diff options
Diffstat (limited to 'academic')
796 files changed, 21077 insertions, 2792 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/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/DRAMSys/DRAMSys.SlackBuild b/academic/DRAMSys/DRAMSys.SlackBuild new file mode 100644 index 0000000000..bf56134fd2 --- /dev/null +++ b/academic/DRAMSys/DRAMSys.SlackBuild @@ -0,0 +1,143 @@ +#!/bin/bash + +# Slackware build script for DRAMSys + +# 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=DRAMSys +VERSION=${VERSION:-20220830} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +COMMIT=09f6dcbb91351e6ee7cadfc7bc8b29d97625db8f + +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 {} \; + + +# 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 + 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" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_CXX_STANDARD=17 \ + $OPT \ + -DCMAKE_BUILD_TYPE=Release ../DRAMSys + make +# make install/strip DESTDIR=$PKG +cd .. + +# 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 + +find $PKG -depth -type d -empty -delete || 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/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/DRAMSys/slack-desc b/academic/DRAMSys/slack-desc new file mode 100644 index 0000000000..b1fe79727d --- /dev/null +++ b/academic/DRAMSys/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------------------------------------------------------| +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/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 d0049728d1..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:-3} +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 diff --git a/academic/EMBOSS/EMBOSS.SlackBuild b/academic/EMBOSS/EMBOSS.SlackBuild index b3546bc77d..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:-3} +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 @@ -106,6 +113,10 @@ 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 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 35ce05e04b..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 2019-2022, 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=${VERSION:-4.11} +VERSION=${VERSION:-4.14} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} -SRCVER=${SRCVER:-4.11} +SRCVER=${SRCVER:-4.14} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -84,33 +84,30 @@ cp $CWD/tetgen1.5.1-beta1.tar.gz 3rdparty/pkg autoreconf -i ./configure \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ --prefix=/usr \ --sysconfdir=/etc \ --disable-mumps \ - --with-petsc=/usr/lib${LIBDIRSUFFIX}/petsc/conf/petscvariables \ --with-mpi=/usr/bin/mpic++ \ --enable-hpddm \ --enable-opengl find . -name Makefile -exec sed -i 's+^gcc+gcc =+' {} \; find . -name Makefile -exec sed -i 's+^dir+dir =+' {} \; +find . -name Makefile -exec sed -i "s:/usr/lib/ff++/:/usr/lib${LIBDIRSUFFIX}/ff++/:" {} \; -## TODO: Enable mumps - FreeFem fails to compile with this option enabled up to now +## TODO: Enable mumps make make install DESTDIR=$PKG -if [ "$ARCH" = "x86_64" ]; then - mv $PKG/usr/lib $PKG/usr/lib${LIBDIRSUFFIX} -fi - 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 990f463359..d936d143c5 100644 --- a/academic/FreeFem/FreeFem.info +++ b/academic/FreeFem/FreeFem.info @@ -1,14 +1,14 @@ PRGNAM="FreeFem" -VERSION="4.11" +VERSION="4.14" HOMEPAGE="https://freefem.org/" -DOWNLOAD="https://github.com/FreeFem/FreeFem-sources/archive/v4.11/FreeFem-sources-4.11.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="b6355b01842204d068ce4530dd45b32f \ +MD5SUM="ca73e2353138e6c6cebdd9cc8df60b7f \ 5465e67079419a69e0116de24fce58fe \ 3d55c197bcbfc611b7ced6f343643756" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="arpack-ng hdf5 suitesparse petsc" +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 index 0fbdebc116..1ee40ab8ca 100644 --- a/academic/Gabedit/Gabedit.SlackBuild +++ b/academic/Gabedit/Gabedit.SlackBuild @@ -112,7 +112,7 @@ 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 ChangeLog License $PKG/usr/doc/$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 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/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/Gridcoin-Research/Gridcoin-Research.SlackBuild b/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild index 84056b7168..9a04eb6fc4 100644 --- a/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild +++ b/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=Gridcoin-Research -VERSION=${VERSION:-5.3.3.0} +VERSION=${VERSION:-5.4.7.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/Gridcoin-Research/Gridcoin-Research.info b/academic/Gridcoin-Research/Gridcoin-Research.info index 48b26b3c2d..a28295c32f 100644 --- a/academic/Gridcoin-Research/Gridcoin-Research.info +++ b/academic/Gridcoin-Research/Gridcoin-Research.info @@ -1,8 +1,8 @@ PRGNAM="Gridcoin-Research" -VERSION="5.3.3.0" +VERSION="5.4.7.0" HOMEPAGE="https://gridcoin.us/" -DOWNLOAD="https://github.com/gridcoin-community/Gridcoin-Research/archive/5.3.3.0/Gridcoin-Research-5.3.3.0.tar.gz" -MD5SUM="101fe4826b60f84321be3f9c5fddd5db" +DOWNLOAD="https://github.com/gridcoin-community/Gridcoin-Research/archive/5.4.7.0/Gridcoin-Research-5.4.7.0.tar.gz" +MD5SUM="8c42dfd8deaa754d78aa248785e724b0" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/Gridcoin-Research/README b/academic/Gridcoin-Research/README index c5d43b5115..2fc9a1a4f5 100644 --- a/academic/Gridcoin-Research/README +++ b/academic/Gridcoin-Research/README @@ -16,8 +16,24 @@ and any other configurations that you require. For details, see https://wiki.gridcoin.us/Gridcoinresearch_config_file and in /usr/share/Gridcoin-Research-$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 25dd19977b..44e4fea74b 100644 --- a/academic/Kst/Kst.SlackBuild +++ b/academic/Kst/Kst.SlackBuild @@ -1,7 +1,7 @@ #!/bin/bash # Slackware build script for Kst -# Copyright 2014-2022 Fellype do Nascimento, Guaratingueta, Brazil +# 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 @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=Kst -VERSION=${VERSION:-20220116_2b8e03e} +VERSION=${VERSION:-20221025_5fdd819} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -51,10 +51,10 @@ TMP=${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 [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC"; SLKLDFLAGS="-L/usr/lib64"; LIBDIRSUFFIX="64" fi diff --git a/academic/Kst/Kst.info b/academic/Kst/Kst.info index 9ade76a485..adff979071 100644 --- a/academic/Kst/Kst.info +++ b/academic/Kst/Kst.info @@ -1,10 +1,10 @@ PRGNAM="Kst" -VERSION="20220116_2b8e03e" -HOMEPAGE="https://kst-plot.kde.org/" -DOWNLOAD="https://ponce.cc/slackware/sources/repo/Kst-20220116_2b8e03e.tar.xz" -MD5SUM="1b6e1fbe3fdfc27441140fd9b761eba4" +VERSION="20221025_5fdd819" +HOMEPAGE="https://apps.kde.org/kst/" +DOWNLOAD="https://sourceforge.net/projects/slackbuildsdirectlinks/files/Kst/Kst-20221025_5fdd819.tar.xz" +MD5SUM="402fac69d4701cd7f223159e70b73439" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="scipy" +REQUIRES="python2-scipy" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/Kst/README b/academic/Kst/README index 87d0adcf94..314ac53aab 100644 --- a/academic/Kst/README +++ b/academic/Kst/README @@ -16,6 +16,7 @@ without KDE, but you get additional features when running on a platform with KDE). Optional dependencies are: +- hdf5 (provides support for the HDF5 file formats) - netcdf (which provides support for files in the netCDF format) - muParser (which is used in the general non-linear fitting plugin) - GetData (which provides support for files in the Dirfile format) diff --git a/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild b/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild index a64fe00125..99d17512b7 100644 --- a/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild +++ b/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild @@ -31,14 +31,8 @@ TAG=${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/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 c63bcee582..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, 2021, 2022 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=${VERSION:-9} +VERSION=${VERSION:-11} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/OpenFOAM/OpenFOAM.info b/academic/OpenFOAM/OpenFOAM.info index 832c21f8af..52786f5932 100644 --- a/academic/OpenFOAM/OpenFOAM.info +++ b/academic/OpenFOAM/OpenFOAM.info @@ -1,10 +1,10 @@ PRGNAM="OpenFOAM" -VERSION="9" +VERSION="11" HOMEPAGE="https://openfoam.org/" -DOWNLOAD="https://github.com/OpenFOAM/OpenFOAM-9/archive/version-9/OpenFOAM-9-version-9.tar.gz \ - https://github.com/OpenFOAM/ThirdParty-9/archive/version-9/ThirdParty-9-version-9.tar.gz" -MD5SUM="c588fcabc7a8b48cd9677411a6c8cb0e \ - 5fd71fcb1dedc7c55a539fd2173f58d3" +DOWNLOAD="https://github.com/OpenFOAM/OpenFOAM-11/archive/version-11/OpenFOAM-11-version-11.tar.gz \ + https://github.com/OpenFOAM/ThirdParty-11/archive/version-11/ThirdParty-11-version-11.tar.gz" +MD5SUM="81862ded202dc13eb285d399e2ce1741 \ + fcd80fb7fa8d011d1a055cd30323ae58" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi CGAL" diff --git a/academic/OpenFOAM/OpenFOAM.sh b/academic/OpenFOAM/OpenFOAM.sh index 1b2052b83b..02c71aa6ed 100644 --- a/academic/OpenFOAM/OpenFOAM.sh +++ b/academic/OpenFOAM/OpenFOAM.sh @@ -1 +1 @@ -. /opt/OpenFOAM/OpenFOAM-9/etc/bashrc +. /opt/OpenFOAM/OpenFOAM-11/etc/bashrc diff --git a/academic/OpenFOAM/README b/academic/OpenFOAM/README index d91ec421c8..a72cf10568 100644 --- a/academic/OpenFOAM/README +++ b/academic/OpenFOAM/README @@ -10,4 +10,4 @@ multi-core processors and multi-processor computers. Optional dependency: graphviz (for documentation with graphs) You can build with multiple jobs by setting the MAKEFLAGS environment -variable. +variable (e.g. export MAKEFLAGS="-j$(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/OpenVSP/doinst.sh b/academic/OpenVSP/doinst.sh new file mode 100644 index 0000000000..aea0f894eb --- /dev/null +++ b/academic/OpenVSP/doinst.sh @@ -0,0 +1,13 @@ +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/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/R/COPYING b/academic/R/COPYING new file mode 100644 index 0000000000..94a9ed024d --- /dev/null +++ b/academic/R/COPYING @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + + Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. If such problems arise substantially in other domains, we +stand ready to extend this provision to those domains in future versions +of the GPL, as needed to protect the freedom of users. + + Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish to +avoid the special danger that patents applied to a free program could +make it effectively proprietary. To prevent this, the GPL assures that +patents cannot be used to render the program non-free. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + <one line to give the program's name and a brief idea of what it does.> + Copyright (C) <year> <name of author> + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + <program> Copyright (C) <year> <name of author> + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +<http://www.gnu.org/licenses/>. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +<http://www.gnu.org/philosophy/why-not-lgpl.html>. diff --git a/academic/R/R.SlackBuild b/academic/R/R.SlackBuild index f918eeba91..3ee98369fc 100644 --- a/academic/R/R.SlackBuild +++ b/academic/R/R.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=R -VERSION=${VERSION:-4.2.0} +VERSION=${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 . \ @@ -115,7 +115,7 @@ 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 {COPYING,README,SVN-REVISION,VERSION,VERSION-NICK} \ +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 diff --git a/academic/R/R.info b/academic/R/R.info index d3d3eded86..45cf892f94 100644 --- a/academic/R/R.info +++ b/academic/R/R.info @@ -1,8 +1,8 @@ PRGNAM="R" -VERSION="4.2.0" +VERSION="4.3.3" HOMEPAGE="https://www.r-project.org/" -DOWNLOAD="https://cran.r-project.org/src/base/R-4/R-4.2.0.tar.gz" -MD5SUM="f1d4b7fec9e15835fdcfb8369ef039c0" +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/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/STAR.SlackBuild b/academic/STAR/STAR.SlackBuild index c72e15ed31..bc4913730e 100644 --- a/academic/STAR/STAR.SlackBuild +++ b/academic/STAR/STAR.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for STAR -# Copyright 2018-2022 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 @@ -25,10 +25,11 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=STAR -VERSION=${VERSION:-2.7.10a} +VERSION=${VERSION:-2.7.11b} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} + # This script is set for processors that support "Advanced Vector Extensions", # (AVX), included since 2008 in Intel processors (Sandy Bridge) and since 2011 # in AMD cpus (Bulldozer). AVX is an implementation of "Single Instruction @@ -46,9 +47,6 @@ if [ -z "$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.$PKGTYPE" exit 0 @@ -119,6 +117,7 @@ cp -a \ source/parametersDefault doc/${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 > $PKG/install/slack-desc diff --git a/academic/STAR/STAR.info b/academic/STAR/STAR.info index 939f358cb0..6c9a4bff5e 100644 --- a/academic/STAR/STAR.info +++ b/academic/STAR/STAR.info @@ -1,10 +1,10 @@ PRGNAM="STAR" -VERSION="2.7.10a" +VERSION="2.7.11b" HOMEPAGE="https://github.com/alexdobin/STAR" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.7.10a/STAR-2.7.10a.tar.gz" -MD5SUM_x86_64="8f0c982f946e1b93a0f499ab44a4b040" +DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.7.11b/STAR-2.7.11b.tar.gz" +MD5SUM_x86_64="9e21d9930989b1be3ffc50b818489d55" REQUIRES="" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/SU2/README b/academic/SU2/README index fd4519ee57..b70ea47277 100644 --- a/academic/SU2/README +++ b/academic/SU2/README @@ -8,12 +8,26 @@ flow, elasticity, electrodynamics, chemically-reacting flows, and many others. Under active development by individuals all around the world on GitHub and is released under an open-source license. -Builds parallel version by default. -For serial version, delete the following configuration lines from -su2.Slackbuild script: +Optional dependencies: mpich or openmpi; OpenBLAS ---enable-mpi ---with-cxx=/usr/bin/mpicxx ---with-cc=/usr/bin/mpicc +Build options can be controlled by passing MESONOPTS to the SlackBuild +script. -and then no need for mpich / openmpi. +Builds parallel version by default if mpich or openmpi installed. If +mpich, use: + +MESONOPTS="-Dcustom-mpi=true -Dextra-deps=mpich" + +For OpenBlas, add "-Denable-openblas=true" + +See the docs for a complete list of options. + +Following installation, add these to your ~/.bashrc: + +export SU2_RUN=/usr/bin +export PATH=$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 69f27f0f98..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 @@ -22,16 +22,10 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# 20220324 bkw: Modified by SlackBuilds.org: mark as unsupported -# on 32-bit, since it won't compile and it's a non-trivial fix. The -# maintainer of this script is welcome to fix the 32-bit build, but -# the SBo admins won't. - - cd $(dirname $0) ; CWD=$(pwd) PRGNAM=SU2 -VERSION=${VERSION:-6.2.0} +VERSION=${VERSION:-7.5.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -44,9 +38,6 @@ if [ -z "$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 @@ -85,33 +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 f19f0bc9f0..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="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://github.com/su2code/SU2/archive/v6.2.0/SU2-6.2.0.tar.gz" -MD5SUM_x86_64="c74d1dbe52d6239c4f9c75cbd3102a90" -REQUIRES="mpich" +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/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 df1270f38e..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=${VERSION:-2.5.0} -BUILD=${BUILD:-2} +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 @@ -196,7 +198,7 @@ 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 @@ -204,6 +206,8 @@ 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/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/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 $PKG diff --git a/academic/aliview/aliview.info b/academic/aliview/aliview.info index a640eb9ba8..41abed4471 100644 --- a/academic/aliview/aliview.info +++ b/academic/aliview/aliview.info @@ -1,8 +1,8 @@ PRGNAM="aliview" -VERSION="1.27" +VERSION="1.28" HOMEPAGE="http://www.ormbunkar.se/aliview/" -DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-versions-all/linux-version-1.27/aliview.tgz" -MD5SUM="5e16b3ce0a9680972f5a271e5d4ac6b9" +DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-versions-all/linux-version-1.28/aliview.tgz" +MD5SUM="1eac87a0f88f3815707df27d3a9970dc" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="zulu-openjdk11" diff --git a/academic/amd/amd.SlackBuild b/academic/amd/amd.SlackBuild index b8c3a202cb..4cca1d563e 100644 --- a/academic/amd/amd.SlackBuild +++ b/academic/amd/amd.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${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/antiprism/antiprism.SlackBuild b/academic/antiprism/antiprism.SlackBuild index 85c57885b0..a294efedfd 100644 --- a/academic/antiprism/antiprism.SlackBuild +++ b/academic/antiprism/antiprism.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 @@ -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" diff --git a/academic/aris/aris.SlackBuild b/academic/aris/aris.SlackBuild index cedc949c26..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 @@ -75,15 +74,14 @@ 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="$SLKCFLAGS -w -Wl,--allow-multiple-definition" \ +CFLAGS="$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/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="$abs_top_builddir"]) + + AC_CONFIG_FILES([ + arpackdef.h +diff --git a/pkg-config/tstAutotoolsInstall.sh.in b/tstAutotoolsInstall.sh.in +old mode 100755 +new mode 100644 +rename from pkg-config/tstAutotoolsInstall.sh.in +rename to tstAutotoolsInstall.sh.in diff --git a/academic/arpack/arpack.SlackBuild b/academic/arpack/arpack.SlackBuild index d77ffd6eb1..cc21abf76f 100644 --- a/academic/arpack/arpack.SlackBuild +++ b/academic/arpack/arpack.SlackBuild @@ -33,7 +33,7 @@ PKGTYPE=${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" diff --git a/academic/avogadroapp/README b/academic/avogadroapp/README index 690df5da4f..692ec7f1c2 100644 --- a/academic/avogadroapp/README +++ b/academic/avogadroapp/README @@ -8,15 +8,16 @@ 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 avogadroapp is built with static libraries. If you -want to enable the building with shared libraries, pass the variable -SHARED=yes to the script: +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=yes ./avogadroapp.SlackBuild - -Note that if you build avogadroapp with shared libraries, hdf5 is -not required as needed dependency. + 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 index 506cf84432..e8b6905bd1 100644 --- a/academic/avogadroapp/avogadroapp.SlackBuild +++ b/academic/avogadroapp/avogadroapp.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=avogadroapp -VERSION=${VERSION:-1.95.1} +VERSION=${VERSION:-1.97.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -43,7 +43,7 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then exit 0 fi -SHAREDLIBS="" ; [ "${SHARED:-no}" = "yes" ] && SHAREDLIBS="-DBUILD_SHARED_LIBS=ON" +SHAREDLIBS="" ; [ "${SHARED:-yes}" = "yes" ] && SHAREDLIBS="-DBUILD_SHARED_LIBS=ON" TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM @@ -68,12 +68,13 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION avogadro-i18n +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.tar.gz +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 diff --git a/academic/avogadroapp/avogadroapp.info b/academic/avogadroapp/avogadroapp.info index f5539dee43..e98567822d 100644 --- a/academic/avogadroapp/avogadroapp.info +++ b/academic/avogadroapp/avogadroapp.info @@ -1,12 +1,12 @@ PRGNAM="avogadroapp" -VERSION="1.95.1" +VERSION="1.97.0" HOMEPAGE="https://github.com/OpenChemistry/avogadroapp" -DOWNLOAD="https://github.com/OpenChemistry/avogadroapp/archive/1.95.1/avogadroapp-1.95.1.tar.gz \ - https://github.com/giandex/misc/raw/main/avogadro-i18n.tar.gz" -MD5SUM="3281a73a93810276a014506041094ee3 \ - 538f178ec33f948f1391f877557718a2" +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 hdf5" +REQUIRES="avogadrolibs" MAINTAINER="Giancarlo Dessì" EMAIL="slack@giand.it" diff --git a/academic/avogadrolibs/README b/academic/avogadrolibs/README index 4877412d76..4990e7bf74 100644 --- a/academic/avogadrolibs/README +++ b/academic/avogadrolibs/README @@ -15,6 +15,7 @@ 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 @@ -26,3 +27,11 @@ 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 index fc45449bca..825baf7b68 100644 --- a/academic/avogadrolibs/avogadrolibs.SlackBuild +++ b/academic/avogadrolibs/avogadrolibs.SlackBuild @@ -25,12 +25,13 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=avogadrolibs -VERSION=${VERSION:-1.95.1} -BUILD=${BUILD:-1} +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 "$( uname -m )" in @@ -48,6 +49,7 @@ fi #These are features which are disabled by default USEHDF5="" ; [ "${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="" ; [ "${LIBMSYM:-yes}" = "no" ] && USELIBMSYM="-DUSE_LIBMSYM=OFF" @@ -58,6 +60,7 @@ USEMMTF="" ; [ "${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" @@ -88,7 +91,8 @@ tar xvf $CWD/crystals-$CVERSION.tar.gz mv molecules-$MVERSION molecules mv crystals-$CVERSION crystals if [ "${PYTHON}" = "yes" ]; then - tar xvf $CWD/avogadrogenerators.tar.gz + tar xvf $CWD/avogenerators-$AVERSION.tar.gz + mv avogenerators-$AVERSION avogadrogenerators fi # Now we can change directory to $PRGNAM-$VERSION @@ -102,8 +106,18 @@ find -L . \ # 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" \ @@ -118,6 +132,7 @@ cd build $USELIBMSYM \ $USESPGLIB \ $USEMMTF \ + $USEVTK \ .. make make install DESTDIR=$PKG @@ -129,7 +144,7 @@ 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 *.md LICENSE $PKG/usr/doc/$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 diff --git a/academic/avogadrolibs/avogadrolibs.info b/academic/avogadrolibs/avogadrolibs.info index 98b38a281f..50472adccb 100644 --- a/academic/avogadrolibs/avogadrolibs.info +++ b/academic/avogadrolibs/avogadrolibs.info @@ -1,14 +1,16 @@ PRGNAM="avogadrolibs" -VERSION="1.95.1" +VERSION="1.97.0" HOMEPAGE="https://github.com/OpenChemistry/avogadrolibs" -DOWNLOAD="https://github.com/OpenChemistry/avogadrolibs/archive/1.95.1/avogadrolibs-1.95.1.tar.gz \ +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/giandex/misc/raw/main/avogadrogenerators.tar.gz" -MD5SUM="8e86fd39799bcc614f8982b3408f30b5 \ + 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 \ - 4d8fe7ddb99069d777bead7d261abac9" + d115ab0f5f4dbf10d2ba2d1191c80a59 \ + e1b3c1d6b951ed83a037567490d75f1d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="molequeue mmtf-cpp libmsym spglib" 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/bcftools/bcftools.SlackBuild b/academic/bcftools/bcftools.SlackBuild index 5f99c3f222..b7a8433557 100644 --- a/academic/bcftools/bcftools.SlackBuild +++ b/academic/bcftools/bcftools.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bcftools -# Copyright 2017-2022 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=${VERSION:-1.15.1} +VERSION=${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 6ac9c62f49..1998ed001c 100644 --- a/academic/bcftools/bcftools.info +++ b/academic/bcftools/bcftools.info @@ -1,8 +1,8 @@ PRGNAM="bcftools" -VERSION="1.15.1" +VERSION="1.19" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.15.1/bcftools-1.15.1.tar.bz2" -MD5SUM="37e0cbdbcbeb844b8592f4a2acb2fe3f" +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/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/bibletime.SlackBuild b/academic/bibletime/bibletime.SlackBuild index 0db263921f..a25bde4b12 100644 --- a/academic/bibletime/bibletime.SlackBuild +++ b/academic/bibletime/bibletime.SlackBuild @@ -27,7 +27,7 @@ # 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) 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 b617f82986..f63d0e2e4c 100644 --- a/academic/boinc/README +++ b/academic/boinc/README @@ -18,14 +18,15 @@ Building 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. (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). See -README.Slackware for details. +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 index 5dc39e60ab..c0f1ceb4e3 100644 --- a/academic/boinc/README.Slackware +++ b/academic/boinc/README.Slackware @@ -2,8 +2,9 @@ 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 files +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. @@ -20,8 +21,14 @@ if [ -x /etc/rc.d/rc.boinc ]; then /etc/rc.d/rc.boinc stop fi -Note: The default configuration enables boinc control on the running -host via boinccmg or boincmgr on th same running host. To truly run +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 c093c71325..8f8330ac87 100644 --- a/academic/boinc/boinc.SlackBuild +++ b/academic/boinc/boinc.SlackBuild @@ -22,17 +22,17 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # -# 01MAY2022: +# 08DEC2022: # Version update -# Removed need for STATIC wxWidgets-3.0 to avoid conflicts. +# switched to wxWidgets-3.2 # Bypass wxconfig symlink for compatibility. cd $(dirname $0) ; CWD=$(pwd) PRGNAM=boinc -VERSION=${VERSION:-7.18.1} -BRANCH=${BRANCH:-7.18} -BUILD=${BUILD:-2} +VERSION=${VERSION:-7.24.1} +BRANCH=${BRANCH:-7.24} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -70,7 +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 [ "$BOINCMGR" = "yes" ]; then @@ -107,7 +107,7 @@ CXXFLAGS="$SLKCFLAGS" \ --disable-shared \ $do_mgr \ --with-x \ - --with-wx-config=/usr/lib$LIBDIRSUFFIX/wx/config/gtk3-unicode-3.0 \ + --with-wx-config=/usr/lib$LIBDIRSUFFIX/wx/config/gtk3-unicode-3.2 \ --build=$ARCH-slackware-linux make diff --git a/academic/boinc/boinc.info b/academic/boinc/boinc.info index 259064a227..4d1bb74cdd 100644 --- a/academic/boinc/boinc.info +++ b/academic/boinc/boinc.info @@ -1,10 +1,10 @@ PRGNAM="boinc" -VERSION="7.18.1" +VERSION="7.24.1" HOMEPAGE="https://boinc.berkeley.edu/" -DOWNLOAD="https://github.com/BOINC/boinc/archive/client_release/7.18/7.18.1/boinc-client_release-7.18-7.18.1.tar.gz" -MD5SUM="039fa9d0ad58a23784a162394ac1c599" +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/rc.boinc.txt b/academic/boinc/rc.boinc.txt index fe3cf94b76..e84583ed0b 100644 --- a/academic/boinc/rc.boinc.txt +++ b/academic/boinc/rc.boinc.txt @@ -1,105 +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=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 /usr/bin/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
+#!/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 d5b59d2871..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} @@ -64,8 +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 \ @@ -73,14 +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 ca9409d9e8..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="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.0/bowtie-1.3.0-src.zip" -MD5SUM_x86_64="2055d1ab066a8f3f015bdffa26509335" +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/bowtie2.SlackBuild b/academic/bowtie2/bowtie2.SlackBuild index 967260c70c..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 2018-2022 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=${VERSION:-2.4.5} +VERSION=${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 diff --git a/academic/bowtie2/bowtie2.info b/academic/bowtie2/bowtie2.info index 1ab264f29c..6942bdcfcd 100644 --- a/academic/bowtie2/bowtie2.info +++ b/academic/bowtie2/bowtie2.info @@ -1,10 +1,10 @@ PRGNAM="bowtie2" -VERSION="2.4.5" +VERSION="2.5.3" HOMEPAGE="https://github.com/BenLangmead/bowtie2/releases" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://github.com/BenLangmead/bowtie2/archive/v2.4.5/bowtie2-2.4.5.tar.gz" -MD5SUM_x86_64="efe20fd1adfd440941c83611a63cc5e3" +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/README b/academic/bpp-core/README new file mode 100644 index 0000000000..6210addd2e --- /dev/null +++ b/academic/bpp-core/README @@ -0,0 +1,8 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ Core Library. diff --git a/academic/bpp-core/bpp-core.SlackBuild b/academic/bpp-core/bpp-core.SlackBuild new file mode 100644 index 0000000000..ea5ae35b52 --- /dev/null +++ b/academic/bpp-core/bpp-core.SlackBuild @@ -0,0 +1,106 @@ +#!/bin/bash + +# Slackware build script for bpp-core + +# Copyright 2017-2022 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=bpp-core +VERSION=${VERSION:-2.4.1} +BUILD=${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" +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 {} \; + +# 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 +cd build + cmake \ + -DCMAKE_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -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 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 +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/bpp-core/bpp-core.info b/academic/bpp-core/bpp-core.info new file mode 100644 index 0000000000..a5d5073b1c --- /dev/null +++ b/academic/bpp-core/bpp-core.info @@ -0,0 +1,10 @@ +PRGNAM="bpp-core" +VERSION="2.4.1" +HOMEPAGE="https://github.com/BioPP/bpp-core/" +DOWNLOAD="https://github.com/BioPP/bpp-core/archive/v2.4.1/bpp-core-2.4.1.tar.gz" +MD5SUM="25040b547ca63e57cb79de5815ef2584" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" 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-core/slack-desc b/academic/bpp-core/slack-desc new file mode 100644 index 0000000000..c26a09a443 --- /dev/null +++ b/academic/bpp-core/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------------------------------------------------------| +bpp-core: bpp-core (Bio++ Core Library) +bpp-core: +bpp-core: Contains the Bio++ Core Library. +bpp-core: +bpp-core: Git: https://github.com/BioPP/bpp-core +bpp-core: +bpp-core: +bpp-core: +bpp-core: +bpp-core: +bpp-core: diff --git a/academic/bpp-phyl-omics/README b/academic/bpp-phyl-omics/README new file mode 100644 index 0000000000..c5ebc164c7 --- /dev/null +++ b/academic/bpp-phyl-omics/README @@ -0,0 +1,8 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ Phylogenetic Omics Library. diff --git a/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild b/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild new file mode 100644 index 0000000000..31a4b60cc8 --- /dev/null +++ b/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for bpp-phyl-omics + +# Copyright 2017-2022 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=bpp-phyl-omics +VERSION=${VERSION:-2.4.1} +BUILD=${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" +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 {} \; + +sed -i "s|cmake-package-location lib/cmake|cmake-package-location lib${LIBDIRSUFFIX}/cmake|" CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$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 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 +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/bpp-phyl-omics/bpp-phyl-omics.info b/academic/bpp-phyl-omics/bpp-phyl-omics.info new file mode 100644 index 0000000000..56f4abcbb4 --- /dev/null +++ b/academic/bpp-phyl-omics/bpp-phyl-omics.info @@ -0,0 +1,10 @@ +PRGNAM="bpp-phyl-omics" +VERSION="2.4.1" +HOMEPAGE="https://github.com/BioPP/bpp-phyl-omics/" +DOWNLOAD="https://github.com/BioPP/bpp-phyl-omics/archive/v2.4.1/bpp-phyl-omics-2.4.1.tar.gz" +MD5SUM="7c1c1d06e0c0ff61ddecc7fcc4064f51" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp-phyl bpp-seq-omics" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp-phyl-omics/slack-desc b/academic/bpp-phyl-omics/slack-desc new file mode 100644 index 0000000000..e76c164009 --- /dev/null +++ b/academic/bpp-phyl-omics/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------------------------------------------------------| +bpp-phyl-omics: bpp-phyl-omics (Bio++ Phylogenetic Omics Library) +bpp-phyl-omics: +bpp-phyl-omics: Contains the Bio++ Phylogenetic Omics Library +bpp-phyl-omics: +bpp-phyl-omics: Git: https://github.com/BioPP/bpp-phyl-omics +bpp-phyl-omics: +bpp-phyl-omics: +bpp-phyl-omics: +bpp-phyl-omics: +bpp-phyl-omics: +bpp-phyl-omics: diff --git a/academic/bpp-phyl/README b/academic/bpp-phyl/README new file mode 100644 index 0000000000..658bbc2751 --- /dev/null +++ b/academic/bpp-phyl/README @@ -0,0 +1,8 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ Phylogenetic Library. diff --git a/academic/bpp-phyl/bpp-phyl.SlackBuild b/academic/bpp-phyl/bpp-phyl.SlackBuild new file mode 100644 index 0000000000..d1de4c4a79 --- /dev/null +++ b/academic/bpp-phyl/bpp-phyl.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for bpp-phyl + +# Copyright 2017-2022 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=bpp-phyl +VERSION=${VERSION:-2.4.1} +BUILD=${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" +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 {} \; + +sed -i "s|cmake-package-location lib/cmake|cmake-package-location lib${LIBDIRSUFFIX}/cmake|" CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$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 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 +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/bpp-phyl/bpp-phyl.info b/academic/bpp-phyl/bpp-phyl.info new file mode 100644 index 0000000000..65631eb491 --- /dev/null +++ b/academic/bpp-phyl/bpp-phyl.info @@ -0,0 +1,10 @@ +PRGNAM="bpp-phyl" +VERSION="2.4.1" +HOMEPAGE="https://github.com/BioPP/bpp-phyl/" +DOWNLOAD="https://github.com/BioPP/bpp-phyl/archive/v2.4.1/bpp-phyl-2.4.1.tar.gz" +MD5SUM="05c58ac05a1f7525888df2b04c4a800c" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp-seq" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp-phyl/slack-desc b/academic/bpp-phyl/slack-desc new file mode 100644 index 0000000000..591618ed14 --- /dev/null +++ b/academic/bpp-phyl/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------------------------------------------------------| +bpp-phyl: bpp-phyl (Bio++ Phylogenetic Library) +bpp-phyl: +bpp-phyl: Contains the Bio++ Phylogenetic Library. +bpp-phyl: +bpp-phyl: Git: https://github.com/BioPP/bpp-phyl +bpp-phyl: +bpp-phyl: +bpp-phyl: +bpp-phyl: +bpp-phyl: +bpp-phyl: diff --git a/academic/bpp-popgen/README b/academic/bpp-popgen/README new file mode 100644 index 0000000000..0772158a82 --- /dev/null +++ b/academic/bpp-popgen/README @@ -0,0 +1,8 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ Population Genetics Library. diff --git a/academic/bpp-popgen/bpp-popgen.SlackBuild b/academic/bpp-popgen/bpp-popgen.SlackBuild new file mode 100644 index 0000000000..11e65b03be --- /dev/null +++ b/academic/bpp-popgen/bpp-popgen.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for bpp-popgen + +# Copyright 2017-2022 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=bpp-popgen +VERSION=${VERSION:-2.4.1} +BUILD=${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" +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 {} \; + +sed -i "s|cmake-package-location lib/cmake|cmake-package-location lib${LIBDIRSUFFIX}/cmake|" CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$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 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 +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/bpp-popgen/bpp-popgen.info b/academic/bpp-popgen/bpp-popgen.info new file mode 100644 index 0000000000..66439c4bbc --- /dev/null +++ b/academic/bpp-popgen/bpp-popgen.info @@ -0,0 +1,10 @@ +PRGNAM="bpp-popgen" +VERSION="2.4.1" +HOMEPAGE="https://github.com/BioPP/bpp-popgen/" +DOWNLOAD="https://github.com/BioPP/bpp-popgen/archive/v2.4.1/bpp-popgen-2.4.1.tar.gz" +MD5SUM="cdc84495e251b6ff4260385adecbea28" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp-seq" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp-popgen/slack-desc b/academic/bpp-popgen/slack-desc new file mode 100644 index 0000000000..f59a1bdccd --- /dev/null +++ b/academic/bpp-popgen/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------------------------------------------------------| +bpp-popgen: bpp-popgen (Bio++ Population Genetics Library) +bpp-popgen: +bpp-popgen: Contains the Bio++ Population Genetics Library. +bpp-popgen: +bpp-popgen: Git: https://github.com/BioPP/bpp-popgen +bpp-popgen: +bpp-popgen: +bpp-popgen: +bpp-popgen: +bpp-popgen: +bpp-popgen: diff --git a/academic/bpp-seq-omics/README b/academic/bpp-seq-omics/README new file mode 100644 index 0000000000..673e95bd2c --- /dev/null +++ b/academic/bpp-seq-omics/README @@ -0,0 +1,10 @@ +Bio++ Phylogenetic library + +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ Sequence Omics Library. diff --git a/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild b/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild new file mode 100644 index 0000000000..c81730ea5a --- /dev/null +++ b/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for bpp-seq-omics + +# Copyright 2017-2022 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=bpp-seq-omics +VERSION=${VERSION:-2.4.1} +BUILD=${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" +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 {} \; + +sed -i "s|cmake-package-location lib/cmake|cmake-package-location lib${LIBDIRSUFFIX}/cmake|" CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$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 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 +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/bpp-seq-omics/bpp-seq-omics.info b/academic/bpp-seq-omics/bpp-seq-omics.info new file mode 100644 index 0000000000..c2e8b54a2f --- /dev/null +++ b/academic/bpp-seq-omics/bpp-seq-omics.info @@ -0,0 +1,10 @@ +PRGNAM="bpp-seq-omics" +VERSION="2.4.1" +HOMEPAGE="https://github.com/BioPP/bpp-seq-omics/" +DOWNLOAD="https://github.com/BioPP/bpp-seq-omics/archive/v2.4.1/bpp-seq-omics-2.4.1.tar.gz" +MD5SUM="fe5d906c557d94ef1341e78f240119d4" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp-seq" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp-seq-omics/slack-desc b/academic/bpp-seq-omics/slack-desc new file mode 100644 index 0000000000..1e75832c17 --- /dev/null +++ b/academic/bpp-seq-omics/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------------------------------------------------------| +bpp-seq-omics: bpp-seq-omics (Bio++ Sequence Omics Library) +bpp-seq-omics: +bpp-seq-omics: Bio++ Sequence Omics Library +bpp-seq-omics: +bpp-seq-omics: Git: https://github.com/BioPP/bpp-seq-omics +bpp-seq-omics: +bpp-seq-omics: +bpp-seq-omics: +bpp-seq-omics: +bpp-seq-omics: +bpp-seq-omics: diff --git a/academic/bpp-seq/README b/academic/bpp-seq/README new file mode 100644 index 0000000000..080d3ae4f6 --- /dev/null +++ b/academic/bpp-seq/README @@ -0,0 +1,8 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ Sequence Library. diff --git a/academic/bpp-seq/bpp-seq.SlackBuild b/academic/bpp-seq/bpp-seq.SlackBuild new file mode 100644 index 0000000000..298386625e --- /dev/null +++ b/academic/bpp-seq/bpp-seq.SlackBuild @@ -0,0 +1,104 @@ +#!/bin/bash + +# Slackware build script for bpp-seq + +# Copyright 2017-2022 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=bpp-seq +VERSION=${VERSION:-2.4.1} +BUILD=${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" +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 {} \; + +sed -i "s|cmake-package-location lib/cmake|cmake-package-location lib${LIBDIRSUFFIX}/cmake|" CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$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 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 +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/bpp-seq/bpp-seq.info b/academic/bpp-seq/bpp-seq.info new file mode 100644 index 0000000000..62742f6d21 --- /dev/null +++ b/academic/bpp-seq/bpp-seq.info @@ -0,0 +1,10 @@ +PRGNAM="bpp-seq" +VERSION="2.4.1" +HOMEPAGE="https://github.com/BioPP/bpp-seq/" +DOWNLOAD="https://github.com/BioPP/bpp-seq/archive/v2.4.1/bpp-seq-2.4.1.tar.gz" +MD5SUM="bdafc80aab9591ff79556138d6555941" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp-core" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp-seq/slack-desc b/academic/bpp-seq/slack-desc new file mode 100644 index 0000000000..7b629858f4 --- /dev/null +++ b/academic/bpp-seq/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------------------------------------------------------| +bpp-seq: bpp-seq (Bio++ Sequence library) +bpp-seq: +bpp-seq: Contains the Bio++ Sequence Library. +bpp-seq: +bpp-seq: Git: https://github.com/BioPP/bpp-seq +bpp-seq: +bpp-seq: +bpp-seq: +bpp-seq: +bpp-seq: +bpp-seq: diff --git a/academic/bpp1.9-numcalc/README b/academic/bpp1.9-numcalc/README new file mode 100644 index 0000000000..a514a0450e --- /dev/null +++ b/academic/bpp1.9-numcalc/README @@ -0,0 +1,10 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ 1.9 (April 2010) NumCalc Library. It can be +installed along the current Bio++ suite libraries, however they better +not be present at compile time. diff --git a/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild b/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild new file mode 100644 index 0000000000..ea548edbdf --- /dev/null +++ b/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/bash + +# Slackware build script for bpp1.9-utils + +# Copyright 2020-2022 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=bpp1.9-numcalc +SRCNAM=bpp-numcalc +VERSION=${VERSION:-1.8.0} +BUILD=${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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" + +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 {} \; + +# Use custom install place, so libs can coexist with latest bpp +export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH" +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" NumCalc.spec + +source /etc/profile.d/gcc5.sh + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" NumCalc/cmake_install.cmake +sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" NumCalc/cmake_install.cmake + + make + make DESTDIR=$PKG 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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +chmod 0644 AUTHORS ChangeLog COPYING +cp -a \ + AUTHORS ChangeLog 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/bpp1.9-numcalc/bpp1.9-numcalc.info b/academic/bpp1.9-numcalc/bpp1.9-numcalc.info new file mode 100644 index 0000000000..026698cbb2 --- /dev/null +++ b/academic/bpp1.9-numcalc/bpp1.9-numcalc.info @@ -0,0 +1,10 @@ +PRGNAM="bpp1.9-numcalc" +VERSION="1.8.0" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-numcalc-1.8.0.tar.gz" +MD5SUM="0d6d51aaefcb4f89816704feae010bc9" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp1.9-utils" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp1.9-numcalc/slack-desc b/academic/bpp1.9-numcalc/slack-desc new file mode 100644 index 0000000000..0b1db4fe56 --- /dev/null +++ b/academic/bpp1.9-numcalc/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------------------------------------------------------| +bpp1.9-numcalc: bpp1.9-numcalc (Bio++ 1.9 NumCalc Library) +bpp1.9-numcalc: +bpp1.9-numcalc: Contains the Bio++ 1.9 NumCalc Library. +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: diff --git a/academic/bpp1.9-phyl/README b/academic/bpp1.9-phyl/README new file mode 100644 index 0000000000..292485c428 --- /dev/null +++ b/academic/bpp1.9-phyl/README @@ -0,0 +1,10 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ 1.9 (April 2010) Phyl Library. It can be +installed along the current Bio++ suite libraries, however they better +not be present at compile time. diff --git a/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild b/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild new file mode 100644 index 0000000000..fa951d6f2e --- /dev/null +++ b/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild @@ -0,0 +1,119 @@ +#!/bin/bash + +# Slackware build script for bpp1.9-phyl + +# Copyright 2020-2022 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=bpp1.9-phyl +SRCNAM=bpp-phyl +VERSION=${VERSION:-1.9.0} +BUILD=${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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" + +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 {} \; + +# CAPS wants TreeTemplateTools to be modified a bit... +patch -p1 -i $CWD/caps_TreeTemplateTools.patch + +# Use custom install place, so libs can coexist with latest bpp +export PATH="/usr/lib${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 \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + + sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Phyl/cmake_install.cmake + sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Phyl/cmake_install.cmake + + make + make DESTDIR=$PKG 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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +chmod 0644 AUTHORS ChangeLog COPYING +cp -a \ + AUTHORS ChangeLog 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/bpp1.9-phyl/bpp1.9-phyl.info b/academic/bpp1.9-phyl/bpp1.9-phyl.info new file mode 100644 index 0000000000..ae873c0a59 --- /dev/null +++ b/academic/bpp1.9-phyl/bpp1.9-phyl.info @@ -0,0 +1,10 @@ +PRGNAM="bpp1.9-phyl" +VERSION="1.9.0" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-phyl-1.9.0.tar.gz" +MD5SUM="1b100b688faca52419e9f782798b8add" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp1.9-seq" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch b/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch new file mode 100644 index 0000000000..b4f79029de --- /dev/null +++ b/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch @@ -0,0 +1,39 @@ +diff -pruN orig/Phyl/TreeTemplateTools.h new/Phyl/TreeTemplateTools.h +--- orig/Phyl/TreeTemplateTools.h 2010-04-01 16:37:04.000000000 +0300 ++++ new/Phyl/TreeTemplateTools.h 2017-02-03 14:33:11.000000000 +0200 +@@ -191,7 +191,7 @@ class TreeTemplateTools + static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception) + { + N* leaf = tree.getNode(leafName); +- if (!leaf->hasfather()) ++ if (!leaf->hasFather()) + throw Exception("TreeTemplateTools::dropLeaf(). Leaf is the only node in the tree, can't remove it."); + N* parent = leaf->getFather(); + if (parent->getNumberOfSons() > 2) +@@ -203,7 +203,7 @@ class TreeTemplateTools + else if (parent->getNumberOfSons() == 2) + { + //We have to delete the parent node as well: +- N* brother = parent->getson(0); ++ N* brother = parent->getSon(0); + if (brother == leaf) brother = parent->getSon(1); + if (!parent->hasFather()) + { +@@ -212,7 +212,7 @@ class TreeTemplateTools + { + brother->setDistanceToFather(brother->getDistanceToFather() + leaf->getDistanceToFather()); + } +- tree->setRootNode(brother); ++ tree.setRootNode(brother); + delete parent; + delete leaf; + } +@@ -223,7 +223,7 @@ class TreeTemplateTools + { + brother->setDistanceToFather(brother->getDistanceToFather() + parent->getDistanceToFather()); + } +- unsigned int pos = gParent->getsonPosition(parent); ++ unsigned int pos = gParent->getSonPosition(parent); + gParent->setSon(pos, brother); + delete parent; + delete leaf; diff --git a/academic/bpp1.9-phyl/slack-desc b/academic/bpp1.9-phyl/slack-desc new file mode 100644 index 0000000000..05245c02f1 --- /dev/null +++ b/academic/bpp1.9-phyl/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------------------------------------------------------| +bpp1.9-phyl: bpp1.9-phyl (Bio++ 1.9 Phyl Library) +bpp1.9-phyl: +bpp1.9-phyl: Contains the Bio++ 1.9 Phyl Library. +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: diff --git a/academic/bpp1.9-seq/README b/academic/bpp1.9-seq/README new file mode 100644 index 0000000000..eaeb91d929 --- /dev/null +++ b/academic/bpp1.9-seq/README @@ -0,0 +1,10 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ 1.9 (April 2010) Seq Library. It can be +installed along the current Bio++ suite libraries, however they better +not be present at compile time. diff --git a/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild b/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild new file mode 100644 index 0000000000..fcea3aef1d --- /dev/null +++ b/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/bash + +# Slackware build script for bpp1.9-seq + +# Copyright 2020-2022 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=bpp1.9-seq +SRCNAM=bpp-seq +VERSION=${VERSION:-1.7.0} +BUILD=${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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" + +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 {} \; + +# Use custom install place, so libs can coexist with latest bpp +export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH" +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Seq.spec + +source /etc/profile.d/gcc5.sh + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + + sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Seq/cmake_install.cmake + sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Seq/cmake_install.cmake + + make + make DESTDIR=$PKG 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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +chmod 0644 AUTHORS ChangeLog COPYING +cp -a \ + AUTHORS ChangeLog 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/bpp1.9-seq/bpp1.9-seq.info b/academic/bpp1.9-seq/bpp1.9-seq.info new file mode 100644 index 0000000000..0d6d9f38df --- /dev/null +++ b/academic/bpp1.9-seq/bpp1.9-seq.info @@ -0,0 +1,10 @@ +PRGNAM="bpp1.9-seq" +VERSION="1.7.0" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-seq-1.7.0.tar.gz" +MD5SUM="4256293637ac4131c0d030f5265b8b8b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp1.9-numcalc" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp1.9-seq/slack-desc b/academic/bpp1.9-seq/slack-desc new file mode 100644 index 0000000000..bd154ce1f1 --- /dev/null +++ b/academic/bpp1.9-seq/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------------------------------------------------------| +bpp1.9-seq: bpp1.9-seq (Bio++ 1.9 Seq Library) +bpp1.9-seq: +bpp1.9-seq: Contains the Bio++ 1.9 Seq Library. +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: diff --git a/academic/bpp1.9-utils/README b/academic/bpp1.9-utils/README new file mode 100644 index 0000000000..5ee42d9632 --- /dev/null +++ b/academic/bpp1.9-utils/README @@ -0,0 +1,10 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ 1.9 (April 2010) Utils Library. It can be +installed along the current Bio++ suite libraries, however they better +not be present at compile time. diff --git a/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild new file mode 100644 index 0000000000..6840376b84 --- /dev/null +++ b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild @@ -0,0 +1,120 @@ +#!/bin/bash + +# Slackware build script for bpp1.9-utils + +# Copyright 2020-2022 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=bpp1.9-utils +SRCNAM=bpp-utils +VERSION=${VERSION:-1.5.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# This is needed for vCAPS to find its libraries at runtime. Thanks Urchlay! +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" + +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 {} \; + +# This is needed on newer systems (-current) +#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${LIBDIRSUFFIX}/Bpp1.9/:g" Utils.spec + +source /etc/profile.d/gcc5.sh + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + +# More about word boundary and sed: +# https://linuxize.com/post/how-to-use-sed-to-find-and-replace-string-in-files/ +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Utils/cmake_install.cmake +sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Utils/cmake_install.cmake + + make + make DESTDIR=$PKG 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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog 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/bpp1.9-utils/bpp1.9-utils.info b/academic/bpp1.9-utils/bpp1.9-utils.info new file mode 100644 index 0000000000..8ee8062200 --- /dev/null +++ b/academic/bpp1.9-utils/bpp1.9-utils.info @@ -0,0 +1,10 @@ +PRGNAM="bpp1.9-utils" +VERSION="1.5.0" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-utils-1.5.0.tar.gz" +MD5SUM="4625b7f2146caa1815ed7dc433d5eb78" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="gcc5" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.copm" diff --git a/academic/bpp1.9-utils/slack-desc b/academic/bpp1.9-utils/slack-desc new file mode 100644 index 0000000000..be9d333c61 --- /dev/null +++ b/academic/bpp1.9-utils/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------------------------------------------------------| +bpp1.9-utils: bpp1.9-utils (Bio++ 1.9 Utils Library) +bpp1.9-utils: +bpp1.9-utils: Contains the Bio++ 1.9 Utils Library. +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: diff --git a/academic/bppsuite/README b/academic/bppsuite/README new file mode 100644 index 0000000000..cc877ea40b --- /dev/null +++ b/academic/bppsuite/README @@ -0,0 +1,11 @@ +Bio++ program suite + +The Bio++ Program Suite is a package of programs using the Bio++ +libraries and dedicated to Phylogenetics and Molecular Evolution. All +programs are independent, but can be combined to perform rather +complex analyses. These programs use the interface helper tools of the +libraries, and hence share the same syntax. They also have several +options in common, which may also be shared by third-party software. + +Detailed documentation can be found (as PDF and HTML) here: +https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 diff --git a/academic/bppsuite/bppsuite.SlackBuild b/academic/bppsuite/bppsuite.SlackBuild new file mode 100644 index 0000000000..4e4bc8c2d2 --- /dev/null +++ b/academic/bppsuite/bppsuite.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/bash + +# Slackware build script for bppsuite + +# Copyright 2017-2022 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=bppsuite +VERSION=${VERSION:-2.4.1} +BUILD=${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" +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_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$PKG +cd .. + +# Place man pages to their proper location +mkdir -p $PKG/usr/man/man1 +mv $PKG/usr/share/man/man1/* $PKG/usr/man/man1 + +# Place info pages to their proper location +mkdir -p $PKG/usr/info +mv $PKG/usr/share/info/* $PKG/usr/info +rm -rf $PKG/usr/share + +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 +gzip -9 $PKG/usr/info/*.info* + +mkdir -p $PKG/usr/doc/$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 +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/bppsuite/bppsuite.info b/academic/bppsuite/bppsuite.info new file mode 100644 index 0000000000..ccd92962fe --- /dev/null +++ b/academic/bppsuite/bppsuite.info @@ -0,0 +1,10 @@ +PRGNAM="bppsuite" +VERSION="2.4.1" +HOMEPAGE="https://github.com/BioPP/" +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-phyl-omics bpp-popgen" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bppsuite/slack-desc b/academic/bppsuite/slack-desc new file mode 100644 index 0000000000..8419aa4f1e --- /dev/null +++ b/academic/bppsuite/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------------------------------------------------------| +bppsuite: bppsuite (Bio++ program suite) +bppsuite: +bppsuite: The Bio++ Program Suite is a package of programs using the Bio++ +bppsuite: libraries and dedicated to Phylogenetics and Molecular Evolution. +bppsuite: All programs are independent, but can be combined to perform +bppsuite: rather complex analyses. These programs use the interface helper +bppsuite: tools of the libraries, and hence share the same syntax. They also +bppsuite: have several options in common, which may also be shared by third- +bppsuite: party software. +bppsuite: +bppsuite: Git: https://github.com/BioPP/bppsuite 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..0172ff5550 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:-2.4.5.7} 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..2bd6e73540 100644 --- a/academic/cadabra2/cadabra2.info +++ b/academic/cadabra2/cadabra2.info @@ -1,10 +1,10 @@ PRGNAM="cadabra2" -VERSION="2.3.6.3" +VERSION="2.4.5.7" 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/2.4.5.7/cadabra2-2.4.5.7.tar.gz" +MD5SUM="0114198388cc3d11e7318a1319b46aae" 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 12df4cd0f4..8b51ed982c 100644 --- a/academic/calc/calc.SlackBuild +++ b/academic/calc/calc.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=calc -VERSION=${VERSION:-2.14.0.14} +VERSION=${VERSION:-2.14.1.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/calc/calc.info b/academic/calc/calc.info index 4ff56c400d..9ba6856746 100644 --- a/academic/calc/calc.info +++ b/academic/calc/calc.info @@ -1,10 +1,10 @@ PRGNAM="calc" -VERSION="2.14.0.14" +VERSION="2.14.1.5" HOMEPAGE="http://www.isthe.com/chongo/tech/comp/calc/" -DOWNLOAD="http://www.isthe.com/chongo/src/calc/calc-2.14.0.14.tar.bz2" -MD5SUM="8a3f3d8a0cf889679e3de699e359688e" +DOWNLOAD="http://www.isthe.com/chongo/src/calc/calc-2.14.1.5.tar.bz2" +MD5SUM="57607be276a3998fa76376e41dc49a03" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Dave Woodfall" +MAINTAINER="D Woodfall" EMAIL="dave@slackbuilds.org" diff --git a/academic/camd/camd.SlackBuild b/academic/camd/camd.SlackBuild index 3b4c52de11..2823459a12 100644 --- a/academic/camd/camd.SlackBuild +++ b/academic/camd/camd.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${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 b2bc1f0870..a4023eccfa 100644 --- a/academic/cap3/README +++ b/academic/cap3/README @@ -14,5 +14,8 @@ 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* you have to download the tarballs manually from a browser, -to read and accept the license. +*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.info b/academic/cap3/cap3.info index 499a2d4859..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="https://slackware.uk/~urchlay/src/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 05ed056313..bc0583a4da 100644 --- a/academic/cdo/cdo.SlackBuild +++ b/academic/cdo/cdo.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cdo -# Copyright 2020-2022 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=${VERSION:-2.0.4} +VERSION=${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 8615f6071c..f3ca4cd66b 100644 --- a/academic/cdo/cdo.info +++ b/academic/cdo/cdo.info @@ -1,10 +1,10 @@ PRGNAM="cdo" -VERSION="2.0.4" +VERSION="2.4.0" HOMEPAGE="https://code.mpimet.mpg.de/projects/cdo" -DOWNLOAD="https://code.mpimet.mpg.de/attachments/download/26761/cdo-2.0.4.tar.gz" -MD5SUM="03c7d59cd80377dfa0b9bbc0ec79a427" -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/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.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 88ed70f889..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 python2-django R" +REQUIRES="python2-numpy python2-django R" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/clustalx/clustalx.SlackBuild b/academic/clustalx/clustalx.SlackBuild index 515802e6b3..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 [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -89,7 +89,7 @@ find -L . \ sed -i 's/static//g' clustalx.pro -qmake +qmake-qt5 #Use our CFLAGS/CXXFLAGS sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile diff --git a/academic/colamd/colamd.SlackBuild b/academic/colamd/colamd.SlackBuild index 9ebc5c4963..3f9a632954 100644 --- a/academic/colamd/colamd.SlackBuild +++ b/academic/colamd/colamd.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${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 d081260b24..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} 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/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/cvc4/cvc4.info b/academic/cvc4/cvc4.info index 8125f26125..379b15bffa 100644 --- a/academic/cvc4/cvc4.info +++ b/academic/cvc4/cvc4.info @@ -7,6 +7,6 @@ MD5SUM="9f7657e21fec3c4042225b0b8f513c34 \ 1b91dea1c7d480b3223f7c8a9aa0e172" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="zulu-openjdk8 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 58b479ac29..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, 2021, 2022 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 @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=dakota -VERSION=${VERSION:-6.15.0} -BUILD=${BUILD:-2} +VERSION=${VERSION:-6.19.0} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -71,7 +71,7 @@ mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION-public-src-cli tar xvf $CWD/$PRGNAM-$VERSION-public-src-cli.tar.gz -cd $PRGNAM-$VERSION-public-src-cli + 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 \ @@ -97,10 +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 $CWD/Users-${VERSION}.pdf $PKG/usr/doc/$PRGNAM-$VERSION/Users.pdf -cp $CWD/Theory-${VERSION}.pdf $PKG/usr/doc/$PRGNAM-$VERSION/Theory.pdf -tar xvf $CWD/html-ref-${VERSION}.tar.gz -C $PKG/usr/doc/$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 e18a31ad04..9e43bb02f6 100644 --- a/academic/dakota/dakota.info +++ b/academic/dakota/dakota.info @@ -1,16 +1,14 @@ PRGNAM="dakota" -VERSION="6.15.0" +VERSION="6.19.0" HOMEPAGE="https://dakota.sandia.gov/" -DOWNLOAD="https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.15.0-public-src-cli.tar.gz \ - https://dakota.sandia.gov/sites/default/files/docs/6.15/Users-6.15.0.pdf \ - https://dakota.sandia.gov/sites/default/files/docs/6.15/html-ref-6.15.0.tar.gz \ - https://dakota.sandia.gov/sites/default/files/docs/6.15/Theory-6.15.0.pdf" -MD5SUM="47136b14a86143d0038735638da4578e \ - ddd67ce8da2646e94bfe7e3e571dbb88 \ - 1060fe37934c1f80c55c6e940e594bc9 \ - 9daff457edb09dd84bc6a6b962d08e90" +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/ds9/README b/academic/ds9/README index 0bed20cece..3569e0678c 100644 --- a/academic/ds9/README +++ b/academic/ds9/README @@ -1,11 +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, +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. 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. +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/petsc/petsc.SlackBuild b/academic/dwave-system/dwave-system.SlackBuild index 99e046805f..c2f1f2e2c0 100644 --- a/academic/petsc/petsc.SlackBuild +++ b/academic/dwave-system/dwave-system.SlackBuild @@ -1,8 +1,8 @@ #!/bin/bash -# -# Slackware build script for petsc. -# -# Copyright 2022 Fellype do Nascimento, Guaratingueta, Brazil. + +# 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 @@ -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=petsc -VERSION=${VERSION:-3.17.0} +PRGNAM="dwave-system" +VERSION=${VERSION:-1.16.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -38,6 +39,9 @@ if [ -z "$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 @@ -76,28 +80,20 @@ 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 {} \; -./configure \ - --prefix=/usr \ - --with-petsc4py \ - .. -make PETSC_DIR=$(pwd) PETSC_ARCH=arch-linux-c-debug all -make install DESTDIR=$PKG +python3 setup.py install --root=$PKG -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -if [ "$ARCH" = "x86_64" ]; then - mv $PKG/usr/lib $PKG/usr/lib${LIBDIRSUFFIX} -fi -# Most of this files are 0 size -rm -rf $PKG/usr/share/petsc/examples +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la -DOCS="CODE_OF_CONDUCT.md LICENSE" +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/ +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 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.info b/academic/ed-v6/ed-v6.info index bb013cb0d9..c7d239ec09 100644 --- a/academic/ed-v6/ed-v6.info +++ b/academic/ed-v6/ed-v6.info @@ -6,5 +6,5 @@ MD5SUM="797a81796fdaf0b35bbce721d08d7bd7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Dave Woodfall" +MAINTAINER="D Woodfall" EMAIL="dave@slackbuilds.org" 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/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/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 339e12ba48..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="zulu-openjdk8" +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 f9fb968b6f..6962abec49 100644 --- a/academic/fet/fet.SlackBuild +++ b/academic/fet/fet.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=fet -VERSION=${VERSION:-6.3.4} +VERSION=${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 5088f7ee2a..2093219a59 100644 --- a/academic/fet/fet.info +++ b/academic/fet/fet.info @@ -1,8 +1,8 @@ PRGNAM="fet" -VERSION="6.3.4" +VERSION="6.19.3" HOMEPAGE="https://www.lalescu.ro/liviu/fet/" -DOWNLOAD="https://www.lalescu.ro/liviu/fet/download/fet-6.3.4.tar.bz2" -MD5SUM="6def269ef595512bf0e75a054a21c573" +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 9f97499f69..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=${VERSION:-20201104_1356} +VERSION=${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=i386 ;; - 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=linux32 -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 @@ -114,6 +105,7 @@ cp -a \ jars \ java \ lib \ + licenses \ luts \ macros \ plugins \ @@ -123,12 +115,6 @@ cp -a \ $PRGNAM \ $PKG/opt/$PRGNAM -if [ "$ARCH" = "x86_64" ]; then - cp -a \ - licenses \ - $PKG/opt/$PRGNAM -fi - # If a file called "ImageJ2.desktop" is not present in the directory # of fiji, it will create (and re-create it if you delete it) the file # "~/.local/share/applications/ImageJ2.desktop" upon start. So, let it @@ -139,7 +125,7 @@ fi 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/fityk.SlackBuild b/academic/fityk/fityk.SlackBuild index 5af5ab5af2..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 @@ -22,16 +22,14 @@ # 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: -# - fix conflict between wxPython/wxGTK3. -# - remove useless INSTALL from doc dir. -# - mention Sphinx as optional dep in README. +# The SlackBuilds.org team contributed with improvements and maintenance of +# this script cd $(dirname $0) ; CWD=$(pwd) PRGNAM=fityk -VERSION=${VERSION:-20210925_e022356} -BUILD=${BUILD:-3} +VERSION=${VERSION:-1.3.2} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -83,7 +81,7 @@ find -L . \ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS -std=c++14" \ -./autogen.sh \ +./configure \ --prefix=/usr \ --bindir=/usr/bin \ --libdir=/usr/lib${LIBDIRSUFFIX} \ diff --git a/academic/fityk/fityk.info b/academic/fityk/fityk.info index f3e514e636..c9bdbeba0a 100644 --- a/academic/fityk/fityk.info +++ b/academic/fityk/fityk.info @@ -1,10 +1,10 @@ PRGNAM="fityk" -VERSION="20210925_e022356" +VERSION="1.3.2" HOMEPAGE="http://fityk.nieto.pl/" -DOWNLOAD="https://ponce.cc/slackware/sources/repo/fityk-20210925_e022356.tar.xz" -MD5SUM="555f230ff835e2f5d29b58f485edfae4" +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/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.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/gcompris-qt/gcompris-qt.SlackBuild b/academic/gcompris-qt/gcompris-qt.SlackBuild index 1d34d6b9d2..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=${VERSION:-2.4} +VERSION=${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 eeef0aa1ff..835328b6ce 100644 --- a/academic/gcompris-qt/gcompris-qt.info +++ b/academic/gcompris-qt/gcompris-qt.info @@ -1,10 +1,10 @@ PRGNAM="gcompris-qt" -VERSION="2.4" +VERSION="4.0" HOMEPAGE="https://gcompris.net/" -DOWNLOAD="https://gcompris.net/download/qt/linux/gcompris-qt-2.4-Linux32.sh" -MD5SUM="bb2f4b23372c22bedba28669cde0158f" -DOWNLOAD_x86_64="https://gcompris.net/download/qt/linux/gcompris-qt-2.4-Linux64.sh" -MD5SUM_x86_64="21f3ea9061b51762dfd254177cf634b9" +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/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/gdstk/gdstk.SlackBuild b/academic/gdstk/gdstk.SlackBuild new file mode 100644 index 0000000000..7a14390770 --- /dev/null +++ b/academic/gdstk/gdstk.SlackBuild @@ -0,0 +1,119 @@ +#!/bin/bash + +# Slackware build script for gdstk + +# 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=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=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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$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 {} + + +#sed -i 's/qh_nextfacet2d/qh_nextfacet/g' src/utils.cpp + +sed -i 's|add_library(gdstk|add_library(gdstk SHARED|g' src/CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DMAN_INSTALL_DIR=/usr/man \ + -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ + -DCMAKE_C_COMPILER_LAUNCHER=ccache \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +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.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/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/gelemental/gelemental.SlackBuild b/academic/gelemental/gelemental.SlackBuild index 277e9ec6c0..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 @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gelemental -VERSION=${VERSION:-2.0.0} -BUILD=${BUILD:-2} +VERSION=${VERSION:-2.0.2} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -100,9 +100,12 @@ 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 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/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/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 855127b779..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=${VERSION:-1.9.4} -BUILD=${BUILD:-2} +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 +109,22 @@ 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 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/gephi/doinst.sh b/academic/gephi/doinst.sh new file mode 100644 index 0000000000..65c7e2eeb9 --- /dev/null +++ b/academic/gephi/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/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/petsc/slack-desc b/academic/gephi/slack-desc index 7abea7ef22..881315966d 100644 --- a/academic/petsc/slack-desc +++ b/academic/gephi/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -petsc: petsc (toolkit for scientific computation) -petsc: -petsc: PETSc, the Portable, Extensible Toolkit for Scientific Computation, -petsc: pronounced PET-see , is a suite of data structures and routines for -petsc: the scalable (parallel) solution of scientific applications modeled -petsc: by partial differential equations. -petsc: -petsc: -petsc: -petsc: -petsc: +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 a66f645265..0b4d1094a2 100644 --- a/academic/gerbv/gerbv.SlackBuild +++ b/academic/gerbv/gerbv.SlackBuild @@ -2,13 +2,34 @@ # 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:-2} +VERSION=${VERSION:-2.10.0} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -20,9 +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 @@ -61,6 +79,8 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +autoreconf -fi + CFLAGS="$SLKCFLAGS -w -Wl,--allow-multiple-definition" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -71,29 +91,38 @@ 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 -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 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/getdp.SlackBuild b/academic/getdp/getdp.SlackBuild index 0763576717..751b64a88c 100644 --- a/academic/getdp/getdp.SlackBuild +++ b/academic/getdp/getdp.SlackBuild @@ -23,7 +23,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=getdp -VERSION=${VERSION:-3.4.0} +VERSION=${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 \ diff --git a/academic/getdp/getdp.info b/academic/getdp/getdp.info index 56a79610bb..bfacafe5f2 100644 --- a/academic/getdp/getdp.info +++ b/academic/getdp/getdp.info @@ -1,8 +1,8 @@ PRGNAM="getdp" -VERSION="3.4.0" +VERSION="3.5.0" HOMEPAGE="http://getdp.info/" -DOWNLOAD="http://getdp.info/src/getdp-3.4.0-source.tgz" -MD5SUM="76472429f7741a42c3ca3d8626e74e30" +DOWNLOAD="http://getdp.info/src/getdp-3.5.0-source.tgz" +MD5SUM="157d6604cc6a26ead0b0b4121216074a" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="arpack-ng OpenBLAS %README%" diff --git a/academic/getfem/getfem.SlackBuild b/academic/getfem/getfem.SlackBuild index 41bb991697..d4567aa2e7 100644 --- a/academic/getfem/getfem.SlackBuild +++ b/academic/getfem/getfem.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for GetFEM # -# Copyright 2022, Fellype do Nascimento, Campinas - Brazil +# Copyright 2022, Fellype do Nascimento, Guaratingueta - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=getfem -VERSION=${VERSION:-5.4.1} +VERSION=${VERSION:-5.4.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/getfem/getfem.info b/academic/getfem/getfem.info index dbde5c03e1..9a61fe097c 100644 --- a/academic/getfem/getfem.info +++ b/academic/getfem/getfem.info @@ -1,10 +1,10 @@ PRGNAM="getfem" -VERSION="5.4.1" +VERSION="5.4.2" HOMEPAGE="https://getfem.org/" -DOWNLOAD="http://download-mirror.savannah.gnu.org/releases/getfem/stable/getfem-5.4.1.tar.gz" -MD5SUM="61988ac13d8a88fceb928b050c988220" +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="scipy3" +REQUIRES="python3-scipy" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" 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 2a501768db..cbc93a7222 100644 --- a/academic/gmsh/README +++ b/academic/gmsh/README @@ -26,3 +26,5 @@ 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/gmsh.SlackBuild b/academic/gmsh/gmsh.SlackBuild index 9d959c11a6..e318452d91 100644 --- a/academic/gmsh/gmsh.SlackBuild +++ b/academic/gmsh/gmsh.SlackBuild @@ -1,7 +1,7 @@ #!/bin/bash # Slackware build script for gmsh -# Copyright 2020-2022 Fellype do Nascimento, Guaratingueta, 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=${VERSION:-4.10.0} +VERSION=${VERSION:-4.12.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -84,7 +84,9 @@ find -L . \ # do it using BUILDSTATICLIB=yes ./gmsh.SlackBuild # default is BUILDSTATICLIB=no if [ "${BUILDSTATICLIB:-no}" = "yes" ]; then - echo "**building a static library for gmsh**" + echo " " + echo "** building a static library for gmsh **" + echo " " mkdir lib cd lib cmake -DDEFAULT=0 \ @@ -94,12 +96,17 @@ if [ "${BUILDSTATICLIB:-no}" = "yes" ]; then -DENABLE_BLAS_LAPACK=1 \ -DENABLE_BUILD_LIB=1 \ -DENABLE_PRIVATE_API=1 \ + -DENABLE_MED=OFF \ + -DENABLE_CGNS=OFF \ -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DCMAKE_INSTALL_DOCDIR:PATH=/usr/share/gmsh \ .. make lib make install/fast DESTDIR=$PKG/ cd .. + echo " " + echo "** finished building the static library **" + echo " " fi mkdir build @@ -113,8 +120,12 @@ cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DENABLE_PRIVATE_API=1 \ -DENABLE_PETSC=OFF \ -DENABLE_SLEPC=OFF \ + -DENABLE_MED=OFF \ + -DENABLE_CGNS=OFF \ .. # 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=$PKG diff --git a/academic/gmsh/gmsh.info b/academic/gmsh/gmsh.info index 914fc10f95..f56d44b835 100644 --- a/academic/gmsh/gmsh.info +++ b/academic/gmsh/gmsh.info @@ -1,10 +1,10 @@ PRGNAM="gmsh" -VERSION="4.10.0" -HOMEPAGE="http://gmsh.info/" -DOWNLOAD="http://gmsh.info/src/gmsh-4.10.0-source.tgz" -MD5SUM="a4e6ba03ef305dbb8c6b698862ea17c6" +VERSION="4.12.2" +HOMEPAGE="https://gmsh.info/" +DOWNLOAD="https://gmsh.info/src/gmsh-4.12.2-source.tgz" +MD5SUM="2c99a1b94d1a4c597b8febb6e9b02f5b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="fltk lapack med OpenCASCADE" +REQUIRES="fltk lapack OpenCASCADE" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/gmsh/slack-desc b/academic/gmsh/slack-desc index 35305eed9d..3fe2e76a5d 100644 --- a/academic/gmsh/slack-desc +++ b/academic/gmsh/slack-desc @@ -11,7 +11,7 @@ gmsh: gmsh: Gmsh is an automatic three-dimensional finite element mesh generator gmsh: with built-in pre- and post-processing facilities. gmsh: -gmsh: Gmsh is copyright (C) 1997-2019 C. Geuzaine and J.-F. Remacle, +gmsh: Gmsh is copyright (C) 1997- C. Geuzaine and J.-F. Remacle, gmsh: and is distributed under the terms of the GNU General Public gmsh: License, Version 2 or later, with an exception to allow for gmsh: easier linking with external libraries. diff --git a/academic/gp2fasta/gp2fasta.SlackBuild b/academic/gp2fasta/gp2fasta.SlackBuild index da6b2fbd44..ce052827b0 100644 --- a/academic/gp2fasta/gp2fasta.SlackBuild +++ b/academic/gp2fasta/gp2fasta.SlackBuild @@ -36,7 +36,7 @@ PKGTYPE=${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" 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/gplates/doinst.sh b/academic/gplates/doinst.sh new file mode 100644 index 0000000000..aea0f894eb --- /dev/null +++ b/academic/gplates/doinst.sh @@ -0,0 +1,13 @@ +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/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 dc4e9069f6..4f6d1c7981 100644 --- a/academic/gpredict/gpredict.SlackBuild +++ b/academic/gpredict/gpredict.SlackBuild @@ -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/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/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=${PKGTYPE:-tgz} diff --git a/academic/gspiceui/gspiceui.info b/academic/gspiceui/gspiceui.info index d2d260e790..223171695c 100644 --- a/academic/gspiceui/gspiceui.info +++ b/academic/gspiceui/gspiceui.info @@ -1,8 +1,8 @@ PRGNAM="gspiceui" -VERSION="1.2.36" +VERSION="1.2.87" HOMEPAGE="http://users.tpg.com.au/micksw012/gspiceui.html" -DOWNLOAD="https://sourceforge.net/projects/gspiceui/files/gSpiceUI/gspiceui-v1.2.36/gspiceui-v1.2.36.tar.gz" -MD5SUM="a385028952ada5aa69acdb7298332c8c" +DOWNLOAD="https://sourceforge.net/projects/gspiceui/files/gSpiceUI/gspiceui-v1.2.87/gspiceui-v1.2.87.tar.gz" +MD5SUM="ae580ac1665674fda3b7029392695157" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="pangox-compat wxGTK3" diff --git a/academic/gtypist/gtypist.SlackBuild b/academic/gtypist/gtypist.SlackBuild index 49e7087d86..b23279fa52 100644 --- a/academic/gtypist/gtypist.SlackBuild +++ b/academic/gtypist/gtypist.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for gtypist # Copyright 2007-2012 Grigorios Bouzakis <grbzks@imap.cc> -# Copyright 2014 Aaditya Bagga <aaditya_gnulinux@zoho.com> +# Copyright 2014 Aaditya <aaditya_gnulinux@zoho.com> # All rights reserved. # # Permission to use, copy, modify, and distribute this software for any purpose @@ -30,7 +30,7 @@ PKGTYPE=${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/gwyddion.SlackBuild b/academic/gwyddion/gwyddion.SlackBuild index 1213aa588f..5f741433c1 100644 --- a/academic/gwyddion/gwyddion.SlackBuild +++ b/academic/gwyddion/gwyddion.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gwyddion -VERSION=${VERSION:-2.61} +VERSION=${VERSION:-2.65} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} diff --git a/academic/gwyddion/gwyddion.info b/academic/gwyddion/gwyddion.info index 8f3042bf2e..6dc1a61df0 100644 --- a/academic/gwyddion/gwyddion.info +++ b/academic/gwyddion/gwyddion.info @@ -1,8 +1,8 @@ PRGNAM="gwyddion" -VERSION="2.61" +VERSION="2.65" HOMEPAGE="http://gwyddion.net" -DOWNLOAD="http://downloads.sourceforge.net/gwyddion/gwyddion-2.61.tar.xz" -MD5SUM="7600fd7d76a930178528d480d7d4db41" +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 d48c4804d0..7bbd8433bf 100644 --- a/academic/harminv/harminv.SlackBuild +++ b/academic/harminv/harminv.SlackBuild @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=harminv -VERSION=${VERSION:-1.4.1} -BUILD=${BUILD:-2} +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 @@ -115,8 +130,6 @@ 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/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/io_lib/io_lib.SlackBuild b/academic/io_lib/io_lib.SlackBuild index 3553a7e4f5..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 @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=io_lib -VERSION=${VERSION:-1.14.14} -BUILD=${BUILD:-2} +VERSION=${VERSION:-1.15.0} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} 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.$PKGTYPE diff --git a/academic/iqtree/iqtree.info b/academic/iqtree/iqtree.info new file mode 100644 index 0000000000..fed2f89662 --- /dev/null +++ b/academic/iqtree/iqtree.info @@ -0,0 +1,10 @@ +PRGNAM="iqtree" +VERSION="2.2.2.7" +HOMEPAGE="http://www.iqtree.org/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-Linux.tar.gz" +MD5SUM_x86_64="8159c4bb33dae900ccd513a19561fd01" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/iqtree/slack-desc b/academic/iqtree/slack-desc new file mode 100644 index 0000000000..cecc57ba48 --- /dev/null +++ b/academic/iqtree/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +iqtree: iqtree (Efficient and versatile phylogenomic software by ML) +iqtree: +iqtree: The IQ-TREE software was created as the successor of IQPNNI and +iqtree: TREE-PUZZLE. IQ-TREE can utilize multicore computers and +iqtree: distributed parallel computing to speed up the analysis. IQ-TREE +iqtree: automatically performs checkpointing to resume an interrupted +iqtree: analysis. +iqtree: +iqtree: http://www.iqtree.org/ +iqtree: https://github.com/Cibiv/IQ-TREE +iqtree: diff --git a/academic/isoelectric-point/isoelectric-point.SlackBuild b/academic/isoelectric-point/isoelectric-point.SlackBuild index 8925785ee6..3e9244579b 100644 --- a/academic/isoelectric-point/isoelectric-point.SlackBuild +++ b/academic/isoelectric-point/isoelectric-point.SlackBuild @@ -32,7 +32,7 @@ PKGTYPE=${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" 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-$VERSION diff --git a/academic/jalview/jalview.info b/academic/jalview/jalview.info index f4231e0581..90b4e3b971 100644 --- a/academic/jalview/jalview.info +++ b/academic/jalview/jalview.info @@ -1,10 +1,10 @@ PRGNAM="jalview" -VERSION="2.11.1.4" +VERSION="2.11.2.7" HOMEPAGE="http://www.jalview.org/" -DOWNLOAD="http://www.jalview.org/getdown/release/jalview-all-2.11.1.4-j1.8.jar" -MD5SUM="725915975f65ce4ae5570578e68d1b03" +DOWNLOAD="http://www.jalview.org/getdown/release/jalview-all-2.11.2.7-j1.8.jar" +MD5SUM="15b9f3e9ca81c56050efea28e530a4c1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="zulu-openjdk11" +REQUIRES="zulu-openjdk8" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/jalview/slack-desc b/academic/jalview/slack-desc index 3afaa82c61..fd372a3f3a 100644 --- a/academic/jalview/slack-desc +++ b/academic/jalview/slack-desc @@ -14,6 +14,6 @@ jalview: It can also work with sequence annotation, secondary structure jalview: information, phylogenetic trees and 3D molecular structures. jalview: jalview: Home: http://www.jalview.org/ -jalview: References: /usr/doc/jalview-2.10.0b1/References +jalview: jalview: jalview: diff --git a/academic/jpicedt/jpicedt.SlackBuild b/academic/jpicedt/jpicedt.SlackBuild index 0de293eb4b..799ef4a103 100644 --- a/academic/jpicedt/jpicedt.SlackBuild +++ b/academic/jpicedt/jpicedt.SlackBuild @@ -30,7 +30,7 @@ PKGTYPE=${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/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/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 fd97e538b1..926705cdc7 100644 --- a/academic/klavaro/klavaro.SlackBuild +++ b/academic/klavaro/klavaro.SlackBuild @@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=klavaro -VERSION=${VERSION:-3.11} +VERSION=${VERSION:-3.14} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -98,7 +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 821ccce71c..eed8101207 100644 --- a/academic/klavaro/klavaro.info +++ b/academic/klavaro/klavaro.info @@ -1,10 +1,10 @@ PRGNAM="klavaro" -VERSION="3.11" +VERSION="3.14" HOMEPAGE="https://klavaro.sourceforge.io/" -DOWNLOAD="https://downloads.sourceforge.net/project/klavaro/klavaro-3.11.tar.bz2" -MD5SUM="05b3c1dab363e6bddaf2d29e74f93ac3" +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/labplot2/README b/academic/labplot2/README index d2d56dd8cd..11b9ca7430 100644 --- a/academic/labplot2/README +++ b/academic/labplot2/README @@ -16,6 +16,8 @@ in LabPlot1. optional dependencies: -- fftw - hdf5 - netcdf +- cfitsio +- matio +- discount diff --git a/academic/labplot2/labplot2.SlackBuild b/academic/labplot2/labplot2.SlackBuild index 66702f9d28..a4b4946d00 100644 --- a/academic/labplot2/labplot2.SlackBuild +++ b/academic/labplot2/labplot2.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for LabPlot # Based on the Slackware 15.0 SlackBuild and AUR PKGBUILD for labplot # -# Copyright 2014-2022, Fellype do Nascimento, Guaratingueta - Brazil +# Copyright 2014-2023, Fellype do Nascimento, Guaratingueta - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,12 +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=${VERSION:-2.9.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-2.10.1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -75,10 +75,6 @@ rm -rf $NAME-$VERSION tar -xJf $CWD/$NAME-$VERSION.tar.xz cd $NAME-$VERSION -# Avoid readstat-1.1.6.tar.gz to be removed and downloaded again from github. -# Use the one downloaded previously instead. -sed -i "s:https\://github.com/WizardMac/ReadStat/releases/download/v\${ext_version}/readstat-\${ext_version}.tar.gz:$CWD/readstat-1.1.6.tar.gz:" src/3rdparty/CMakeLists.txt - chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -86,14 +82,17 @@ 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_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 diff --git a/academic/labplot2/labplot2.info b/academic/labplot2/labplot2.info index e2d5be4ad8..fca8ba5bad 100644 --- a/academic/labplot2/labplot2.info +++ b/academic/labplot2/labplot2.info @@ -1,10 +1,8 @@ PRGNAM="labplot2" -VERSION="2.9.0" +VERSION="2.10.1" HOMEPAGE="https://labplot.kde.org/" -DOWNLOAD="https://download.kde.org/stable/labplot/2.9.0/labplot-2.9.0.tar.xz \ - https://github.com/WizardMac/ReadStat/releases/download/v1.1.6/readstat-1.1.6.tar.gz" -MD5SUM="6a189f66f610954aa54461f4faf9815d \ - b95f9385ecd629f665d8c5d7e2570398" +DOWNLOAD="https://download.kde.org/stable/labplot/labplot-2.10.1.tar.xz" +MD5SUM="b3cdfe029d64fa834e0990e9b5ab446f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" 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 16627cf661..21465899c3 100644 --- a/academic/libghemical/libghemical.SlackBuild +++ b/academic/libghemical/libghemical.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 @@ -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 [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" diff --git a/academic/link-grammar/link-grammar.SlackBuild b/academic/link-grammar/link-grammar.SlackBuild index f172bb8094..a7686f7c7a 100644 --- a/academic/link-grammar/link-grammar.SlackBuild +++ b/academic/link-grammar/link-grammar.SlackBuild @@ -15,7 +15,7 @@ PKGTYPE=${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/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/mathics.info b/academic/mathics/mathics.info index bbdedfb2fd..4f4c0e7aa2 100644 --- a/academic/mathics/mathics.info +++ b/academic/mathics/mathics.info @@ -5,6 +5,6 @@ DOWNLOAD="https://files.pythonhosted.org/packages/35/68/72d4ec12fe91c3cf569fe95b MD5SUM="f221aaf0ef9a27e2953429a32fe94652" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="numpy sympy" +REQUIRES="python2-numpy python2-sympy" MAINTAINER="David Melik" EMAIL="dchmelik@gmail.com" diff --git a/academic/mathjax2/mathjax2.SlackBuild b/academic/mathjax2/mathjax2.SlackBuild index bf881b5c17..fb1d4ce3a2 100644 --- a/academic/mathjax2/mathjax2.SlackBuild +++ b/academic/mathjax2/mathjax2.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for mathjax2 -# Copyright 2022 Isaac Yu <isaacyu1@isaacyu1.com> +# Copyright 2022 Isaac Yu <isaacyu@protonmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is diff --git a/academic/mathjax2/mathjax2.info b/academic/mathjax2/mathjax2.info index f9d9fc1356..66b659c608 100644 --- a/academic/mathjax2/mathjax2.info +++ b/academic/mathjax2/mathjax2.info @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Isaac Yu" -EMAIL="isaacyu1@isaacyu1.com" +EMAIL="isaacyu@protonmail.com" 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 fc39a0e21c..9c12742701 100644 --- a/academic/matio/matio.SlackBuild +++ b/academic/matio/matio.SlackBuild @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=matio -VERSION=${VERSION:-1.5.9} -BUILD=${BUILD:-2} +VERSION=${VERSION:-1.5.23} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} 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 8f38e6eaf3..629d20e14d 100644 --- a/academic/meep/meep.SlackBuild +++ b/academic/meep/meep.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=meep -VERSION=${VERSION:-1.17.1} +VERSION=${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 \ 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=${PKGTYPE:-tgz} diff --git a/academic/meme-suite/meme-suite.info b/academic/meme-suite/meme-suite.info index 081ac95959..f0d7634d52 100644 --- a/academic/meme-suite/meme-suite.info +++ b/academic/meme-suite/meme-suite.info @@ -1,8 +1,8 @@ PRGNAM="meme-suite" -VERSION="5.3.3" +VERSION="5.5.4" HOMEPAGE="https://meme-suite.org/" -DOWNLOAD="https://meme-suite.org/meme-software/5.3.3/meme-5.3.3.tar.gz" -MD5SUM="97b258e6a6627ada02404a2224b13e92" +DOWNLOAD="https://meme-suite.org/meme-software/5.5.4/meme-5.5.4.tar.gz" +MD5SUM="eed938a859b551209af3c4adf7e41fa1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi perl-HTML-Template perl-JSON meme-db-gomo meme-db-motif meme-db-tgene" diff --git a/academic/mendeleydesktop/mendeleydesktop.SlackBuild b/academic/mendeleydesktop/mendeleydesktop.SlackBuild index e9b7410cc2..bdc072f10d 100644 --- a/academic/mendeleydesktop/mendeleydesktop.SlackBuild +++ b/academic/mendeleydesktop/mendeleydesktop.SlackBuild @@ -35,15 +35,12 @@ PKGTYPE=${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/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 f71064c95b..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.$PKGTYPE" exit 0 @@ -121,6 +118,16 @@ make prefix=$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/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 168041188c..706e1316ed 100644 --- a/academic/nco/nco.SlackBuild +++ b/academic/nco/nco.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for nco -# Copyright 2020-2022 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 @@ -26,8 +26,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=nco -VERSION=${VERSION:-5.0.7} -BUILD=${BUILD:-2} +VERSION=${VERSION:-5.2.4} +BUILD=${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" \ @@ -115,6 +113,8 @@ 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 adc8b81456..b6064e2b16 100644 --- a/academic/nco/nco.info +++ b/academic/nco/nco.info @@ -1,8 +1,8 @@ PRGNAM="nco" -VERSION="5.0.7" +VERSION="5.2.4" HOMEPAGE="http://nco.sf.net" -DOWNLOAD="https://github.com/nco/nco/archive/5.0.7/nco-5.0.7.tar.gz" -MD5SUM="9fc5f4dac6ecb7c9152a32d824389c67" +DOWNLOAD="https://github.com/nco/nco/archive/5.2.4/nco-5.2.4.tar.gz" +MD5SUM="b46ed9dcdc1a2c857811cb5698a0460c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="netcdf udunits antlr2" diff --git a/academic/ngspice/ngspice.SlackBuild b/academic/ngspice/ngspice.SlackBuild index e8bc20f348..db12c3aab6 100644 --- a/academic/ngspice/ngspice.SlackBuild +++ b/academic/ngspice/ngspice.SlackBuild @@ -9,7 +9,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ngspice -VERSION=${VERSION:-36} +VERSION=${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-$VERSION-manual.pdf # The shared library enabled by "--with-ngshared" -install -Dm755 ./release/src/.libs/libngspice.so.0.0.2 \ - "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0.0.2" +install -Dm755 ./release/src/.libs/libngspice.so.0.0.9 \ + "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0.0.9" -ln -s "libngspice.so.0.0.2" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0" -ln -s "libngspice.so.0.0.2" "$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 $TMP/$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 607252830b..d7fa1f2449 100644 --- a/academic/ngspice/ngspice.info +++ b/academic/ngspice/ngspice.info @@ -1,12 +1,12 @@ PRGNAM="ngspice" -VERSION="36" +VERSION="42" HOMEPAGE="http://ngspice.sourceforge.net/" -DOWNLOAD="https://sourceforge.net/projects/ngspice/files/ng-spice-rework/36/ngspice-36.tar.gz \ - https://sourceforge.net/projects/ngspice/files/ng-spice-rework/36/ngspice-36-manual.pdf" -MD5SUM="9c34c41bfeaf8b5c530357344b3777a7 \ - 0e30dbf0eeffc11de98c1a0a7722fc46" +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 d5c51fca32..a0f531e127 100644 --- a/academic/octave/README +++ b/academic/octave/README @@ -20,9 +20,9 @@ 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. +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 diff --git a/academic/octave/octave.SlackBuild b/academic/octave/octave.SlackBuild index 162ebf1629..7fba88f533 100644 --- a/academic/octave/octave.SlackBuild +++ b/academic/octave/octave.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for octave -# Copyright 2012-2022 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=${VERSION:-6.4.0} +VERSION=${VERSION:-8.4.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -44,15 +44,12 @@ if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then fi TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="AUTHORS BUGS CITATION COPYING ChangeLog INSTALL* NEWS README" -if [ "$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 [ "$ARCH" = "i686" ]; then @@ -67,13 +64,17 @@ else fi # Use GraphicsMagick by default. Fall back on ImageMagick from the full -# Slackware install if it's not present. Requires a patch for this bug: -# https://savannah.gnu.org/bugs/?49653 +# Slackware install if it's not present. # # GraphicsMagick is default due to the fact that the Octave devs mainly test # with that, and went several releases before noticing ImageMagick was broken. # If ImageMagick doesn't work, install GraphicsMagick, or set MAGICK="". -MAGICK=${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 @@ -92,7 +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 < $CWD/patches/atlas-lib-rename.diff autoreconf -vif @@ -101,19 +101,16 @@ autoreconf -vif # If you live far enough east or west that the date contained in version.texi # does not match that file's timestamp when printed accounting for your # timezone, then the docs get rebuilt with your local date. -# -# The TeX environment in Slackware 14.1 fails to build the DVI and PDF -# targets in Octave 3.8.1. Maybe it works with a recent version of TeXLive? find . -name stamp-vti -exec touch {} + ./configure \ --prefix=/usr \ - --libdir=/usr/lib${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 \ ${MAGICK} \ @@ -123,7 +120,8 @@ find . -name stamp-vti -exec touch {} + FFLAGS="$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 37218af730..13eccf569d 100644 --- a/academic/octave/octave.info +++ b/academic/octave/octave.info @@ -1,8 +1,8 @@ PRGNAM="octave" -VERSION="6.4.0" +VERSION="8.4.0" HOMEPAGE="https://www.gnu.org/software/octave/" -DOWNLOAD="https://ftpmirror.gnu.org/gnu/octave/octave-6.4.0.tar.lz" -MD5SUM="10ff993735afadcf0fcf1bd68e9e1fb3" +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/573.patch.gz b/academic/openboard/573.patch.gz Binary files differdeleted file mode 100644 index 16865b5382..0000000000 --- a/academic/openboard/573.patch.gz +++ /dev/null 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 671171bdb8..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 @@ -26,9 +26,9 @@ 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:-2} +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.$PKGTYPE" exit 0 @@ -53,16 +50,12 @@ OUTPUT=${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 [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2" - LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" - LIBDIRSUFFIX="" fi set -e @@ -89,10 +82,6 @@ sed -i "s|lquazip5|lquazip1-qt5|g" OpenBoard.pro # Thanks to Robby Workman for the idea QUAZIPVER=`pkg-config --modversion quazip1-qt5` sed -i "s|QuaZip-Qt5-1.1|QuaZip-Qt5-$QUAZIPVER|g" OpenBoard.pro plugins/cffadaptor/UBCFFAdaptor.pro -zcat $CWD/573.patch.gz | patch -p1 - -# Patch to run in a window -patch -p1 < $CWD/run-in-a-window.patch qmake-qt5 OpenBoard.pro -spec linux-g++ make @@ -110,6 +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 36214ea14d..20a8614784 100644 --- a/academic/openboard/openboard.info +++ b/academic/openboard/openboard.info @@ -1,8 +1,8 @@ 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" diff --git a/academic/openboard/quazip.patch b/academic/openboard/quazip.patch index 678e22fa55..6a5cb79865 100644 --- a/academic/openboard/quazip.patch +++ b/academic/openboard/quazip.patch @@ -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/QuaZip-Qt5-1.1/quazip" +--- 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/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 a74dd7c25a..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=${PKGTYPE:-tgz} @@ -86,8 +86,8 @@ find -L . \ # manuals installed by paml. sed -i 's|QApplication::applicationDirPath()|"/usr"|g' mainwindow.cpp sed -i 's|+= "/pamlx.conf"|= "~/.pamlX/pamlx.conf"|g' mainwindow.cpp -sed -i 's|/doc/|/doc/paml-4.9j/|g' mainwindow.cpp -sed -i 's|/doc/|/doc/paml-4.9j/|g' pamlhistorydialog.cpp +sed -i 's|/doc/|/doc/paml-4.10.6/|g' mainwindow.cpp +sed -i 's|/doc/|/doc/paml-4.10.6/|g' pamlhistorydialog.cpp # If you want the "Help" menu to use something else than Okular for # viewing the PDF documentation, uncomment the appropriate line below diff --git a/academic/parmetis/parmetis.SlackBuild b/academic/parmetis/parmetis.SlackBuild index c106737a06..6511e58083 100644 --- a/academic/parmetis/parmetis.SlackBuild +++ b/academic/parmetis/parmetis.SlackBuild @@ -34,7 +34,7 @@ SRCNAM="$(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/petsc/README b/academic/petsc/README deleted file mode 100644 index 435fff0276..0000000000 --- a/academic/petsc/README +++ /dev/null @@ -1,11 +0,0 @@ -PETSc, the Portable, Extensible Toolkit for Scientific Computation, -pronounced PET-see (/ˈpɛt-siː/), is a suite of data structures and -routines for the scalable (parallel) solution of scientific -applications modeled by partial differential equations. It supports -MPI, and GPUs through CUDA, HIP or OpenCL, as well as hybrid MPI-GPU -parallelism; it also supports the NEC-SX Tsubasa Vector Engine. PETSc -(sometimes called PETSc/TAO) also contains the TAO, the Toolkit for -Advanced Optimization, software library. - -PETSc is developed as open-source, requests and contributions are -welcome. diff --git a/academic/petsc/petsc.info b/academic/petsc/petsc.info deleted file mode 100644 index bd0bdf3848..0000000000 --- a/academic/petsc/petsc.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="petsc" -VERSION="3.17.0" -HOMEPAGE="https://petsc.org/" -DOWNLOAD="https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.17.0.tar.gz" -MD5SUM="54ecb6055e7e219aff2c30d99f2f603e" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="numpy3 OpenBLAS openmpi" -MAINTAINER="Fellype do Nascimento" -EMAIL="fellype (at) gmail (dot) com" 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 2c8ee6b842..5ce9f314c9 100644 --- a/academic/pianobooster/pianobooster.info +++ b/academic/pianobooster/pianobooster.info @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="" MD5SUM_x86_64="" 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/plus42/doinst.sh b/academic/plus42/doinst.sh new file mode 100644 index 0000000000..4e8ba7071d --- /dev/null +++ b/academic/plus42/doinst.sh @@ -0,0 +1,4 @@ +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/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/README b/academic/prank-msa/README new file mode 100644 index 0000000000..03d714280f --- /dev/null +++ b/academic/prank-msa/README @@ -0,0 +1,32 @@ +PRANK: Probabilistic Alignment Kit + +PRANK is a probabilistic multiple alignment program for DNA, codon and +amino-acid sequences. It is based on a novel algorithm that treats +insertions correctly and avoids over-estimation of the number of +deletion events. + +In addition, PRANK borrows ideas from maximum likelihood (ML) methods +used in phylogenetics and correctly takes into account the evolutionary +distances between sequences. + +Lastly, PRANK allows for defining a potential structure for sequences to +be aligned and then, simultaneously with the alignment, predicts the +locations of structural units in the sequences. + +NOTE! +The dependencies listed in the REQUIRED field are not needed for +building PRANK. They are, however, highly recommended for the complete +functionality of the program: + +1) Progressive alignment requires a guide tree. If no tree is provided, +PRANK constructs one by calling MAFFT to make a quick alignment and +infers an NJ tree from the evolutionary distances based on that. + +2) The standard PRANK algorithm is based on an exhaustive search of the +best pairwise solution. PRANK uses Exonerate to anchor the pairwise +alignments and thus speed up the process. + +3) To improve the ancestral reconstruction, PRANK uses BppAncestor from +the BppSuite. + +NOTE 2: This will not build on a 32bit system. diff --git a/academic/prank-msa/prank-msa.SlackBuild b/academic/prank-msa/prank-msa.SlackBuild new file mode 100644 index 0000000000..a3c6791cdd --- /dev/null +++ b/academic/prank-msa/prank-msa.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/bash + +# Slackware build script for prank-msa + +# Copyright 2017-2022 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=prank-msa +SRCNAM=prank.source +VERSION=${VERSION:-170427} +BUILD=${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 +tar xvf $CWD/${SRCNAM}.${VERSION}.tgz +cd $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 {} \; + +cd src + +# Use our FLAGS +sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i "/^CXXFLAGS/s/=/+=/" Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make + +# Install the binary +install -D -m755 prank $PKG/usr/bin/prank + +# Place the man page in its proper location +install -D -m644 prank.1 $PKG/usr/man/man1/prank.1 + +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 ../VERSION_HISTORY $PKG/usr/doc/$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/prank-msa/prank-msa.info b/academic/prank-msa/prank-msa.info new file mode 100644 index 0000000000..ab3041d52b --- /dev/null +++ b/academic/prank-msa/prank-msa.info @@ -0,0 +1,10 @@ +PRGNAM="prank-msa" +VERSION="170427" +HOMEPAGE="http://wasabiapp.org/software/prank/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="http://wasabiapp.org/download/prank/prank.source.170427.tgz" +MD5SUM_x86_64="a5cda14dc4e5efe1f14b84eb7a7caabd" +REQUIRES="bppsuite mafft exonerate" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/prank-msa/slack-desc b/academic/prank-msa/slack-desc new file mode 100644 index 0000000000..3a6b88e42b --- /dev/null +++ b/academic/prank-msa/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------------------------------------------------------| +prank-msa: prank-msa (A probabilistic multiple alignment program) +prank-msa: +prank-msa: PRANK is a probabilistic multiple alignment program for DNA, +prank-msa: codon and amino-acid sequences. +prank-msa: +prank-msa: Home: http://wasabiapp.org/software/prank/ +prank-msa: +prank-msa: +prank-msa: +prank-msa: +prank-msa: 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 adfdf57c99..17b31eb664 100644 --- a/academic/pspp/pspp.SlackBuild +++ b/academic/pspp/pspp.SlackBuild @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=pspp -VERSION=${VERSION:-1.4.1} +VERSION=${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 @@ -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 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 5456d0253a..702e496e28 100644 --- a/academic/pspp/pspp.info +++ b/academic/pspp/pspp.info @@ -1,10 +1,10 @@ PRGNAM="pspp" -VERSION="1.4.1" +VERSION="2.0.0" HOMEPAGE="http://www.gnu.org/software/pspp/" -DOWNLOAD="http://ftpmirror.gnu.org/pspp/pspp-1.4.1.tar.gz" -MD5SUM="7852af2e4f5ac1b57bd2c1636dca7b40" +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/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 872cf0be27..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 \ - ab1f71f1d38096af86048866c0bbd3d8" +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 2489d6cd26..17d0db3198 100644 --- a/academic/pysam/pysam.SlackBuild +++ b/academic/pysam/pysam.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for pysam -# Copyright 2017-2022 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=${VERSION:-0.19.0} -BUILD=${BUILD:-1} +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 now at htslib-1.15; SBo-htslib is at 1.15.1: -# can 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 2df162ea2d..d71c4d96bd 100644 --- a/academic/pysam/pysam.info +++ b/academic/pysam/pysam.info @@ -1,10 +1,10 @@ PRGNAM="pysam" -VERSION="0.19.0" +VERSION="0.21.0" HOMEPAGE="https://github.com/pysam-developers/pysam" -DOWNLOAD="https://pypi.python.org/packages/source/p/pysam/pysam-0.19.0.tar.gz" -MD5SUM="010374b2a33238c6e3236a1bcfded096" +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/scipy/scipy.SlackBuild b/academic/python2-scipy/python2-scipy.SlackBuild index 273d144b3e..683c91db3d 100644 --- a/academic/scipy/scipy.SlackBuild +++ b/academic/python2-scipy/python2-scipy.SlackBuild @@ -2,7 +2,7 @@ # Build script for the Python SciPy package -# Copyright 2011-2018 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 +25,16 @@ # 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=scipy -VERSION=${VERSION:-1.2.2} -BUILD=${BUILD:-2} +PRGNAM=python2-scipy +SRCNAM=scipy +VERSION=${VERSION:-1.2.3} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -53,7 +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 @@ -61,9 +63,9 @@ 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 . \ @@ -79,12 +81,12 @@ DEBUG=$(echo "$DEBUG"|cut -b 1|tr a-z A-Z) if [ "$DEBUG" = "N" ] then - 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 else - python setup.py build --debug - python 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/scipy3/README b/academic/python3-scipy/README index 6bde98595e..c4b1d1d862 100644 --- a/academic/scipy3/README +++ b/academic/python3-scipy/README @@ -15,10 +15,12 @@ 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. +If you need to build scipy for debugging, set DEBUG=YES. NOTE: this is for Python 3. If you need Python 2 support, install -scipy. +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/scipy3/scipy3.SlackBuild b/academic/python3-scipy/python3-scipy.SlackBuild index 8e7d540308..7586beabdc 100644 --- a/academic/scipy3/scipy3.SlackBuild +++ b/academic/python3-scipy/python3-scipy.SlackBuild @@ -3,7 +3,8 @@ # Build script for the Python SciPy package to be used with python 3 # Copyright 2016-2019 Serban Udrea <s.udrea@gsi.de> -# Copyright 2022 Isaac Yu <isaacyu1@isaacyu1.com> +# 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, @@ -31,9 +32,9 @@ cd $(dirname $0) ; CWD=$(pwd) -PRGNAM="scipy3" +PRGNAM="python3-scipy" SRCNAM="scipy" -VERSION=${VERSION:-1.8.1} +VERSION=${VERSION:-1.12.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -46,16 +47,13 @@ if [ -z "$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 @@ -69,29 +67,33 @@ 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 - python3 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 + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -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 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 $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/qhull/qhull.info b/academic/qhull/qhull.info index 2124edbf51..f296e70bab 100644 --- a/academic/qhull/qhull.info +++ b/academic/qhull/qhull.info @@ -1,10 +1,10 @@ PRGNAM="qhull" -VERSION="2015.2" +VERSION="8.0.2" HOMEPAGE="http://www.qhull.org/" -DOWNLOAD="http://www.qhull.org/download/qhull-2015-src-7.2.0.tgz" -MD5SUM="e6270733a826a6a7c32b796e005ec3dc" +DOWNLOAD="http://www.qhull.org/download/qhull-2020-src-8.0.2.tgz" +MD5SUM="295f7332269a38279478f555cc185296" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Jason Graham" -EMAIL="jgraha8@gmail.com" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.qhull2020_2023-11-19@lockywolf.net" diff --git a/academic/qrupdate/qrupdate.SlackBuild b/academic/qrupdate/qrupdate.SlackBuild index e98a100038..859089ed67 100644 --- a/academic/qrupdate/qrupdate.SlackBuild +++ b/academic/qrupdate/qrupdate.SlackBuild @@ -47,13 +47,13 @@ if [ ! -z "${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/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.$PKGTYPE diff --git a/academic/ramulator/ramulator.info b/academic/ramulator/ramulator.info new file mode 100644 index 0000000000..1be349e32f --- /dev/null +++ b/academic/ramulator/ramulator.info @@ -0,0 +1,10 @@ +PRGNAM="ramulator" +VERSION="20220503" +HOMEPAGE="https://github.com/CMU-SAFARI/ramulator" +DOWNLOAD="https://github.com/CMU-SAFARI/ramulator/archive/743b940b70a8e18bcffb14eec22d2ed731059540/ramulator-743b940b70a8e18bcffb14eec22d2ed731059540.tar.gz" +MD5SUM="c8eb022ef2465831704bc8551bfa1a36" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/ramulator/slack-desc b/academic/ramulator/slack-desc new file mode 100644 index 0000000000..ab7d81704f --- /dev/null +++ b/academic/ramulator/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +ramulator: ramulator (a fast and cycle-accurate DRAM simulator) +ramulator: +ramulator: +ramulator: +ramulator: Ramulator is a fast and cycle-accurate DRAM simulator that +ramulator: supports a wide array of commercial, as well as academic, +ramulator: DRAM standards. +ramulator: +ramulator: +ramulator: +ramulator: diff --git a/academic/rbio/rbio.SlackBuild b/academic/rbio/rbio.SlackBuild index d5595a7d6d..ba45380aac 100644 --- a/academic/rbio/rbio.SlackBuild +++ b/academic/rbio/rbio.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${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 ca62905ea0..3f7a5201e2 100644 --- a/academic/root/README +++ b/academic/root/README @@ -15,6 +15,22 @@ arguments. Compilation takes quite a while, thus consider to build ROOT like that: # MAKEFLAGS=-j5 ./root.SlackBuild -REQUIREMENTS: gl2ps libAfterImage numpy3 tbb ftgl +REQUIREMENTS: gl2ps libAfterImage python3-numpy tbb ftgl -NOTE: ROOT's python TMVA requires numpy3 built over blas. +NOTES: + - ROOT's python TMVA requires python3-numpy being built over blas. + + - 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 + + - 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 + + - 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 9725527197..1dc6bb4194 100644 --- a/academic/root/root.SlackBuild +++ b/academic/root/root.SlackBuild @@ -20,7 +20,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=root -VERSION=${VERSION:-6.24.06} +VERSION=${VERSION:-6.28.08} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -90,6 +90,7 @@ cmake ../src \ -Dbuiltin_davix=OFF \ -Dbuiltin_fftw3=OFF \ -Dbuiltin_gsl=OFF \ + -Dbuiltin_gtest=OFF \ -Dbuiltin_openssl=OFF \ -Dbuiltin_tbb=OFF \ -Dbuiltin_vc=OFF \ @@ -215,7 +216,9 @@ cp -a README/ README.md LICENSE LGPL2_1.txt ../src/CONTRIBUTING.md \ find $PKG/usr/doc/$PRGNAM-$VERSION -type f -exec chmod 644 {} \; cp -a README/ LICENSE \ $PKG$PREFIX -chmod -R 644 $PKG$PREFIX/README +# 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 diff --git a/academic/root/root.info b/academic/root/root.info index de20662e7e..9343758408 100644 --- a/academic/root/root.info +++ b/academic/root/root.info @@ -1,10 +1,10 @@ PRGNAM="root" -VERSION="6.24.06" +VERSION="6.28.08" HOMEPAGE="https://root.cern" -DOWNLOAD="https://root.cern/download/root_v6.24.06.source.tar.gz" -MD5SUM="267e08ba9bf957e82b4236f3c50f0219" +DOWNLOAD="https://root.cern/download/root_v6.28.08.source.tar.gz" +MD5SUM="3eca7fadb7867232fa74a7262644b05d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="gl2ps libAfterImage numpy3 tbb ftgl" +REQUIRES="gl2ps libAfterImage python3-numpy tbb ftgl" MAINTAINER="Andrei Rabusov" EMAIL="arabusov@gmail.com" 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 90988eef3d..ea640b1291 100644 --- a/academic/rpy2/rpy2.SlackBuild +++ b/academic/rpy2/rpy2.SlackBuild @@ -2,7 +2,7 @@ # # SlackBuild for rpy2 # -# Copyright 2020-2022 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=${VERSION:-3.5.1} +VERSION=${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 c30e984424..2c3adced95 100644 --- a/academic/rpy2/rpy2.info +++ b/academic/rpy2/rpy2.info @@ -1,10 +1,10 @@ PRGNAM="rpy2" -VERSION="3.5.1" +VERSION="3.5.16" HOMEPAGE="https://rpy2.github.io/" -DOWNLOAD="https://pypi.python.org/packages/source/r/rpy2/rpy2-3.5.1.tar.gz" -MD5SUM="b9981a0cc73efe1b08c8174b943f2788" +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/sage-bin.info b/academic/sage-bin/sage-bin.info index 9907eb8cb1..9d85b66d3b 100644 --- a/academic/sage-bin/sage-bin.info +++ b/academic/sage-bin/sage-bin.info @@ -1,9 +1,9 @@ PRGNAM="sage-bin" VERSION="9.4" -HOMEPAGE="http://www.sagemath.org" +HOMEPAGE="https://www.sagemath.org" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="http://mirrors.mit.edu/sage/linux/64bit/sage-9.4-Debian_GNU_Linux_11-x86_64.tar.bz2 \ +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 \ diff --git a/academic/sage/sage.SlackBuild b/academic/sage/sage.SlackBuild index 55235ef6e0..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 Jan 2022. +# Last update June 2023. # # All rights reserved. # @@ -27,7 +27,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=sage -VERSION=${VERSION:-9.4} +VERSION=${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 364237c41a..70070f617e 100644 --- a/academic/sage/sage.info +++ b/academic/sage/sage.info @@ -1,8 +1,8 @@ PRGNAM="sage" -VERSION="9.4" +VERSION="10.1" HOMEPAGE="http://www.sagemath.org" -DOWNLOAD="http://mirrors.mit.edu/sage/src/sage-9.4.tar.gz" -MD5SUM="66d4e2cc18095df56f99f5420d70a33b" +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 3ce93d2d42..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 2017-2022 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=${VERSION:-1.15.1} +VERSION=${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 716fa50acc..eef9473b1e 100644 --- a/academic/samtools/samtools.info +++ b/academic/samtools/samtools.info @@ -1,8 +1,8 @@ PRGNAM="samtools" -VERSION="1.15.1" +VERSION="1.19.2" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2" -MD5SUM="b71d1aa1de9749773b1a04bf54281ca0" +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 62e21593e3..6ebdd91a51 100644 --- a/academic/scidavis/scidavis.SlackBuild +++ b/academic/scidavis/scidavis.SlackBuild @@ -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 3292d81154..7904927c3f 100644 --- a/academic/scidavis/scidavis.info +++ b/academic/scidavis/scidavis.info @@ -1,8 +1,14 @@ 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" diff --git a/academic/scipy/scipy.info b/academic/scipy/scipy.info deleted file mode 100644 index d6f9f0522c..0000000000 --- a/academic/scipy/scipy.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="scipy" -VERSION="1.2.2" -HOMEPAGE="https://www.scipy.org/" -DOWNLOAD="https://github.com/scipy/scipy/releases/download/v1.2.2/scipy-1.2.2.tar.gz" -MD5SUM="d94de858fba4f24de7d6dd16f1caeb5d" -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/scipy3.info b/academic/scipy3/scipy3.info deleted file mode 100644 index fef2e009fe..0000000000 --- a/academic/scipy3/scipy3.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="scipy3" -VERSION="1.8.1" -HOMEPAGE="https://www.scipy.org/" -DOWNLOAD="https://github.com/scipy/scipy/releases/download/v1.8.1/scipy-1.8.1.tar.gz" -MD5SUM="df5ce79288fc457238aeef18e8f70dfc" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="numpy3 lapack pybind11 python3-pythran" -MAINTAINER="Isaac Yu" -EMAIL="isaacyu1@isaacyu1.com" 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/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 c95c76d4b5..d1968b049b 100644 --- a/academic/seaview/seaview.info +++ b/academic/seaview/seaview.info @@ -1,10 +1,10 @@ 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" +REQUIRES="fltk PDFlib-Lite Gblocks PhyML clustalo muscle treerecs" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" 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/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/sim/slack-desc b/academic/sim/slack-desc new file mode 100644 index 0000000000..c38253a06f --- /dev/null +++ b/academic/sim/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------------------------------------------------------| +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/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 2eb048865e..bc40d92965 100644 --- a/academic/smath-studio/smath-studio.info +++ b/academic/smath-studio/smath-studio.info @@ -1,9 +1,9 @@ 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="" 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 $PKG/usr/bin diff --git a/academic/solfege/solfege.SlackBuild b/academic/solfege/solfege.SlackBuild index 7dd3799cf8..4b69490ae4 100644 --- a/academic/solfege/solfege.SlackBuild +++ b/academic/solfege/solfege.SlackBuild @@ -13,7 +13,7 @@ PKGTYPE=${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/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/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 15ae507453..4704b3906b 100644 --- a/academic/suitesparse/README +++ b/academic/suitesparse/README @@ -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 eeed0ddcac..774fbc1a19 100644 --- a/academic/suitesparse/suitesparse.SlackBuild +++ b/academic/suitesparse/suitesparse.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for suitesparse -# Copyright 2017-2022 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=${VERSION:-5.11.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-5.13.0} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -82,6 +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=$PKG/usr/include/suitesparse \ diff --git a/academic/suitesparse/suitesparse.info b/academic/suitesparse/suitesparse.info index c69b1cd585..929ec6e26f 100644 --- a/academic/suitesparse/suitesparse.info +++ b/academic/suitesparse/suitesparse.info @@ -1,8 +1,8 @@ PRGNAM="suitesparse" -VERSION="5.11.0" +VERSION="5.13.0" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.11.0/SuiteSparse-5.11.0.tar.gz" -MD5SUM="909a75e6abca32a329a593a96dc00de7" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.13.0/SuiteSparse-5.13.0.tar.gz" +MD5SUM="e9e7bc594b77ae4b58d943cdc286d679" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="lapack OpenBLAS chrpath" diff --git a/academic/suitesparseconfig/suitesparseconfig.SlackBuild b/academic/suitesparseconfig/suitesparseconfig.SlackBuild index 6b32fdb34a..8ebbedcfc1 100644 --- a/academic/suitesparseconfig/suitesparseconfig.SlackBuild +++ b/academic/suitesparseconfig/suitesparseconfig.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${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 6facf19883..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 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 b6d1650404..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=${VERSION:-1.9.0_1} -BUILD=${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 f0606e9dfb..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="1.9.0_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/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 > $PKG/install/slack-desc diff --git a/academic/tiemu/tiemu.info b/academic/tiemu/tiemu.info index d665780f3f..5f6b445bdc 100644 --- a/academic/tiemu/tiemu.info +++ b/academic/tiemu/tiemu.info @@ -6,5 +6,5 @@ MD5SUM="2736440d717a0ee97cdb35189814fc93" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="libticalcs2" -MAINTAINER="shelldweller" -EMAIL="shelldweller@beauxbead.com" +MAINTAINER="B. Watson" +EMAIL="urchlay@slackware.uk" diff --git a/academic/tkgate/tkgate.SlackBuild b/academic/tkgate/tkgate.SlackBuild index 3d09c6f107..cbcf6001b4 100644 --- a/academic/tkgate/tkgate.SlackBuild +++ b/academic/tkgate/tkgate.SlackBuild @@ -33,7 +33,7 @@ PKGTYPE=${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/treerecs/README b/academic/treerecs/README new file mode 100644 index 0000000000..283164480a --- /dev/null +++ b/academic/treerecs/README @@ -0,0 +1,38 @@ +Treerecs: a tree reconciliation tool + +Treerecs is an open-source (species- and gene-) tree reconciliation +software distributed under the GNU AGPL licence. It can correct, +rearrange and (re-)root gene trees with regard to a given species tree. +It was designed to be both efficient and easy to install and to use. + +Features +- Correct gene trees with regard to a reference species tree +- Root or re-root gene trees +- Contract gene-tree branches whose support is lower than a given + threshold, thus creating polytomies (multifurcations) that can be + resolved therefater +- Sample solutions with equivalent scores +- Produce a graphical representation of the reconciled trees +- Supported formats + +Treerecs supports the following formats: Newick, NHX, PhyloXML, +recPhyloXML, SVG (graphical output). + +A program that can drive Treerecs, providing a GUI is Seaview, also +available at SBo. The SlacBuild script builds two additional programs: + +1) ALEevaluate_undated: an executable of the ALE (Amalgamated likelihood +estimation, https://github.com/ssolo/ALE), by Szollosi GJ et al). This +version has other mapping options and a different implementation in +Bio++ use. + +2) genetreeEditor: a small program which provides editing of gene names +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 +https://www.biorxiv.org/content/10.1101/782946v1 diff --git a/academic/treerecs/doinst.sh b/academic/treerecs/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/treerecs/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/treerecs/slack-desc b/academic/treerecs/slack-desc new file mode 100644 index 0000000000..319b6b6f7b --- /dev/null +++ b/academic/treerecs/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------------------------------------------------------| +treerecs: treerecs (Treerecs: a tree reconciliation tool) +treerecs: +treerecs: Treerecs is an open-source (species- and gene-) tree reconciliation +treerecs: software. It can correct, rearrange and (re-)root gene trees with +treerecs: regard to a given species tree. +treerecs: +treerecs: https://project.inria.fr/treerecs/ +treerecs: https://gitlab.inria.fr/Phylophile/Treerecs +treerecs: +treerecs: +treerecs: diff --git a/academic/treerecs/treerecs.SlackBuild b/academic/treerecs/treerecs.SlackBuild new file mode 100644 index 0000000000..14e1cebfe0 --- /dev/null +++ b/academic/treerecs/treerecs.SlackBuild @@ -0,0 +1,123 @@ +#!/bin/bash + +# Slackware build script for treerecs + +# Copyright 2020-2023 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. + +# Thanks to David Parsons for clarifications about the scipt and suggestions! + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=treerecs +SRCNAM=Treerecs +VERSION=${VERSION:-1.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${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 $SRCNAM-v${VERSION} +tar xvf $CWD/$SRCNAM-v${VERSION}.tar.gz +cd $SRCNAM-v${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 {} \; + +# 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 \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_BUILD_TYPE=Release .. + make +cd .. + +# This is the program executable. Using "make install DESTDIR=$PKG" +# works, but it simply puts treerecs in /usr/local/bin and that's it +install -D -m755 build/bin/$PRGNAM $PKG/usr/bin/$PRGNAM + +# Include the extra binaries +install -D -m755 build/bin/misc/ALEevaluate_undated $PKG/usr/bin/ALEevaluate_undated +install -D -m755 build/bin/misc/genetreeEditor $PKG/usr/bin/genetreeEditor + +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 + +# Copy some examples and the icon just in case +mkdir -p $PKG/usr/share/$PRGNAM +cp -a examples ${PRGNAM}_icon.png $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS COPYING CONTRIBUTING.md README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cp -a build/bin/misc/README.md $PKG/usr/doc/$PRGNAM-$VERSION/README-misc.md +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.$PKGTYPE diff --git a/academic/treerecs/treerecs.info b/academic/treerecs/treerecs.info new file mode 100644 index 0000000000..f6a81aa05b --- /dev/null +++ b/academic/treerecs/treerecs.info @@ -0,0 +1,10 @@ +PRGNAM="treerecs" +VERSION="1.2" +HOMEPAGE="https://project.inria.fr/treerecs/" +DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/-/archive/v1.2/Treerecs-v1.2.tar.gz" +MD5SUM="a85d2dc0047278bfb0017c2b69824b56" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/treeviewx/treeviewx.info b/academic/treeviewx/treeviewx.info index 8de22d44fb..14ab2567b3 100644 --- a/academic/treeviewx/treeviewx.info +++ b/academic/treeviewx/treeviewx.info @@ -1,7 +1,7 @@ PRGNAM="treeviewx" VERSION="0.5.1_20100723" HOMEPAGE="https://github.com/rdmpage" -DOWNLOAD="http://deb.debian.org/debian/pool/main/t/treeviewx/treeviewx_0.5.1+20100823.orig.tar.gz" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/treeviewx/treeviewx_0.5.1+20100823.orig.tar.gz" MD5SUM="8059a306b723e6fb4d3befcf302b2920" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/tuxtype2/tuxtype2.SlackBuild b/academic/tuxtype2/tuxtype2.SlackBuild index cc3eb64ffc..ad7e5240be 100644 --- a/academic/tuxtype2/tuxtype2.SlackBuild +++ b/academic/tuxtype2/tuxtype2.SlackBuild @@ -33,7 +33,7 @@ PKGTYPE=${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 b0a0c8064c..181b318651 100644 --- a/academic/ugene/README +++ b/academic/ugene/README @@ -38,28 +38,25 @@ 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) - tophat (Splice junction mapper for RNA-Seq reads) diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild index 6ccec594dd..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 @@ -25,8 +25,8 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ugene -VERSION=${VERSION:-38.1} -BUILD=${BUILD:-2} +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 @@ -84,19 +81,46 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Fix libraries and man pages paths -sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri -sed -i "s:/share/man:/man:g" src/ugene_globals.pri -sed -i "s:Werror=maybe-uninitialized:Wno-error=maybe-uninitialized:g - s:Werror=uninitialized:Wno-error=uninitialized:g" \ - src/ugene_globals.pri +#sed -i "s:/lib:/lib${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 -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 $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info index 14652ce6a2..8f9bf4bdf6 100644 --- a/academic/ugene/ugene.info +++ b/academic/ugene/ugene.info @@ -1,10 +1,10 @@ PRGNAM="ugene" -VERSION="38.1" +VERSION="48.1" HOMEPAGE="http://ugene.net/" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://github.com/ugeneunipro/ugene/archive/38.1/ugene-38.1.tar.gz" -MD5SUM_x86_64="4add1b1c0216ce42e588e982a3d7147e" +DOWNLOAD_x86_64="https://github.com/ugeneunipro/ugene/archive/48.1/ugene-48.1.tar.gz" +MD5SUM_x86_64="5662a9e58d6ad19a8be7410f12139072" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/umfpack/umfpack.SlackBuild b/academic/umfpack/umfpack.SlackBuild index 447c4d03c9..3da82b0df8 100644 --- a/academic/umfpack/umfpack.SlackBuild +++ b/academic/umfpack/umfpack.SlackBuild @@ -50,13 +50,13 @@ if [ ! -z "${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/01_caps_verbose.patch b/academic/vCAPS_coevolution/01_caps_verbose.patch new file mode 100644 index 0000000000..7f64d80f34 --- /dev/null +++ b/academic/vCAPS_coevolution/01_caps_verbose.patch @@ -0,0 +1,114 @@ +diff -pruN orig/caps.cpp new/caps.cpp +--- orig/caps.cpp 2012-12-15 17:13:23.000000000 +0200 ++++ new/caps.cpp 2020-09-09 23:07:46.080566000 +0300 +@@ -14,7 +14,7 @@ + #include <gsl/gsl_statistics.h> + #include<sys/time.h> + #include<iomanip> +- ++#include <bits/stdc++.h> + + + +@@ -69,6 +69,8 @@ + const gsl_rng_type * T; + gsl_rng *r; + ++vector<double> totaltempnew; ++double alphathresh = 0; + int main(int argc, char *argv[]){ + + +@@ -543,16 +545,27 @@ int main(int argc, char *argv[]){ + + + print_splash(output); ++ OUTPUT << "\n\File1: " << files[i] << endl; + vec1.print_to_fasta(output.c_str()); ++ OUTPUT << "\n\nFile2: " << files[j] << endl; + vec2.print_to_fasta(output.c_str()); + int length1 = vec1.sequences[0].length(); + int length2 = vec2.sequences[0].length(); + ++ OUTPUT << "\n\nLength1: " << length1 << endl; ++ OUTPUT << "Length2: " << length2 << endl; + + + if(tree_in ==0){ + tree1 = create_input_tree(vec1.names, vec1.sequences); + tree2 = create_input_tree(vec2.names, vec2.sequences); ++ ++ // Output the CAPS generated trees to the .out file of each pair ++ string temptre1 = TreeTemplateTools::treeToParenthesis(*tree1, true); ++ string temptre2 = TreeTemplateTools::treeToParenthesis(*tree2, true); ++ OUTPUT << "\n" << endl; ++ OUTPUT << "CAPS generated tree 1: " << temptre1 << endl; ++ OUTPUT << "CAPS generated tree 2: " << temptre2 << endl; + }/*else if(tree_in ==1 && variable==1){ + + std::auto_ptr<DistanceMatrix> DS; +@@ -666,6 +679,7 @@ int main(int argc, char *argv[]){ + int value = floor(((totaltemp.size())*(1-(threshval))))+1; + + threshold = totaltemp[value]; ++ totaltempnew = totaltemp; + + + /*=======================================================*/ +@@ -870,6 +884,30 @@ int Chi_squared (int num_pairs, int num_ + + } /* ----- end of function Chi_squared ----- */ + ++/* ++ * === FUNCTION ====================================================================== ++ * Name: find_alpha ++ * Description: Find the index of an element in a vector totaltemp ++ * Help from: https://www.geeksforgeeks.org/how-to-find-index-of-a-given-element-in-a-vector-in-cpp/ ++ * https://stackoverflow.com/questions/8647635/elegant-way-to-find-closest-value-in-a-vector-from-above ++ * Author: Petar Petrov, University of Turku (Finland); pebope@utu.fi ++ * ===================================================================================== ++ */ ++double getIndex(std::vector<double> const& v, double K) ++{ ++ auto const it = std::lower_bound(v.begin(), v.end(), fabs(K)); ++ //auto it = std::upper_bound(v.begin(), v.end(), fabs(K)); ++ ++ if (it != v.end()) { ++ int index = distance(v.begin(), it); ++ alphathresh = (((int)1+(double)v.size()-(int)index)/(double)v.size()); ++ return alphathresh; ++ //cerr << index << "\t" << alphathresh << endl; ++ } ++ else { ++ cerr << "ELEMENT NOT FOUND!" << endl; ++ } ++} + + + +@@ -890,9 +928,9 @@ int print_inter(vector<double>& Correl1, + output << endl << endl; + + output << "Coevolving Pairs of amino acid sites\n"; +- output << "=============================================================================\n"; +- output << "Col1(real)\tCol2(real)\tDmean1\t\tDmean2\t\tCorrelation\tBootstrap value\n\n"; +- output << "=============================================================================\n"; ++ output << "================================================================================================================================\n"; ++ output << "Col1(real)\tCol2(real)\tDmean1\t\tDmean2\t\tCorrelation\tBootstrap value\tP-value1\tP-value2\tMean P-value\tCorrelation1\tCorrelation2\n\n"; ++ output << "================================================================================================================================\n"; + + //double mean = average_vec<double>(Correl); + //double SD = SD_vf(Correl, mean); +@@ -951,9 +989,11 @@ int print_inter(vector<double>& Correl1, + + // } + ++ double Alpha1 = getIndex(totaltempnew, Correl1[cor]); ++ double Alpha2 = getIndex(totaltempnew, Correl2[cor]); + //if(bootval>=bootcut && re1<=8 && re2<=8 ){ + if(bootval>=bootcut){ +- output << i+1 << "(" << i-gaps1+1 << ")\t\t" << j+1 << "(" << (j+1)-gaps2 << ")\t\t" << averDi << "\t\t" << averDj << "\t\t" << (Correl1[cor]+Correl2[cor])/2 << "\t" << bootval << endl; ++ output << i+1 << "(" << i-gaps1+1 << ")\t\t" << j+1 << "(" << (j+1)-gaps2 << ")\t\t" << averDi << "\t\t" << averDj << "\t" << (Correl1[cor]+Correl2[cor])/2 << "\t" << bootval << "\t" << Alpha1 << "\t" << Alpha2 << "\t" << (Alpha1+Alpha2)/2 << "\t" << Correl1[cor] << "\t" << Correl2[cor] << endl; + signif.push_back(((Correl1[cor]+Correl2[cor])/2)); + ++pairs; + vector<int> tem; 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 new file mode 100644 index 0000000000..b8b4a71a4b --- /dev/null +++ b/academic/vCAPS_coevolution/README @@ -0,0 +1,33 @@ +vCAPS: (verbose) Coevolution Analysis using Protein Sequences + +CAPS is aimed at measuring the coevolution between amino acid sites +belonging to the same protein (intra-molecular coevolution) or to two +functionally or physically interacting proteins (inter-molecular +coevolution). The Software implements an improved method to detect +intra-molecular coevolution as published in Genetics (Fares and Travers, +2006) and also inter-protein coevolution analysis. The improved scoring +of amino acid sites is obtained by maximum likelihood ancestral state +reconstruction along with simulations to assess significance. + +This is a modified version of "CAPS_coevolution", used in the AutoCoEv +pipeline: +https://github.com/mattilalab/autocoev + +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 + +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 + +The mathematical model has been described separately: +A novel method for detecting intramolecular coevolution: adding a +further dimension to selective constraints analyses. Fares MA, Travers +SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113 diff --git a/academic/vCAPS_coevolution/References b/academic/vCAPS_coevolution/References new file mode 100644 index 0000000000..e8236cd282 --- /dev/null +++ b/academic/vCAPS_coevolution/References @@ -0,0 +1,14 @@ +If you use CAPS in your research, please include the following citations: + +CAPS: coevolution analysis using protein sequences. +Fares MA, McNally D. +Bioinformatics. 2006 Nov 15;22(22):2821-2. +PMID: 17005535 +https://www.ncbi.nlm.nih.gov/pubmed/17005535 + +The mathematical model has been described separately: +A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. +Fares MA, Travers SA. +Genetics. 2006 May;173(1):9-23. +PMID: 16547113 +https://www.ncbi.nlm.nih.gov/pubmed/16547113 diff --git a/academic/vCAPS_coevolution/slack-desc b/academic/vCAPS_coevolution/slack-desc new file mode 100644 index 0000000000..5cd78f0770 --- /dev/null +++ b/academic/vCAPS_coevolution/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------------------------------------------------------| +vCAPS_coevolution: vCAPS_coevolution (Coevolution Analysis using Protein Sequences) +vCAPS_coevolution: +vCAPS_coevolution: CAPS is aimed at measuring the coevolution between amino acid +vCAPS_coevolution: sites belonging to the same protein (intra-molecular coevolution) +vCAPS_coevolution: or to two functionally or physically interacting proteins (inter- +vCAPS_coevolution: molecular coevolution). In addition, a test which assesses +vCAPS_coevolution: whether two proteins are interacting is implemented. +vCAPS_coevolution: +vCAPS_coevolution: Home: http://bioinf.gen.tcd.ie/~faresm/software/software.html +vCAPS_coevolution: +vCAPS_coevolution: diff --git a/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild b/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild new file mode 100644 index 0000000000..f00aea698e --- /dev/null +++ b/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild @@ -0,0 +1,129 @@ +#!/bin/bash + +# Slackware build script for vCAPS_coevolution + +# Copyright 2020-2022 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=vCAPS_coevolution +VERSION=${VERSION:-2.0_2UN} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=caps +SRCVER=2.0 +BINNAM=vCAPS + +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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${SRCNAM}${SRCVER}_src +unzip $CWD/${SRCNAM}2_src.zip +cd ${SRCNAM}${SRCVER}_src +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 is needed for gcc in Slackware 14.2 +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 $LIBDIRPATH:" Makefile + +# Find the legacy bpp libraries +sed -i "s:-lbpp-phyl:-L/usr/lib${LIBDIRSUFFIX}/Bpp1.9 -lbpp-phyl:g" Makefile +sed -i "s:-lbpp-numcalc:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-numcalc:g" Makefile +sed -i "s:-lbpp-utils:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-utils:g" Makefile +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 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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + caps_manual.pdf \ + $PKG/usr/doc/$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/vCAPS_coevolution/vCAPS_coevolution.info b/academic/vCAPS_coevolution/vCAPS_coevolution.info new file mode 100644 index 0000000000..48545099b1 --- /dev/null +++ b/academic/vCAPS_coevolution/vCAPS_coevolution.info @@ -0,0 +1,10 @@ +PRGNAM="vCAPS_coevolution" +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="" +REQUIRES="bpp1.9-phyl" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" 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/verilog/verilog.info b/academic/verilog/verilog.info index d2cdfbc5b0..a78c9fe87d 100644 --- a/academic/verilog/verilog.info +++ b/academic/verilog/verilog.info @@ -1,7 +1,7 @@ PRGNAM="verilog" VERSION="11.0" HOMEPAGE="http://iverilog.icarus.com/" -DOWNLOAD="ftp://icarus.com/pub/eda/verilog/v11/verilog-11.0.tar.gz" +DOWNLOAD="https://jaist.dl.sourceforge.net/project/iverilog/iverilog/11.0/verilog-11.0.tar.gz" MD5SUM="a3f7a618a4f499244ec6ee928574f03d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" 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/voro++/voro++.SlackBuild b/academic/voro++/voro++.SlackBuild new file mode 100644 index 0000000000..563f9f3e56 --- /dev/null +++ b/academic/voro++/voro++.SlackBuild @@ -0,0 +1,118 @@ +#!/bin/bash + +# Slackware build script for voro++ + +# 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=voro++ +VERSION=${VERSION:-0.4.6} +BUILD=${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 +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 {} \; + + +# the default make build the examples +# let's keep source only +sed -i '15s/^/#/;24s/^/#/' Makefile + +# 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 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 + +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 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 +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/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-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 b8f069e748..a73a47e760 100644 --- a/academic/wehi-weasel/wehi-weasel.info +++ b/academic/wehi-weasel/wehi-weasel.info @@ -1,8 +1,8 @@ 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="zulu-openjdk11" 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 68391f9136..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 @@ -78,9 +74,9 @@ 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/x48/x48.info b/academic/x48/x48.info index f2e81ceaf5..d6301da61e 100644 --- a/academic/x48/x48.info +++ b/academic/x48/x48.info @@ -7,7 +7,7 @@ DOWNLOAD="https://sourceforge.net/projects/x48.berlios/files/x48-0.6.4.tar.bz2 \ https://literature.hpcalc.org/community/hp48g-ug-en.pdf" MD5SUM="700e631f8924a991b35d8a86ce60aab7 \ a08249c9a75d52671045dbb9c35321fa \ - c87d60754afa7401d8f0a836fb7e40ee \ + 1e91e669ed5bc126049f35f43e12805a \ 9efd58fc89b6ea89bc00d6dbff6812a3" DOWNLOAD_x86_64="" MD5SUM_x86_64="" 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/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 18e4308115..8bfc0a4705 100644 --- a/academic/xflr5/xflr5.SlackBuild +++ b/academic/xflr5/xflr5.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for xflr5 -# Copyright 2020-2022 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=${VERSION:-6.54} +VERSION=${VERSION:-6.61} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -87,6 +87,11 @@ sed -i "s/target\.path = \$\$PREFIX\/lib/target\.path = \$\$PREFIX\/lib${LIBDIRS 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 $CWD/link_directly.patch.gz | patch -p0 + qmake-qt5 \ PREFIX=/usr \ QMAKE_CFLAGS+="$SLKCFLAGS" \ diff --git a/academic/xflr5/xflr5.info b/academic/xflr5/xflr5.info index 484e3aca95..947ad8f4ea 100644 --- a/academic/xflr5/xflr5.info +++ b/academic/xflr5/xflr5.info @@ -1,8 +1,8 @@ PRGNAM="xflr5" -VERSION="6.54" +VERSION="6.61" HOMEPAGE="http://www.xflr5.com/xflr5.htm" -DOWNLOAD="http://sourceforge.net/projects/slackbuildsdirectlinks/files/xflr5/xflr5-6.54.tar.gz" -MD5SUM="a005dabe15ff93bc441655228e10c291" +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/xiphos.SlackBuild b/academic/xiphos/xiphos.SlackBuild index d7638e29e2..3471341e36 100644 --- a/academic/xiphos/xiphos.SlackBuild +++ b/academic/xiphos/xiphos.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for xiphos -# Copyright 2015-2022 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 @@ -22,6 +22,8 @@ # 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 @@ -85,7 +87,6 @@ find -L . \ echo "#define GLIB_VERSION_MIN_REQUIRED (GLIB_VERSION_2_26)" >>cmake/config.h.cmake.in mkdir -p build cd build -echo "1" cmake -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ diff --git a/academic/xiphos/xiphos.info b/academic/xiphos/xiphos.info index 2e531b0cac..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 webkit2gtk 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/6f6b2fa82b8a0cf24ac50899a6d53cd9fd329d2b.patch b/academic/xsimd/6f6b2fa82b8a0cf24ac50899a6d53cd9fd329d2b.patch deleted file mode 100644 index 6e09ea5bf5..0000000000 --- a/academic/xsimd/6f6b2fa82b8a0cf24ac50899a6d53cd9fd329d2b.patch +++ /dev/null @@ -1,48 +0,0 @@ -From 6f6b2fa82b8a0cf24ac50899a6d53cd9fd329d2b Mon Sep 17 00:00:00 2001 -From: serge-sans-paille <serge.guelton@telecom-bretagne.eu> -Date: Fri, 13 May 2022 11:34:53 +0200 -Subject: [PATCH] Do not run tests on unsupported architectures - ---- - test/test_batch_manip.cpp | 5 +++++ - test/test_sum.hpp | 3 +++ - 2 files changed, 8 insertions(+) - -diff --git a/test/test_batch_manip.cpp b/test/test_batch_manip.cpp -index 45c8939f8..b8ca978d3 100644 ---- a/test/test_batch_manip.cpp -+++ b/test/test_batch_manip.cpp -@@ -9,6 +9,9 @@ - * The full license is in the file LICENSE, distributed with this software. * - ****************************************************************************/ - -+#include "xsimd/xsimd.hpp" -+#ifndef XSIMD_NO_SUPPORTED_ARCHITECTURE -+ - #include "test_utils.hpp" - - namespace xsimd -@@ -212,3 +215,5 @@ TYPED_TEST(swizzle_test, swizzle_dup) - { - this->swizzle_dup(); - } -+ -+#endif -diff --git a/test/test_sum.hpp b/test/test_sum.hpp -index 89af1a236..e5edeaf0f 100644 ---- a/test/test_sum.hpp -+++ b/test/test_sum.hpp -@@ -1,6 +1,7 @@ - #ifndef XSIMD_TEST_SUM_HPP - #define XSIMD_TEST_SUM_HPP - #include "xsimd/xsimd.hpp" -+#ifndef XSIMD_NO_SUPPORTED_ARCHITECTURE - - struct sum - { -@@ -29,3 +30,5 @@ extern template float sum::operator()(xsimd::avx, float const*, unsigned); - #endif - - #endif -+ -+#endif diff --git a/academic/xsimd/xsimd.SlackBuild b/academic/xsimd/xsimd.SlackBuild index 5938fdb195..f15fa4eb2b 100644 --- a/academic/xsimd/xsimd.SlackBuild +++ b/academic/xsimd/xsimd.SlackBuild @@ -1,7 +1,9 @@ #!/bin/bash # Slackware build script for xsimd -# Copyright 2022 Isaac Yu <isaacyu1@isaacyu1.com> + +# 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 @@ -24,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=xsimd -VERSION=${VERSION:-8.1.0} +VERSION=${VERSION:-11.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -37,9 +39,6 @@ if [ -z "$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.$PKGTYPE" exit 0 @@ -51,16 +50,12 @@ OUTPUT=${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 -fPIC" - LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" - LIBDIRSUFFIX="" fi set -e @@ -71,8 +66,6 @@ cd $TMP rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION -# https://github.com/xtensor-stack/xsimd/pull/742 -patch -p1 -i $CWD/6f6b2fa82b8a0cf24ac50899a6d53cd9fd329d2b.patch chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ diff --git a/academic/xsimd/xsimd.info b/academic/xsimd/xsimd.info index cf1d4b7475..8a24d36307 100644 --- a/academic/xsimd/xsimd.info +++ b/academic/xsimd/xsimd.info @@ -1,10 +1,10 @@ PRGNAM="xsimd" -VERSION="8.1.0" +VERSION="11.1.0" HOMEPAGE="https://github.com/QuantStack/xsimd" -DOWNLOAD="https://github.com/QuantStack/xsimd/archive/8.1.0/xsimd-8.1.0.tar.gz" -MD5SUM="e3edf90fcdf1d11297ed74bda96d7fbd" +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="gtest" -MAINTAINER="Isaac Yu" -EMAIL="isaacyu1@isaacyu1.com" +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/yices2/yices2.SlackBuild b/academic/yices2/yices2.SlackBuild new file mode 100644 index 0000000000..7d80ee1a9e --- /dev/null +++ b/academic/yices2/yices2.SlackBuild @@ -0,0 +1,131 @@ +#!/bin/bash + +# Slackware build script for yices2 + +# 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=yices2 +VERSION=${VERSION:-2.6.4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=yices-$VERSION-src + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( 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 $PRGNAM-Yices-$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 \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +if [ "${MCSAT:-no}" == "yes" ]; then + OPT="--enable-mcsat" +fi + +autoconf +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + $OPT \ + --docdir=/usr/doc/$PRGNAM-$VERSION + +make +make install DESTDIR=$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 + +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/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/z3.SlackBuild b/academic/z3/z3.SlackBuild index 9793ed0be3..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 @@ -22,14 +22,10 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# 20220323 bkw: Modified by SlackBuilds.org: -# - update for v4.8.12 (previous version failed to build on 32-bit 15.0). -# - always include python3 bindings (since python3 is in core Slackware now). - cd $(dirname $0) ; CWD=$(pwd) PRGNAM=z3 -VERSION=${VERSION:-4.8.12} +VERSION=${VERSION:-4.11.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -94,7 +90,8 @@ cd ../doc python mk_api_doc.py cd .. -# Copy the Python3 bindings to python3.X/site-packages. +# The Python bindings are installed for Python2 by default but work on +# Python3 too. Copy them to python3.X/site-packages. PYTHON_VERSION=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') PYLIB=$PKG/usr/lib${LIBDIRSUFFIX}/python${PYTHON_VERSION}/site-packages mkdir -p $PYLIB @@ -106,11 +103,11 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr 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 762fe838ac..b3b6178ae5 100644 --- a/academic/z3/z3.info +++ b/academic/z3/z3.info @@ -1,8 +1,8 @@ PRGNAM="z3" -VERSION="4.8.12" +VERSION="4.11.2" HOMEPAGE="https://github.com/Z3Prover/z3/wiki" -DOWNLOAD="https://github.com/Z3Prover/z3/archive/z3-4.8.12/z3-z3-4.8.12.tar.gz" -MD5SUM="73fd07d094685039b03aed9e38040d13" +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" |
