_SOURCE["INDI"]="$CWD/indi-$CPM_INDI_VERSION.zip" +CPM_SOURCE["GLM"]="$CWD/glm-$CPM_GLM_VERSION.7z" +CPM_SOURCE["NLOPT"]="$CWD/nlopt-$CPM_NLOPT_VERSION.tar.gz" +CPM_DEST["SHOWMYSKY"]="$CPM_CACHE_DIR/showmysky-qt5-subbuild/showmysky-qt5-populate-prefix/src/$CPM_SHOWMYSKY_VERSION.tar.gz" +CPM_DEST["QXLSX"]="$CPM_CACHE_DIR/qxlsxqt5-subbuild/qxlsxqt5-populate-prefix/src/v$CPM_QXSLX_VERSION.tar.gz" +CPM_DEST["INDI"]="$CPM_CACHE_DIR/indiclient-subbuild/indiclient-populate-prefix/src/v$CPM_INDI_VERSION.zip" +CPM_DEST["GLM"]="$CPM_CACHE_DIR/glm-subbuild/glm-populate-prefix/src/glm-$CPM_GLM_VERSION.7z" +CPM_DEST["NLOPT"]="$CPM_CACHE_DIR/nlopt-subbuild/nlopt-populate-prefix/src/$CPM_NLOPT_VERSION.tar.gz" + +for dep in "${!CPM_SOURCE[@]}" +do + mkdir -p "$(dirname "${CPM_DEST[$dep]}")" + ln -s "${CPM_SOURCE[$dep]}" "${CPM_DEST[$dep]}" +done + +# End of CPM deps management + +mkdir -p build +cd build + cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_BUILD_TYPE="release" \ - .. + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DPYTHON_EXECUTABLE=/usr/bin/python3 \ + -DCMAKE_INSTALL_LIBDIR=/usr/lib${LIBDIRSUFFIX} \ + -DCMAKE_INSTALL_MANDIR=/usr/man \ + -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG cd - +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -mv $PKG/usr/share/man $PKG/usr +# upstream doesn't honor the CMAKE_INSTALL_MANDIR. Move files manually, for now +mv $PKG/usr/share/man $PKG/usr/ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a CREDITS.md COPYING ChangeLog README.md $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CREDITS.md COPYING ChangeLog README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/stellarium/stellarium.info b/academic/stellarium/stellarium.info index 7ff88d8138..df1c008e58 100644 --- a/academic/stellarium/stellarium.info +++ b/academic/stellarium/stellarium.info @@ -1,8 +1,18 @@ PRGNAM="stellarium" -VERSION="0.21.0" +VERSION="23.4" HOMEPAGE="http://www.stellarium.org" -DOWNLOAD="https://github.com/Stellarium/stellarium/releases/download/v0.21.0/stellarium-0.21.0.tar.gz" -MD5SUM="333646917111ffc31692aa4f316cbc26" +DOWNLOAD="https://github.com/Stellarium/stellarium/releases/download/v23.4/stellarium-23.4.tar.xz \ +https://github.com/10110111/CalcMySky/archive/refs/tags/v0.3.1/CalcMySky-v0.3.1.tar.gz \ +https://github.com/QtExcel/QXlsx/archive/refs/tags/v1.4.6/QXlsx-v1.4.6.tar.gz \ +https://github.com/indilib/indi/archive/v1.8.5/indi-1.8.5.zip \ +https://github.com/g-truc/glm/releases/download/0.9.9.8/glm-0.9.9.8.7z \ +https://github.com/stevengj/nlopt/archive/refs/tags/v2.7.1/nlopt-v2.7.1.tar.gz" +MD5SUM="c44271c128de0f2830ce465574e28ce8 \ +88def58da627a30135cd1871fffa5577 \ +fdc7a2bf239bd0ff84f6058694dcd9f9 \ +14a092a9eb2117e5c51ba3302197e097 \ +c8342552801ebeb31497288192c4e793 \ +ed1a3000a1c8c248d51df126dfcfaa78" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/stellarsolver/README b/academic/stellarsolver/README new file mode 100644 index 0000000000..7bf9e1a087 --- /dev/null +++ b/academic/stellarsolver/README @@ -0,0 +1,11 @@ +stellarsolver Astrometric Plate Solver + +stellarsolver is a cross platform SEP-based star extractor and +astrometry.net-based internal astrometric solver. Also refered to as +Plate solving or Astrometric calibration of an astronomical image, +this is a technique used in astronomy and applied on celestial images. +the astrometric solution it is possible to calculate the celestial +coordinates of any object on the image or synchronize the telescope +mount or satellite pointing position to the center of the image taken. + +stellarsolver is required to compile Kstars with INDI support. diff --git a/academic/stellarsolver/doinst.sh b/academic/stellarsolver/doinst.sh new file mode 100644 index 0000000000..19b813d022 --- /dev/null +++ b/academic/stellarsolver/doinst.sh @@ -0,0 +1,7 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 +fi diff --git a/academic/stellarsolver/slack-desc b/academic/stellarsolver/slack-desc new file mode 100644 index 0000000000..c56b7376e3 --- /dev/null +++ b/academic/stellarsolver/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +stellarsolver: stellarsolver (Astrometric Plate Solver) +stellarsolver: +stellarsolver: stellarsolver is a cross platform SEP-based star extractor and +stellarsolver: astrometry.net-based internal astrometric solver. +stellarsolver: +stellarsolver: +stellarsolver: +stellarsolver: https://github.com/rlancaste/stellarsolver +stellarsolver: +stellarsolver: +stellarsolver: diff --git a/academic/stellarsolver/stellarsolver.SlackBuild b/academic/stellarsolver/stellarsolver.SlackBuild new file mode 100644 index 0000000000..8dec189d67 --- /dev/null +++ b/academic/stellarsolver/stellarsolver.SlackBuild @@ -0,0 +1,112 @@ +#!/bin/bash + +# Slackware build script for stellarsolver + +# Copyright 2022 Edward W. Koenig, Vancouver, WA, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=stellarsolver +VERSION=${VERSION:-2.4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +case "$ARCH" in + x86_64) ;; + arm*) ;; + *) echo "Unsupported ARCH '$ARCH'"; exit 1 ;; +esac + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +export CFLAGS="$SLKCFLAGS" +export CXXFLAGS="$SLKCFLAGS" +mkdir -p build +cd build + cmake \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + -DBUILD_TESTER=ON .. + make + make install DESTDIR=$PKG +cd .. + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README.md LICENSE $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/stellarsolver/stellarsolver.info b/academic/stellarsolver/stellarsolver.info new file mode 100644 index 0000000000..e9d567c16f --- /dev/null +++ b/academic/stellarsolver/stellarsolver.info @@ -0,0 +1,10 @@ +PRGNAM="stellarsolver" +VERSION="2.4" +HOMEPAGE="https://github.com/rlancaste/stellarsolver" +DOWNLOAD="https://github.com/rlancaste/stellarsolver/archive/2.4/stellarsolver-2.4.tar.gz" +MD5SUM="a4a92e7c2dc296d7fcbc814134d45886" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="wcslib" +MAINTAINER="Edward W. Koenig" +EMAIL="kingbeowulf@linuxgalaxy.org" diff --git a/academic/suitesparse/README b/academic/suitesparse/README index a0a5eb5679..4704b3906b 100644 --- a/academic/suitesparse/README +++ b/academic/suitesparse/README @@ -1,5 +1,5 @@ -suitesparse is a collection of libraries for computations involving sparse -matrices. The package includes the following libraries: +suitesparse is a collection of libraries for computations involving +sparse matrices. The package includes the following libraries: AMD: approximate minimum degree ordering. CAMD: constrained approximate minimum degree ordering. @@ -25,8 +25,7 @@ by default. SlackBuilds.org also has all the parts of this suite as individual builds - DO NOT try and install the individual parts and the suite; -pick one or the other. +choose one or the other. -For Slackware 14.2, suitesparse's version is being held at 5.7.2. -Later versions (5.8.n) are not compatible with 14.2 supplied version -of mpfr (3.1.4). +For Slackware 15.0, suitesparse's version is being held at 5.13.0. +Later versions are not compatible with 15.0 supplied version of cmake. diff --git a/academic/suitesparse/suitesparse.SlackBuild b/academic/suitesparse/suitesparse.SlackBuild index 40600ba9dc..774fbc1a19 100644 --- a/academic/suitesparse/suitesparse.SlackBuild +++ b/academic/suitesparse/suitesparse.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for suitesparse -# Copyright 2017-2021 Christoph Willing, Brisbane Australia +# Copyright 2017-2023 Christoph Willing, Brisbane Australia # All rights reserved. # Thanks to Pablo Santamaria for previous versions # @@ -27,8 +27,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=suitesparse SRCNAM=SuiteSparse -VERSION=${VERSION:-5.10.1} -BUILD=${BUILD:-1} +VERSION=${VERSION:-5.13.0} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -40,9 +40,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -85,6 +82,7 @@ mkdir -p $PKG/usr/include/suitesparse mkdir -p $PKG/usr/lib$LIBDIRSUFFIX mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +export BLAS="$(pkg-config --libs openblas)" make make install \ INSTALL_INCLUDE=$PKG/usr/include/suitesparse \ diff --git a/academic/suitesparse/suitesparse.info b/academic/suitesparse/suitesparse.info index ba56ee4881..929ec6e26f 100644 --- a/academic/suitesparse/suitesparse.info +++ b/academic/suitesparse/suitesparse.info @@ -1,8 +1,8 @@ PRGNAM="suitesparse" -VERSION="5.10.1" +VERSION="5.13.0" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.10.1/SuiteSparse-5.10.1.tar.gz" -MD5SUM="68bb912f3cf3d2b01f30ebafef690302" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.13.0/SuiteSparse-5.13.0.tar.gz" +MD5SUM="e9e7bc594b77ae4b58d943cdc286d679" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="lapack OpenBLAS chrpath" diff --git a/academic/suitesparseconfig/suitesparseconfig.SlackBuild b/academic/suitesparseconfig/suitesparseconfig.SlackBuild index 6b32fdb34a..8ebbedcfc1 100644 --- a/academic/suitesparseconfig/suitesparseconfig.SlackBuild +++ b/academic/suitesparseconfig/suitesparseconfig.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/sword-data-kjv/README b/academic/sword-data-kjv/README index 1ecea1c77b..7f1f855900 100644 --- a/academic/sword-data-kjv/README +++ b/academic/sword-data-kjv/README @@ -1,6 +1,6 @@ -sword-data-kjv is a data package containing the king james with strongs -dictionarys for sword. -This packages the King James Version bible with strongs refereneces +sword-data-kjv is a data package containing the King James bible with +Strongs dictionaries. +This packages the King James Version bible with strongs references and the strongs Hebrew and Greek dictionaries for use with the sword engine/library V1.7.0 or higher. This and many other bibles and dictionaries can be downloaded from the www.crosswire.org web site. As @@ -16,7 +16,8 @@ works fine. See the .info file for an example of url location when using wget. most sword based bible programs, such as bibletime or xiphos -(gnomesword) have a facility to download more content using their gui. +(previously called gnomesword) have a facility to download more content +using their gui. Please Note: you need at least sword 1.7.0 or higher to read this data. -It has been tested with sword 1.7.0 1.7.5a1 and 1.8.1 +It has been tested with sword 1.7.0 1.7.5a1 1.8.1 and 1.9.0 diff --git a/academic/sword-data-kjv/sword-data-kjv.SlackBuild b/academic/sword-data-kjv/sword-data-kjv.SlackBuild index dfee4e68a4..198bb6bc89 100644 --- a/academic/sword-data-kjv/sword-data-kjv.SlackBuild +++ b/academic/sword-data-kjv/sword-data-kjv.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for sword-data-kjv -# Copyright 2015-2021 Tim Dickson, email: tim at googlemail.com +# Copyright 2015-2023 Tim Dickson, email: tim at googlemail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=sword-data-kjv -VERSION=${VERSION:-1.8.1_1} -BUILD=${BUILD:-1} +VERSION=${VERSION:-1.9.0_2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -53,7 +53,7 @@ cd $TMP rm -rf $PRGNAM-$VERSION #check if sword is installed and get data location, otherwise use default -DATADEST="/usr/shared/sword/" +DATADEST="/usr/share/sword/" if [ -e /etc/sword.conf ]; then DATADEST=`cat /etc/sword.conf|grep DataPath|awk -F"=" '{print $2}'` if [ "x$DATADEST" = "x" ]||[ "x$DATDEST" = "x/" ]; then @@ -67,10 +67,10 @@ fi mkdir -p $PKG${DATADEST} cd $PKG${DATADEST} -chown -R root:root . unzip $CWD/KJV.zip unzip $CWD/StrongsGreek.zip unzip $CWD/StrongsHebrew.zip +chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ -o -perm 511 \) -exec chmod 755 {} \; -o \ diff --git a/academic/sword-data-kjv/sword-data-kjv.info b/academic/sword-data-kjv/sword-data-kjv.info index 0bbedb43ef..11c62693b1 100644 --- a/academic/sword-data-kjv/sword-data-kjv.info +++ b/academic/sword-data-kjv/sword-data-kjv.info @@ -1,11 +1,11 @@ PRGNAM="sword-data-kjv" -VERSION="1.8.1_1" +VERSION="1.9.0_2" HOMEPAGE="http://www.crosswire.org/sword/modules/" DOWNLOAD="http://www.crosswire.org/ftpmirror/pub/sword/packages/rawzip/KJV.zip \ http://www.crosswire.org/ftpmirror/pub/sword/packages/rawzip/StrongsGreek.zip \ http://www.crosswire.org/ftpmirror/pub/sword/packages/rawzip/StrongsHebrew.zip" -MD5SUM="7488aadfd5b72c96b4601a0135c5786a \ - 2acde501e6a33e84feeeaa62f8e53d89 \ +MD5SUM="f55dab4fb1515c1b0b229148319d074d \ + 5b2816b8b424033a72850eb64355f104 \ 3cbbc69d7410efc9d1d7f6f6b30e3415" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/sword/sword.SlackBuild b/academic/sword/sword.SlackBuild index ac8a20bae0..7ec9c9c693 100644 --- a/academic/sword/sword.SlackBuild +++ b/academic/sword/sword.SlackBuild @@ -27,7 +27,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=sword -VERSION=${VERSION:-1.8.1} +VERSION=${VERSION:-1.9.0} BUILD=${BUILD:-3} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -74,9 +74,6 @@ cd $TMP rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION -#patch to fix pre-chapter text, required for xiphos. when sword tag>1.8.1 -#remove this patch as it will be included. -patch -p0 -i $CWD/$PRGNAM.diff chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ @@ -85,11 +82,10 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; #now patch the automake stuff so it doesn't error on slackware's newer version -#thanks to aur.archlinux.org for the information... -#since update to 1.8.1 first patch has to be commented out. we will get a bunch of -#warnings, but at least the library compiles -#sed -i 's/AM_INIT_AUTOMAKE$/AM_INIT_AUTOMAKE\(\[subdir\-objects\]\)/g' configure.ac sed -i 's/ftemplate-depth-25/ftemplate-depth\=125/g' configure.ac +#patch to remove subdir-objects warnings +sed -i 's/1.6/1.6 subdir-objects/g' lib/Makefile.am + ./autogen.sh #add workaround for compiling with more recent (>=61) versions of icu4c CFLAGS="$SLKCFLAGS -DU_USING_ICU_NAMESPACE=1" \ @@ -111,6 +107,8 @@ cp -a AUTHORS ChangeLog CODINGSTYLE COPYING INSTALL LICENSE NEWS README \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh diff --git a/academic/sword/sword.diff b/academic/sword/sword.diff deleted file mode 100644 index ac57df456c..0000000000 --- a/academic/sword/sword.diff +++ /dev/null @@ -1,75 +0,0 @@ -Index: src/mgr/stringmgr.cpp -=================================================================== ---- src/mgr/stringmgr.cpp (revision 3718) -+++ src/mgr/stringmgr.cpp (revision 3721) -@@ -20,6 +20,7 @@ - * - */ - -+#include <ctype.h> - #include <stringmgr.h> - #include <swlog.h> - #include <localemgr.h> -Index: src/modules/filters/osisxhtml.cpp -=================================================================== ---- src/modules/filters/osisxhtml.cpp (revision 3718) -+++ src/modules/filters/osisxhtml.cpp (revision 3721) -@@ -849,7 +849,11 @@ - else if (tag.isEndTag()) { - outText("</div>", buf, u); - } -- else if (!(type == "colophon")) outText(tag, buf, u); -+ else if (!(type == "colophon")) { -+ if (tag.getAttribute("sID")) tag.setEmpty(false); -+ if (tag.getAttribute("eID")) tag.setEndTag(true); -+ outText(tag, buf, u); -+ } - - } - else if (!strcmp(tag.getName(), "span")) { -Index: src/utilfuns/utilxml.cpp -=================================================================== ---- src/utilfuns/utilxml.cpp (revision 3718) -+++ src/utilfuns/utilxml.cpp (revision 3721) -@@ -291,13 +291,16 @@ - tag.append('/'); - - tag.append(getName()); -- for (StringPairMap::iterator it = attributes.begin(); it != attributes.end(); it++) { -- //tag.appendFormatted(" %s=\"%s\"", it->first.c_str(), it->second.c_str()); -- tag.append(' '); -- tag.append(it->first.c_str()); -- tag.append((strchr(it->second.c_str(), '\"')) ? "=\'" : "=\""); -- tag.append(it->second.c_str()); -- tag.append((strchr(it->second.c_str(), '\"'))? '\'' : '\"'); -+ -+ if (!isEndTag()) { -+ for (StringPairMap::iterator it = attributes.begin(); it != attributes.end(); it++) { -+ //tag.appendFormatted(" %s=\"%s\"", it->first.c_str(), it->second.c_str()); -+ tag.append(' '); -+ tag.append(it->first.c_str()); -+ tag.append((strchr(it->second.c_str(), '\"')) ? "=\'" : "=\""); -+ tag.append(it->second.c_str()); -+ tag.append((strchr(it->second.c_str(), '\"'))? '\'' : '\"'); -+ } - } - - if (isEmpty()) -Index: include/utilxml.h -=================================================================== ---- include/utilxml.h (revision 3718) -+++ include/utilxml.h (revision 3721) -@@ -75,6 +75,13 @@ - * otherwise, we return if we're a simple XML end </tag>. - */ - bool isEndTag(const char *eID = 0) const; -+ inline void setEndTag(bool value) { -+ if (!parsed) -+ parse(); -+ endTag = value; -+ if (value) -+ empty = false; -+ } - - const StringList getAttributeNames() const; - int getAttributePartCount(const char *attribName, char partSplit = '|') const; diff --git a/academic/sword/sword.info b/academic/sword/sword.info index bafb795e6c..8417f0c7ec 100644 --- a/academic/sword/sword.info +++ b/academic/sword/sword.info @@ -1,8 +1,8 @@ PRGNAM="sword" -VERSION="1.8.1" +VERSION="1.9.0" HOMEPAGE="http://www.crosswire.org/sword" -DOWNLOAD="http://crosswire.org/ftpmirror/pub/sword/source/v1.8/sword-1.8.1.tar.gz" -MD5SUM="ddab24192104b15cbec72e569145ccd1" +DOWNLOAD="http://crosswire.org/ftpmirror/pub/sword/source/v1.9/sword-1.9.0.tar.gz" +MD5SUM="7b86ab627993ef295307e3729d8edef2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/t_coffee/README b/academic/t_coffee/README index f5f6689f7d..a52a9692f0 100644 --- a/academic/t_coffee/README +++ b/academic/t_coffee/README @@ -8,6 +8,8 @@ to combine sequence information with protein structural information 3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA secondary structures (R-Coffee). +examples are installed in /usr/share/t_coffee/ + For detailed information and citation: T-Coffee: A novel method for multiple sequence alignments. Notredame, Higgins,Heringa,JMB,302(205-217)2000 diff --git a/academic/t_coffee/t_coffee.SlackBuild b/academic/t_coffee/t_coffee.SlackBuild index 0da6aae740..94d3e3918d 100644 --- a/academic/t_coffee/t_coffee.SlackBuild +++ b/academic/t_coffee/t_coffee.SlackBuild @@ -25,13 +25,12 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=t_coffee -VERSION=${VERSION:-13.41.0_git28bdc39} +VERSION=${VERSION:-13.45.58.c355d11} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -TARNAM=tcoffee -COMMIT=28bdc39911d10d8597db8513f9515fb2ed7a9158 +TARNAM=T-COFFEE_distribution_Version if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -72,9 +71,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf ${TARNAM}-${COMMIT} -tar xvf $CWD/${TARNAM}-${COMMIT}.tar.gz -cd ${TARNAM}-${COMMIT} +rm -rf ${TARNAM}_${VERSION} +tar xvf $CWD/${TARNAM}_${VERSION}.tar.gz +cd ${TARNAM}_${VERSION} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -83,17 +82,20 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" t_coffee/src/makefile +sed -i "s|-O3 -Wno-write-strings|$SLKCFLAGS|" t_coffee_source/makefile -CFLAGS="$SLKCFLAGS" make t_coffee -C t_coffee/src -install -D -m755 t_coffee/src/$PRGNAM $PKG/usr/bin/$PRGNAM +CFLAGS="$SLKCFLAGS" make t_coffee -C t_coffee_source +install -D -m755 t_coffee_source/$PRGNAM $PKG/usr/bin/$PRGNAM + +mkdir -p $PKG/usr/share/t_coffee +cp -a example $PKG/usr/share/t_coffee/ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - HOW_BUILD_WORKS.md README.md docs/*.rst \ + README doc license.txt \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References diff --git a/academic/t_coffee/t_coffee.info b/academic/t_coffee/t_coffee.info index ec75e49f23..355fa22ca2 100644 --- a/academic/t_coffee/t_coffee.info +++ b/academic/t_coffee/t_coffee.info @@ -1,8 +1,8 @@ PRGNAM="t_coffee" -VERSION="13.41.0_git28bdc39" +VERSION="13.45.58.c355d11" HOMEPAGE="http://www.tcoffee.org/" -DOWNLOAD="https://github.com/cbcrg/tcoffee/archive/28bdc39/tcoffee-28bdc39911d10d8597db8513f9515fb2ed7a9158.tar.gz" -MD5SUM="3392d55a2817575ce90c1c3e94e08c0b" +DOWNLOAD="https://ponce.cc/slackware/sources/repo/T-COFFEE_distribution_Version_13.45.58.c355d11.tar.gz" +MD5SUM="8b5d42142b531f913429dd9c2d4c8b27" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/tiemu/tiemu.SlackBuild b/academic/tiemu/tiemu.SlackBuild index 4e76a95846..85b1e0094f 100644 --- a/academic/tiemu/tiemu.SlackBuild +++ b/academic/tiemu/tiemu.SlackBuild @@ -2,7 +2,8 @@ # Slackbuild for tiemu -# Written by shelldweller <shelldweller@beauxbead.com> +# Written by shelldweller <email removed> +# Now maintained by B. Watson <urchlay@slackware.uk> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +23,15 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20230224 bkw: BUILD=2 +# - new maintainer. +# - remove INSTALL and ABOUT-NLS from doc dir (generic, useless). + cd $(dirname $0) ; CWD=$(pwd) PRGNAM=tiemu VERSION=${VERSION:-3.03} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,9 +43,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -73,11 +75,8 @@ rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION-nogdb.tar.gz cd $PRGNAM-$VERSION chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +find -L . -perm /111 -a \! -perm 755 -a -exec chmod 755 {} \+ -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} \+ # A few necessary patches # https://aur.archlinux.org/packages/tiemu/#comment-667308 @@ -98,22 +97,16 @@ CXXFLAGS="$SLKCFLAGS" \ --disable-gdb make - -DESTDIR=$PKG make install - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a ABOUT-NLS AUTHORS BUGS COPYING ChangeLog INSTALL LICENSES NEWS \ - README RELEASE TODO docs/ \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -find $PKG/usr/doc -name "Makefile" -delete -find $PKG/usr/doc -type f -exec chmod 644 {} \; +make install DESTDIR=$PKG +strip $PKG/usr/bin/$PRGNAM +gzip -9 $PKG/usr/man/man*/* + +PKGDOC=$PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKGDOC +cp -a AUTHORS BUGS COPYING ChangeLog LICENSES NEWS \ + README RELEASE TODO docs/ \ + $PKGDOC +cat $CWD/$PRGNAM.SlackBuild > $PKGDOC/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/tiemu/tiemu.info b/academic/tiemu/tiemu.info index d665780f3f..5f6b445bdc 100644 --- a/academic/tiemu/tiemu.info +++ b/academic/tiemu/tiemu.info @@ -6,5 +6,5 @@ MD5SUM="2736440d717a0ee97cdb35189814fc93" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="libticalcs2" -MAINTAINER="shelldweller" -EMAIL="shelldweller@beauxbead.com" +MAINTAINER="B. Watson" +EMAIL="urchlay@slackware.uk" diff --git a/academic/tilem/tilem.SlackBuild b/academic/tilem/tilem.SlackBuild index 1f12f5e80f..cbff9b3731 100644 --- a/academic/tilem/tilem.SlackBuild +++ b/academic/tilem/tilem.SlackBuild @@ -76,7 +76,7 @@ find -L . \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -p \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; -CFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -w -Wl,--allow-multiple-definition" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ diff --git a/academic/tkgate/tkgate.SlackBuild b/academic/tkgate/tkgate.SlackBuild index 3d09c6f107..cbcf6001b4 100644 --- a/academic/tkgate/tkgate.SlackBuild +++ b/academic/tkgate/tkgate.SlackBuild @@ -33,7 +33,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -51,8 +51,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/topdraw/topdraw.info b/academic/topdraw/topdraw.info index caaad940bb..8080d97ea6 100644 --- a/academic/topdraw/topdraw.info +++ b/academic/topdraw/topdraw.info @@ -1,7 +1,7 @@ PRGNAM="topdraw" VERSION="sep2002" HOMEPAGE="http://crystal.scb.uwa.edu.au/charlie/software/topdraw/" -DOWNLOAD="http://crystal.scb.uwa.edu.au/charlie/software/topdraw/topdraw.zip" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/topdraw/topdraw.zip" MD5SUM="9827abf8ea33ea7f0811873661565925" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/tophat/tophat.SlackBuild b/academic/tophat/tophat.SlackBuild index 17db0b0b1f..22d1b532bf 100644 --- a/academic/tophat/tophat.SlackBuild +++ b/academic/tophat/tophat.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=tophat VERSION=${VERSION:-2.1.2} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -86,6 +86,7 @@ patch -p1 < $CWD/make_pair.patch CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ +CPPFLAGS="$SLKCFLAGS -std=c++14" \ ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ diff --git a/academic/treebest-ensembl/README b/academic/treebest-ensembl/README index b6639d304d..f91a651be9 100644 --- a/academic/treebest-ensembl/README +++ b/academic/treebest-ensembl/README @@ -10,16 +10,18 @@ TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. -This is the Ensembl Compara modifications version. The main new features -are: +This is the Ensembl Compara modifications version. The main new +features are: 1) -s option in treebest sdi, to allow a user-defined species tree. T node-tag in the NHX output: a bit-field listing the input trees 2) that support the node. 3) -I option in treebest nj, to carry on the T tags from the input tree -4) -Z option in treebest best, to redefine the PhyML variable MIN_DIFF_LK -5) -X option in treebest best, to give a higher weight to the likelihood - that comes from the reconciliation with the species tree (default 1) +4) -Z option in treebest best, to redefine the PhyML variable + MIN_DIFF_LK +5) -X option in treebest best, to give a higher weight to the + likelihood that comes from the reconciliation with the species tree + (default 1) 6) -I option in treebest best, to start from the input tree instead of building one 7) Species-intersection scores are now also reported as floating-point diff --git a/academic/treerecs/README b/academic/treerecs/README index e338496bfb..283164480a 100644 --- a/academic/treerecs/README +++ b/academic/treerecs/README @@ -30,8 +30,9 @@ Bio++ use. using species names and format conversion (Newick, Nhx or PhyloXML) . For more information, see preprint at bioRxiv: -Treerecs: an integrated phylogenetic tool, from sequences to reconciliations -Nicolas Comte, Benoit Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, -Vincent Daubin, Simon Penel, Celine Scornavacca, Manolo Gouy, Alexandros -Stamatakis, Eric Tannier, View ORCID ProfileDavid P. Parsons +Treerecs: an integrated phylogenetic tool, from sequences to +reconciliations. Nicolas Comte, Benoit Morel, Damir Hasic, Laurent +Guéguen, Bastien Boussau, Vincent Daubin, Simon Penel, Celine +Scornavacca, Manolo Gouy, Alexandros Stamatakis, Eric Tannier. +View ORCID ProfileDavid P. Parsons https://www.biorxiv.org/content/10.1101/782946v1 diff --git a/academic/treerecs/treerecs.SlackBuild b/academic/treerecs/treerecs.SlackBuild index abaf7ba814..14e1cebfe0 100644 --- a/academic/treerecs/treerecs.SlackBuild +++ b/academic/treerecs/treerecs.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for treerecs -# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -27,13 +27,12 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=treerecs +SRCNAM=Treerecs VERSION=${VERSION:-1.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -SRCNAM=Treerecs - if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -42,9 +41,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -83,6 +79,11 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# GCC 12 explicitly requires these +# https://stackoverflow.com/a/68149587 +sed -i "45i #include <limits>" ext/bpp/bpp-core/src/Bpp/Graph/GlobalGraph.cpp +sed -i "26i #include <utility>" src/treerecs/containers/AbstractGrid.h + mkdir -p build cd build cmake \ diff --git a/academic/treeviewx/treeviewx.info b/academic/treeviewx/treeviewx.info index 8de22d44fb..14ab2567b3 100644 --- a/academic/treeviewx/treeviewx.info +++ b/academic/treeviewx/treeviewx.info @@ -1,7 +1,7 @@ PRGNAM="treeviewx" VERSION="0.5.1_20100723" HOMEPAGE="https://github.com/rdmpage" -DOWNLOAD="http://deb.debian.org/debian/pool/main/t/treeviewx/treeviewx_0.5.1+20100823.orig.tar.gz" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/treeviewx/treeviewx_0.5.1+20100823.orig.tar.gz" MD5SUM="8059a306b723e6fb4d3befcf302b2920" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/trimmomatic/trimmomatic.info b/academic/trimmomatic/trimmomatic.info index f4e2d484a4..9572a0f8fb 100644 --- a/academic/trimmomatic/trimmomatic.info +++ b/academic/trimmomatic/trimmomatic.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmom MD5SUM="271ed9dca91132eee0c960e0ae487bcd" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmailc.com" diff --git a/academic/tuxmath/0001-src-menu_lan.c-Remove-unused-duplicate-lan_player_in.patch b/academic/tuxmath/0001-src-menu_lan.c-Remove-unused-duplicate-lan_player_in.patch new file mode 100644 index 0000000000..ee192e9470 --- /dev/null +++ b/academic/tuxmath/0001-src-menu_lan.c-Remove-unused-duplicate-lan_player_in.patch @@ -0,0 +1,26 @@ +From c471e2a94798787afbad4e547a1e2485ef9835db Mon Sep 17 00:00:00 2001 +From: Adrian Bunk <bunk@debian.org> +Date: Sun, 3 Jan 2021 14:22:29 +0200 +Subject: src/menu_lan.c: Remove unused duplicate lan_player_info definition + +This broke the build with gcc 10: +https://bugs.debian.org/976513 +--- + src/menu_lan.c | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/src/menu_lan.c b/src/menu_lan.c +index 4512eb1..d85f2c6 100644 +--- a/src/menu_lan.c ++++ b/src/menu_lan.c +@@ -37,7 +37,6 @@ along with this program. If not, see <http://www.gnu.org/licenses/>. */ + + + /* lan_player_type now defined in network.h */ +-lan_player_type lan_player_info[MAX_CLIENTS]; + + /* Local function prototypes: ------------------- */ + void draw_player_table(void); +-- +2.20.1 + diff --git a/academic/tuxmath/0002-rename-blits-to-tmblits.patch b/academic/tuxmath/0002-rename-blits-to-tmblits.patch new file mode 100644 index 0000000000..c5b5108acf --- /dev/null +++ b/academic/tuxmath/0002-rename-blits-to-tmblits.patch @@ -0,0 +1,54 @@ +Bug-Debian: https://bugs.debian.org/986623 +Forwarded: no +Last-Update: 2021-04-20 + +--- tuxmath-2.0.3.orig/src/titlescreen.c ++++ tuxmath-2.0.3/src/titlescreen.c +@@ -55,7 +55,7 @@ struct blit { + SDL_Rect *srcrect; + SDL_Rect *dstrect; + unsigned char type; +-} blits[MAX_UPDATES]; ++} tmblits[MAX_UPDATES]; + + // Lessons available for play + char **lesson_list_titles = NULL; +@@ -1019,8 +1019,8 @@ void init_blits(void) { + int i; + + for (i = 0; i < MAX_UPDATES; ++i) { +- blits[i].srcrect = &srcupdate[i]; +- blits[i].dstrect = &dstupdate[i]; ++ tmblits[i].srcrect = &srcupdate[i]; ++ tmblits[i].dstrect = &dstupdate[i]; + } + } + +@@ -1032,14 +1032,14 @@ void update_screen(int *frame) { + + /* -- First erase everything we need to -- */ + for (i = 0; i < numupdates; i++) +- if (blits[i].type == 'E') +- SDL_LowerBlit(blits[i].src, blits[i].srcrect, screen, blits[i].dstrect); ++ if (tmblits[i].type == 'E') ++ SDL_LowerBlit(tmblits[i].src, tmblits[i].srcrect, screen, tmblits[i].dstrect); + // SNOW_erase(); + + /* -- then draw -- */ + for (i = 0; i < numupdates; i++) +- if (blits[i].type == 'D') +- SDL_BlitSurface(blits[i].src, blits[i].srcrect, screen, blits[i].dstrect); ++ if (tmblits[i].type == 'D') ++ SDL_BlitSurface(tmblits[i].src, tmblits[i].srcrect, screen, tmblits[i].dstrect); + // SNOW_draw(); + + /* -- update the screen only where we need to! -- */ +@@ -1067,7 +1067,7 @@ void add_rect(SDL_Rect* src, SDL_Rect* d + return; + } + +- update = &blits[numupdates++]; ++ update = &tmblits[numupdates++]; + + update->srcrect->x = src->x; + update->srcrect->y = src->y; diff --git a/academic/tuxmath/tuxmath.SlackBuild b/academic/tuxmath/tuxmath.SlackBuild index 45b07f6215..8128007c5e 100644 --- a/academic/tuxmath/tuxmath.SlackBuild +++ b/academic/tuxmath/tuxmath.SlackBuild @@ -8,13 +8,13 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=tuxmath VERSION=${VERSION:-2.0.3} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -32,8 +32,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" elif [ "$ARCH" = "x86_64" ]; then @@ -58,7 +58,11 @@ find -L . \ # Fix .desktop. sed -i -e '/^##/d' -e '/^X/d' -e 's|Math;||' $PRGNAM.desktop -CFLAGS="$SLKCFLAGS" \ +patch -p1 < $CWD/0001-src-menu_lan.c-Remove-unused-duplicate-lan_player_in.patch +patch -p1 < $CWD/0002-rename-blits-to-tmblits.patch + +LDFLAGS="-std=gnu11" \ +CFLAGS="$SLKCFLAGS -std=gnu11 -fcommon" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ diff --git a/academic/tuxtype2/tuxtype2.SlackBuild b/academic/tuxtype2/tuxtype2.SlackBuild index cc3eb64ffc..ad7e5240be 100644 --- a/academic/tuxtype2/tuxtype2.SlackBuild +++ b/academic/tuxtype2/tuxtype2.SlackBuild @@ -33,7 +33,7 @@ PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -51,8 +51,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/ucsc-blat/ucsc-blat.SlackBuild b/academic/ucsc-blat/ucsc-blat.SlackBuild index d643808d48..5529adc0ac 100644 --- a/academic/ucsc-blat/ucsc-blat.SlackBuild +++ b/academic/ucsc-blat/ucsc-blat.SlackBuild @@ -34,12 +34,16 @@ SRCNAM=blatSuite if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi +if ! [ "$ARCH" = "x86_64" ] && ! [[ $ARCH =~ i?86 ]]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information # could be useful to other scripts. @@ -54,11 +58,6 @@ OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP diff --git a/academic/ucsc-blat/ucsc-blat.info b/academic/ucsc-blat/ucsc-blat.info index c2b6884091..6f97e59c99 100644 --- a/academic/ucsc-blat/ucsc-blat.info +++ b/academic/ucsc-blat/ucsc-blat.info @@ -1,9 +1,9 @@ PRGNAM="ucsc-blat" VERSION="34" HOMEPAGE="https://users.soe.ucsc.edu/~kent/" -DOWNLOAD="http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip" +DOWNLOAD="https://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip" MD5SUM="ec9fbe02fed2f15051893001da5db767" -DOWNLOAD_x86_64="http://hgwdev.cse.ucsc.edu/~kent/exe/opteron/blatSuite.34.zip" +DOWNLOAD_x86_64="https://hgwdev.cse.ucsc.edu/~kent/exe/opteron/blatSuite.34.zip" MD5SUM_x86_64="bf9042aa85a04ce85b24cef11011faee" REQUIRES="" MAINTAINER="Petar Petrov" diff --git a/academic/ugene/README b/academic/ugene/README index de420023f9..181b318651 100644 --- a/academic/ugene/README +++ b/academic/ugene/README @@ -38,30 +38,27 @@ program. All of them are available at SlackBuilds.org: - bowtie2 (A tool for aligning sequencing reads) - bwa (Burrows-Wheeler Aligner) - cap3 (CAP3: A DNA sequence assembly program) -- cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System) -- cistrome-conductGO (Find the top-n highest expressed TFs) -- cistrome-extra (Cistrome Applications Harvard extra apps) -- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq) -- cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos) -- clark-ugene (Ugene's forked CLAssifier based on Reduced K-mers) - clustalo (Clustal Omega) - clustalw (Multiple Sequence Alignment) - cufflinks (A reference-guided assembler for RNA-Seq experiments) - cutadapt (Trim adapters from high-throughput sequencing reads) -- diamond (A sequence aligner for protein and translated DNA) - fastqc (A quality control tool for high throughput sequence data) +- FastTree (Infers approximately-ML phylogenetic trees) - HMMER (Biosequence analysis using profile hidden Markov models) -- kraken (Assign taxonomic labels to short DNA sequences) -- MetaPhlAn (Metagenomic Phylogenetic Analysis) -- ncbi-blast (BLAST: Basic Local Alignment Search Tool) +- iqtree (Efficient and versatile phylogenomic software by ML) +- kalign (A fast multiple sequence alignment program) +- MetaPhlAn2 (Metagenomic Phylogenetic Analysis) +- mafft (A multiple sequence alignment program) +- mrbayes (MrBayes: Bayesian Inference of Phylogeny) - ncbi-blast+ (BLAST+ Command Line Applications) - PhyML (Phylogenetic estimation using Maximum Likelihood) - samtools-legacy (Sequence Alignment/Map Tools) - snpEff (Genetic variant annotation and effect prediction toolbox) - spades (SPAdes Genome Assembler) - spidey (mRNA-to-genomic alignment) +- stringtie (Assembler of RNA-Seq alignments) - t_coffee (A multiple sequence alignment program) -- tabix-legacy (Generic indexer for TAB-delimited genome position files ) +- tabix-legacy (Generic indexer for TAB-delimited genome position files) - tophat (Splice junction mapper for RNA-Seq reads) - trimmomatic (A flexible read trimming tool for Illumina NGS data) - vcftools (A program package designed for working with VCF files) diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild index c33b11ecb9..3a6f9ff280 100644 --- a/academic/ugene/ugene.SlackBuild +++ b/academic/ugene/ugene.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for ugene -# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ugene -VERSION=${VERSION:-38.1} +VERSION=${VERSION:-48.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -84,16 +81,46 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Fix libraries and man pages paths -sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri -sed -i "s:/share/man:/man:g" src/ugene_globals.pri +#sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri +#sed -i "s:/share/man:/man:g" src/ugene_globals.pri +#sed -i "s:Werror=maybe-uninitialized:Wno-error=maybe-uninitialized:g +# s:Werror=uninitialized:Wno-error=uninitialized:g" \ +# src/ugene_globals.pri -qmake-qt5 $QMAKECONFIG -r \ +qmake-qt5 $QMAKECONFIG -r PREFIX=/usr/lib${LIBDIRSUFFIX}/$PRGNAM \ QMAKE_CFLAGS="$SLKCFLAGS" \ -QMAKE_CXXFLAGS="$SLKCFLAGS" \ +QMAKE_CXXFLAGS="$SLKCFLAGS -std=c++11" \ UGENE_EXCLUDE_LIST_ENABLED=1 make + +# Apparently, this has to be done twice to generate the right installation files +# https://github.com/ugeneunipro/ugene/issues/683#issuecomment-1046370388 +qmake-qt5 $QMAKECONFIG -r PREFIX=/usr/lib${LIBDIRSUFFIX}/$PRGNAM \ +QMAKE_CFLAGS="$SLKCFLAGS" \ +QMAKE_CXXFLAGS="$SLKCFLAGS -std=c++11" \ +UGENE_EXCLUDE_LIST_ENABLED=1 +make + make install INSTALL_ROOT=$PKG +mkdir -p $PKG/usr/share/{applications,pixmaps} +mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM.desktop $PKG/usr/share/applications +mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/usr/man/man1 +mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM.1.gz $PKG/usr/man/man1 + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM . +cd - + +# Do not associate with my fasta files... +sed -i '/MimeType/d' $PKG/usr/share/applications/$PRGNAM.desktop + +# use just one categiry +sed -i "s:Education;Science:Education:" $PKG/usr/share/applications/$PRGNAM.desktop + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info index 3c98a2c536..8f9bf4bdf6 100644 --- a/academic/ugene/ugene.info +++ b/academic/ugene/ugene.info @@ -1,10 +1,10 @@ PRGNAM="ugene" -VERSION="38.1" +VERSION="48.1" HOMEPAGE="http://ugene.net/" -DOWNLOAD="https://github.com/ugeneunipro/ugene/archive/38.1/ugene-38.1.tar.gz" -MD5SUM="4add1b1c0216ce42e588e982a3d7147e" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/ugeneunipro/ugene/archive/48.1/ugene-48.1.tar.gz" +MD5SUM_x86_64="5662a9e58d6ad19a8be7410f12139072" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/umfpack/README b/academic/umfpack/README index 954cb8b964..921b1dcd4b 100644 --- a/academic/umfpack/README +++ b/academic/umfpack/README @@ -3,12 +3,16 @@ systems, Ax=b, using the Unsymmetric MultiFrontal method. This package is part of SuiteSparse. -This requires a BLAS implementation. Choose one of these package sets: +This requires a BLAS implementation. Choose one of these package +sets: + * OpenBLAS * atlas * blas (the Netlib reference implementation) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. + +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib reference +implementations; other packages that require a BLAS or LAPACK +implementation may not build if they are not configured to detect/use +alternate implementations. diff --git a/academic/umfpack/umfpack.SlackBuild b/academic/umfpack/umfpack.SlackBuild index 447c4d03c9..3da82b0df8 100644 --- a/academic/umfpack/umfpack.SlackBuild +++ b/academic/umfpack/umfpack.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/umfpack/umfpack.info b/academic/umfpack/umfpack.info index 9b8e8496a8..003572719c 100644 --- a/academic/umfpack/umfpack.info +++ b/academic/umfpack/umfpack.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/Suit MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas suitesparseconfig amd cholmod" +REQUIRES="cholmod" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/units/doinst.sh b/academic/units/doinst.sh new file mode 100644 index 0000000000..40e776ac68 --- /dev/null +++ b/academic/units/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/install-info ]; then + /usr/bin/install-info --info-dir=usr/info usr/info/units.info.gz 1> /dev/null 2>&1 +fi diff --git a/academic/units/douninst.sh b/academic/units/douninst.sh new file mode 100644 index 0000000000..0273142e5c --- /dev/null +++ b/academic/units/douninst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/install-info -a -d usr/info ]; then + ( + cd usr/info + rm -f dir + for i in *.info*; do + /usr/bin/install-info $i dir 1>/dev/null 2>&1 + done + ) +fi diff --git a/academic/units/units.SlackBuild b/academic/units/units.SlackBuild index 760f771dfd..e9586ecb36 100644 --- a/academic/units/units.SlackBuild +++ b/academic/units/units.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for gnu units -# Copyright (c) 2010-2021 Gregory J. L. Tourte <artourter@gmail.com> +# Copyright (c) 2010-2024 Gregory J. L. Tourte <artourter@gmail.com> # Previously maintained by Yalla-One <yallaone@gmail.com> # All rights reserved. # @@ -27,7 +27,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=units -VERSION=${VERSION:-2.21} +VERSION=${VERSION:-2.23} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -76,11 +76,8 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - + -perm /111 -a \! -perm 755 -a -exec chmod 755 {} + -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} + PYTHON=/usr/bin/python3 \ CFLAGS="$SLKCFLAGS" \ @@ -93,6 +90,7 @@ CXXFLAGS="$SLKCFLAGS" \ --infodir=/usr/info \ --localstatedir=/var \ --datadir=/usr/share \ + --sharedstatedir=/usr/share \ --build=$ARCH-slackware-linux make @@ -109,11 +107,13 @@ rm -f $PKG/usr/info/dir gzip -9 $PKG/usr/info/*.info* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a INSTALL COPYING ChangeLog NEWS README $PKG/usr/doc/$PRGNAM-$VERSION +cp -a COPYING NEWS README units.pdf $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/douninst.sh > $PKG/install/douninst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/units/units.info b/academic/units/units.info index 195a9c1a75..cab93752fb 100644 --- a/academic/units/units.info +++ b/academic/units/units.info @@ -1,8 +1,8 @@ PRGNAM="units" -VERSION="2.21" +VERSION="2.23" HOMEPAGE="https://www.gnu.org/software/units/" -DOWNLOAD="https://ftpmirror.gnu.org/units/units-2.21.tar.gz" -MD5SUM="8fc4884bf5f7dab10b5a31bdf7726c2d" +DOWNLOAD="https://ftpmirror.gnu.org/units/units-2.23.tar.gz" +MD5SUM="2cb4f754dcde5b2409e656f5d8d4a474" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="Unidecode" diff --git a/academic/vCAPS_coevolution/caps_verbose.patch b/academic/vCAPS_coevolution/01_caps_verbose.patch index 7f64d80f34..7f64d80f34 100644 --- a/academic/vCAPS_coevolution/caps_verbose.patch +++ b/academic/vCAPS_coevolution/01_caps_verbose.patch diff --git a/academic/vCAPS_coevolution/02_caps_sort_input.patch b/academic/vCAPS_coevolution/02_caps_sort_input.patch new file mode 100644 index 0000000000..917bca7cab --- /dev/null +++ b/academic/vCAPS_coevolution/02_caps_sort_input.patch @@ -0,0 +1,38 @@ +diff -pruN old/caps.cpp new/caps.cpp +--- old/caps.cpp 2022-01-20 09:30:24.409886691 +0200 ++++ new/caps.cpp 2022-01-20 09:39:10.669845265 +0200 +@@ -1,4 +1,5 @@ + #include<iostream> ++#include <algorithm> + #include<fstream> + #include"BCFasta.h" + #include"file_manip.h" +@@ -15,7 +16,7 @@ + #include<sys/time.h> + #include<iomanip> + #include <bits/stdc++.h> +- ++#include <vector> + + + #include <Seq/SequenceApplicationTools.h> +@@ -69,6 +70,10 @@ + const gsl_rng_type * T; + gsl_rng *r; + ++// make sure filenames are sorted! ++// https://stackoverflow.com/a/34757557 ++bool compareFunction (std::string a, std::string b) {return a<b;} ++ + vector<double> totaltempnew; + double alphathresh = 0; + int main(int argc, char *argv[]){ +@@ -189,6 +194,8 @@ int main(int argc, char *argv[]){ + + vector<string> files; + files = Folder_to_vector(mystring.c_str()); ++ // make sure filenames are sorted! ++ std::sort(files.begin(),files.end(),compareFunction); + + Fasta_vector file; + file.ref_num=0; diff --git a/academic/vCAPS_coevolution/README b/academic/vCAPS_coevolution/README index 27ebb623a0..b8b4a71a4b 100644 --- a/academic/vCAPS_coevolution/README +++ b/academic/vCAPS_coevolution/README @@ -9,20 +9,21 @@ intra-molecular coevolution as published in Genetics (Fares and Travers, of amino acid sites is obtained by maximum likelihood ancestral state reconstruction along with simulations to assess significance. -In addition, a test which assesses whether two proteins are interacting -is implemented. +This is a modified version of "CAPS_coevolution", used in the AutoCoEv +pipeline: +https://github.com/mattilalab/autocoev -NOTE: -This applies an _unofficial_ patch to enable more verbose output of the -program, including CAPS generated phylogenetic trees and p-values of the -pairwise results. The produced executable is called "vCAPS" and can be -installed along "caps" from CAPS_coevolution. Building CAPS from source -requires the Bio++ 1.9 suite, also available at SBo, which can be safely -installed along the current version. Fore details of the patch see pre- -print at bioRxiv by Petrov et al.: -https://doi.org/10.1101/2020.09.29.315374 +It applies two _unofficial_ patches: +- 01_caps_verbose: makes the program output its generated trees, as well + as the p-value for each correlated amino acid pair +- 02_caps_sort_input: introduce a function to sort input file names -CITING: +The produced executable is called "vCAPS" and can be installed along +"caps" from CAPS_coevolution. Building CAPS from source requires the +Bio++ 1.9 suite libraries, but make sure the current versions of the +bppsuite (and its dependencies) are NOT installed at build time. + +Citing CAPS: CAPS: coevolution analysis using protein sequences. Fares MA, McNally D. Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535 diff --git a/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild b/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild index 9b000762b1..f00aea698e 100644 --- a/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild +++ b/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for vCAPS_coevolution -# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=vCAPS_coevolution -VERSION=${VERSION:-2.0_1UN} +VERSION=${VERSION:-2.0_2UN} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -42,9 +42,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -68,7 +65,6 @@ else LIBDIRSUFFIX="" fi -# This is needed for vCAPS to find its libraries at runtime. Thanks Urchlay! LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" set -e @@ -87,7 +83,7 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # This is needed for gcc in Slackware 14.2 -sed -i "s:CC=g++ -g:CC=g++ -g -std=c++11:" Makefile +sed -i "s:CC=g++ -g:CC=g++-5 -g -std=c++11:" Makefile # Use our CFLAGS and the custom (legacy) lib path sed -i "s:CFLAGS=:CFLAGS=$SLKCFLAGS $LIBDIRPATH:" Makefile @@ -101,14 +97,21 @@ sed -i "s:-lbpp-seq:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-seq:g" Makefile # Rename the produced executable sed -i "s:-o caps:-o $BINNAM:" Makefile -# Use our unofficial patch -patch -p1 -i $CWD/caps_verbose.patch +# Use our patches +patch -p1 -i $CWD/01_caps_verbose.patch +patch -p1 -i $CWD/02_caps_sort_input.patch + +# we already specified g++-5 above, so no need for this +#source /etc/profile.d/gcc5.sh make all # Install the binary produced from our patched source, as "vCAPS" install -D -m755 $BINNAM $PKG/usr/bin/$BINNAM +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + mkdir -p $PKG/usr/share/$PRGNAM cp -a sample structures trees TLR1.fa.out $PKG/usr/share/$PRGNAM diff --git a/academic/vCAPS_coevolution/vCAPS_coevolution.info b/academic/vCAPS_coevolution/vCAPS_coevolution.info index 84ebd91d4c..48545099b1 100644 --- a/academic/vCAPS_coevolution/vCAPS_coevolution.info +++ b/academic/vCAPS_coevolution/vCAPS_coevolution.info @@ -1,7 +1,7 @@ PRGNAM="vCAPS_coevolution" -VERSION="2.0_1UN" -HOMEPAGE="http://bioinf.gen.tcd.ie/~faresm/software/software.html" -DOWNLOAD="http://bioinf.gen.tcd.ie/~faresm/software/files/caps2_src.zip" +VERSION="2.0_2UN" +HOMEPAGE="http://bioinf.gen.tcd.ie/caps/home.html" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/caps2_src.zip" MD5SUM="0914007c32ed22a9cb8a47b55cd18a39" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/velocyto/README b/academic/velocyto/README new file mode 100644 index 0000000000..24fd05629e --- /dev/null +++ b/academic/velocyto/README @@ -0,0 +1,2 @@ + Velocyto is a library for the analysis of RNA velocity. It includes +a command line tool and an analysis pipeline. diff --git a/academic/velocyto/slack-desc b/academic/velocyto/slack-desc new file mode 100644 index 0000000000..58988e9bed --- /dev/null +++ b/academic/velocyto/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +velocyto: velocyto (library for the analysis of RNA velocity) +velocyto: +velocyto: +velocyto: +velocyto: Velocyto is a library for the analysis of RNA velocity. It includes +velocyto: a command line tool and an analysis pipeline. +velocyto: +velocyto: +velocyto: +velocyto: +velocyto: diff --git a/academic/velocyto/velocyto.SlackBuild b/academic/velocyto/velocyto.SlackBuild new file mode 100644 index 0000000000..145f7344ee --- /dev/null +++ b/academic/velocyto/velocyto.SlackBuild @@ -0,0 +1,107 @@ +#!/bin/bash + +# Slackware build script for velocyto + +# Copyright 2023 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=velocyto +VERSION=${VERSION:-0.17.17} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=$PRGNAM.py + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +python3 setup.py build +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE doc \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/velocyto/velocyto.info b/academic/velocyto/velocyto.info new file mode 100644 index 0000000000..ea72fc71d8 --- /dev/null +++ b/academic/velocyto/velocyto.info @@ -0,0 +1,10 @@ +PRGNAM="velocyto" +VERSION="0.17.17" +HOMEPAGE="https://velocyto.org" +DOWNLOAD="https://github.com/velocyto-team/velocyto.py/archive/0.17.17/velocyto.py-0.17.17.tar.gz" +MD5SUM="e85f92edf103fdaf51fbc998c4e1701d" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-numpy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/verilator/slack-desc b/academic/verilator/slack-desc index 1bb74ecb6d..9cdfb77535 100644 --- a/academic/verilator/slack-desc +++ b/academic/verilator/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| verilator: verilator (the fastest free Verilog HDL simulator) verilator: -verilator: Verilator is invoked with parameters similar to GCC or Synopsys’s VCS. -verilator: It "Verilates" the specified synthesizable Verilog or SystemVerilog -verilator: code by reading it, performing lint checks, and optionally inserting -verilator: assertion checks and coverage-analysis points. It outputs single- or -verilator: multi-threaded .cpp and .h files, the "Verilated" code. +verilator: Verilator is invoked with parameters similar to GCC or Synopsys's +verilator: VCS. It "Verilates" the specified synthesizable Verilog or +verilator: SystemVerilog code by reading it, performing lint checks, and +verilator: optionally inserting assertion checks and coverage-analysis points. +verilator: It outputs single- or verilator: multi-threaded .cpp and .h files, +verilator: the "Verilated" code. verilator: verilator: homepage: https://www.veripool.org/wiki/verilator verilator: -verilator: diff --git a/academic/verilator/verilator.SlackBuild b/academic/verilator/verilator.SlackBuild index b59dfd9623..4db86c835f 100644 --- a/academic/verilator/verilator.SlackBuild +++ b/academic/verilator/verilator.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=verilator -VERSION=${VERSION:-4.030} +VERSION=${VERSION:-4.218} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -70,7 +70,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tgz +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -79,6 +79,8 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +autoconf -f + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -101,7 +103,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - LICENSE Changes Artistic README.adoc verilator.txt verilator.pdf \ + LICENSE Changes Artistic README.rst \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/verilator/verilator.info b/academic/verilator/verilator.info index 7dc1f41490..22dccf1cf7 100644 --- a/academic/verilator/verilator.info +++ b/academic/verilator/verilator.info @@ -1,10 +1,10 @@ PRGNAM="verilator" -VERSION="4.030" +VERSION="4.218" HOMEPAGE="https://www.veripool.org/wiki/verilator" -DOWNLOAD="https://www.veripool.org/ftp/verilator-4.030.tgz" -MD5SUM="f412f817a8eeb142f6d27684e5fd4809" +DOWNLOAD="https://github.com/verilator/verilator/archive/v4.218/verilator-4.218.tar.gz" +MD5SUM="b237c0524327fc82aa4f3af93ecb9371" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="verilog" MAINTAINER="Charles Daniels" EMAIL="charles [at] cdaniels [dot] net" diff --git a/academic/verilog/verilog.SlackBuild b/academic/verilog/verilog.SlackBuild index c54239ae9f..797f1bcf9b 100644 --- a/academic/verilog/verilog.SlackBuild +++ b/academic/verilog/verilog.SlackBuild @@ -6,14 +6,14 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=verilog -VERSION=${VERSION:-0.9.7} +VERSION=${VERSION:-11.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -31,8 +31,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -69,6 +69,8 @@ CXXFLAGS="$SLKCFLAGS" \ --localstatedir=/var \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ + --enable-shared \ + --disable-static \ --build=$ARCH-slackware-linux make -j1 diff --git a/academic/verilog/verilog.info b/academic/verilog/verilog.info index 3386e5387d..a78c9fe87d 100644 --- a/academic/verilog/verilog.info +++ b/academic/verilog/verilog.info @@ -1,8 +1,8 @@ PRGNAM="verilog" -VERSION="0.9.7" +VERSION="11.0" HOMEPAGE="http://iverilog.icarus.com/" -DOWNLOAD="ftp://icarus.com/pub/eda/verilog/v0.9/verilog-0.9.7.tar.gz" -MD5SUM="1a8c3f13360078a5e266a0c852bbec57" +DOWNLOAD="https://jaist.dl.sourceforge.net/project/iverilog/iverilog/11.0/verilog-11.0.tar.gz" +MD5SUM="a3f7a618a4f499244ec6ee928574f03d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/veusz/veusz.info b/academic/veusz/veusz.info index d724e40c5d..4b02fb8b23 100644 --- a/academic/veusz/veusz.info +++ b/academic/veusz/veusz.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/veusz/veusz/releases/download/veusz-3.3.1/veusz-3.3 MD5SUM="1c7d42d6f87ea3b98fafc8dc52dbbc58" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="numpy3" +REQUIRES="python3-numpy" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/voro++/README b/academic/voro++/README new file mode 100644 index 0000000000..886a2a1030 --- /dev/null +++ b/academic/voro++/README @@ -0,0 +1,7 @@ + Voro++ is a software library for carrying out three-dimensional +computations of the Voronoi tessellation. A distinguishing feature of +the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is +particularly well-suited for applications that rely on cell-based +statistics, where features of Voronoi cells (eg. volume, centroid, +number of faces) can be used to analyze a system of particles. diff --git a/academic/voro++/slack-desc b/academic/voro++/slack-desc new file mode 100644 index 0000000000..a0482548d5 --- /dev/null +++ b/academic/voro++/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +voro++: voro++ (A 3D Voronoi cell software library) +voro++: +voro++: Voro++ is a software library for carrying out three-dimensional +voro++: computations of the Voronoi tessellation. A distinguishing feature of +voro++: the Voro++ library is that it carries out cell-based calculations, +voro++: computing the Voronoi cell for each particle individually. It is +voro++: particularly well-suited for applications that rely on cell-based +voro++: statistics, where features of Voronoi cells (eg. volume, centroid, +voro++: number of faces) can be used to analyze a system of particles. +voro++: +voro++: diff --git a/academic/coq/coq.SlackBuild b/academic/voro++/voro++.SlackBuild index ac1985a5dc..563f9f3e56 100644 --- a/academic/coq/coq.SlackBuild +++ b/academic/voro++/voro++.SlackBuild @@ -1,8 +1,8 @@ #!/bin/bash -# Slackware build script for coq +# Slackware build script for voro++ -# Copyright 2020 Nick Smallbone <nick@smallbone.se>, Gothenburg, Sweden +# Copyright 2022 William PC - Seattle, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,11 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + cd $(dirname $0) ; CWD=$(pwd) -PRGNAM=coq -VERSION=${VERSION:-8.9.0} +PRGNAM=voro++ +VERSION=${VERSION:-0.4.6} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -51,12 +52,16 @@ PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" else + SLKCFLAGS="-O2" LIBDIRSUFFIX="" fi @@ -75,29 +80,23 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Configure findlib so it can find camlp5. -cp /etc/findlib.conf . -sed -i "s@path=\"@path=\"/usr/lib${LIBDIRSUFFIX}/ocaml:@" findlib.conf -export OCAMLFIND_CONF=$(pwd)/findlib.conf -CONFIG_ARGS= -if [ z$COQIDE = zyes ];then - CONFIG_ARGS+=" -coqide opt" -else - CONFIG_ARGS+=" -coqide no" -fi +# the default make build the examples +# let's keep source only +sed -i '15s/^/#/;24s/^/#/' Makefile -./configure \ - -prefix /usr \ - -libdir /usr/lib${LIBDIRSUFFIX}/$PRGNAM \ - -configdir /etc/xdg/$PRGNAM \ - -mandir /usr/man \ - -docdir /usr/doc/$PRGNAM-$VERSION \ - -arch $ARCH \ - $CONFIG_ARGS +# comment the include line of example's Makefiles +# then add the right path for include files +sed -i 's/^include ../#&/; /#include/aE_INC=-I/usr/include/voro++' examples/*/Makefile +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ make -make install COQINSTALLPREFIX=$PKG +make install PREFIX=$PKG/usr + +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a examples $PKG/usr/share/$PRGNAM-$VERSION +cp -a scripts $PKG/usr/share/$PRGNAM-$VERSION find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -107,8 +106,9 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - CHANGES.md CONTRIBUTING.md CREDITS INSTALL LICENSE README.md \ + LICENSE html \ $PKG/usr/doc/$PRGNAM-$VERSION +chmod 755 $PKG/usr/doc/$PRGNAM-$VERSION/html cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/voro++/voro++.info b/academic/voro++/voro++.info new file mode 100644 index 0000000000..0bfd5007a7 --- /dev/null +++ b/academic/voro++/voro++.info @@ -0,0 +1,10 @@ +PRGNAM="voro++" +VERSION="0.4.6" +HOMEPAGE="https://crd.lbl.gov/divisions/amcr/mathematics-dept/math/software/voro-a-three-dimensional-voronoi-library-in-c/" +DOWNLOAD="https://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz" +MD5SUM="2338b824c3b7b25590e18e8df5d68af9" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/wcalc/README b/academic/wcalc/README new file mode 100644 index 0000000000..c1522dce07 --- /dev/null +++ b/academic/wcalc/README @@ -0,0 +1,13 @@ +wcalc (command-line scientific calculator) + +Wcalc is a very capable command-line calculator. It has standard +functions (sin, asinh, and sqrt for example, in either radians or +degrees), many pre-defined constants (pi, e, c, G, etc.), support +for using variables, "active" variables, a command history, +hex/octal/binary input and output, unit conversions, embedded +comments, and the ability to save history to a file and load it +from a file. Wcalc evaluates expressions using the standard order of +operations. + +Wcalc uses intuitive expressions. For example, Wcalc will evaluate +5sin 4!-7*2(4%6)^2 to be -221.96631678. diff --git a/academic/wcalc/doinst.sh b/academic/wcalc/doinst.sh new file mode 100644 index 0000000000..65c7e2eeb9 --- /dev/null +++ b/academic/wcalc/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/wcalc/icons/128.png b/academic/wcalc/icons/128.png Binary files differnew file mode 100644 index 0000000000..cafefc348c --- /dev/null +++ b/academic/wcalc/icons/128.png diff --git a/academic/wcalc/icons/16.png b/academic/wcalc/icons/16.png Binary files differnew file mode 100644 index 0000000000..ab6bf4aba0 --- /dev/null +++ b/academic/wcalc/icons/16.png diff --git a/academic/wcalc/icons/32.png b/academic/wcalc/icons/32.png Binary files differnew file mode 100644 index 0000000000..5077cee603 --- /dev/null +++ b/academic/wcalc/icons/32.png diff --git a/academic/wcalc/icons/48.png b/academic/wcalc/icons/48.png Binary files differnew file mode 100644 index 0000000000..e188f42fa7 --- /dev/null +++ b/academic/wcalc/icons/48.png diff --git a/academic/wcalc/slack-desc b/academic/wcalc/slack-desc new file mode 100644 index 0000000000..f7e41e97e1 --- /dev/null +++ b/academic/wcalc/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +wcalc: wcalc (command-line scientific calculator) +wcalc: +wcalc: Wcalc is a very capable command-line calculator. It has standard +wcalc: functions (sin, asinh, and sqrt for example, in either radians or +wcalc: degrees), many pre-defined constants (pi, e, c, G, etc.), support +wcalc: for using variables, "active" variables, a command history, +wcalc: hex/octal/binary input and output, unit conversions, embedded +wcalc: comments, and the ability to save history to a file and load it +wcalc: from a file. Wcalc evaluates expressions using the standard order of +wcalc: operations. +wcalc: diff --git a/academic/wcalc/wcalc.SlackBuild b/academic/wcalc/wcalc.SlackBuild new file mode 100644 index 0000000000..21bd7932cd --- /dev/null +++ b/academic/wcalc/wcalc.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for wcalc + +# Written by B. Watson (urchlay@slackware.uk) + +# Licensed under the WTFPL. See http://www.wtfpl.net/txt/copying/ for details. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=wcalc +VERSION=${VERSION:-2.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +# the * in the next line is in case '?viasf=1' is appended to the filename... +tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2* +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . -perm /111 -a \! -perm 755 -a -exec chmod 755 {} + -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} + + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --disable-static \ + --build=$ARCH-slackware-linux + +make +make install-strip DESTDIR=$PKG +gzip -9 $PKG/usr/man/man*/* + +# Icons extracted from graphics/TheW.icns in the source. +for i in $CWD/icons/*.png; do + px="$( basename $i .png )" + sz="${px}x${px}" + dir=$PKG/usr/share/icons/hicolor/$sz/apps + mkdir -p $dir + cat $i > $dir/$PRGNAM.png +done + +mkdir -p $PKG/usr/share/pixmaps +ln -s ../icons/hicolor/48x48/apps/$PRGNAM.png $PKG/usr/share/pixmaps/$PRGNAM.png + +# .desktop file written by SlackBuild author. +mkdir -p $PKG/usr/share/applications +cat $CWD/$PRGNAM.desktop > $PKG/usr/share/applications/$PRGNAM.desktop + +PKGDOC=$PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKGDOC +cp -a AUTHORS COPYRIGHT ChangeLog NEWS README $PKGDOC +cat $CWD/$PRGNAM.SlackBuild > $PKGDOC/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wcalc/wcalc.desktop b/academic/wcalc/wcalc.desktop new file mode 100644 index 0000000000..a47430d238 --- /dev/null +++ b/academic/wcalc/wcalc.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Version=1.0 +Type=Application +Name=WCalc +Comment=Scientific Calculator +Exec=wcalc +Icon=wcalc +Terminal=true +StartupNotify=false +Categories=Science;Math diff --git a/academic/wcalc/wcalc.info b/academic/wcalc/wcalc.info new file mode 100644 index 0000000000..12bcbc0131 --- /dev/null +++ b/academic/wcalc/wcalc.info @@ -0,0 +1,10 @@ +PRGNAM="wcalc" +VERSION="2.5" +HOMEPAGE="https://w-calc.sourceforge.net/" +DOWNLOAD="https://downloads.sourceforge.net/project/w-calc/Wcalc/2.5/wcalc-2.5.tar.bz2" +MD5SUM="45b02ba339a813ffc65f154d1e54a04b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="B. Watson" +EMAIL="urchlay@slackware.uk" diff --git a/academic/wehi-cellsymphony/wehi-cellsymphony.info b/academic/wehi-cellsymphony/wehi-cellsymphony.info index d5a3c58eb1..e6a94638b3 100644 --- a/academic/wehi-cellsymphony/wehi-cellsymphony.info +++ b/academic/wehi-cellsymphony/wehi-cellsymphony.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.frankbattye.com.au/downloads/CellSymphony.jar" MD5SUM="d7c3b806491f7922742271a4dfcdb58c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/wehi-deid/wehi-deid.info b/academic/wehi-deid/wehi-deid.info index 074a0e8f91..6b465458a5 100644 --- a/academic/wehi-deid/wehi-deid.info +++ b/academic/wehi-deid/wehi-deid.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.frankbattye.com.au/downloads/DeID.jar" MD5SUM="bd938d07b0471cf9ed9f32b778ded63d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/wehi-hackit/wehi-hackit.info b/academic/wehi-hackit/wehi-hackit.info index 2f96e41d08..043df91eec 100644 --- a/academic/wehi-hackit/wehi-hackit.info +++ b/academic/wehi-hackit/wehi-hackit.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.frankbattye.com.au/downloads/Hackit.jar" MD5SUM="1b498994d569b147a461b698633078e1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/wehi-weasel/wehi-weasel.SlackBuild b/academic/wehi-weasel/wehi-weasel.SlackBuild index 7a81f34196..17332d1bb0 100644 --- a/academic/wehi-weasel/wehi-weasel.SlackBuild +++ b/academic/wehi-weasel/wehi-weasel.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for wehi-weasel -# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=wehi-weasel -VERSION=${VERSION:-3.7.1.18} +VERSION=${VERSION:-3.8.0.18} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -46,7 +46,7 @@ OUTPUT=${OUTPUT:-/tmp} SRCNAM=wsl JARNAM=Weasel -SRCVER=37118 +SRCVER=38018 SRCDIST=unix LICENSE=WeaselLicence.doc diff --git a/academic/wehi-weasel/wehi-weasel.info b/academic/wehi-weasel/wehi-weasel.info index 1545b68aeb..a73a47e760 100644 --- a/academic/wehi-weasel/wehi-weasel.info +++ b/academic/wehi-weasel/wehi-weasel.info @@ -1,10 +1,10 @@ PRGNAM="wehi-weasel" -VERSION="3.7.1.18" +VERSION="3.8.0.18" HOMEPAGE="http://www.frankbattye.com.au/Weasel/" DOWNLOAD="http://www.frankbattye.com.au/Weasel/WeaselDownload.html" -MD5SUM="d9154f7e71dbd1a8311f8cbd03b44090" +MD5SUM="f7dfb4363b6d60a7781a212b06afbc98" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adoptopenjdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/wise/README b/academic/wise/README new file mode 100644 index 0000000000..6fe23af5ad --- /dev/null +++ b/academic/wise/README @@ -0,0 +1,7 @@ +Wise compares a protein sequence to a genomic DNA sequence, allowing for +introns and frameshifting errors. + +The Wise package is now a rather stately bioinformatics package that has +been around for a while. Its key programs are genewise, a program for +aligning proteins or protein HMMs to DNA, and dynamite a rather cranky +"macro language" which automates the production of dynamic programming. diff --git a/academic/wise/patches/01_welcome-csh.patch b/academic/wise/patches/01_welcome-csh.patch new file mode 100644 index 0000000000..3a9057e062 --- /dev/null +++ b/academic/wise/patches/01_welcome-csh.patch @@ -0,0 +1,22 @@ +Author: Philipp Benner <mail@philipp-benner.de> +Description: Avoid dependency from csh + +--- wise-2.4.1.orig/src/makefile ++++ wise-2.4.1/src/makefile +@@ -109,7 +109,7 @@ + bin : + mkdir bin + cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin +- csh welcome.csh ++ ./welcome.csh + + libs : + (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a ) +--- wise-2.4.1.orig/src/welcome.csh ++++ wise-2.4.1/src/welcome.csh +@@ -1,4 +1,4 @@ +-#!/bin/tcsh -f ++#!/bin/sh + + echo "" + echo "Welcome to Wise2.4" diff --git a/academic/wise/patches/02_isnumber.patch b/academic/wise/patches/02_isnumber.patch new file mode 100644 index 0000000000..a6ae90856d --- /dev/null +++ b/academic/wise/patches/02_isnumber.patch @@ -0,0 +1,14 @@ +Author: Philipp Benner <mail@philipp-benner.de> +Description: Replace isnumber() (which does not exist on linux) by isdigit(). + +--- wise-2.4.1.orig/src/models/phasemodel.c ++++ wise-2.4.1/src/models/phasemodel.c +@@ -20,7 +20,7 @@ + if( line[0] == '#' ) { + continue; + } +- if( !isnumber(line[0]) ) { ++ if( !isdigit(line[0]) ) { + warn("Bad looking line in intron file, %s",line); + continue; + } diff --git a/academic/wise/patches/03_doc-nodycache.patch b/academic/wise/patches/03_doc-nodycache.patch new file mode 100644 index 0000000000..6fe7b1893c --- /dev/null +++ b/academic/wise/patches/03_doc-nodycache.patch @@ -0,0 +1,15 @@ +Author Philipp Benner <mail@philipp-benner.de> +Description: Documentation bugfix. + +--- wise-2.4.1.orig/docs/wise2.tex ++++ wise-2.4.1/docs/wise2.tex +@@ -1617,7 +1617,8 @@ + \item[-hithelp] more detailed help on hitlist formats + \item[-dymem] memory style [default/linear/explicit] + \item[-kbyte] memory amount to use [4000] +-\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes) ++\item[-dycache] implicitly cache dy matrix usage (default) ++\item[-nodycache] do not implicitly cache dy matrix usage + \item[-dydebug] drop into dynamite dp matrix debugger + \item[-paldebug] print PackAln after debugger run if used + \item[-help] show help options diff --git a/academic/wise/patches/04_wise2-pdflatex-update.patch b/academic/wise/patches/04_wise2-pdflatex-update.patch new file mode 100644 index 0000000000..bbaf2861d7 --- /dev/null +++ b/academic/wise/patches/04_wise2-pdflatex-update.patch @@ -0,0 +1,38 @@ +Author Philipp Benner <mail@philipp-benner.de> +Description: Make wise2.tex pdflatex compatible. + +--- wise-2.4.1.orig/docs/wise2.tex ++++ wise-2.4.1/docs/wise2.tex +@@ -1,6 +1,7 @@ + + \documentclass{article} +-\usepackage{epsfig} ++%\usepackage{epsfig} ++\usepackage{graphicx} + + \begin{document} + \newcommand{\programtext}[1]{{\tt #1}} +@@ -707,8 +708,9 @@ + \begin{figure} + \begin{center} + \leavevmode +-\epsfxsize 300pt +-\epsfbox{genewise21.eps} ++%\epsfxsize 300pt ++%\epsfbox{genewise21.eps} ++%\includegraphics[scale=0.75]{genewise21.pdf} + \newline + \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the + arrows between them transitions. Black transitions are standard +@@ -898,8 +900,9 @@ + \begin{figure} + \begin{center} + \leavevmode +-\epsfxsize 300pt +-\epsfbox{genewise6.eps} ++%\epsfxsize 300pt ++%\epsfbox{genewise6.eps} ++%\includegraphics[scale=0.75]{genewise6.pdf} + \newline + \caption{GeneWise6:23} + \label{Figure:genewise623} diff --git a/academic/wise/patches/05_glib2.patch b/academic/wise/patches/05_glib2.patch new file mode 100644 index 0000000000..908506524a --- /dev/null +++ b/academic/wise/patches/05_glib2.patch @@ -0,0 +1,703 @@ +Author: Barry deFreese <bdefreese@debian.org> +Description: To build wise2 with the Glib version 2.0 instead of 1.2. +Forwarded: birney@sanger.ac.uk +--- wise-2.4.1.orig/src/makefile ++++ wise-2.4.1/src/makefile +@@ -31,13 +31,13 @@ + + + # Intel icc flags +-# CFLAGS = -c -O3 -axWK -ipo `glib-config --cflags` ++# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0` + + # alpha flags (-pthread) +-# CFLAGS = -c -O3 -pthread `glib-config --cflags` ++# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0` + + # normal linux/bsd/mac flags +-CFLAGS = -c -O3 `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0` + + + EXTRALIBS = -lm +--- wise-2.4.1.orig/src/snp/makefile ++++ wise-2.4.1/src/snp/makefile +@@ -5,9 +5,9 @@ + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -16,7 +16,7 @@ + $(CC) $(CFLAGS) $(INCFLAGS) $? + + test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o +- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) ++ $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LDFLAGS) + + INCFLAGS = -I../base/ -I../dynlibsrc/ + DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn +--- wise-2.4.1.orig/src/corba/makefile ++++ wise-2.4.1/src/corba/makefile +@@ -3,9 +3,9 @@ + CC = cc + INCFLAGS = -I../base/ -I../dynlibsrc + #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ +-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` +-LFLAGS = -L../base/ -lm -lpthread ++#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ ++CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` ++LDFLAGS += -L../base/ -lm -lpthread + AR_OPTIONS = ru + + +@@ -14,18 +14,18 @@ + orbit-idl hspscan_corba.idl + + test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o +- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o +- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- wise-2.4.1.orig/src/models/makefile ++++ wise-2.4.1/src/models/makefile +@@ -62,46 +62,46 @@ + # $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) wise2xhmmer2.c + + testgenestat : testgenestat.o genestats.o pwmdna.o +- $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + test_aligng : test_aligng.o aligngenemodel.o pwmdna.o +- $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + makepwm : makepwm.o pwmdna.o +- $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + testwise2xhmmer2.o : testwise2xhmmer2.c + $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) testwise2xhmmer2.c + + testwise2xhmmer2 : testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o +- $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LFLAGS) ++ $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LDFLAGS) + + plan7test.o : plan7test.c + $(CC) $(CFLAGS) -I../HMMer2/ plan7test.c + + plan7test : plan7test.o plan7.o wise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o +- $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LFLAGS) ++ $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LDFLAGS) + + seqstat : seqstat.o +- $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LDFLAGS) + + mutatedna : mutatedna.o +- $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LDFLAGS) + + revcomp : revcomp.o +- $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LDFLAGS) + + stupid_motif_scan : stupid_motif_scan.o +- $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LDFLAGS) + + seqtrunc : seqtrunc.o +- $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LDFLAGS) + + seqlist : seqlist.o +- $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LDFLAGS) + + testpwm : testpwm.o pwmdna.o +- $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) -lefence ++ $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) -lefence + + + threestate : $(MODELOBJ) +@@ -111,29 +111,29 @@ + pwise : $(MODELOBJ) threestatemat.o threestatedisplay.o + + test : test.o proteinsw.o protprotdis.o +- $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LFLAGS) ++ $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LDFLAGS) + + testanc : testanc.o proteinsw.o abc.o pba.o sw_wrap.o +- $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_tf : test_transfactor.o transfactor.o pwmdna.o +- $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LDFLAGS) -ldyna -lwisebase + + motifwise : motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + motifcluster : motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + motifdiff : motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + + cdtest : cdtest.o cdna2genomic.o d2d_display.o +- $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LDFLAGS) + + prob2bits : prob2bits.o +- $(CC) -o prob2bits $(LFLAGS) -ldyna_glib -ldyna -lwisebase ++ $(CC) -o prob2bits $(LDFLAGS) -ldyna_glib -ldyna -lwisebase + + quick : + cc -O -c -I../dynlibsrc/ -I../base/ genewise6.c +@@ -180,161 +180,161 @@ + $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. + + oldpostwise : oldpostwise.o $(NEWG) +- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase ++ $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase + + testdna : testdna.o dnaalign.o seqaligndisplay.o +- $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + dnal : dnal.o dnaalign.o seqaligndisplay.o +- $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + scanwisep.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $? + + hsp2aln_sw.o : hsp2aln_sw.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + scanwisep_mysql.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c + + scanwisep_mysql : scanwisep_mysql.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) -lpthread -lZ ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LDFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) $(LDFLAGS) -lpthread -lZ + + + scanwisep_corba.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_CORBA -I../corba -I../external/mott `orbit-config --cflags server` scanwisep.c + + scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LDFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread + + + scanwisep_wiseserver.o : scanwisep.c + $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c + + scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c + + scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + + + + scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + test_gwhsp : test_gwhsp.o genewisehsp.o +- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + localcishit.o : localcishit.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + promoterwise.o : promoterwise.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o +- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o +- $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread ++ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread + + pswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + efpswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) ++ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) + + dba : dbac.o dba.o slimdba.o bigdba.o dbadisplay.o +- $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + lba : lba.o largeblockdp.o seqaligndisplay.o +- $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + fastdba : fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o +- $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + evopairwise : evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o +- $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_threestatehsp : test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o threestatehsp.o +- $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + makerandomdb : makerandomdb.o +- $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o +- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o +- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase ++ $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase + + + efgw : genewise.o $(NEWG) +- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence ++ $(CC) -g -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + edb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o +- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o +- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o +- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o +- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + HMMER_LIBS = ../HMMer2/ +@@ -345,11 +345,11 @@ + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` +-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` +-#LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ ++CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` ++#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++#LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ + +-LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` ++LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -360,7 +360,7 @@ + + + #test : test.o libwisedb.a +-# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LFLAGS) ++# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LDFLAGS) + + + # +--- wise-2.4.1.orig/src/dnaindex/makefile ++++ wise-2.4.1/src/dnaindex/makefile +@@ -27,53 +27,53 @@ + + + kwise : kwise.o $(ASSEMBLY_OBJ) +- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) +- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + + findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) +- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + make_shotgun : make_shotgun.o shotgun.o +- $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS) + + test_dnanumber : test_dnanumber.o dnanumber.o +- $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) + + test_linkindex : test_linkindex.o linkindex.o dnanumber.o +- $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) + + test_forwardindex : test_forwardindex.o forwardindex.o +- $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LDFLAGS) + + test_euler : test_euler.o eulerindex.o singleseqspace.o +- $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + test_kmer : test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_contig.o kmer_assembly_error.o assembly.o +- $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LDFLAGS) + + kmer_stat : kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o +- $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LDFLAGS) + + test_compara : test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o +- $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) + + bigseqwise : bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o +- $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) + + + + + show_euler : show_euler.o eulerindex.o singleseqspace.o +- $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + CC = cc +-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` + + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm + + + .c.o : +--- wise-2.4.1.orig/src/dnaindex/assembly/makefile ++++ wise-2.4.1/src/dnaindex/assembly/makefile +@@ -3,33 +3,33 @@ + .SUFFIXES : .dy + + test_basegraph : test_basegraph.o basegraph.o +- $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LDFLAGS) -ldyna -lwisebase + + test_assemblygraph : test_assemblygraph.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + + test_graphtangle : test_graphtangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o +- $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LDFLAGS) -ldyna -lwisebase + + + pathwise : pathwise.o supertangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o grapherror.o graphmanager.o depthmanager.o +- $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LDFLAGS) -ldyna -lwisebase + + + badkmer : badkmer.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + + + CC = cc +-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` + + +-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm + + + .c.o : +--- wise-2.4.1.orig/src/dynlibsrc/makefile ++++ wise-2.4.1/src/dynlibsrc/makefile +@@ -84,11 +84,11 @@ + CC = cc + INCFLAGS = -I../base/ + #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-CFLAGS = -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0` + #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ +-LFLAGS = -g -L../base/ -lm ++LDFLAGS += -g -L../base/ -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -133,47 +133,47 @@ + # + + test_genomic : genomic.o test_genomic.o sequence.o codon.o +- $(CC) -o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS)-o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm + + test_tree : tree.o test_tree.o +- $(CC) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm + + test_intallocator : intallocator.o test_intallocator.o +- $(CC) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm + + test_psi : test_psi.o proteinstreamedindex.o +- $(CC) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm + + test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a +- $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + + test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a +- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + + test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` + + test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` + + + testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o +- $(CC) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm + + testseqalign : seqalign.o testseqalign.o sequence.o codon.o +- $(CC) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm + + testanc : libdyna.a +- $(CC) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm + + testdb : testdb.o sequencedb.o sequence.o codon.o probability.o +- $(CC) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm + + testpdb : testpdb.o protein.o proteindb.o complexevalset.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o histogram.o +- $(CC) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm + + testpb : testpairbase.o pairbase.o pairbaseseq.o sequence.o seqalign.o codon.o probability.o complexsequence.o complexevalset.o +- $(CC) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- wise-2.4.1.orig/src/network/makefile ++++ wise-2.4.1/src/network/makefile +@@ -3,8 +3,8 @@ + + CC = cc + INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex +-CFLAGS = -O2 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` ++CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -13,7 +13,7 @@ + + + scanwise_server : wise_proteinindex_server.o net_hspscan.o ../dynlibsrc/libdyna.a ../dynlibsrc/libdyna_glib.a ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o +- $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LFLAGS) -lpthread ++ $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LDFLAGS) -lpthread + + + .c.o : +--- wise-2.4.1.orig/src/other_programs/makefile ++++ wise-2.4.1/src/other_programs/makefile +@@ -3,8 +3,8 @@ + .SUFFIXES : .dy + + CC = cc +-CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../dynlibsrc -lm `glib-config --libs` ++CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- wise-2.4.1.orig/src/base/makefile ++++ wise-2.4.1/src/base/makefile +@@ -19,9 +19,9 @@ + + + +-#CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH +-CFLAGS = -c -O2 -DUNIX -pthread +-LFLAGS = -g -lm ++#CFLAGS += -c -g -DUNIX -DWISE_MEMORY_WATCH ++CFLAGS += $(CPPFLAGS) -c -DUNIX -pthread ++LDFLAGS += -g -lm + DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D + AR_OPTIONS = ru + +--- wise-2.4.1.orig/src/HMMer2/Makefile ++++ wise-2.4.1/src/HMMer2/Makefile +@@ -13,7 +13,7 @@ + ## your compiler and compiler flags + # + CC = cc +-CFLAGS = -g ++CFLAGS += $(CPPFLAGS) -g + + ## machine specific definitions + # +@@ -75,25 +75,25 @@ + all: $(PROGS) + + hmmalign: $(OBJ) hmmalign.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) + + hmmbuild: $(OBJ) hmmbuild.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) + + hmmcalibrate: $(OBJ) hmmcalibrate.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) + + hmmconvert: $(OBJ) hmmconvert.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) + + hmmemit: $(OBJ) hmmemit.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) + + hmmpfam: $(OBJ) hmmpfam.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) + + hmmsearch: $(OBJ) hmmsearch.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) + + ####### + ## Target used in making Shiva test suite diff --git a/academic/wise/patches/06_getline.patch b/academic/wise/patches/06_getline.patch new file mode 100644 index 0000000000..341cdae82e --- /dev/null +++ b/academic/wise/patches/06_getline.patch @@ -0,0 +1,305 @@ +Author: Philipp Benner <philipp@debian.org> +Last-Update: Sat, 31 Oct 2009 21:25:52 +0000 +Bug-Debian: http://bugs.debian.org/552821 +Description: Fixed conflicting definitions of getline(). + +--- wise-2.4.1.orig/src/HMMer2/sqio.c ++++ wise-2.4.1/src/HMMer2/sqio.c +@@ -213,7 +213,7 @@ + } + } + +-/* Function: getline() ++/* Function: getline_() + * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] + * + * Purpose: read a line from a sequence file into V->sbuffer. +@@ -229,7 +229,7 @@ + * Returns: (void) + */ + static void +-getline(struct ReadSeqVars *V) ++getline_(struct ReadSeqVars *V) + { + char *cp; + +@@ -299,7 +299,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ getline_(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -327,7 +327,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ getline_(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -336,7 +336,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ getline_(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -345,7 +345,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ getline_(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -359,7 +359,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -377,7 +377,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ getline_(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -389,7 +389,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ getline_(V); + } + + static int +@@ -411,7 +411,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ getline_(V); + } + + if (! feof(V->f)) +@@ -420,7 +420,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ getline_(V); + } + + +@@ -438,7 +438,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ getline_(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -449,7 +449,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ getline_(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -482,11 +482,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ getline_(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ getline_(V); + } + + static int +@@ -515,7 +515,7 @@ + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ getline_(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -535,7 +535,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ getline_(V); + } + + static int +@@ -555,12 +555,12 @@ + if ((sptr = strtok(NULL, "\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); + /* workaround for long NCBI NR lines */ +- while (V->longline && ! feof(V->f)) getline(V); ++ while (V->longline && ! feof(V->f)) getline_(V); + + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ getline_(V); + } + + +@@ -587,7 +587,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ getline_(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -596,7 +596,7 @@ + } + + do { +- getline(V); ++ getline_(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -620,7 +620,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -636,7 +636,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ getline_(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -647,7 +647,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ getline_(V); + } + + static void +@@ -669,7 +669,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ getline_(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -681,7 +681,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -689,7 +689,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ getline_(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -721,14 +721,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ getline_(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ getline_(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -736,7 +736,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -816,7 +816,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ getline_(dbfp); + + return dbfp; + } +@@ -833,7 +833,7 @@ + Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); + + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ getline_(sqfp); + } + + +@@ -853,7 +853,7 @@ + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ getline_(sqfp); + } + } + +@@ -949,7 +949,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ getline_(V); + } while (! feof(V->f)); + break; + diff --git a/academic/wise/patches/07_ld--as-needed.patch b/academic/wise/patches/07_ld--as-needed.patch new file mode 100644 index 0000000000..51ee254370 --- /dev/null +++ b/academic/wise/patches/07_ld--as-needed.patch @@ -0,0 +1,52 @@ +Description: Fix FTBFS with ld --as-needed. +Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935 + +--- wise-2.4.1.orig/src/models/makefile ++++ wise-2.4.1/src/models/makefile +@@ -215,7 +215,7 @@ + $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c + + scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread $(LDFLAGS) + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c +@@ -275,7 +275,7 @@ + $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o + $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) +@@ -300,16 +300,16 @@ + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + edb : estwisedb.o $(NEWG) + $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +@@ -331,7 +331,7 @@ + $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o + $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) diff --git a/academic/wise/patches/08_mayhem.patch b/academic/wise/patches/08_mayhem.patch new file mode 100644 index 0000000000..c54c7c66ab --- /dev/null +++ b/academic/wise/patches/08_mayhem.patch @@ -0,0 +1,103 @@ +Author: Philipp Benner <philipp@debian.org> +Last-Update: Sun, 07 Jul 2013 13:33:01 +0200 +Description: Fix run time errors detected by Mayhem + +--- wise-2.4.1.orig/src/models/dbac.c ++++ wise-2.4.1/src/models/dbac.c +@@ -535,8 +535,12 @@ + * + */ + +- one = read_fasta_file_Sequence(*argv++); +- two = read_fasta_file_Sequence(*argv++); ++ if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) { ++ fatal("Unable to read the sequence in file"); ++ } ++ if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) { ++ fatal("Unable to read the sequence in file"); ++ } + + uppercase_Sequence(one); + uppercase_Sequence(two); +--- wise-2.4.1.orig/src/models/estwise.c ++++ wise-2.4.1/src/models/estwise.c +@@ -313,7 +313,7 @@ + } + } + +- if( reverse == TRUE ) { ++ if( cdna && reverse == TRUE ) { + if( tstart > tend ) { + warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend); + } +@@ -323,7 +323,7 @@ + cdna = cdna_temp; + } + +- if( target_abs == TRUE ) { ++ if( cdna && target_abs == TRUE ) { + cdna->baseseq->offset = 1; + cdna->baseseq->end = strlen(cdna->baseseq->seq); + } +@@ -472,8 +472,11 @@ + } + + cp = flat_cDNAParser(indel_error); +- cm = flat_CodonMapper(ct); +- sprinkle_errors_over_CodonMapper(cm,subs_error); ++ ++ if( ct ) { ++ cm = flat_CodonMapper(ct); ++ sprinkle_errors_over_CodonMapper(cm,subs_error); ++ } + + return ret; + +--- wise-2.4.1.orig/src/models/genewise.c ++++ wise-2.4.1/src/models/genewise.c +@@ -550,8 +550,10 @@ + ret = FALSE; + } + +- gen->baseseq->offset = 1; +- gen->baseseq->end = strlen(gen->baseseq->seq); ++ if ( gen ) { ++ gen->baseseq->offset = 1; ++ gen->baseseq->end = strlen(gen->baseseq->seq); ++ } + } + + if( alg_str != NULL ) { +--- wise-2.4.1.orig/src/models/estwisedb.c ++++ wise-2.4.1/src/models/estwisedb.c +@@ -688,8 +688,11 @@ + + + cps = flat_cDNAParser(indel_error); +- cm = flat_CodonMapper(ct); +- sprinkle_errors_over_CodonMapper(cm,subs_error); ++ ++ if( ct ) { ++ cm = flat_CodonMapper(ct); ++ sprinkle_errors_over_CodonMapper(cm,subs_error); ++ } + + return ret; + +--- wise-2.4.1.orig/src/models/promoterwise.c ++++ wise-2.4.1/src/models/promoterwise.c +@@ -147,8 +147,12 @@ + + lchs = standard_LocalCisHitScore(NMaskType_VARIABLE); + +- query = read_fasta_file_Sequence(argv[1]); +- target = read_fasta_file_Sequence(argv[2]); ++ if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) { ++ fatal("Unable to read the sequence in query file"); ++ } ++ if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) { ++ fatal("Unable to read the sequence in target file"); ++ } + + for(i=0;i<query->len;i++) { + query->seq[i] = toupper(query->seq[i]); diff --git a/academic/wise/patches/09_dnal-add-return-statement.patch b/academic/wise/patches/09_dnal-add-return-statement.patch new file mode 100644 index 0000000000..62931ed624 --- /dev/null +++ b/academic/wise/patches/09_dnal-add-return-statement.patch @@ -0,0 +1,17 @@ +Author: Dejan Latinovic <Dejan.Latinovic@imgtec.com> +Last-Update: Mon, 4 Aug 2014 17:10:38 +0000 +Bug-Debian: http://bugs.debian.org/751277 +Description: Make sure dnal has a valid return value + This affects a bug reported against python-biopython. + +--- wise-2.4.1.orig/src/models/dnal.c ++++ wise-2.4.1/src/models/dnal.c +@@ -75,6 +75,8 @@ + + if( show_alb == TRUE ) + dump_ascii_AlnBlock(alb,stdout); ++ ++ return 0; + } + + diff --git a/academic/wise/patches/10_fix_path_to_data_files.patch b/academic/wise/patches/10_fix_path_to_data_files.patch new file mode 100644 index 0000000000..f437241cd1 --- /dev/null +++ b/academic/wise/patches/10_fix_path_to_data_files.patch @@ -0,0 +1,337 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Mon, 04 Aug 2014 19:25:58 +0200 +Description: Brute force patch to fix the PATH to the data files to make the + tools finding the needed data for the test suite + . + In principle the PATH should be configurable and the test suite script even + contains a parameter (-cf) for this - but this seems to be ignored. + . + The correct way to deal with this would be a configuration option but I had + no intend to spend to much time into some software that was declared to be + orphaned (superseded by exonerate). So this primitive patch works to run + the test suite successfully (which is not the case without the patch). + +--- a/src/models/estwise.c ++++ b/src/models/estwise.c +@@ -484,8 +484,8 @@ boolean build_objects(void) + + void build_defaults(void) + { +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + +--- a/src/models/estwisedb.c ++++ b/src/models/estwisedb.c +@@ -78,7 +78,7 @@ char * qend_str = NULL; + int qend = -1; + + +-char * matrix_file = "BLOSUM62.bla"; ++char * matrix_file = "/usr/share/wise/BLOSUM62.bla"; + CompMat * mat = NULL; + + char * gap_str = "12"; +@@ -849,8 +849,8 @@ void show_version(FILE * ofp) + + void build_defaults(void) + { +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + } +--- a/src/models/pswdb.c ++++ b/src/models/pswdb.c +@@ -40,7 +40,7 @@ int max_desc = 500; + + char * querydb = NULL; + char * targetdb = NULL; +-char * matrix_file = "BLOSUM62.bla"; ++char * matrix_file = "/usr/share/wise/BLOSUM62.bla"; + char * output_file = "-"; + + char * cutoff_str = NULL; +@@ -65,7 +65,7 @@ void show_help(FILE * ofp) + fprintf(ofp,"\npswdb <options> <query_db> <target_db>\nSeqs in fasta format\n" + "\t-g gap penalty (default 12)\n" + "\t-e ext penatly (default 2)\n" +- "\t-m comp matrix (default BLOSUM62.bla)\n" ++ "\t-m comp matrix (default /usr/share/wise/BLOSUM62.bla)\n" + "\t-abc use the abc model\n" + "\t-a a penalty for above (default 120)\n" + "\t-b b penalty for above (default 10)\n" +@@ -397,7 +397,7 @@ int main(int argc,char *argv[]) + + matrix_file = strip_out_assigned_argument(&argc,argv,"m"); + if( matrix_file == NULL) +- matrix_file = "BLOSUM62.bla"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + /* database implementation stuff */ + dbsi = new_DBSearchImpl_from_argv(&argc,argv); +--- a/src/models/genewisedb.c ++++ b/src/models/genewisedb.c +@@ -77,7 +77,7 @@ int qend = -1; + char * gene_file = NULL; + GeneFrequency21 * gf = NULL; + +-char * matrix_file = "BLOSUM62.bla"; ++char * matrix_file = "/usr/share/wise/BLOSUM62.bla"; + CompMat * mat = NULL; + + char * gap_str = "12"; +@@ -1015,9 +1015,9 @@ void show_version(FILE * ofp) + + void build_defaults(void) + { +- gene_file = "human.gf"; +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ gene_file = "/usr/share/wise/human.gf"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + } +--- a/src/models/genewise.c ++++ b/src/models/genewise.c +@@ -749,10 +749,10 @@ boolean build_objects(void) + + void build_defaults(void) + { +- gene_file = "human.gf"; +- new_gene_file = "gene.stat"; +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ gene_file = "/usr/share/wise/human.gf"; ++ new_gene_file = "/usr/share/wise/gene.stat"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + } +--- a/src/models/scanwisep.c ++++ b/src/models/scanwisep.c +@@ -157,7 +157,7 @@ ScanWiseHSPImpl * new_ScanWiseHSPImpl_fr + out->use_multiscan = FALSE; + out->ior_file = NULL; + out->direct_sequence = NULL; +- out->matrix_file = "BLOSUM62.bla"; ++ out->matrix_file = "/usr/share/wise/BLOSUM62.bla"; + out->step = 32; + out->host = "localhost"; + out->port = 4050; +@@ -546,7 +546,7 @@ int main(int argc,char ** argv) + + /* ugly, but we don't want to bounce matrices around the network... */ + +- mat = read_Blast_file_CompMat("BLOSUM62.bla"); ++ mat = read_Blast_file_CompMat("/usr/share/wise/BLOSUM62.bla"); + + erroroff(REPORT); + +--- a/src/models/psw.c ++++ b/src/models/psw.c +@@ -24,7 +24,7 @@ void show_help(FILE * ofp) + "\tOPTIONS\n" + "\t-g gap penalty (default 12)\n" + "\t-e ext penatly (default 2)\n" +- "\t-m comp matrix (default BLOSUM62.bla)\n" ++ "\t-m comp matrix (default /usr/share/wise/BLOSUM62.bla)\n" + "\t-abc use the abc model\n" + "\t-a a penalty for above (default 120)\n" + "\t-b b penalty for above (default 10)\n" +@@ -126,7 +126,7 @@ int main(int argc,char ** argv) + + comp_file = strip_out_assigned_argument(&argc,argv,"m"); + if( comp_file == NULL) +- comp_file = "BLOSUM62.bla"; ++ comp_file = "/usr/share/wise/BLOSUM62.bla"; + + if( (temp = strip_out_assigned_argument(&argc,argv,"dpenv")) != NULL ) { + dpenv = read_DPEnvelope_file(temp); +--- a/src/test/basic_cdna.out ++++ b/src/test/basic_cdna.out +@@ -3,13 +3,13 @@ This program is freely distributed under + Copyright (c) GRL limited: portions of the code are from separate copyrights + + Query protein: roa1_drome +-Comp Matrix: BLOSUM62.bla ++Comp Matrix: /usr/share/wise/BLOSUM62.bla + Gap open: 12 + Gap extension: 2 + Start/End default + Target Sequence HSHNCPA1 + Strand: both +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Algorithm 333 +--- a/src/test/basic_genomic.out ++++ b/src/test/basic_genomic.out +@@ -3,17 +3,17 @@ This program is freely distributed under + Copyright (c) GRL limited: portions of the code are from separate copyright + + Query protein: roa1_drome +-Comp Matrix: BLOSUM62.bla ++Comp Matrix: /usr/share/wise/BLOSUM62.bla + Gap open: 12 + Gap extension: 2 + Start/End default + Target Sequence HSHNCPA1 + Strand: forward + Start/End (protein) default +-Gene Parameter file: gene.stat ++Gene Parameter file: /usr/share/wise/gene.stat + Splice site model: GT/AG only + GT/AG bits penalty -9.96 +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-06 + Indel error: 1e-06 + Null model syn +--- a/src/test/pswdb.out ++++ b/src/test/pswdb.out +@@ -12,7 +12,7 @@ Gap open: 12 + Gap extension: 2 + Query info from: road.pep + Database info from: pep.fa +-Comp Matrix: BLOSUM62.bla ++Comp Matrix: /usr/share/wise/BLOSUM62.bla + [Warning: Can't fit histogram to a db smaller than 1,000] + + +--- a/src/models/genestats.c ++++ b/src/models/genestats.c +@@ -22,7 +22,7 @@ void show_help_GeneModelParam(FILE * ofp + fprintf(ofp," -splice_score_offset [%.1f] score offset for splice sites\n",DEFAULT_SPLICE_OFFSET_SCORE); + fprintf(ofp," -[no]splice_gtag make just gtag splice sites (default is gtag, ie no model)\n"); + fprintf(ofp," -splice_gtag_prob [0.001] probability for gt/ag \n"); +- fprintf(ofp," -genestats [gene.stat]\n"); ++ fprintf(ofp," -genestats [/usr/share/wise/gene.stat]\n"); + + } + +@@ -270,7 +270,7 @@ GeneModelParam * std_GeneModelParam(void + out->min_collar = -5.0; + out->max_collar = +5.0; + out->score_offset = DEFAULT_SPLICE_OFFSET_SCORE; +- out->gene_stats_file = stringalloc("gene.stat"); ++ out->gene_stats_file = stringalloc("/usr/share/wise/gene.stat"); + out->use_gtag_splice = TRUE; + + out->prob_for_gtag = 0.001; +--- a/src/models/genestats.dy ++++ b/src/models/genestats.dy +@@ -103,7 +103,7 @@ void show_help_GeneModelParam(FILE * ofp + fprintf(ofp," -splice_score_offset [%.1f] score offset for splice sites\n",DEFAULT_SPLICE_OFFSET_SCORE); + fprintf(ofp," -[no]splice_gtag make just gtag splice sites (default is gtag, ie no model)\n"); + fprintf(ofp," -splice_gtag_prob [0.001] probability for gt/ag \n"); +- fprintf(ofp," -genestats [gene.stat]\n"); ++ fprintf(ofp," -genestats [/usr/share/wise/gene.stat]\n"); + + } + +@@ -290,7 +290,7 @@ GeneModelParam * std_GeneModelParam(void + out->min_collar = -5.0; + out->max_collar = +5.0; + out->score_offset = DEFAULT_SPLICE_OFFSET_SCORE; +- out->gene_stats_file = stringalloc("gene.stat"); ++ out->gene_stats_file = stringalloc("/usr/share/wise/gene.stat"); + out->use_gtag_splice = TRUE; + + out->prob_for_gtag = 0.001; +--- a/src/models/testgenestat.c ++++ b/src/models/testgenestat.c +@@ -23,7 +23,7 @@ int main(int argc,char ** argv) + + seq = read_fasta_file_Sequence("../../test_data/human.genomic"); + +- ifp = openfile("gene.stat","r"); ++ ifp = openfile("/usr/share/wise/gene.stat","r"); + + st = read_GeneStats(ifp); + +--- a/src/test/hmm_genomic.out ++++ b/src/test/hmm_genomic.out +@@ -7,10 +7,10 @@ Start/End local + Target Sequence HSHNCPA1 + Strand: forward + Start/End (protein) local +-Gene Parameter file: gene.stat ++Gene Parameter file: /usr/share/wise/gene.stat + Splice site model: GT/AG only + GT/AG bits penalty -9.96 +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-06 + Indel error: 1e-06 + Null model syn +--- a/src/test/hmm_cdna.out ++++ b/src/test/hmm_cdna.out +@@ -6,7 +6,7 @@ Query model: unnamed + Start/End default + Target Sequence HSHNCPA1 + Strand: both +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Algorithm 333L +--- a/src/test/genewise-db.out ++++ b/src/test/genewise-db.out +@@ -12,8 +12,8 @@ Search mode: Single protein vs + Protein info from: rrm.HMM + Dna info from: dna.db + Start/End (protein) global +-Gene Paras: human.gf +-Codon Table: codon.table ++Gene Paras: /usr/share/wise/human.gf ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Model splice? model +--- a/src/test/genewise-db-lite.out ++++ b/src/test/genewise-db-lite.out +@@ -12,8 +12,8 @@ Search mode: Single protein vs + Protein info from: rrm.HMM + Dna info from: dna.db + Start/End (protein) global +-Gene Paras: human.gf +-Codon Table: codon.table ++Gene Paras: /usr/share/wise/human.gf ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Model splice? model +--- a/src/test/estwise-db.out ++++ b/src/test/estwise-db.out +@@ -13,7 +13,7 @@ Search mode: Single protein vs + Protein info from: rrm.HMM + Dna info from: dna.db + Start/End local +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 0.01 + Indel error: 0.01 + Null model: synchronous +--- a/src/test/genewisedb-pfam.out ++++ b/src/test/genewisedb-pfam.out +@@ -12,8 +12,8 @@ Search mode: Single genomic vs + Protein info from: rrm.HMM + Dna info from: short.dna + Start/End (protein) default +-Gene Paras: human.gf +-Codon Table: codon.table ++Gene Paras: /usr/share/wise/human.gf ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Model splice? model diff --git a/academic/wise/patches/11_consistent_manual_dates.patch b/academic/wise/patches/11_consistent_manual_dates.patch new file mode 100644 index 0000000000..eaea1eec90 --- /dev/null +++ b/academic/wise/patches/11_consistent_manual_dates.patch @@ -0,0 +1,53 @@ +Description: Use fixed dates for manuals. + These make the build reproducible. I have picked the file modificatin dates of + the corresponding source .tex files. +Author: Sascha Steinbiss <sascha@steinbiss.name> +--- a/docs/dynamite.tex ++++ b/docs/dynamite.tex +@@ -1,4 +1,5 @@ + \documentstyle{article} ++\pdftrailerid{} + \begin{document} + + \newcommand{\programtext}[1]{{\tt #1}} +@@ -10,6 +11,7 @@ + Hinxton, Cambridge CB10 1SA,\\ + England.\\ + Email: birney@sanger.ac.uk} ++\date{18/6/2001} + + \maketitle + +--- a/docs/wise2.tex ++++ b/docs/wise2.tex +@@ -1,5 +1,6 @@ + + \documentclass{article} ++\pdftrailerid{} + %\usepackage{epsfig} + \usepackage{graphicx} + +@@ -13,6 +14,7 @@ + Hinxton, Cambridge CB10 1SD,\\ + England.\\ + Email: birney@ebi.ac.uk} ++\date{18/6/2001} + + \maketitle + +--- a/docs/wise2api.tex ++++ b/docs/wise2api.tex +@@ -1,4 +1,5 @@ + \documentstyle{article} ++\pdftrailerid{} + \begin{document} + + \newcommand{\programtext}[1]{{\tt #1}} +@@ -10,6 +11,7 @@ + Hinxton, Cambridge CB10 1SA,\\ + England.\\ + Email: birney@sanger.ac.uk} ++\date{18/6/2001} + + \maketitle + diff --git a/academic/wise/patches/cross.patch b/academic/wise/patches/cross.patch new file mode 100644 index 0000000000..f6da1363d0 --- /dev/null +++ b/academic/wise/patches/cross.patch @@ -0,0 +1,266 @@ +Date: Sat, 18 Apr 2020 11:59:09 +0200 +From: Helmut Grohne <helmut@subdivi.de> +Bug-Debian: https://bugs.debian.org/958094 +Description: Do not hard code the build architecture pkg-config + +--- a/src/corba/makefile ++++ b/src/corba/makefile +@@ -1,9 +1,10 @@ + + + CC = cc ++PKG_CONFIG ?= pkg-config + INCFLAGS = -I../base/ -I../dynlibsrc + #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ ++#CFLAGS += -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ + CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` + LDFLAGS += -L../base/ -lm -lpthread + AR_OPTIONS = ru +@@ -14,18 +15,18 @@ hspscan_corba.c : hspscan_corba.idl + orbit-idl hspscan_corba.idl + + test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o +- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o +- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- a/src/dnaindex/assembly/makefile ++++ b/src/dnaindex/assembly/makefile +@@ -26,10 +26,11 @@ arraymatcher : arraymatcher.o assemblygr + + + CC = cc +-CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` ++PKG_CONFIG ?= pkg-config ++CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `$(PKG_CONFIG) --cflags glib-2.0` + + +-LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm ++LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm + + + .c.o : +--- a/src/dnaindex/makefile ++++ b/src/dnaindex/makefile +@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ) + + + kwise : kwise.o $(ASSEMBLY_OBJ) +- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0` + + arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) +- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0` + + + findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) +- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0` + + make_shotgun : make_shotgun.o shotgun.o + $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS) +@@ -70,10 +70,11 @@ show_euler : show_euler.o eulerindex.o s + $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + CC = cc +-CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++PKG_CONFIG ?= pkg-config ++CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0` + + +-LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm + + + .c.o : +--- a/src/dynlibsrc/makefile ++++ b/src/dynlibsrc/makefile +@@ -82,11 +82,12 @@ DYNHELPEROBJ = packaln.o \ + + + CC = cc ++PKG_CONFIG ?= pkg-config + INCFLAGS = -I../base/ + #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` +-#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` +-#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` ++#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` ++#CFLAGS += -c -pthread -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` + #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ + LDFLAGS += -g -L../base/ -lm + AR_OPTIONS = ru +@@ -148,13 +149,13 @@ test_shadowindex : test_shadowindex.o sh + $(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + + test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a +- $(CC) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_seqhash `$(PKG_CONFIG) --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + + test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` ++ $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `$(PKG_CONFIG) --libs glib-2.0` + + test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` ++ $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `$(PKG_CONFIG) --libs glib-2.0` + + + testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o +--- a/src/makefile ++++ b/src/makefile +@@ -23,6 +23,7 @@ + # Most likely you have a non ANSI C compiler + # CC = /opt/intel_cc_80/bin/icc + CC = cc ++PKG_CONFIG ?= pkg-config + + # These are the CFLAGS to use. These days Wise2 is inherently + # pthreaded, and everything is compiled with threads. However +@@ -31,13 +32,13 @@ CC = cc + + + # Intel icc flags +-# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0` ++# CFLAGS += -c -axWK -ipo `$(PKG_CONFIG) --cflags glib-2.0` + + # alpha flags (-pthread) +-# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0` ++# CFLAGS += -c -pthread `$(PKG_CONFIG) --cflags glib-2.0` + + # normal linux/bsd/mac flags +-CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -c `$(PKG_CONFIG) --cflags glib-2.0` + + + EXTRALIBS = -lm +--- a/src/models/makefile ++++ b/src/models/makefile +@@ -192,10 +192,10 @@ psw : psw.o seqaligndisplay.o proteinsw. + $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + scanwisep.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `$(PKG_CONFIG) --cflags glib-2.0` $? + + hsp2aln_sw.o : hsp2aln_sw.c +- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $? + + scanwisep_mysql.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c +@@ -226,25 +226,25 @@ scanwisep_compress : scanwisep_compress. + + + scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + test_gwhsp : test_gwhsp.o genewisehsp.o +- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + localcishit.o : localcishit.c +- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $? + + promoterwise.o : promoterwise.c +- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $? + + promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o +- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o + $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread +@@ -343,13 +343,14 @@ HMMER_DEFINE = + + + CC = cc ++PKG_CONFIG ?= pkg-config + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` +-#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0` ++#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0` + #LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ + +-LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0` ++LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `$(PKG_CONFIG) --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- a/src/network/makefile ++++ b/src/network/makefile +@@ -2,9 +2,10 @@ + .SUFFIXES : .dy + + CC = cc ++PKG_CONFIG ?= pkg-config + INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex +-CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` +-LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` ++CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `$(PKG_CONFIG) --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `$(PKG_CONFIG) --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- a/src/other_programs/makefile ++++ b/src/other_programs/makefile +@@ -3,8 +3,9 @@ + .SUFFIXES : .dy + + CC = cc +-CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` +-LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` ++PKG_CONFIG ?= pkg-config ++CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `$(PKG_CONFIG) --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `$(PKG_CONFIG) --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- a/src/snp/makefile ++++ b/src/snp/makefile +@@ -3,11 +3,12 @@ + + + CC = cc ++PKG_CONFIG ?= pkg-config + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0` + +-LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lpthread -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 diff --git a/academic/wise/patches/spelling.patch b/academic/wise/patches/spelling.patch new file mode 100644 index 0000000000..cb46f070ce --- /dev/null +++ b/academic/wise/patches/spelling.patch @@ -0,0 +1,702 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Fri, 22 Sep 2017 09:18:47 +0200 +Description: Fix spelling issues + +--- a/src/dynlibsrc/hscore.c ++++ b/src/dynlibsrc/hscore.c +@@ -413,7 +413,7 @@ DataScore * new_DataScore_from_storage(H + if( hs->st_len == 0 ) { + new = new_DataScoreStorage(); + if( new == NULL ) { +- warn("could not make inital data score storage!"); ++ warn("could not make initial data score storage!"); + return NULL; + } + add_st_Hscore(hs,new); +--- a/src/dynlibsrc/hscore.dy ++++ b/src/dynlibsrc/hscore.dy +@@ -422,7 +422,7 @@ DataScore * new_DataScore_from_storage(H + if( hs->st_len == 0 ) { + new = new_DataScoreStorage(); + if( new == NULL ) { +- warn("could not make inital data score storage!"); ++ warn("could not make initial data score storage!"); + return NULL; + } + add_st_Hscore(hs,new); +--- a/docs/dynamite.tex ++++ b/docs/dynamite.tex +@@ -2839,7 +2839,7 @@ needs at least one offset to be non zero + Once all the semantics of the Dynamite blueprint is ok, the compiler then turns its + attention to the calc lines. This is like a mini-parser operating inside the dynamite + parser, but unlike the dynamite parser, this once was written in yacc/lex and is +-a more vanilla parser enviroment. ++a more vanilla parser environment. + + \subsubsection{Parser Syntax error on calc line} + +--- a/docs/wise2.tex ++++ b/docs/wise2.tex +@@ -121,7 +121,7 @@ Warning Error + Could not read a GeneFrequency file in human.gf + ... + \end{verbatim} +-This means that the enviroment variable WISECONFIGDIR has not been ++This means that the environment variable WISECONFIGDIR has not been + set up correctly. You need to find where the distribution was downloaded + to (a directory called something like wise2.1.16b) and inside that + directory should be the configuration directory wisecfg. You need to +@@ -427,7 +427,7 @@ sequence flag) as well. An example run w + \begin{verbatim} + genewisedb -pfam Pfam -dnas myseq.fa + \end{verbatim} +-If you have set up the HMMER package to work with Pfam using the enviroment ++If you have set up the HMMER package to work with Pfam using the environment + variable HMMERDB, Wise2 will also pick that up as well. + + +@@ -675,7 +675,7 @@ mathematically it is almost that easy: t + of the probability. + + Perhaps a better known example is the relationship between the old +-profile technology, as developped by Gribskov and Gibson along with ++profile technology, as developed by Gribskov and Gibson along with + others, and its probabilistic partner, profile Hidden Markov Models + (profile HMMs). In terms of the actual algorithm these two methods + are very similar: it is simply that the profile HMM has a strong +@@ -1639,7 +1639,7 @@ Of course there are many options to chan + \subsection{dba - Dna Block Aligner} + \label{sec:dba} + +-dba - standing for Dna Block Aligner, was developped by Niclas Jareborg, ++dba - standing for Dna Block Aligner, was developed by Niclas Jareborg, + Richard Durbin and Ewan Birney for characterising shared regulatory regions + of genomic DNA, either in upstream regions or introns of genes + +--- a/src/base/wisefile.c ++++ b/src/base/wisefile.c +@@ -329,7 +329,7 @@ FILE * openfile(const char * filename,co + * + * + * +- * Arg: envname [READ ] enviroment variable to read from [NullString] ++ * Arg: envname [READ ] environment variable to read from [NullString] + * Arg: filename [UNKN ] Undocumented argument [char *] + * Arg: name [READ ] filename to open [NullString] + * Arg: env [UNKN ] Undocumented argument [char *] +@@ -344,17 +344,17 @@ FILE * envopenfile(char * filename,char + char path [512]; + + if( filename == NULL || env == NULL ) { +- warn("Passed a NULL filename or enviroment name into Envfile. Should trap this elsewhere"); ++ warn("Passed a NULL filename or environment name into Envfile. Should trap this elsewhere"); + return NULL; + } + + if( (envp = getenv(env)) == NULL ) { +- /* fail gracefully - somebody might query a number of enviroment variables */ ++ /* fail gracefully - somebody might query a number of environment variables */ + return NULL; + } + + if( strlen(filename) + strlen(envp) < 490 ) { +- warn("Really long filename/enviroment variables [%s] [%s] Can't cope!",filename,envp); ++ warn("Really long filename/environment variables [%s] [%s] Can't cope!",filename,envp); + return NULL; + } + sprintf(path,"%s/%s",filename,envp); +--- a/src/base/wisefile.dy ++++ b/src/base/wisefile.dy +@@ -302,7 +302,7 @@ in HMMer2. You call it as + + %arg + name r filename to open +-envname r enviroment variable to read from ++envname r environment variable to read from + return a valid file pointer or NULL + %% + FILE * envopenfile(char * filename,char * env) +@@ -311,17 +311,17 @@ FILE * envopenfile(char * filename,char + char path [512]; + + if( filename == NULL || env == NULL ) { +- warn("Passed a NULL filename or enviroment name into Envfile. Should trap this elsewhere"); ++ warn("Passed a NULL filename or environment name into Envfile. Should trap this elsewhere"); + return NULL; + } + + if( (envp = getenv(env)) == NULL ) { +- /* fail gracefully - somebody might query a number of enviroment variables */ ++ /* fail gracefully - somebody might query a number of environment variables */ + return NULL; + } + + if( strlen(filename) + strlen(envp) < 490 ) { +- warn("Really long filename/enviroment variables [%s] [%s] Can't cope!",filename,envp); ++ warn("Really long filename/environment variables [%s] [%s] Can't cope!",filename,envp); + return NULL; + } + sprintf(path,"%s/%s",filename,envp); +--- a/src/base/wisefile.h ++++ b/src/base/wisefile.h +@@ -143,7 +143,7 @@ FILE * Wise2_openfile(const char * filen + * + * + * +- * Arg: envname [READ ] enviroment variable to read from [NullString] ++ * Arg: envname [READ ] environment variable to read from [NullString] + * Arg: filename [UNKN ] Undocumented argument [char *] + * Arg: name [READ ] filename to open [NullString] + * Arg: env [UNKN ] Undocumented argument [char *] +--- a/LICENSE ++++ b/LICENSE +@@ -19,7 +19,7 @@ an acknowledgement of the authorship nee + + The HMMer2 libaries (Sean Eddy's HMM package) and the models directory + (The algorithms for the Wise2 package, and final executable programs) +-are both distributed under a Gnu General Public License (GPL). This ++are both distributed under a GNU General Public License (GPL). This + means that the entire package as it is distributed with these portions + in is also licensed under GPL, due to the 'infectious' nature of the + GPL. +--- a/docs/wise3arch.tex ++++ b/docs/wise3arch.tex +@@ -49,7 +49,7 @@ clear up a considerable amount of confus + + \subsection{Committment to open source, freely available code} + +-The Wise2 package has been licensed under the Gnu Public License since ++The Wise2 package has been licensed under the GNU General Public License since + its inception. In addition, parts of the package has even less + restrictive Licenses. I have a strong committment to keep Wise a + freely available, open source package. The aim of the open +--- a/src/corba/scanwise_protein_index.c ++++ b/src/corba/scanwise_protein_index.c +@@ -19,7 +19,7 @@ char * program_name = "scanwise_protein_ + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/assembly/badkmer.c ++++ b/src/dnaindex/assembly/badkmer.c +@@ -25,7 +25,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EBI 2003\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/assembly/pathwise.c ++++ b/src/dnaindex/assembly/pathwise.c +@@ -40,7 +40,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EBI 2003\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/bigseqwise.c ++++ b/src/dnaindex/bigseqwise.c +@@ -10,7 +10,7 @@ char * program_name = "bigseqwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/findbad_kmer.c ++++ b/src/dnaindex/findbad_kmer.c +@@ -13,7 +13,7 @@ char * program_name = "findbad_kmer"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/kwise.c ++++ b/src/dnaindex/kwise.c +@@ -15,7 +15,7 @@ char * program_name = "kwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/alignwise.c ++++ b/src/models/alignwise.c +@@ -61,7 +61,7 @@ void show_Gene_debug(AlnBlock * alb,Sequ + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/amplimer_resolver.c ++++ b/src/models/amplimer_resolver.c +@@ -10,7 +10,7 @@ char * program_name = "amplimer_resolver + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/cdnawise.c ++++ b/src/models/cdnawise.c +@@ -15,7 +15,7 @@ void show_version(FILE * ofp) + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); + + +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL (2001) and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/clonewise.c ++++ b/src/models/clonewise.c +@@ -25,7 +25,7 @@ int mismatch_score = -1; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/dbac.c ++++ b/src/models/dbac.c +@@ -363,7 +363,7 @@ void show_version(FILE * ofp) + fprintf(ofp," Released %s\n",RELEASE_DAY); + fprintf(ofp," Compiled %s\n",COMPILE_DATE); + fprintf(ofp,"dba was written by Niclas Jareborg, Ewan Birney and Richard Durbin\n"); +- fprintf(ofp,"Copyright (c) 1998,1999,2000,2001 GRL ltd. It is distributed under a Gnu Public License\n"); ++ fprintf(ofp,"Copyright (c) 1998,1999,2000,2001 GRL ltd. It is distributed under a GNU General Public License\n"); + fprintf(ofp,"See GNULICENSE in source directory for more information\n"); + } + +--- a/src/models/dnal.c ++++ b/src/models/dnal.c +@@ -104,7 +104,7 @@ void show_short_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/dnawise.c ++++ b/src/models/dnawise.c +@@ -8,7 +8,7 @@ char * program_name = "dnawise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/editdist.c ++++ b/src/models/editdist.c +@@ -8,7 +8,7 @@ char * program_name = "editdist"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/estwise.c ++++ b/src/models/estwise.c +@@ -557,7 +557,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/estwisedb.c ++++ b/src/models/estwisedb.c +@@ -807,7 +807,7 @@ boolean show_header(FILE * ofp) + fprintf(ofp,"-------------------------------------------------------------\n"); + fprintf(ofp,"Wise2 - database searching mode\n"); + fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY); +- fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n"); ++ fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n"); + fprintf(ofp," See -version for more info on copyright\n"); + fprintf(ofp,"Bugs and credits to Ewan Birney <birney@sanger.ac.uk>\n"); + fprintf(ofp,"-------------------------------------------------------------\n\n"); +@@ -836,7 +836,7 @@ boolean show_header(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/evopairwise.c ++++ b/src/models/evopairwise.c +@@ -15,7 +15,7 @@ char * program_name = "evopairwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/fivestar.c ++++ b/src/models/fivestar.c +@@ -14,7 +14,7 @@ char * program_name = "fivestar"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/fivestarscan.c ++++ b/src/models/fivestarscan.c +@@ -14,7 +14,7 @@ char * program_name = "fivestarscan"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/fivestarsearch.c ++++ b/src/models/fivestarsearch.c +@@ -12,7 +12,7 @@ char * program_name = "fivestarsearch"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/genewise.c ++++ b/src/models/genewise.c +@@ -858,7 +858,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/genewisedb.c ++++ b/src/models/genewisedb.c +@@ -505,7 +505,7 @@ boolean show_header(FILE * ofp) + { + fprintf(ofp,"Wise2 - database searching mode\n"); + fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY); +- fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n"); ++ fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n"); + fprintf(ofp," See -version for more info on copyright\n"); + fprintf(ofp,"Bugs and credits to Ewan Birney <birney@sanger.ac.uk>\n"); + fprintf(ofp,"-----------------------------------------------------\n\n"); +@@ -1003,7 +1003,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/genomewise.c ++++ b/src/models/genomewise.c +@@ -16,7 +16,7 @@ void show_utr_exon_genomewise(AlnBlock * + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/lba.c ++++ b/src/models/lba.c +@@ -8,7 +8,7 @@ char * program_name = "lba"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/motifcluster.c ++++ b/src/models/motifcluster.c +@@ -8,7 +8,7 @@ char * program_name = "motifcluster"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/motifdiff.c ++++ b/src/models/motifdiff.c +@@ -8,7 +8,7 @@ char * program_name = "motifdiff"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/motifwise.c ++++ b/src/models/motifwise.c +@@ -8,7 +8,7 @@ char * program_name = "motifwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/oldpostwise.c ++++ b/src/models/oldpostwise.c +@@ -375,7 +375,7 @@ void show_help(char * help_arg) + void show_version(void) + { + fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(stdout,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(stdout,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(stdout,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/promotercluster.c ++++ b/src/models/promotercluster.c +@@ -7,7 +7,7 @@ char * program_name = "promotercluster"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/promoterwise.c ++++ b/src/models/promoterwise.c +@@ -15,7 +15,7 @@ char * program_name = "promoterwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/pseudowise.c ++++ b/src/models/pseudowise.c +@@ -13,7 +13,7 @@ char * program_name = "pseudowise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/psw.c ++++ b/src/models/psw.c +@@ -259,7 +259,7 @@ int main(int argc,char ** argv) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/pswdb.c ++++ b/src/models/pswdb.c +@@ -95,7 +95,7 @@ void show_help(FILE * ofp) + void show_version(void) + { + fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(stdout,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(stdout,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(stdout,"The source code is copyright (c) EMBL 1998 and others\n"); + fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n"); +@@ -347,7 +347,7 @@ boolean show_header(FILE * ofp) + fprintf(ofp,"-------------------------------------------------------------\n"); + fprintf(ofp,"Wise2 - Protein vs. Protein\n"); + fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY); +- fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n"); ++ fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n"); + fprintf(ofp," See -version for more info on copyright\n"); + fprintf(ofp,"Bugs and credits to: Richard Copley <copley@embl-heidelberg.de>\n"); + fprintf(ofp," Ewan Birney <birney@sanger.ac.uk>\n"); +--- a/src/models/scanwisep.c ++++ b/src/models/scanwisep.c +@@ -421,7 +421,7 @@ HitList * HitList_from_HSP_HSP2HitListIm + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/statwise.c ++++ b/src/models/statwise.c +@@ -11,7 +11,7 @@ char * codon_table = "codon.table"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/sywise.c ++++ b/src/models/sywise.c +@@ -12,7 +12,7 @@ char * codon_table = "codon.table"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/network/wise_proteinindex_server.c ++++ b/src/network/wise_proteinindex_server.c +@@ -26,7 +26,7 @@ char * program_name = "scanwise_server"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/test/estwise-db.out ++++ b/src/test/estwise-db.out +@@ -1,7 +1,7 @@ + ------------------------------------------------------------- + Wise2 - database searching mode + Program: estwisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ------------------------------------------------------------- +--- a/src/test/genewise-db-lite.out ++++ b/src/test/genewise-db-lite.out +@@ -1,6 +1,6 @@ + Wise2 - database searching mode + Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ----------------------------------------------------- +--- a/src/test/genewise-db.out ++++ b/src/test/genewise-db.out +@@ -1,6 +1,6 @@ + Wise2 - database searching mode + Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ----------------------------------------------------- +--- a/src/test/genewisedb-pfam.out ++++ b/src/test/genewisedb-pfam.out +@@ -1,6 +1,6 @@ + Wise2 - database searching mode + Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ----------------------------------------------------- +--- a/src/test/pswdb.out ++++ b/src/test/pswdb.out +@@ -1,7 +1,7 @@ + ------------------------------------------------------------- + Wise2 - Protein vs. Protein + Program: pswdb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to: Richard Copley <copley@embl-heidelberg.de> + Ewan Birney <birney@sanger.ac.uk> +--- a/src/models/genefrequency.c ++++ b/src/models/genefrequency.c +@@ -636,7 +636,7 @@ double double_from_line(char * buffer) + ret = strtod(runner,&end); + + if( end == runner || isalnum((int)*end) ) { +- warn("Bad conversion of string [%s] to double [%f] occured",runner,ret); ++ warn("Bad conversion of string [%s] to double [%f] occurred",runner,ret); + } + + return ret; +--- a/src/models/genefrequency.dy ++++ b/src/models/genefrequency.dy +@@ -597,7 +597,7 @@ double double_from_line(char * buffer) + ret = strtod(runner,&end); + + if( end == runner || isalnum((int)*end) ) { +- warn("Bad conversion of string [%s] to double [%f] occured",runner,ret); ++ warn("Bad conversion of string [%s] to double [%f] occurred",runner,ret); + } + + return ret; +--- a/src/models/seqerror.dy ++++ b/src/models/seqerror.dy +@@ -42,7 +42,7 @@ Sequence * seq + SequenceErrorSet * ses + %info + This holds a sequence and what +-errors have occured in it. ++errors have occurred in it. + %% + + +--- a/src/models/seqerror.h ++++ b/src/models/seqerror.h +@@ -72,7 +72,7 @@ typedef struct Wise2_SequenceErrorSet Wi + /* Object ErrorSequence + * + * Descrip: This holds a sequence and what +- * errors have occured in it. ++ * errors have occurred in it. + * + * + */ diff --git a/academic/wise/slack-desc b/academic/wise/slack-desc new file mode 100644 index 0000000000..c99b9025f0 --- /dev/null +++ b/academic/wise/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +wise: wise (Compare protein to DNA sequence) +wise: +wise: Wise compares a protein sequence to a genomic DNA sequence, +wise: allowing for introns and frameshifting errors. +wise: +wise: https://www.ebi.ac.uk/~birney/wise2/ +wise: https://www.ebi.ac.uk/Tools/psa/genewise/ +wise: +wise: +wise: +wise: diff --git a/academic/wise/wise.SlackBuild b/academic/wise/wise.SlackBuild new file mode 100644 index 0000000000..84230832be --- /dev/null +++ b/academic/wise/wise.SlackBuild @@ -0,0 +1,131 @@ +#!/bin/bash + +# Slackware build script for <wise> + +# Copyright 2023 Petar Petrov, slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=wise +VERSION=${VERSION:-2.4.1} +BUILD=${BUILD:-2} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/${PRGNAM}_${VERSION}.orig.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +patch -p1 -i $CWD/patches/01_welcome-csh.patch +patch -p1 -i $CWD/patches/02_isnumber.patch +patch -p1 -i $CWD/patches/03_doc-nodycache.patch +patch -p1 -i $CWD/patches/04_wise2-pdflatex-update.patch +patch -p1 -i $CWD/patches/05_glib2.patch +patch -p1 -i $CWD/patches/06_getline.patch +patch -p1 -i $CWD/patches/07_ld--as-needed.patch +patch -p1 -i $CWD/patches/08_mayhem.patch +patch -p1 -i $CWD/patches/09_dnal-add-return-statement.patch +patch -p1 -i $CWD/patches/10_fix_path_to_data_files.patch +patch -p1 -i $CWD/patches/11_consistent_manual_dates.patch +patch -p1 -i $CWD/patches/spelling.patch +patch -p1 -i $CWD/patches/cross.patch + +# This prevents some weird build breaks. Thanks to Urchlay. His explanation: +# +# The .c files that are in the tarball, were already built from the .dy +# files. However, some of them get patched, e.g. wisefile.c and wisefile.dy +# both have a modification time of the current time/date, which is why make +# thinks it needs to rebuild the wisefile.c. When make is run, it looks at +# the timestamps and decided wisefile.c is older than wisefile.dy (which it +# is, ever so slightly, assuming the filesystem's timestamp resolution is +# fine enough). What the solution does is force the timestamp on all the +# .dy files to be older than the generated .c files, so make won't think it +# needs to run dyc to generate the .c files. +find src -name \*.dy -print0 | xargs -0 touch -d '2000-01-01' + +cd src +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make all + +mkdir -p $PKG/usr/bin +mkdir -p $PKG/usr/share/$PRGNAM + +cd bin +for i in * ; do + install -m 755 $i $PKG/usr/bin/$i +done + +cd ../.. +cp -a test_data wisecfg/* $PKG/usr/share/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README docs/{*.tex,*.eps,papers} \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wise/wise.info b/academic/wise/wise.info new file mode 100644 index 0000000000..1aafd927ee --- /dev/null +++ b/academic/wise/wise.info @@ -0,0 +1,10 @@ +PRGNAM="wise" +VERSION="2.4.1" +HOMEPAGE="https://www.ebi.ac.uk/Tools/psa/genewise/" +DOWNLOAD="http://deb.debian.org/debian/pool/main/w/wise/wise_2.4.1.orig.tar.gz" +MD5SUM="9e90132c19a653831ce63b5af7f08302" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/wmcalc/doinst.sh b/academic/wmcalc/doinst.sh index 2cb6861d40..f79396baf0 100644 --- a/academic/wmcalc/doinst.sh +++ b/academic/wmcalc/doinst.sh @@ -1,3 +1,7 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then if [ -x /usr/bin/gtk-update-icon-cache ]; then /usr/bin/gtk-update-icon-cache usr/share/icons/hicolor >/dev/null 2>&1 diff --git a/academic/wmcalc/wmcalc.SlackBuild b/academic/wmcalc/wmcalc.SlackBuild index cf228dd147..7cab2d19df 100644 --- a/academic/wmcalc/wmcalc.SlackBuild +++ b/academic/wmcalc/wmcalc.SlackBuild @@ -25,8 +25,9 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# Now maintained by B. Watson <yalhcru@gmail.com> +# Now maintained by B. Watson <urchlay@slackware.uk> +# 20221226 bkw: add missing update-desktop-database to doinst.sh, BUILD=2. # 20180911 bkw: update for v0.7. # 20160816 bkw: @@ -47,7 +48,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=wmcalc VERSION=${VERSION:-0.7} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/wmcalc/wmcalc.info b/academic/wmcalc/wmcalc.info index 09b7df1b66..2894313a5b 100644 --- a/academic/wmcalc/wmcalc.info +++ b/academic/wmcalc/wmcalc.info @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="B. Watson" -EMAIL="yalhcru@gmail.com" +EMAIL="urchlay@slackware.uk" diff --git a/academic/wxMaxima/wxMaxima.SlackBuild b/academic/wxMaxima/wxMaxima.SlackBuild index 8480fdecab..feb51615b1 100644 --- a/academic/wxMaxima/wxMaxima.SlackBuild +++ b/academic/wxMaxima/wxMaxima.SlackBuild @@ -22,6 +22,9 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20230627 bkw: Modified by SlackBuilds.org, BUILD=2: +# - use DESTDIR properly, to avoid baking $PKG into the binary. + # Mar 2021 - updated for v. 21.01, Judah Milgram, milgram at cgpp com cd $(dirname $0) ; CWD=$(pwd) @@ -29,7 +32,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=wxMaxima SRCNAM=wxmaxima VERSION=${VERSION:-21.01.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -41,9 +44,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -55,16 +55,12 @@ OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" - LIBDIRSUFFIX="" fi set -e @@ -73,14 +69,14 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $SRCNAM-Version-$VERSION -tar xvf $CWD/Version-$VERSION.tar.gz +tar xvf $CWD/$SRCNAM-Version-$VERSION.tar.gz cd $SRCNAM-Version-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} + -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + BUILDDIR=build mkdir -p $BUILDDIR @@ -88,11 +84,11 @@ mkdir -p $BUILDDIR export PATH="/opt/cmake-202x/bin:$PATH" cmake \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_INSTALL_PREFIX=$PKG/usr \ + -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Release \ -G Ninja -S . -B $BUILDDIR cmake --build $BUILDDIR -cmake --install $BUILDDIR +DESTDIR=$PKG cmake --install $BUILDDIR find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/wxMaxima/wxMaxima.info b/academic/wxMaxima/wxMaxima.info index 699d9e17eb..b1cffd86c3 100644 --- a/academic/wxMaxima/wxMaxima.info +++ b/academic/wxMaxima/wxMaxima.info @@ -1,7 +1,7 @@ PRGNAM="wxMaxima" VERSION="21.01.0" HOMEPAGE="https://wxmaxima-developers.github.io/wxmaxima/" -DOWNLOAD="https://github.com/wxMaxima-developers/wxmaxima/archive/Version-21.01.0.tar.gz" +DOWNLOAD="https://github.com/wxMaxima-developers/wxmaxima/archive/Version-21.01.0/wxmaxima-Version-21.01.0.tar.gz" MD5SUM="2c9b97c786806172aa6ed000784e995e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/x48/README b/academic/x48/README new file mode 100644 index 0000000000..b5cd057318 --- /dev/null +++ b/academic/x48/README @@ -0,0 +1,5 @@ +x48 is a vintage emulator capable of providing a faithful replication +of the HP48 Calculator. It requires a copy of the ROM software. + +The user can initialize an HP48GX(r) ROM in $HOME/.hp48 with: +x48 -initialize -reset -rom /usr/doc/x48-0.6.4/gxrom-r diff --git a/academic/x48/slack-desc b/academic/x48/slack-desc new file mode 100644 index 0000000000..80dc45794a --- /dev/null +++ b/academic/x48/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +x48: x48 (HP48 Calculator emulator) +x48: +x48: x48 is a vintage emulator capable of providing a faithful replication +x48: of the HP48 Calculator. It requires a copy of the ROM software. +x48: +x48: The user can initialize an HP48GX(r) ROM in $HOME/.hp48 with: +x48: x48 -initialize -reset -rom /usr/doc/x48-0.6.4/gxrom-r +x48: +x48: http://www.hpcc.org/calculators/hp48.html +x48: +x48: diff --git a/academic/x48/x48.SlackBuild b/academic/x48/x48.SlackBuild new file mode 100644 index 0000000000..84e9c4207f --- /dev/null +++ b/academic/x48/x48.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/bash + +# Slackware build script for x48 + +# Copyright 2022 Lorenzo Trevisan, Caorle, Venice, Italy +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=x48 +VERSION=${VERSION:-0.6.4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 -C $PRGNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +cd $PRGNAM-$VERSION + +sed -i -e '698s=inline int=static inline int=' ./src/emulate.c + +./autogen.sh +./configure \ + --prefix=/usr \ + --mandir=/usr/man + +make +make install DESTDIR=$PKG + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README ChangeLog AUTHORS \ + $PKG/usr/doc/$PRGNAM-$VERSION +cp $CWD/hp48g-qsg-en.pdf $PKG/usr/doc/$PRGNAM-$VERSION +cp $CWD/hp48g-ug-en.pdf $PKG/usr/doc/$PRGNAM-$VERSION +bunzip2 -k -c $CWD/gxrom-r.bz2 > $PKG/usr/doc/$PRGNAM-$VERSION/gxrom-r +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/x48/x48.info b/academic/x48/x48.info new file mode 100644 index 0000000000..d6301da61e --- /dev/null +++ b/academic/x48/x48.info @@ -0,0 +1,16 @@ +PRGNAM="x48" +VERSION="0.6.4" +HOMEPAGE="http://www.hpcc.org/calculators/hp48.html" +DOWNLOAD="https://sourceforge.net/projects/x48.berlios/files/x48-0.6.4.tar.bz2 \ + https://sourceforge.net/projects/x48.berlios/files/gxrom-r.bz2 \ + https://literature.hpcalc.org/community/hp48g-qsg-en.pdf \ + https://literature.hpcalc.org/community/hp48g-ug-en.pdf" +MD5SUM="700e631f8924a991b35d8a86ce60aab7 \ + a08249c9a75d52671045dbb9c35321fa \ + 1e91e669ed5bc126049f35f43e12805a \ + 9efd58fc89b6ea89bc00d6dbff6812a3" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Lorenzo Trevisan" +EMAIL="lorenzo.trevisan@gmail.com" diff --git a/academic/xcircuit/README b/academic/xcircuit/README index b8eca76d61..0dba86217d 100644 --- a/academic/xcircuit/README +++ b/academic/xcircuit/README @@ -1,5 +1,4 @@ -XCircuit is a UNIX/X11 (and Windows, if you have an X-Server running, -or Windows API, if not) program for drawing publishable-quality +XCircuit is a program for drawing publishable-quality electrical circuit schematic diagrams and related figures, and produce circuit netlists through schematic capture. XCircuit regards circuits as inherently hierarchical, and writes both hierarchical PostScript @@ -8,3 +7,5 @@ in and retrieved from libraries which are fully editable. XCircuit does not separate artistic expression from circuit drawing; it maintains flexiblity in style without compromising the power of schematic capture. + +ngspice is an optional dependency diff --git a/academic/xcircuit/slack-desc b/academic/xcircuit/slack-desc index 8d83821bbe..dc34decbd6 100644 --- a/academic/xcircuit/slack-desc +++ b/academic/xcircuit/slack-desc @@ -6,9 +6,9 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -xcircuit: xcircuit (circuit design tool) -xcircuit: XCircuit is a UNIX/X11 (and Windows, if you have an X-Server running, -xcircuit: or Windows API, if not) program for drawing publishable-quality +xcircuit: xcircuit (Circuit drawing and schematic capture program) +xcircuit: +xcircuit: XCircuit is a UNIX/X11 program for drawing publishable-quality xcircuit: electrical circuit schematic diagrams and related figures, and xcircuit: produce circuit netlists through schematic capture. XCircuit regards xcircuit: circuits as inherently hierarchical, and writes both hierarchical diff --git a/academic/xcircuit/xcircuit.SlackBuild b/academic/xcircuit/xcircuit.SlackBuild index 5c6eb3eb37..9429418716 100644 --- a/academic/xcircuit/xcircuit.SlackBuild +++ b/academic/xcircuit/xcircuit.SlackBuild @@ -1,27 +1,44 @@ #!/bin/bash -# Slackware build script for grace +# Slackware build script for xcircuit + # Written by B. Jogai <jogaib {at} comcast [dot] net> +# Copyright 2023 Johannes Schoepfer, Germany +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. cd $(dirname $0) ; CWD=$(pwd) PRGNAM=xcircuit -VERSION=${VERSION:-3.7.54} +VERSION=${VERSION:-3.10.30} BUILD=${BUILD:-1} TAG=${TAG:-"_SBo"} PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -31,8 +48,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -55,10 +72,10 @@ tar xvf $CWD/$PRGNAM-$VERSION.tgz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; CFLAGS="$SLKCFLAGS" \ ./configure \ @@ -66,27 +83,28 @@ CFLAGS="$SLKCFLAGS" \ --bindir=/usr/bin \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --mandir=/usr/man \ - --with-x \ + --with-cairo \ --with-ngspice \ --with-tcl=/usr/lib${LIBDIRSUFFIX} \ + --with-tk=/usr/lib${LIBDIRSUFFIX} \ --build=$ARCH-slackware-linux \ make make DESTDIR=$PKG install +[ "$ARCH" = "x86_64" ] && mv $PKG/usr/lib $PKG/usr/lib$LIBDIRSUFFIX + find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true # Add desktop menu entries -mkdir -p $PKG/usr/share/{applications,pixmaps} -cat $CWD/xcircuit.png > $PKG/usr/share/pixmaps/xcircuit.png -cat $CWD/xcircuit.desktop > $PKG/usr/share/applications/xcircuit.desktop - -# Copy the man pages from the lib to the man directory. -# Don't move it in case the program needs it there for some reason. -rm -rf $PKG/usr/man -mkdir -p $PKG/usr/man/man1 -cp $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM-3.7/man/*.1 $PKG/usr/man/man1 +mkdir -p $PKG/usr/share/{applications,icons} +convert $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM-*.*/pixmaps/$PRGNAM.gif \ + $PKG/usr/share/icons/$PRGNAM.png +cat $CWD/$PRGNAM.desktop > $PKG/usr/share/applications/$PRGNAM.desktop + +mkdir $PKG/usr/man +mv $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM-*.*/man $PKG/usr/man/man1 find $PKG/usr/man -type f -exec gzip -9 {} \; mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/xcircuit/xcircuit.desktop b/academic/xcircuit/xcircuit.desktop index f687451b21..8ff88e11c3 100644 --- a/academic/xcircuit/xcircuit.desktop +++ b/academic/xcircuit/xcircuit.desktop @@ -1,8 +1,9 @@ [Desktop Entry] Type=Application Exec=xcircuit -Name=xcircuit -GenericName=Circuit drawing program +Name=Xcircuit +Comment=A program for drawing publishable-quality electrical circuit schematic diagrams Icon=xcircuit Terminal=false -Categories=Qt;KDE;Graphics;Development; +StartupNotify=false +Categories=Development; diff --git a/academic/xcircuit/xcircuit.info b/academic/xcircuit/xcircuit.info index 02b589bf38..e7e79a3d25 100644 --- a/academic/xcircuit/xcircuit.info +++ b/academic/xcircuit/xcircuit.info @@ -1,10 +1,10 @@ PRGNAM="xcircuit" -VERSION="3.7.54" +VERSION="3.10.30" HOMEPAGE="http://opencircuitdesign.com/xcircuit/" -DOWNLOAD="http://opencircuitdesign.com/xcircuit/archive/xcircuit-3.7.54.tgz" -MD5SUM="25e60837e5db6b4ff71615505493a481" +DOWNLOAD="http://opencircuitdesign.com/xcircuit/archive/xcircuit-3.10.30.tgz" +MD5SUM="f83be9d40d5bea00f27391b979bb1f76" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Glenn Becker" -EMAIL="glenn.becker@gmail.com" +MAINTAINER="Johannes Schoepfer" +EMAIL="slackbuilds@schoepfer.info" diff --git a/academic/xcircuit/xcircuit.png b/academic/xcircuit/xcircuit.png Binary files differdeleted file mode 100644 index 85cc4da406..0000000000 --- a/academic/xcircuit/xcircuit.png +++ /dev/null diff --git a/academic/xephem/slack-desc b/academic/xephem/slack-desc index 7af4a92da3..6a8ac39af8 100644 --- a/academic/xephem/slack-desc +++ b/academic/xephem/slack-desc @@ -8,11 +8,11 @@ |-----handy-ruler------------------------------------------------------| xephem: xephem (Astronomy program) xephem: -xephem: The scientific-grade interactive astronomical ephemeris -xephem: software package for UNIX-like* systems. -xephem: -xephem: Note that this is not free software: read the license -xephem: agreement carefully. +xephem: XEphem is an interactive astronomy program for all UNIX platforms. +xephem: Originally written by Elwood Downey in the 1990s, it has graciously +xephem: been released under the MIT License. It is now maintained by an +xephem: MIT License. It is now maintained by an "XEphem" organization, +xephem: with its source code residing at https://github.com/XEphem/XEphem. xephem: xephem: xephem: diff --git a/academic/xephem/xephem.SlackBuild b/academic/xephem/xephem.SlackBuild index 70af0d12aa..8747d3db80 100644 --- a/academic/xephem/xephem.SlackBuild +++ b/academic/xephem/xephem.SlackBuild @@ -7,10 +7,11 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=xephem -VERSION=${VERSION:-3.7.7} +VERSION=${VERSION:-4.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +SRCNAM="XEphem" if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -51,9 +52,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tgz -cd $PRGNAM-$VERSION +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ @@ -67,7 +68,7 @@ sed -i 's/^CFLAGS =/override CFLAGS +=/g' GUI/xephem/Makefile cd GUI/xephem patch -p3 < $CWD/00_trailmenu.patch - make -j1 CFLAGS="$SLKCFLAGS" CLDFLAGS="" MOTIFL="/usr/lib$LIBDIRSUFFIX" || exit 1 + make -j1 CFLAGS="$SLKCFLAGS" CLDFLAGS="" MOTIFL="/usr/lib$LIBDIRSUFFIX" mkdir -p $PKG/usr/{bin,man/man1,share/xephem} cp xephem $PKG/usr/bin cp XEphem.png $PKG/usr/share/xephem @@ -100,7 +101,7 @@ find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - Copyright INSTALL README \ + INSTALL LICENSE README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/xephem/xephem.info b/academic/xephem/xephem.info index 4a17ddb0d2..69028f4e5b 100644 --- a/academic/xephem/xephem.info +++ b/academic/xephem/xephem.info @@ -1,8 +1,8 @@ PRGNAM="xephem" -VERSION="3.7.7" -HOMEPAGE="http://www.clearskyinstitute.com/xephem/" -DOWNLOAD="http://www.clearskyinstitute.com/xephem/xephem-3.7.7.tgz" -MD5SUM="27c67061a89085bf2b0d4e9deb758a79" +VERSION="4.1.0" +HOMEPAGE="https://xephem.github.io/XEphem/Site/xephem.html" +DOWNLOAD="https://github.com/XEphem/XEphem/archive/4.1.0/XEphem-4.1.0.tar.gz" +MD5SUM="14b5aafd6d8cbfe3d261fc4661e04caa" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/xflr5/README b/academic/xflr5/README index 1521ecb74b..628905a5a5 100644 --- a/academic/xflr5/README +++ b/academic/xflr5/README @@ -1,6 +1,6 @@ -XFLR5 is an analysis tool for airfoils, wings, and planes operating at low -Reynolds numbers. It includes: +XFLR5 is an analysis tool for airfoils, wings, and planes operating at +low Reynolds numbers. It includes: 1. XFoil's Direct and Inverse analysis capabilities -2. Wing design and analysis capabilities based on Lifting Line Theory, on the - Vortex Lattice Method, and on a 3D Panel Method +2. Wing design and analysis capabilities based on Lifting Line Theory, + on the Vortex Lattice Method, and on a 3D Panel Method diff --git a/academic/xflr5/link_directly.patch b/academic/xflr5/link_directly.patch deleted file mode 100644 index 722a238556..0000000000 --- a/academic/xflr5/link_directly.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- xflr5-gui/xflr5-gui.pro 2019-12-26 23:06:50.168628145 -0500 -+++ xflr5-gui/xflr5-gui.pro.new 2019-12-26 23:07:01.925796901 -0500 -@@ -128,8 +128,8 @@ - QMAKE_CFLAGS_WARN_ON -= -W3 - QMAKE_CFLAGS_WARN_ON += -W4 - --LIBS += -L../xflr5-engine -lxflr5-engine --LIBS += -L../XFoil-lib -lXFoil -+LIBS += ../xflr5-engine/libxflr5-engine.so -+LIBS += ../XFoil-lib/libXFoil.so - - include(xflr5v6.pri) - diff --git a/academic/xflr5/link_directly.patch.gz b/academic/xflr5/link_directly.patch.gz Binary files differnew file mode 100644 index 0000000000..232529802f --- /dev/null +++ b/academic/xflr5/link_directly.patch.gz diff --git a/academic/xflr5/xflr5.SlackBuild b/academic/xflr5/xflr5.SlackBuild index 83ccd67623..8bfc0a4705 100644 --- a/academic/xflr5/xflr5.SlackBuild +++ b/academic/xflr5/xflr5.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for xflr5 -# Copyright 2020 Daniel Prosser, Lexington Park, MD, USA +# Copyright 2020-2023 Daniel Prosser, Lexington Park, MD, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=xflr5 -VERSION=${VERSION:-6.47} +VERSION=${VERSION:-6.61} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -69,9 +69,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM -tar xvf $CWD/${PRGNAM}_v${VERSION}_src.tar.gz -cd $PRGNAM +rm -rf ${PRGNAM}-${VERSION} +tar -xzvf $CWD/${PRGNAM}-${VERSION}.tar.gz +cd ${PRGNAM}-${VERSION} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -82,11 +82,15 @@ find -L . \ # Change default path for libraries installation sed -i "s/target\.path = \$\$PREFIX\/lib/target\.path = \$\$PREFIX\/lib${LIBDIRSUFFIX}/g" \ XFoil-lib/XFoil-lib.pro -sed -i "s/target\.path = \$\$PREFIX\/lib/target\.path = \$\$PREFIX\/lib${LIBDIRSUFFIX}/g" \ - xflr5-engine/xflr5-engine.pro -# Fix linking -patch -p0 < $CWD/link_directly.patch +# Fix some hardcoded paths in launcher +sed -i "s/Exec=\/usr\/local\/bin\/xflr5/Exec=\/usr\/bin\/xflr5/g" linux/xflr5.desktop +sed -i "s/Icon=\/usr\/local\/share\/xflr5\/xflr5.png/Icon=xflr5/g" linux/xflr5.desktop + +# Fix linking XFoil-lib +# Note: this patch *must* be gzipped, as it contain a mix of \n and \r\n +# line endings, and git would strip the \r's. +zcat $CWD/link_directly.patch.gz | patch -p0 qmake-qt5 \ PREFIX=/usr \ @@ -101,11 +105,11 @@ make install INSTALL_ROOT=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -mkdir -p $PKG/usr/share/icons/hicolor/64x64/apps -cp -a xflr5-gui/images/xflr5_64.png $PKG/usr/share/icons/hicolor/64x64/apps +mkdir -p $PKG/usr/share/icons/hicolor/128x128/apps +cp -a res/xflr5.png $PKG/usr/share/icons/hicolor/128x128/apps mkdir -p $PKG/usr/share/applications -cp -a $CWD/xflr5.desktop $PKG/usr/share/applications +cp -a linux/xflr5.desktop $PKG/usr/share/applications mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a License.txt $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/xflr5/xflr5.desktop b/academic/xflr5/xflr5.desktop deleted file mode 100644 index 4559ab869f..0000000000 --- a/academic/xflr5/xflr5.desktop +++ /dev/null @@ -1,10 +0,0 @@ -[Desktop Entry] -Comment=an analysis tool for airfoils, wings, and planes -Exec=xflr5 -GenericName=Aircraft analysis tool -Icon=xflr5_64 -Name=xflr5 -StartupNotify=true -Terminal=false -Type=Application -Categories=Education;Science; diff --git a/academic/xflr5/xflr5.info b/academic/xflr5/xflr5.info index 2829af9238..947ad8f4ea 100644 --- a/academic/xflr5/xflr5.info +++ b/academic/xflr5/xflr5.info @@ -1,8 +1,8 @@ PRGNAM="xflr5" -VERSION="6.47" +VERSION="6.61" HOMEPAGE="http://www.xflr5.com/xflr5.htm" -DOWNLOAD="https://ayera.dl.sourceforge.net/project/xflr5/6.47/xflr5_v6.47_src.tar.gz" -MD5SUM="272484cc3fe077af31bbe2ad7ef4205b" +DOWNLOAD="http://sourceforge.net/projects/slackbuildsdirectlinks/files/xflr5/xflr5-6.61.tar.gz" +MD5SUM="ddedf9a123e67dfbf206901f6d6d59f1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/xiphos/README b/academic/xiphos/README index 166b55e9b6..e430c8f0fe 100644 --- a/academic/xiphos/README +++ b/academic/xiphos/README @@ -4,13 +4,3 @@ Sword project by the CrossWire Bible Society. computer reading of the text using festival has not been tested. if it works let me know, and i'll remove these two lines from the readme. - -xiphos version 4.2.1 requires sword v1.8.1-3 or higher -and biblesync v2.0.1 or higher - -xiphos needs a version of cmake 3.11 or higher. A private version is -included in the slackbuild to enable xiphos to be built. If you want to -use a different cmake to that included here, pass CMVERSION with the -version you need (and make sure that the source tar.gz is available) -There are a few new dependencies as the documentation is now created by -the build process rather than shipped preprocessed in the source. diff --git a/academic/xiphos/xiphos.SlackBuild b/academic/xiphos/xiphos.SlackBuild index e7f907c745..3471341e36 100644 --- a/academic/xiphos/xiphos.SlackBuild +++ b/academic/xiphos/xiphos.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for xiphos -# Copyright 2015-2020 Tim Dickson, email: dickson.tim@googlemail.com +# Copyright 2015-2023 Tim Dickson, email: dickson.tim@googlemail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +#note: webkit2gtk is a dep, but is already included as a dep of yelp. + cd $(dirname $0) ; CWD=$(pwd) PRGNAM=xiphos VERSION=${VERSION:-4.2.1} -BUILD=${BUILD:-3} +BUILD=${BUILD:-5} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -73,8 +75,6 @@ rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION -#we will use a newer version of cmake (at least 3.11) - #sane permissions for everything chown -R root:root . find -L . \ @@ -82,18 +82,11 @@ find -L . \ -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# -#lets make newer cmake available to the xiphos build -OLDPATH=$PATH -export PATH=/opt/cmake-202x/bin:$PATH - -# patch navbar_versekey.gtkbuilder to work with gtk shipped with slackware 14.2 -# patch won't be needed for slackware 15 -sed -i "s/3.20/3.14/g" ui/navbar_versekey.gtkbuilder +#patch to make work with newer glib +echo "#define GLIB_VERSION_MIN_REQUIRED (GLIB_VERSION_2_26)" >>cmake/config.h.cmake.in mkdir -p build cd build -export "PATH=/opt/cmake-202x/bin:$PATH" cmake -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ @@ -104,7 +97,6 @@ cmake -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DDBUS=OFF -DSTRIP=ON -DPOSTINST=OFF -DGTKHTML=ON .. #cmake should have created make file so restore PATH -export PATH=$OLDPATH make make install DESTDIR=$PKG cd .. diff --git a/academic/xiphos/xiphos.info b/academic/xiphos/xiphos.info index 46582994ec..70245d07d3 100644 --- a/academic/xiphos/xiphos.info +++ b/academic/xiphos/xiphos.info @@ -1,10 +1,10 @@ PRGNAM="xiphos" VERSION="4.2.1" -HOMEPAGE="http://xiphos.org" +HOMEPAGE="https://xiphos.org" DOWNLOAD="https://github.com/crosswire/xiphos/releases/download/4.2.1/xiphos-4.2.1.tar.gz" MD5SUM="77d8a99c063433bea3006954710b2fd5" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="sword webkitgtk3 biblesync rarian gtkhtml libminizip appstream-glib yelp" +REQUIRES="sword biblesync rarian gtkhtml libminizip appstream-glib yelp" MAINTAINER="Tim Dickson" EMAIL="dickson.tim@googlemail.com" diff --git a/academic/xoscope/xoscope.SlackBuild b/academic/xoscope/xoscope.SlackBuild index 575917c0dc..3e29b53dd8 100644 --- a/academic/xoscope/xoscope.SlackBuild +++ b/academic/xoscope/xoscope.SlackBuild @@ -47,13 +47,13 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="AUTHORS COPYING ChangeLog INSTALL NEWS README TODO* hardware" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" diff --git a/academic/xschem/README b/academic/xschem/README new file mode 100644 index 0000000000..9af371c59b --- /dev/null +++ b/academic/xschem/README @@ -0,0 +1,18 @@ +Xschem is a schematic capture program, it allows creation of +hierarchical representation of circuits with a top down approach . By +focusing on interfaces, hierarchy and instance properties a complex +system can be described in terms of simpler building blocks. A VHDL +or Verilog or Spice netlist can be generated from the drawn schematic, +allowing the simulation of the circuit. Key feature of the program is +its drawing engine written in C and using directly the Xlib drawing +primitives; this gives very good speed performance, even on very big +circuits. The user interface is built with the Tcl-Tk toolkit, tcl is +also the extension language used. - hierarchical schematic drawings, +no limits on size - any object in the schematic can have any sort of +properties (generics in VHDL, parameters in Spice or Verilog) - new +Spice/Verilog primitives can be created, and the netlist format can +be defined by the user -tcl extension language allows the creation +of scripts; any user command in the drawing window has an associated +tcl comand - VHDL / Verilog / Spice netlist, ready for simulation - +Behavioral VHDL / Verilog code can be embedded as one of the properties +of the schematic block. diff --git a/academic/xschem/doinst.sh b/academic/xschem/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/xschem/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/xschem/slack-desc b/academic/xschem/slack-desc new file mode 100644 index 0000000000..cf6956bfb7 --- /dev/null +++ b/academic/xschem/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +xschem: xschem (schematic capture program) +xschem: +xschem: It support various simulators, build it waveform viewer and it can +xschem: connect with other waveform viewer like gaw and BeSpice +xschem: +xschem: +xschem: +xschem: +xschem: +xschem: +xschem: diff --git a/academic/xschem/xschem.SlackBuild b/academic/xschem/xschem.SlackBuild new file mode 100644 index 0000000000..1c513ac5c2 --- /dev/null +++ b/academic/xschem/xschem.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/bash + +# Slackware build script for xschem + +# Copyright 2023 Alfredo USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=xschem +VERSION=${VERSION:-3.4.4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + +make install PREFIX=/usr DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mv $PKG/usr/share/man $PKG/usr/ + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/share/applications +mkdir -p $PKG/usr/share/pixmaps/$PRGNAM/ +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications/ +cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps/$PRGNAM/ + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +mv $PKG/usr/share/doc/$PRGNAM/* $PKG/usr/doc/$PRGNAM-$VERSION/ +rmdir $PKG/usr/share/doc/$PRGNAM/ +rmdir $PKG/usr/share/doc/ +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/xschem/xschem.desktop b/academic/xschem/xschem.desktop new file mode 100644 index 0000000000..8706de83a2 --- /dev/null +++ b/academic/xschem/xschem.desktop @@ -0,0 +1,11 @@ +[Desktop Entry] +Exec=/usr/bin/xschem +InitialPreference=2 +MimeType=application/xscheme; +Name=xscheme +Comment=Schematic capture +Icon=/usr/share/pixmaps/xschem/xschem.png +Terminal=false +Type=Application +Categories=Graphics; +Keywords=CAD;simualtion;design;drawing; diff --git a/academic/xschem/xschem.fig b/academic/xschem/xschem.fig new file mode 100644 index 0000000000..79265fe77e --- /dev/null +++ b/academic/xschem/xschem.fig @@ -0,0 +1,10 @@ +#FIG 3.2 Produced by xfig version 3.2.8b +Landscape +Center +Inches +Letter +100.00 +Single +-2 +1200 2 +4 0 4 50 -1 18 16 0.0000 4 210 1185 225 600 XSCHEM\001 diff --git a/academic/xschem/xschem.info b/academic/xschem/xschem.info new file mode 100644 index 0000000000..7a6abe4add --- /dev/null +++ b/academic/xschem/xschem.info @@ -0,0 +1,10 @@ +PRGNAM="xschem" +VERSION="3.4.4" +HOMEPAGE="https://xschem.sourceforge.io/stefan/index.html" +DOWNLOAD="https://sourceforge.net/projects/xschem/files/xschem-3.4.4.tar.gz" +MD5SUM="d9dbdce18579fb6dc4c08ac942dd8001" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="A. Tomasini" +EMAIL="alto dot tom at gmail dot com" diff --git a/academic/xschem/xschem.png b/academic/xschem/xschem.png Binary files differnew file mode 100644 index 0000000000..9892fbaf2f --- /dev/null +++ b/academic/xschem/xschem.png diff --git a/academic/xsimd/README b/academic/xsimd/README new file mode 100644 index 0000000000..bd2c62b1bb --- /dev/null +++ b/academic/xsimd/README @@ -0,0 +1,11 @@ +SIMD (Single Instruction, Multiple Data) is a feature of microprocessors +that has been available for many years. SIMD instructions perform a +single operation on a batch of values at once, and thus provide a way +to significantly accelerate code execution. However, these instructions +differ between microprocessor vendors and compilers. + +xsimd provides a unified means for using these features for library +authors. Namely, it enables manipulation of batches of numbers with +the same arithmetic operators as for single values. It also provides +accelerated implementation of common mathematical functions operating +on batches. diff --git a/academic/xsimd/slack-desc b/academic/xsimd/slack-desc new file mode 100644 index 0000000000..cea4fc827a --- /dev/null +++ b/academic/xsimd/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +xsimd: xsimd (C++ wrappers for SIMD intrinsics) +xsimd: +xsimd: xsimd provides a unified means for using SIMD features for library +xsimd: authors. Namely, it enables manipulation of batches of numbers with +xsimd: the same arithmetic operators as for single values. It also provides +xsimd: accelerated implementation of common mathematical functions operating +xsimd: on batches. +xsimd: +xsimd: +xsimd: +xsimd: diff --git a/academic/abella/abella.SlackBuild b/academic/xsimd/xsimd.SlackBuild index eb30ac337f..f15fa4eb2b 100644 --- a/academic/abella/abella.SlackBuild +++ b/academic/xsimd/xsimd.SlackBuild @@ -1,6 +1,9 @@ #!/bin/bash -# Slackware build script for abella -# Copyright 2019 Jefferson Rocha <root@slackjeff.com.br> + +# Slackware build script for xsimd + +# Copyright 2022-2023 Isaac Yu <isaacyu@protonmail.com> +# Copyright 2023 Jeremy Hansen <jebrhansen+SBo@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -20,18 +23,22 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -#==========================VARS cd $(dirname $0) ; CWD=$(pwd) -PRGNAM=abella -VERSION=${VERSION:-2.0.6} +PRGNAM=xsimd +VERSION=${VERSION:-11.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -ARCH=noarch -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -41,21 +48,24 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -#Root? -[ "$UID" -ne '0' ] && { echo "Need root."; exit 1 ;} +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi -#=========================START set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP - rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION - -# Fix Permissions chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -63,23 +73,24 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Generate bin -make -strip -s $PRGNAM +mkdir build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DBUILD_TESTS=yes \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$PKG +cd .. -mkdir -p $PKG/usr/bin -cp "$PRGNAM" $PKG/usr/bin +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION - -# Send original Docs and archives -for create in "$PRGNAM.SlackBuild" 'LICENSE' 'CHANGES'; do - if [ "$create" = $PRGNAM.SlackBuild ]; then - cp $CWD/$create $PKG/usr/doc/$PRGNAM-$VERSION/ - else - cp $create $PKG/usr/doc/$PRGNAM-$VERSION/ - fi -done +cp -a LICENSE README.md $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/xsimd/xsimd.info b/academic/xsimd/xsimd.info new file mode 100644 index 0000000000..8a24d36307 --- /dev/null +++ b/academic/xsimd/xsimd.info @@ -0,0 +1,10 @@ +PRGNAM="xsimd" +VERSION="11.1.0" +HOMEPAGE="https://github.com/QuantStack/xsimd" +DOWNLOAD="https://github.com/QuantStack/xsimd/archive/11.1.0/xsimd-11.1.0.tar.gz" +MD5SUM="29ffd841d6491fddfbfaedeffc637f02" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="doctest" +MAINTAINER="Jeremy Hansen" +EMAIL="jebrhansen+SBo@gmail.com" diff --git a/academic/yices2/README b/academic/yices2/README new file mode 100644 index 0000000000..65774f7f8c --- /dev/null +++ b/academic/yices2/README @@ -0,0 +1,14 @@ + Yices 2 is an SMT solver that decides the satisfiability of formulas +containing uninterpreted function symbols with equality, real and +integer arithmetic, bitvectors, scalar types, and tuples. Yices 2 +supports both linear and nonlinear arithmetic. + + Yices 2 can process input written in the SMT-LIB notation (both +versions 2.0 and 1.2 are supported). Alternatively, you can write +specifications using Yices 2's own specification language, which +includes tuples and scalar types. You can also use Yices 2 as a +library in your software. + + + If you want to enable non-linear real and integer arithmetic +set MCSAT=yes, this requires libpoly and libcudd. diff --git a/academic/yices2/slack-desc b/academic/yices2/slack-desc new file mode 100644 index 0000000000..a575d6fc35 --- /dev/null +++ b/academic/yices2/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +yices2: yices2 (Satisfiability modulo theories solver) +yices2: +yices2: +yices2: +yices2: Yices 2 is an SMT solver that decides the satisfiability of +yices2: formulas containing uninterpreted function symbols with equality, +yices2: real and integer arithmetic, bitvectors, scalar types, and tuples. +yices2: Yices 2 supports both linear and nonlinear arithmetic. +yices2: +yices2: +yices2: diff --git a/academic/drawtiming/drawtiming.SlackBuild b/academic/yices2/yices2.SlackBuild index d8f4095833..7d80ee1a9e 100644 --- a/academic/drawtiming/drawtiming.SlackBuild +++ b/academic/yices2/yices2.SlackBuild @@ -1,8 +1,8 @@ #!/bin/bash -# Slackware build script for drawtiming +# Slackware build script for yices2 -# Copyright 2014 R. S. Ananda Murthy, Mysore, India +# Copyright 2022 William PC - Seattle, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,23 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + cd $(dirname $0) ; CWD=$(pwd) -PRGNAM=drawtiming -VERSION=${VERSION:-0.7.1} +PRGNAM=yices2 +VERSION=${VERSION:-2.6.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +SRCNAM=yices-$VERSION-src + if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -STARTDIR=$(pwd) # If the variable PRINT_PACKAGE_NAME is set, then this script will report what # the name of the created package would be, and then exit. This information # could be useful to other scripts. @@ -51,8 +53,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -70,21 +72,22 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION +rm -rf $PRGNAM-Yices-$VERSION +tar xvf $CWD/$SRCNAM.tar.gz +cd $PRGNAM-Yices-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -patch -p1 < $STARTDIR/InitializeMagick.diff -patch -p1 < $STARTDIR/manpage-fix.diff -patch -p1 < $STARTDIR/missing-includes.diff -patch -p1 < $STARTDIR/switch_LDFLAGS_LDADD.diff +if [ "${MCSAT:-no}" == "yes" ]; then + OPT="--enable-mcsat" +fi + +autoconf CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -93,25 +96,35 @@ CXXFLAGS="$SLKCFLAGS" \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --build=$ARCH-slackware-linux + $OPT \ + --docdir=/usr/doc/$PRGNAM-$VERSION + make -make DESTDIR=$PKG install +make install DESTDIR=$PKG + +# install docs and fix permissions +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -av doc/*.* $PKG/usr/doc/$PRGNAM-$VERSION +find $PKG/usr/doc/$PRGNAM-$VERSION -type d -exec chmod 755 '{}' \; + +# installing examples +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a examples $PKG/usr/share/$PRGNAM-$VERSION + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/samples -cp -r $TMP/$PRGNAM-$VERSION/samples/* $PKG/usr/doc/$PRGNAM-$VERSION/samples -rm $PKG/usr/doc/$PRGNAM-$VERSION/samples/runsamples.sh -rm $PKG/usr/doc/$PRGNAM-$VERSION/samples/Makefile* -cp -a COPYING INSTALL NEWS README AUTHORS THANKS $PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE.txt README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install -cat $CWD/doinst.sh > $PKG/install/doinst.sh cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG diff --git a/academic/yices2/yices2.info b/academic/yices2/yices2.info new file mode 100644 index 0000000000..2811b191e2 --- /dev/null +++ b/academic/yices2/yices2.info @@ -0,0 +1,10 @@ +PRGNAM="yices2" +VERSION="2.6.4" +HOMEPAGE="https://yices.csl.sri.com" +DOWNLOAD="https://yices.csl.sri.com/releases/2.6.4/yices-2.6.4-src.tar.gz" +MD5SUM="6863fb6c44345e4b72490d16a7ee9f27" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/z3/README b/academic/z3/README index a1f132277a..a1c4c5a806 100644 --- a/academic/z3/README +++ b/academic/z3/README @@ -1,12 +1,8 @@ Z3 is an automated theorem prover and satisfiability modulo theories -(SMT) solver. Given a formula in first-order logic, it attempts to -either prove the formula or find a counterexample. Z3 supports +(SMT) solver. Given a formula in first-order logic, it attempts +to either prove the formula or find a counterexample. Z3 supports arithmetic, reasoning about arrays, and several other built-in theories. Input problems are written in SMT-LIB format. -This package includes the z3 program as well as the C++ and -Python APIs. By default the Python 2 version of the API is built; -if you also want the Python 3 version, run the SlackBuild with -PYTHON3=yes, like so: - - PYTHON3=yes ./z3.SlackBuild +This package includes the z3 program as well as the C++, Python2, and +Python3 APIs. diff --git a/academic/z3/z3.SlackBuild b/academic/z3/z3.SlackBuild index 5add6450b6..af9aa52dad 100644 --- a/academic/z3/z3.SlackBuild +++ b/academic/z3/z3.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for z3 -# Copyright 2019 Nick Smallbone, Gothenburg, Sweden +# Copyright 2019-2022 Nick Smallbone, Gothenburg, Sweden # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=z3 -VERSION=${VERSION:-4.8.7} +VERSION=${VERSION:-4.11.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -70,14 +67,14 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +tar xvf $CWD/$PRGNAM-$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -93,25 +90,24 @@ cd ../doc python mk_api_doc.py cd .. -if [ z$PYTHON3 = zyes ]; then - # Copy the Python bindings to python3.X/site-packages. - PYTHON_VERSION=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') - PYLIB=$PKG/usr/lib${LIBDIRSUFFIX}/python${PYTHON_VERSION}/site-packages - mkdir -p $PYLIB - cp -a build/python/z3 $PYLIB/z3 - find $PYLIB/z3 -name '*.pyc' -delete -fi +# The Python bindings are installed for Python2 by default but work on +# Python3 too. Copy them to python3.X/site-packages. +PYTHON_VERSION=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') +PYLIB=$PKG/usr/lib${LIBDIRSUFFIX}/python${PYTHON_VERSION}/site-packages +mkdir -p $PYLIB +cp -a build/python/z3 $PYLIB/z3 +find $PYLIB/z3 -name '*.pyc' -delete find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - README.md RELEASE_NOTES LICENSE.txt \ + README.md RELEASE_NOTES.md LICENSE.txt Parameters.md \ $PKG/usr/doc/$PRGNAM-$VERSION mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/examples cp -a \ - examples/c examples/c++ examples/maxsat examples/python examples/tptp \ + examples/c examples/c++ examples/maxsat examples/python examples/tptp examples/SMT-LIB2 \ $PKG/usr/doc/$PRGNAM-$VERSION/examples find $PKG/usr/doc/$PRGNAM-$VERSION/examples -name CMakeLists.txt -delete cp -a \ diff --git a/academic/z3/z3.info b/academic/z3/z3.info index 71512a125f..b3b6178ae5 100644 --- a/academic/z3/z3.info +++ b/academic/z3/z3.info @@ -1,8 +1,8 @@ PRGNAM="z3" -VERSION="4.8.7" +VERSION="4.11.2" HOMEPAGE="https://github.com/Z3Prover/z3/wiki" -DOWNLOAD="https://github.com/Z3Prover/z3/archive/z3-4.8.7.tar.gz" -MD5SUM="18e7332ab136c1d8686ea719ed7107ed" +DOWNLOAD="https://github.com/Z3Prover/z3/archive/z3-4.11.2/z3-z3-4.11.2.tar.gz" +MD5SUM="35afb5c6658bc07c11d73ef7f08ff272" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/zotero-gtk2/README b/academic/zotero-gtk2/README new file mode 100644 index 0000000000..ca62239484 --- /dev/null +++ b/academic/zotero-gtk2/README @@ -0,0 +1,35 @@ +This is the last GTK2 version of Zotero. It will conflict with the +latest one, so don't install both. + +Zotero is a free, easy-to-use tool to help you collect, organize, +cite, and share research. + +Zotero is the only software that automatically senses research on +the web. Need an article from JSTOR or a preprint from arXiv.org? +A news story from the New York Times or a book from a library? +Zotero has you covered, everywhere. + +Zotero helps you organize your research any way you want. You can +sort items into collections and tag them with keywords. Or create +saved searches that automatically fill with relevant materials as +you work. + +Zotero instantly creates references and bibliographies for any +text editor, and directly inside Word, LibreOffice, and Google +Docs. With support for over 100,000 citation styles, you can +format your work to match any style guide or publication. + +Zotero can optionally synchronize your data across devices, +keeping your notes, files, and bibliographic records seamlessly +up to date. If you decide to sync, you can also always access +your research from any web browser. + +Zotero lets you co-write a paper with a colleague, distribute +course materials to students, or build a collaborative +bibliography. You can share a Zotero library with as many +people you like, at no cost. + +Zotero is open source and developed by an independent, +nonprofit organization that has no financial interest in your +private information. With Zotero, you always stay in control +of your own data. diff --git a/academic/zotero-gtk2/doinst.sh b/academic/zotero-gtk2/doinst.sh new file mode 100644 index 0000000000..65c7e2eeb9 --- /dev/null +++ b/academic/zotero-gtk2/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/zotero-gtk2/slack-desc b/academic/zotero-gtk2/slack-desc new file mode 100644 index 0000000000..fa0f527cb5 --- /dev/null +++ b/academic/zotero-gtk2/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +zotero-gtk2: zotero-gtk2 (Collect, organize, cite, and share research sources) +zotero-gtk2: +zotero-gtk2: Zotero is a free, easy-to-use tool to help you collect, organize, +zotero-gtk2: cite, and share research. This is the last GTK2 version of Zotero. +zotero-gtk2: If you are looking for the newest one, install "zotero", instead. +zotero-gtk2: +zotero-gtk2: Homepage: https://www.zotero.org/ +zotero-gtk2: +zotero-gtk2: +zotero-gtk2: +zotero-gtk2: diff --git a/academic/zotero-gtk2/zotero-gtk2.SlackBuild b/academic/zotero-gtk2/zotero-gtk2.SlackBuild new file mode 100644 index 0000000000..a758a63504 --- /dev/null +++ b/academic/zotero-gtk2/zotero-gtk2.SlackBuild @@ -0,0 +1,93 @@ +#!/bin/bash + +# Slackware build script for <zotero-gtk2> + +# Copyright 2023 Petar Petrov slackalaxy at gmail dot com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=zotero-gtk2 +SRCNAM=Zotero +VERSION=${VERSION:-4.0.28} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i686 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +if [ "$ARCH" != "i686" ] && [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-${VERSION}_linux-$ARCH +tar xvf $CWD/$SRCNAM-${VERSION}_linux-$ARCH.tar.bz2 +cd ${SRCNAM}_linux-$ARCH +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +sed -i -e 's:MOZ_PROGRAM="":MOZ_PROGRAM="/opt/zotero/zotero":g' run-zotero.sh + +mkdir -p $PKG/opt/zotero +cp -a * $PKG/opt/zotero + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../../opt/zotero/run-zotero.sh zotero + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/zotero.desktop $PKG/usr/share/applications +cp $CWD/zotero.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/zotero-gtk2/zotero-gtk2.info b/academic/zotero-gtk2/zotero-gtk2.info new file mode 100644 index 0000000000..2feff911d9 --- /dev/null +++ b/academic/zotero-gtk2/zotero-gtk2.info @@ -0,0 +1,10 @@ +PRGNAM="zotero-gtk2" +VERSION="4.0.28" +HOMEPAGE="https://www.zotero.org/" +DOWNLOAD="https://download.zotero.org/client/release/4.0.28/Zotero-4.0.28_linux-i686.tar.bz2" +MD5SUM="a5cb40b79b26dbe4fb29b8e9fdb61a9f" +DOWNLOAD_x86_64="https://download.zotero.org/client/release/4.0.28/Zotero-4.0.28_linux-x86_64.tar.bz2" +MD5SUM_x86_64="55f743aa7c08ca16d933e91faf43a2fc" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy at gmail dot com" diff --git a/academic/zotero-gtk2/zotero.desktop b/academic/zotero-gtk2/zotero.desktop new file mode 100644 index 0000000000..24e542f951 --- /dev/null +++ b/academic/zotero-gtk2/zotero.desktop @@ -0,0 +1,7 @@ +[Desktop Entry] +Type=Application +Name=Zotero Standalone +Icon=zotero +Exec=zotero %f +Categories=Office +Terminal=false diff --git a/academic/zotero/zotero.png b/academic/zotero-gtk2/zotero.png Binary files differindex fe80851fb3..fe80851fb3 100644 --- a/academic/zotero/zotero.png +++ b/academic/zotero-gtk2/zotero.png diff --git a/academic/zotero/README b/academic/zotero/README index 5979cc3be2..90a652ecda 100644 --- a/academic/zotero/README +++ b/academic/zotero/README @@ -1,15 +1,32 @@ -Zotero [zoh-TAIR-oh] is a free, easy-to-use tool to help you collect, -organize, cite, and share your research sources. - -Zotero collects all your research in a single, searchable interface. -You can add PDFs, images, audio / video files, snapshots of web pages, -and really anything else. Zotero automatically indexes the full-text -content of your library, enabling you to find exactly what you are -looking for with just a few keystrokes. - -Zotero is the only research tool that automatically senses content in -your web browser, allowing you to add it to your personal library with -a single click. Whether you're searching for a preprint on arXiv.org, -a journal article from JSTOR, a news story from the New York Times, or -a book from your university library catalog, Zotero has you covered -with support for thousands of sites. +Zotero is a free, easy-to-use tool to help you collect, organize, +cite, and share research. + +Zotero is the only software that automatically senses research on +the web. Need an article from JSTOR or a preprint from arXiv.org? +A news story from the New York Times or a book from a library? +Zotero has you covered, everywhere. + +Zotero helps you organize your research any way you want. You can +sort items into collections and tag them with keywords. Or create +saved searches that automatically fill with relevant materials as +you work. + +Zotero instantly creates references and bibliographies for any +text editor, and directly inside Word, LibreOffice, and Google +Docs. With support for over 100,000 citation styles, you can +format your work to match any style guide or publication. + +Zotero can optionally synchronize your data across devices, +keeping your notes, files, and bibliographic records seamlessly +up to date. If you decide to sync, you can also always access +your research from any web browser. + +Zotero lets you co-write a paper with a colleague, distribute +course materials to students, or build a collaborative +bibliography. You can share a Zotero library with as many +people you like, at no cost. + +Zotero is open source and developed by an independent, +nonprofit organization that has no financial interest in your +private information. With Zotero, you always stay in control +of your own data. diff --git a/academic/zotero/doinst.sh b/academic/zotero/doinst.sh index 5fb28930db..65c7e2eeb9 100644 --- a/academic/zotero/doinst.sh +++ b/academic/zotero/doinst.sh @@ -1,3 +1,9 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/zotero/slack-desc b/academic/zotero/slack-desc index d051f78252..fc426aba92 100644 --- a/academic/zotero/slack-desc +++ b/academic/zotero/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| zotero: zotero (Collect, organize, cite, and share research sources) zotero: -zotero: Zotero automatically senses content in your web browser, allowing -zotero: you to add it to your personal library. Zotero collects all your -zotero: research in a single, searchable interface. You can add PDFs, -zotero: images, audio / video files, snapshots of web pages, and really -zotero: anything else. Zotero automatically indexes the full-text content -zotero: of your library, enabling you to find exactly what you are looking -zotero: for with just a few keystrokes. +zotero: Zotero is a free, easy-to-use tool to help you collect, organize, +zotero: cite, and share research. +zotero: +zotero: +zotero: +zotero: zotero: zotero: Homepage: https://www.zotero.org/ +zotero: diff --git a/academic/zotero/zotero.SlackBuild b/academic/zotero/zotero.SlackBuild index c8a15a366b..db10f91ca6 100644 --- a/academic/zotero/zotero.SlackBuild +++ b/academic/zotero/zotero.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for zotero -# Copyright 2018-2020 Andrew Payne phalange@komputermatrix.com +# Copyright 2018-2024 Andrew Payne phalange@komputermatrix.com # Copyright 2014-2018 Petar Petrov slackalaxy@gmail.com # All rights reserved. # @@ -27,7 +27,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=zotero SRCNAM=Zotero -VERSION=${VERSION:-5.0.85} +VERSION=${VERSION:-6.0.35} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -76,15 +76,27 @@ mkdir -p $PKG/{usr/bin,opt/$PRGNAM} cp -a * $PKG/opt/$PRGNAM ln -s /opt/$PRGNAM/zotero $PKG/usr/bin/$PRGNAM +# put the icons in the right place +mkdir -p $PKG/usr/share/icons/hicolor/{16x16,32x32,48x48,256x256,scalable}/apps +cp $PKG/opt/$PRGNAM/chrome/icons/default/default16.png \ + $PKG/usr/share/icons/hicolor/16x16/apps/zotero.png +cp $PKG/opt/$PRGNAM/chrome/icons/default/default32.png \ + $PKG/usr/share/icons/hicolor/32x32/apps/zotero.png +cp $PKG/opt/$PRGNAM/chrome/icons/default/default48.png \ + $PKG/usr/share/icons/hicolor/48x48/apps/zotero.png +cp $PKG/opt/$PRGNAM/chrome/icons/default/default256.png \ + $PKG/usr/share/icons/hicolor/256x256/apps/zotero.png +cp $PKG/opt/$PRGNAM/chrome/icons/default/main-window.ico \ + $PKG/usr/share/icons/hicolor/scalable/apps/zotero.ico + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -mkdir -p $PKG/usr/share/{applications,pixmaps} -cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications -cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps/$PRGNAM.png +mkdir -p $PKG/usr/share/applications +cat $CWD/$PRGNAM.desktop > $PKG/usr/share/applications/$PRGNAM.desktop mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/zotero/zotero.desktop b/academic/zotero/zotero.desktop index 24e542f951..277ba1f7aa 100644 --- a/academic/zotero/zotero.desktop +++ b/academic/zotero/zotero.desktop @@ -1,6 +1,6 @@ [Desktop Entry] Type=Application -Name=Zotero Standalone +Name=Zotero Icon=zotero Exec=zotero %f Categories=Office diff --git a/academic/zotero/zotero.info b/academic/zotero/zotero.info index 564a6702dd..ef23199303 100644 --- a/academic/zotero/zotero.info +++ b/academic/zotero/zotero.info @@ -1,10 +1,10 @@ PRGNAM="zotero" -VERSION="5.0.85" +VERSION="6.0.35" HOMEPAGE="https://www.zotero.org/" -DOWNLOAD="https://download.zotero.org/client/release/5.0.85/Zotero-5.0.85_linux-i686.tar.bz2" -MD5SUM="196d758dc19a658a54d30877fe0c41b2" -DOWNLOAD_x86_64="https://download.zotero.org/client/release/5.0.85/Zotero-5.0.85_linux-x86_64.tar.bz2" -MD5SUM_x86_64="6509c159079ed59c2c95ac0132dc2328" +DOWNLOAD="https://download.zotero.org/client/release/6.0.35/Zotero-6.0.35_linux-i686.tar.bz2" +MD5SUM="2fc1598b9221cfd545913b97061661d7" +DOWNLOAD_x86_64="https://download.zotero.org/client/release/6.0.35/Zotero-6.0.35_linux-x86_64.tar.bz2" +MD5SUM_x86_64="9fe5026af4b30da8a50b40f576602704" REQUIRES="" MAINTAINER="Andrew Payne" EMAIL="phalange@komputermatrix.com" |
