diff options
Diffstat (limited to 'academic')
633 files changed, 10596 insertions, 3281 deletions
diff --git a/academic/CAFS_divergence/README b/academic/CAFS_divergence/README index 9320c24786..61ae3acb06 100644 --- a/academic/CAFS_divergence/README +++ b/academic/CAFS_divergence/README @@ -1,24 +1,25 @@ CAFS: Clustering Analysis of Functional Shifts -CAFS is a simple and fast method for Clustering functionally divergent (FD) -genes by Functional Category. +CAFS is a simple and fast method for Clustering functionally divergent +(FD) genes by Functional Category. -The method implemented in CAFS is one of several sequence-based methods -for identifying the 'interesting' subset of substitutions that might -underpin functional divergence. These methods are based on the idea of that -functionally-important residues are highly conserved, so that evolutionary -rates tend to be low at important sites. Functional divergence can then be -identified by comparing rates (or levels of conservation) between two -clades of proteins at a homologous site. Alternatively, a significant -change in amino acid identity (such as a large, positively-charged residue -in one group of sequences versus a small, neutral residue in the other) -could indicate functional divergence even without a change in rate. +The method implemented in CAFS is one of several sequence-based +methods for identifying the 'interesting' subset of substitutions +that might underpin functional divergence. These methods are based +on the idea of that functionally-important residues are highly +conserved, so that evolutionary rates tend to be low at important +sites. Functional divergence can then be identified by comparing +rates (or levels of conservation) between two clades of proteins at +a homologous site. Alternatively, a significant change in amino acid +identity (such as a large, positively-charged residue in one group of +sequences versus a small, neutral residue in the other) could indicate +functional divergence even without a change in rate. This program analyses alignments and provides the user with the best putative sites under functional divergence. -NOTE: This only repackages the 64bit binary provided from upstream. A 32bit -executable is not available. +NOTE: This only repackages the 64bit binary provided from upstream. A +32bit executable is not available. Citing: Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA (2011). diff --git a/academic/mpmath/mpmath.SlackBuild b/academic/DendroPy/DendroPy.SlackBuild index 190ef3fa80..83d5387ca2 100644 --- a/academic/mpmath/mpmath.SlackBuild +++ b/academic/DendroPy/DendroPy.SlackBuild @@ -1,8 +1,8 @@ #!/bin/sh -# Slackware build script for mpmath +# Slackware build script for DendroPy -# Copyright SlackBuilds.org Project, David Melik, 2015, Spokane, WA, USA +# Copyright 2019 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,8 +22,8 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=mpmath -VERSION=${VERSION:-0.19} +PRGNAM=DendroPy +VERSION=${VERSION:-4.4.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -75,8 +75,9 @@ 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 CHANGES LICENSE PKG-INFO $PKG/usr/doc/$PRGNAM-$VERSION +cp -a *.rst $PKG/usr/doc/$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 diff --git a/academic/DendroPy/DendroPy.info b/academic/DendroPy/DendroPy.info new file mode 100644 index 0000000000..9fd1030ffa --- /dev/null +++ b/academic/DendroPy/DendroPy.info @@ -0,0 +1,10 @@ +PRGNAM="DendroPy" +VERSION="4.4.0" +HOMEPAGE="https://dendropy.org/" +DOWNLOAD="https://github.com/jeetsukumaran/DendroPy/archive/v4.4.0/DendroPy-4.4.0.tar.gz" +MD5SUM="171d9f435bc990778a0460a8224b3d76" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/DendroPy/README b/academic/DendroPy/README new file mode 100644 index 0000000000..c4f5fc4dce --- /dev/null +++ b/academic/DendroPy/README @@ -0,0 +1,18 @@ +DendroPy Phylogenetic Computing Library + +DendroPy is a Python library for phylogenetic computing. It provides +classes and functions for the simulation, processing, and manipulation +of phylogenetic trees and character matrices, and supports the reading +and writing of phylogenetic data in a range of formats, such as NEXUS, +NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing +some useful phylogenetic operations, such as data conversion and tree +posterior distribution summarization, are also distributed and installed +as part of the libary. DendroPy can thus function as a stand-alone +library for phylogenetics, a component of more complex multi-library +phyloinformatic pipelines, or as a scripting "glue" that assembles and +drives such pipelines. + +If you use this library either in whole or in part in your analysis, +or use any code derived from it, please cite it as: +Sukumaran, J. and Mark T. Holder. 2010. DendroPy: A Python library for +phylogenetic computing. Bioinformatics 26: 1569-1571. diff --git a/academic/DendroPy/References b/academic/DendroPy/References new file mode 100644 index 0000000000..755cb8d31f --- /dev/null +++ b/academic/DendroPy/References @@ -0,0 +1,9 @@ +Citation +If you use this library either in whole or in part in your analysis, or use any code derived from it, please cite it as: + +Sukumaran, J. and Mark T. Holder. 2010. DendroPy: A Python library for phylogenetic computing. Bioinformatics 26: 1569-1571. +Note that, in the interests of scientific reproducibility, in addition to noting the primary citation for DendroPy as given above in the reference section, you should note in the text of your publications (e.g., in the “Methods” section, or, at the very least, in the “Supplemental Materials” section) the specific version of DendroPy that you used (e.g., “DendroPy version 4.0.0, revision 78e6a63”). You can get useful information about your DendroPy installation by typing “python -m dendropy”. + +If you use or reference any part of this documentation, you can cite it as: + +Sukumaran, J. and Mark T. Holder. The DendroPy Phylogenetic Computing Library Documentation. Retrieved March 04, 2019, from http://dendropy.org/.
\ No newline at end of file diff --git a/academic/DendroPy/slack-desc b/academic/DendroPy/slack-desc new file mode 100644 index 0000000000..dca4b30208 --- /dev/null +++ b/academic/DendroPy/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------------------------------------------------------| +DendroPy: DendroPy (A Phylogenetic Computing Library) +DendroPy: +DendroPy: DendroPy is a Python library for phylogenetic computing. It +DendroPy: provides classes and functions for the simulation, processing, +DendroPy: and manipulation of phylogenetic trees and character matrices, +DendroPy: and supports the reading and writing of phylogenetic data in a +DendroPy: range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, +DendroPy: etc. +DendroPy: +DendroPy: https://dendropy.org/ +DendroPy: diff --git a/academic/FCSalyzer/FCSalyzer.SlackBuild b/academic/FCSalyzer/FCSalyzer.SlackBuild index 427e3759b8..e39624d4f3 100644 --- a/academic/FCSalyzer/FCSalyzer.SlackBuild +++ b/academic/FCSalyzer/FCSalyzer.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for FCSalyzer -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,12 +23,12 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=FCSalyzer -VERSION=${VERSION:-0.9.16_alpha} +VERSION=${VERSION:-0.9.18_alpha} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} ARCH=noarch -SRCVER=0.9.16-alpha +SRCVER=0.9.18-alpha CWD=$(pwd) TMP=${TMP:-/tmp/SBo} @@ -40,10 +40,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -mkdir $PRGNAM-$VERSION -cd $PRGNAM-$VERSION +rm -rf ${PRGNAM}\ ${SRCVER} unzip $CWD/${PRGNAM}\ ${SRCVER}.zip +cd ${PRGNAM}\ ${SRCVER} chown -R root:root . find -L . \ @@ -52,7 +51,7 @@ 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}\ ${SRCVER}.jar $PKG/usr/bin/$PRGNAM.jar +install -D -m755 ${PRGNAM}.jar $PKG/usr/bin/$PRGNAM.jar mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ diff --git a/academic/FCSalyzer/FCSalyzer.info b/academic/FCSalyzer/FCSalyzer.info index 4a078ba501..9e4a0d1d4e 100644 --- a/academic/FCSalyzer/FCSalyzer.info +++ b/academic/FCSalyzer/FCSalyzer.info @@ -1,8 +1,8 @@ PRGNAM="FCSalyzer" -VERSION="0.9.16_alpha" +VERSION="0.9.18_alpha" HOMEPAGE="https://sourceforge.net/projects/fcsalyzer/" -DOWNLOAD="https://sourceforge.net/projects/fcsalyzer/files/Version%200.9.16-alpha/FCSalyzer%200.9.16-alpha.zip" -MD5SUM="eec3ba0cf815ac076917d04c233291e8" +DOWNLOAD="https://sourceforge.net/projects/fcsalyzer/files/Version%200.9.18-alpha/FCSalyzer%200.9.18-alpha.zip" +MD5SUM="9926d1af7b9865615a525c0e1bf0ada2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="jdk" diff --git a/academic/FreeFem/FreeFem.SlackBuild b/academic/FreeFem/FreeFem.SlackBuild new file mode 100644 index 0000000000..08df0908f8 --- /dev/null +++ b/academic/FreeFem/FreeFem.SlackBuild @@ -0,0 +1,105 @@ +#!/bin/sh + +# Slackware build script for FreeFem +# Based on the Slackware 14.2 SlackBuild and on PKGBUILD script for freefem from AUR +# +# Copyright 2019-2020, Fellype do Nascimento, Campinas - Brazil +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=FreeFem +VERSION=${VERSION:-4.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +SRCVER=${SRCVER:-4.5} # Variable used in some versions that are numbered as x.y-z + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + SPEC="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + SPEC="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + SPEC="-spec linux-g++-64" +fi + + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-sources-$SRCVER +tar xvf $CWD/$PRGNAM-sources-$SRCVER.tar.gz +cd $PRGNAM-sources-$SRCVER +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p 3rdparty/pkg +cp $CWD/metis-5.1.0.tar.gz 3rdparty/pkg +cp $CWD/tetgen1.5.1-beta1.tar.gz 3rdparty/pkg + +autoreconf -i + +./configure \ + --prefix=/usr \ + --sysconfdir=/etc \ + --disable-mumps \ + --with-mpi=/usr/bin/mpic++ \ + --enable-hpddm \ + --enable-opengl + +find . -name Makefile -exec sed -i 's+^gcc+gcc =+' {} \; +find . -name Makefile -exec sed -i 's+^dir+dir =+' {} \; + +## TODO: Enable mumps - FreeFem fails to compile with this option enabled up to now + +make +make install DESTDIR=$PKG + +find "$PKG"/usr/lib/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 +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:-tgz} diff --git a/academic/FreeFem/FreeFem.info b/academic/FreeFem/FreeFem.info new file mode 100644 index 0000000000..c61fc4c006 --- /dev/null +++ b/academic/FreeFem/FreeFem.info @@ -0,0 +1,14 @@ +PRGNAM="FreeFem" +VERSION="4.5" +HOMEPAGE="https://freefem.org/" +DOWNLOAD="https://github.com/FreeFem/FreeFem-sources/archive/v4.5/FreeFem-sources-4.5.tar.gz \ + http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz \ + http://www.tetgen.org/1.5/src/tetgen1.5.1-beta1.tar.gz" +MD5SUM="4df8fe1c1bc2c042df1f74371e846748 \ + 5465e67079419a69e0116de24fce58fe \ + 3d55c197bcbfc611b7ced6f343643756" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="arpack-ng hdf5 openmpi suitesparse" +MAINTAINER="Fellype do Nascimento" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/FreeFem/README b/academic/FreeFem/README new file mode 100644 index 0000000000..c9a6765f55 --- /dev/null +++ b/academic/FreeFem/README @@ -0,0 +1,13 @@ +FreeFem is a high level multiphysics finite element software + +FreeFEM is a popular 2D and 3D partial differential equations (PDE) +solver used by thousands of researchers across the world. It allows +you to easily implement your own physics modules using the provided +FreeFEM language. FreeFEM offers a large list of finite elements, +like the Lagrange, Taylor-Hood, etc., usable in the continuous and +discontinuous Galerkin method framework. + +FreeFEM has it own internal mesher, called BAMG, and is compatible +with the best open-source mesh and visualization software like Tetgen, +Gmsh, Mmg and ParaView. Written in C++ to optimize for speed, FreeFEM +is interfaced with the popular mumps, PETSc and HPDDM solvers. diff --git a/academic/FreeFem/slack-desc b/academic/FreeFem/slack-desc new file mode 100644 index 0000000000..d2225acde6 --- /dev/null +++ b/academic/FreeFem/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------------------------------------------------------| +FreeFem: FreeFem (A high level multiphysics finite element software) +FreeFem: +FreeFem: FreeFem is a software aimed for non-linear multiphysics in 2D and 3D +FreeFem: +FreeFem: FreeFem++ offers a fast interpolation algorithm and a language for +FreeFem: the manipulation of data on multiple meshes. +FreeFem: +FreeFem: For more information visit: https://freefem.org/ +FreeFem: +FreeFem: +FreeFem: diff --git a/academic/GeoGebra/GeoGebra.info b/academic/GeoGebra/GeoGebra.info index b95c04a42f..60db5293eb 100644 --- a/academic/GeoGebra/GeoGebra.info +++ b/academic/GeoGebra/GeoGebra.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/slackbuildsdirectlinks/files/GeoGebra MD5SUM="55e025c1671d074428a0adb66e1fa3d8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="openjdk" +REQUIRES="openjdk7" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild b/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild index 26e033c901..dfc3aeaf19 100644 --- a/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild +++ b/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for Gridcoin-Research -# Copyright 2018 Edward W. Koenig, Vancouver, WA, USA +# Copyright 2018-2021 Edward W. Koenig, Vancouver, WA, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,11 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - PRGNAM=Gridcoin-Research -VERSION=${VERSION:-4.0.1.0} +VERSION=${VERSION:-5.3.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +NUMJOBS=${NUMJOBS:-1} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -93,12 +93,12 @@ CXXFLAGS="$SLKCFLAGS" \ --localstatedir=/var \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ - --with-gui=auto \ + --with-gui=yes \ $useqr \ $usepnp \ --build=$ARCH-slackware-linux -make +make -j${NUMJOBS} make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ @@ -117,17 +117,16 @@ cp -a $CWD/gridcoinresearch.conf $PKG/etc/$PRGNAM mkdir -p $PKG/usr/share/pixmaps $PKG/usr/share/applications cp -a $TMP/$PRGNAM-$VERSION/share/pixmaps/* $PKG/usr/share/pixmaps -cp -a $CWD/Gridcoin-Research.desktop $PKG/usr/share/applications mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/doc -# we can delete the redundant man pages -rm -f $PKG/usr/doc/$PRGNAM-$VERSION/gridcoinresearch.* -rm -f $PKG/usr/doc/$PRGNAM-$VERSION/gridcoinresearchd.* cp -a \ - COPYING CHANGELOG.md README.md VULNERABILITY_RESPONSE_PROCESS.md \ + COPYING CHANGELOG.md README.md SECURITY.md CONTRIBUTING.md \ $PKG/usr/doc/$PRGNAM-$VERSION cp -a doc/* $PKG/usr/doc/$PRGNAM-$VERSION/doc cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +# we can delete the redundant man pages +rm -f $PKG/usr/doc/$PRGNAM-$VERSION/gridcoinresearch.* +rm -f $PKG/usr/doc/$PRGNAM-$VERSION/gridcoinresearchd.* mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/Gridcoin-Research/Gridcoin-Research.desktop b/academic/Gridcoin-Research/Gridcoin-Research.desktop deleted file mode 100644 index 5e6896f326..0000000000 --- a/academic/Gridcoin-Research/Gridcoin-Research.desktop +++ /dev/null @@ -1,9 +0,0 @@ -[Desktop Entry] -Type=Application -Name=Gridcoin -Comment=Gridcoin is an open source cryptocurrency (Ticker: GRC) which securely rewards volunteer computing performed on the BOINC platform. -Exec=gridcoinresearch -Icon=grc -Categories=Education;Science; -Terminal=false -Hidden=false diff --git a/academic/Gridcoin-Research/Gridcoin-Research.info b/academic/Gridcoin-Research/Gridcoin-Research.info index ba68c247b5..a3675fa047 100644 --- a/academic/Gridcoin-Research/Gridcoin-Research.info +++ b/academic/Gridcoin-Research/Gridcoin-Research.info @@ -1,8 +1,8 @@ PRGNAM="Gridcoin-Research" -VERSION="4.0.1.0" +VERSION="5.3.1.0" HOMEPAGE="https://gridcoin.us/" -DOWNLOAD="https://github.com/gridcoin-community/Gridcoin-Research/archive/4.0.1.0/Gridcoin-Research-4.0.1.0.tar.gz" -MD5SUM="a018151f4ea4727369bd50b2caccbfe6" +DOWNLOAD="https://github.com/gridcoin-community/Gridcoin-Research/archive/5.3.1.0/Gridcoin-Research-5.3.1.0.tar.gz" +MD5SUM="773b104454e9c35f0594e28d88e04ed7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/Gridcoin-Research/README b/academic/Gridcoin-Research/README index ac7e670e22..bc15acbd92 100644 --- a/academic/Gridcoin-Research/README +++ b/academic/Gridcoin-Research/README @@ -1,16 +1,19 @@ -Gridcoin is an open source cryptocurrency (Ticker: GRC) which securely rewards -volunteer computing performed on the BOINC platform. BOINC is an open source -volunteer computing grid which combines the processing power of individual users -for the purposes of scientific research. +Gridcoin is an open source cryptocurrency (Ticker: GRC) which securely +rewards volunteer computing performed on the BOINC platform. BOINC is +an open source volunteer computing grid which combines the processing +power of individual users for the purposes of scientific research. -QT5, qrencode and miniupnpc are optional (available on SBo) to build GUI, QR -and UPnP support. QT5 will be detected automatically, for the others, run -script as +QT5, qrencode and miniupnpc are optional (available on SBo) to build +GUI, QR and UPnP support. QT5 will be detected automatically, for the +others, run script as QRENC=yes ./Gridcoin-Research.SlackBuild UPNP=yes ./Gridcoin-Research.SlackBuild -You will need to edit the configuration file gridcoinresearch.conf in -/etc/Gridcoin-Research/ and place it in your home directory ~/.GridcoinResearch/ -to provide the location of your boinc data and any other configurations that you -require. For details, see https://wiki.gridcoin.us/Gridcoinresearch_config_file +You will need to edit the configuration file gridcoinresearch.conf +in /etc/Gridcoin-Research/ and place it in your home directory +~/.GridcoinResearch/ to provide the location of your boinc data +and any other configurations that you require. For details, see +https://wiki.gridcoin.us/Gridcoinresearch_config_file + +**NOTE: Recommended Leisure update** diff --git a/academic/Gridcoin-Research/doinst.sh b/academic/Gridcoin-Research/doinst.sh index 5fb28930db..fd1bca3b49 100644 --- a/academic/Gridcoin-Research/doinst.sh +++ b/academic/Gridcoin-Research/doinst.sh @@ -1,3 +1,8 @@ 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/Gridcoin-Research/gridcoinresearch.conf b/academic/Gridcoin-Research/gridcoinresearch.conf index 7ab2e07a3f..1c66a0b640 100644 --- a/academic/Gridcoin-Research/gridcoinresearch.conf +++ b/academic/Gridcoin-Research/gridcoinresearch.conf @@ -2,44 +2,38 @@ #################### Example gridcoinresearch.conf file ##################### ############################################################################# ## -## For further details on this configuration file please see: -## http://wiki.gridcoin.us/Gridcoinresearch_config_file -## ## Default gridcoinresearch.conf location: ## ## Win: %AppData%\GridcoinResearch\ ## Linux: ~/.GridcoinResearch/ -## MacOS: /Users/USERNAME/Library/Application/Support/GridcoinResearch/ +## macOS: /Users/USERNAME/Library/Application/Support/GridcoinResearch/ ## -## Single # lines are commands, remove the # in Front of the Command to use it +## Single # lines are commands, remove the # in Front of the command to use it ## Double ## lines are comments ## ############################################################################# ####################### Required Settings (All OS's) ######################## ############################################################################# -## Community provided list of addnodes available at -## http://wiki.gridcoin.us/List_of_Addnodes +## Community provided list of addnodes available at https://github.com/gridcoin-community/Gridcoin-Wiki/wiki/List-of-Addnodes #~~~~~Copy & Paste Addnodes here~~~~~ #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -## BOINC account settings, i.e. your BOINC CPID & E-Mail -## Use INVESTOR for Investor or Pool Mining -PrimaryCPID=INVESTOR -email=INVESTOR +## BOINC account E-Mail +## Use blank or INVESTOR for Investor or Pool Mining +## Note the PrimaryCPID field is deprecated and ignored since the 4.0.5.0 +## release. +email= -## Port 32749/TCP required for Inbound Connections +## Port 32749/TCP open or forwarded required for Inbound Connections ## (Not required but highly recommended) -listen=1 +#listen=1 ## Required for Headless set-ups #daemon=1 -## Blocks client from upgrading on its own. -suppressupgrade=true - ############################################################################# ############# RPC Settings for Remote Access and Headless Users ############# ############ Warning: Set a Good Password and Secure Your System ############ @@ -50,25 +44,46 @@ suppressupgrade=true #rpcallowip=<IP Address of Remote System> #rpcport=<Port for RPC Communication> #rpcuser=<A Username for RPC> -#rpcpassword=<A GOOD Password for RPC> +#rpcpassword=<A STRONG Password for RPC> ############################################################################# ######################## Optional BOINC settings ############################ ########### (Required if BOINC installed to non-default location) ########### ############################################################################# +## Windows (Note the double backslashes are necessary) +#boincdatadir=C:\\ProgramData\\BOINC\\ + ## Linux -boincdatadir=$HOME/.boinc_data/ +#boincdatadir=/var/lib/boinc-client/ + +## macOS +#boincdatadir=/Library/Application Support/BOINC Data/ ############################################################################# ######################## Optional Network settings ########################## ############################################################################# -## Maximum number of inbound+outbound connections.Default 125 -maxconnections=125 -## Maximum number of outbound connections.Default 8 -maxoutboundconnections=8 +## Maximum number of inbound+outbound connections. Default 125 +#maxconnections=125 +## Maximum number of outbound connections. Default 8 +#maxoutboundconnections=8 ## Manually Set-up Ports #upnp=false #externalip=<Your IP Address> -#port=32748
\ No newline at end of file + +############################################################################# +############################## Other Entries ################################ +############################################################################# + +## See detailed Other Entries description section below. + +#debug=true +#debug=<category> + +#enablestakesplit=1 +#stakingefficiency=<percentage between 75 and 98, defaults to 90> +#minstakesplitvalue=<value in GRC, minimum and defaults to 800> + +#enablesidestaking=1 +#sidestake=<address>,<allocation percentage> diff --git a/academic/HMMER/HMMER.SlackBuild b/academic/HMMER/HMMER.SlackBuild index 02b15867cd..e0e4f5bfcf 100644 --- a/academic/HMMER/HMMER.SlackBuild +++ b/academic/HMMER/HMMER.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for HMMER -# Copyright 2016-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,11 +23,12 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=HMMER -SRCNAM=hmmer -VERSION=${VERSION:-3.2.1} +VERSION=${VERSION:-3.3.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +SRCNAM=hmmer + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -93,11 +94,11 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r # Include some tutorial examples mkdir -p $PKG/usr/share/$PRGNAM -cp -a tutorial/* $PKG/usr/share/$PRGNAM +cp -a testsuite tutorial $PKG/usr/share/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - INSTALL LICENSE README.md RELEASE-$VERSION Userguide.pdf \ + INSTALL LICENSE README.md RELEASE-$VERSION.md Userguide.pdf \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/HMMER/HMMER.info b/academic/HMMER/HMMER.info index 2de753666b..80f7a1ebe5 100644 --- a/academic/HMMER/HMMER.info +++ b/academic/HMMER/HMMER.info @@ -1,10 +1,10 @@ PRGNAM="HMMER" -VERSION="3.2.1" +VERSION="3.3.1" HOMEPAGE="http://hmmer.org/" -DOWNLOAD="http://eddylab.org/software/hmmer/hmmer-3.2.1.tar.gz" -MD5SUM="4e0ad5ed45462d4e36807d21e6d82b69" +DOWNLOAD="http://eddylab.org/software/hmmer/hmmer-3.3.1.tar.gz" +MD5SUM="07da6661a17bd4ddbaded4a0dc9c5b6d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="python3" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/IGV/IGV.SlackBuild b/academic/IGV/IGV.SlackBuild new file mode 100644 index 0000000000..746d394ea4 --- /dev/null +++ b/academic/IGV/IGV.SlackBuild @@ -0,0 +1,84 @@ +#!/bin/sh + +# Slackware build script for IGV + +# Copyright 2020 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. + +PRGNAM=IGV +VERSION=${VERSION:-2.8.12} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +JDK=jdk-11 + +if [ -z "$ARCH" ]; then + ARCH="$( uname -m )" +fi + +if [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" >&2 + exit 1 +fi + +CWD=$(pwd) +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 ${PRGNAM}_Linux_${VERSION} +unzip $CWD/${PRGNAM}_Linux_${VERSION}_WithJava.zip +cd ${PRGNAM}_Linux_${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 {} \; + +# 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 + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp IGV_64.png $PKG/usr/share/pixmaps/$PRGNAM.png +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a readme.txt $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../../opt/$PRGNAM/igv.sh igv +cd - + +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:-tgz} diff --git a/academic/IGV/IGV.desktop b/academic/IGV/IGV.desktop new file mode 100644 index 0000000000..9dad30517e --- /dev/null +++ b/academic/IGV/IGV.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Type=Application +Exec=igv +Terminal=false +Name=IGV +Icon=IGV +Comment=Integrative Genomics Viewer +Categories=Education; diff --git a/academic/IGV/IGV.info b/academic/IGV/IGV.info new file mode 100644 index 0000000000..f54e6a3a2d --- /dev/null +++ b/academic/IGV/IGV.info @@ -0,0 +1,10 @@ +PRGNAM="IGV" +VERSION="2.8.12" +HOMEPAGE="http://software.broadinstitute.org/software/igv/home" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_Linux_2.8.12_WithJava.zip" +MD5SUM_x86_64="7ee4f59615726723964bd9e023baf136" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/IGV/README b/academic/IGV/README new file mode 100644 index 0000000000..7c1ec02a11 --- /dev/null +++ b/academic/IGV/README @@ -0,0 +1,7 @@ +The Integrative Genomics Viewer (IGV) is a high-performance and easy-to- +use, interactive tool for the visual exploration of genomic data. It +supports flexible integration of all the common types of genomic data +and metadata, investigator-generated or publicly available, loaded from +local or cloud sources. + +Please, check the package's documentation folder for citing information. diff --git a/academic/IGV/References b/academic/IGV/References new file mode 100644 index 0000000000..cdbdf3e743 --- /dev/null +++ b/academic/IGV/References @@ -0,0 +1,17 @@ +To cite your use of IGV in your publication, please reference one or more of: + +James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, +Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. +Nature Biotechnology 29, 24–26 (2011). (Free PMC article here). + +Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov. +Integrative Genomics Viewer (IGV): high-performance genomics data visualization +and exploration. Briefings in Bioinformatics 14, 178-192 (2013). + +James T. Robinson, Helga Thorvaldsdóttir, Aaron M. Wenger, Ahmet Zehir, Jill P. +Mesirov. Variant Review with the Integrative Genomics Viewer (IGV). Cancer +Research 77(21) 31-34 (2017). + +James T. Robinson, Helga Thorvaldsdóttir, Douglass Turner, Jill P. Mesirov. +igv.js: an embeddable JavaScript implementation of the Integrative Genomics +Viewer (IGV). bioRxiv 2020.05.03075499. diff --git a/academic/IGV/doinst.sh b/academic/IGV/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/IGV/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/IGV/slack-desc b/academic/IGV/slack-desc new file mode 100644 index 0000000000..c02edd24c9 --- /dev/null +++ b/academic/IGV/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------------------------------------------------------| +IGV: IGV (Integrative Genomics Viewer) +IGV: +IGV: The Integrative Genomics Viewer (IGV) is a high-performance and easy +IGV: to use, interactive tool for the visual exploration of genomic data. +IGV: It supports flexible integration of all the common types of genomic +IGV: data and metadata, investigator-generated or publicly available, +IGV: loaded from local or cloud sources. +IGV: +IGV: http://software.broadinstitute.org/software/igv/home +IGV: +IGV: diff --git a/academic/ITK/ITK.SlackBuild b/academic/ITK/ITK.SlackBuild index 2bffadf6d9..fd9e8128f0 100644 --- a/academic/ITK/ITK.SlackBuild +++ b/academic/ITK/ITK.SlackBuild @@ -2,7 +2,7 @@ # SlackBuild script for ITK -# Copyright 2018 Benjamin Trigona-Harany <slackbuilds@jaxartes.net> +# Copyright 2018-2021 Benjamin Trigona-Harany <slackbuilds@jaxartes.net> # All rights reserved. # # Redistribution and use in source and binary forms, with or without @@ -26,7 +26,7 @@ PRGNAM=ITK SRCNAM=InsightToolkit -VERSION=${VERSION:-4.13.1} +VERSION=${VERSION:-5.1.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -63,7 +63,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $SRCNAM-$VERSION -tar xvf $CWD/$SRCNAM-$VERSION.tar.xz +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz cd $SRCNAM-$VERSION chown -R root:root . find -L . \ @@ -78,24 +78,25 @@ sed -i "s|/opj_config.h|& \$\{CMAKE_CURRENT_BINARY_DIR\}/openjpeg_mangle.h|" \ mkdir -p build cd build + export "PATH=/opt/cmake-202x/bin:$PATH" cmake \ - -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_C_FLAGS="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ - -DITK_FORBID_DOWNLOADS:BOOL=ON \ - -DITK_WRAP_PYTHON:BOOL=OFF \ - -DBUILD_SHARED_LIBS:BOOL=ON \ - -DBUILD_EXAMPLES:BOOL=OFF \ - -DITK_USE_SYSTEM_LIBRARIES:BOOL=ON \ - -DITK_USE_SYSTEM_DCMTK:BOOL=ON \ - -DITK_USE_SYSTEM_DOUBLECONVERSION:BOOL=ON \ - -DITK_USE_SYSTEM_EXPAT:BOOL=ON \ - -DITK_USE_SYSTEM_FFTW:BOOL=ON \ - -DITK_USE_SYSTEM_HDF5:BOOL=ON \ - -DITK_USE_SYSTEM_JPEG:BOOL=ON \ - -DITK_USE_SYSTEM_PNG:BOOL=ON \ - -DITK_USE_SYSTEM_TIFF:BOOL=ON \ - -DITK_USE_SYSTEM_ZLIB:BOOL=ON \ + -DITK_FORBID_DOWNLOADS=ON \ + -DITK_WRAP_PYTHON=OFF \ + -DBUILD_SHARED_LIBS=ON \ + -DBUILD_EXAMPLES=OFF \ + -DITK_USE_SYSTEM_LIBRARIES=ON \ + -DITK_USE_SYSTEM_DCMTK=ON \ + -DITK_USE_SYSTEM_EIGEN=OFF \ + -DITK_USE_SYSTEM_EXPAT=ON \ + -DITK_USE_SYSTEM_FFTW=ON \ + -DITK_USE_SYSTEM_HDF5=ON \ + -DITK_USE_SYSTEM_JPEG=ON \ + -DITK_USE_SYSTEM_PNG=ON \ + -DITK_USE_SYSTEM_TIFF=ON \ + -DITK_USE_SYSTEM_ZLIB=ON \ -DCMAKE_BUILD_TYPE=Release .. make install DESTDIR=$PKG cd .. diff --git a/academic/ITK/ITK.info b/academic/ITK/ITK.info index fd6573bc1d..9479aaaac9 100644 --- a/academic/ITK/ITK.info +++ b/academic/ITK/ITK.info @@ -1,10 +1,10 @@ PRGNAM="ITK" -VERSION="4.13.1" +VERSION="5.1.2" HOMEPAGE="https://itk.org" -DOWNLOAD="https://sourceforge.net/projects/itk/files/itk/4.13/InsightToolkit-4.13.1.tar.xz" -MD5SUM="bc7296e7faccdcb5656a7669d4d875d2" +DOWNLOAD="https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.2/InsightToolkit-5.1.2.tar.gz" +MD5SUM="e939fc61e7354eba20f98fbd7b034ec2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="double-conversion gtest hdf5" +REQUIRES="cmake-202x double-conversion gtest hdf5" MAINTAINER="Benjamin Trigona-Harany" EMAIL="slackbuilds@jaxartes.net" diff --git a/academic/ITK/README b/academic/ITK/README index f152989931..ea82c00fc2 100644 --- a/academic/ITK/README +++ b/academic/ITK/README @@ -1,4 +1,4 @@ ITK is an open-source software toolkit for performing registration and -segmentation. Segmentation is the process of identifying and classifying data -found in a digitally sampled representation. Registration is the task of -aligning or developing correspondences between data. +segmentation. Segmentation is the process of identifying and classifying +data found in a digitally sampled representation. Registration is the +task of aligning or developing correspondences between data. diff --git a/academic/ITK/slack-desc b/academic/ITK/slack-desc index 3713cd3ece..79a20f8176 100644 --- a/academic/ITK/slack-desc +++ b/academic/ITK/slack-desc @@ -14,6 +14,6 @@ ITK: classifying data found in a digitally sampled representation. ITK: Registration is the task of aligning or developing correspondences ITK: between data. ITK: -ITK: +ITK: ITK: ITK: diff --git a/academic/Kst/README b/academic/Kst/README index cfad9f4c4b..cb1ad83042 100644 --- a/academic/Kst/README +++ b/academic/Kst/README @@ -8,14 +8,15 @@ Kst is very user-friendly (both the community and the program itself!). Kst contains many powerful built-in features and is expandable with plugins and extensions. -Kst is licensed under the GPL, and is as such freely available for anyone. +Kst is licensed under the GPL, and is as such freely available for +anyone. Note that KDE libraries are an optional dependency (i.e. you can run Kst without KDE, but you get additional features when running on a platform with KDE). Optional dependencies are: -- gsl (a lot of very useful data analysis plugins are based) - RECOMMENDED +- gsl (many very useful data analysis plugins are based) - RECOMMENDED - 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 new file mode 100644 index 0000000000..48492049c4 --- /dev/null +++ b/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild @@ -0,0 +1,92 @@ +#!/bin/sh + +# Slackware build script for MetaPhlAn2 + +# Copyright 2019-2020 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. + +PRGNAM=MetaPhlAn2 +VERSION=${VERSION:-2.9.5.3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=metaphlan2 +AUTHOR=biobakery +COMMIT=3a075f914593 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +ARCH=noarch + +set -e + +# Construct the source tarball name. +if [ -e $CWD/$COMMIT.tar.gz ]; then + TARBALL=${COMMIT} +else + TARBALL=${AUTHOR}-${SRCNAM}-${COMMIT} +fi + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${AUTHOR}-${SRCNAM}-${COMMIT} +tar xvf $CWD/$TARBALL.tar.gz +cd ${AUTHOR}-${SRCNAM}-${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 {} \; + +mkdir -p $PKG/usr/share/$PRGNAM +cp -a \ + *.py utils strainphlan_src \ + $PKG/usr/share/$PRGNAM + +mkdir $PKG/usr/bin +cd $PKG/usr/bin + ln -s ../share/$PRGNAM/metaphlan2.py + ln -s ../share/$PRGNAM/strainphlan.py +cd - + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README.md changeset.txt license.txt strainphlan_tutorial \ + $PKG/usr/doc/$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:-tgz} diff --git a/academic/MetaPhlAn2/MetaPhlAn2.info b/academic/MetaPhlAn2/MetaPhlAn2.info new file mode 100644 index 0000000000..f01033053b --- /dev/null +++ b/academic/MetaPhlAn2/MetaPhlAn2.info @@ -0,0 +1,10 @@ +PRGNAM="MetaPhlAn2" +VERSION="2.9.5.3" +HOMEPAGE="http://huttenhower.sph.harvard.edu/metaphlan2" +DOWNLOAD="https://bitbucket.org/biobakery/metaphlan2/get/3a075f914593.tar.gz" +MD5SUM="956f8f6897a40e15cec38eb26cdcf97c" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="pysam biopython msgpack-python pandas scipy DendroPy bowtie2 muscle samtools-legacy bcftools ncbi-blast+ RAxML" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/MetaPhlAn2/README b/academic/MetaPhlAn2/README new file mode 100644 index 0000000000..55665c56e1 --- /dev/null +++ b/academic/MetaPhlAn2/README @@ -0,0 +1,36 @@ +MetaPhlAn2 is a computational tool for profiling the composition of +microbial communities (Bacteria, Archaea and Eukaryotes) from meta- +genomic shotgun sequencing data (i.e. not 16S) with species-level. + +With the newly added StrainPhlAn module, it is now possible to perform +accurate strain-level microbial profiling. MetaPhlAn2 relies on ~1.5M +unique clade-specific marker genes. The latest marker information file +`mpa_v29_CHOCOPhlAn_201901_marker_info.txt.bz2` can be found in the +Download page (https://bitbucket.org/biobakery/metaphlan2/downloads/) +identified from ~100,000 reference genomes (~99,500 bacterial and +archaeal and ~500 eukaryotic), allowing: + +* unambiguous taxonomic assignments; +* accurate estimation of organismal relative abundance; +* species-level resolution for bacteria, archaea, eukaryotes, viruses; +* strain identification and tracking +* orders of magnitude speedups compared to existing methods. +* metagenomic strain-level population genomics + +If you use MetaPhlAn2, please cite: +MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Duy Tin Truong, +Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart, +Edoardo Pasolli, Adrian Tett, Curtis Huttenhower & Nicola Segata. Nature +Methods 12, 902-903 (2015) + +If you use StrainPhlAn, please cite the MetaPhlAn2 paper and the +following StrainPhlAn paper: +Microbial strain-level population structure and genetic diversity from +metagenomes. Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis +Huttenhower, & Nicola Segata. Genome Research 27:626-638 (2017) + +NOTE! +The script places the python files in /usr/share/MetaPhlAn2 and creates +symlinks to /usr/bin. If you are using metaphlan2.py with Ugene, it may +not work with the symlink. Instead, just point Ugene directly to +/usr/share/MetaPhlAn2/metaphlan2.py diff --git a/academic/MetaPhlAn2/References b/academic/MetaPhlAn2/References new file mode 100644 index 0000000000..5e3629e893 --- /dev/null +++ b/academic/MetaPhlAn2/References @@ -0,0 +1,7 @@ +If you use MetaPhlAn2, please cite: + +[**MetaPhlAn2 for enhanced metagenomic taxonomic profiling.**](http://www.nature.com/nmeth/journal/v12/n10/pdf/nmeth.3589.pdf) *Duy Tin Truong, Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower & Nicola Segata*. Nature Methods 12, 902-903 (2015) + +If you use StrainPhlAn, please cite the MetaPhlAn2 paper and the following StrainPhlAn paper: + +[**Microbial strain-level population structure and genetic diversity from metagenomes.**](http://genome.cshlp.org/content/27/4/626.full.pdf) *Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, & Nicola Segata*. Genome Research 27:626-638 (2017) diff --git a/academic/MetaPhlAn2/slack-desc b/academic/MetaPhlAn2/slack-desc new file mode 100644 index 0000000000..3f6ccd01df --- /dev/null +++ b/academic/MetaPhlAn2/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------------------------------------------------------| +MetaPhlAn2: MetaPhlAn2 (Metagenomic Phylogenetic Analysis) +MetaPhlAn2: +MetaPhlAn2: MetaPhlAn is a computational tool for profiling the composition of +MetaPhlAn2: microbial communities from metagenomic shotgun sequencing data. +MetaPhlAn2: MetaPhlAn relies on unique clade-specific marker genes identified +MetaPhlAn2: from ~17,000 reference genomes (~13,500 bacterial and archaeal, +MetaPhlAn2: ~3,500 viral, and ~110 eukaryotic). +MetaPhlAn2: +MetaPhlAn2: http://huttenhower.sph.harvard.edu/metaphlan2 +MetaPhlAn2: https://bitbucket.org/biobakery/metaphlan2/ +MetaPhlAn2: diff --git a/academic/Mnemosyne/Mnemosyne.SlackBuild b/academic/Mnemosyne/Mnemosyne.SlackBuild index 0245781426..6de86d1a48 100644 --- a/academic/Mnemosyne/Mnemosyne.SlackBuild +++ b/academic/Mnemosyne/Mnemosyne.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=Mnemosyne -VERSION=${VERSION:-2.5} +VERSION=${VERSION:-2.6.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/Mnemosyne/Mnemosyne.info b/academic/Mnemosyne/Mnemosyne.info index 2247dc0b2e..8d6fc3ac9a 100644 --- a/academic/Mnemosyne/Mnemosyne.info +++ b/academic/Mnemosyne/Mnemosyne.info @@ -1,8 +1,8 @@ PRGNAM="Mnemosyne" -VERSION="2.5" -HOMEPAGE="http://www.mnemosyne-proj.org/download-mnemosyne.php" -DOWNLOAD="https://downloads.sourceforge.net/project/mnemosyne-proj/mnemosyne/mnemosyne-2.5/Mnemosyne-2.5.tar.gz" -MD5SUM="fcae31625523437049cc64c7b0c226b8" +VERSION="2.6.1" +HOMEPAGE="https://mnemosyne-proj.org/" +DOWNLOAD="https://downloads.sourceforge.net/project/mnemosyne-proj/mnemosyne/mnemosyne-2.6.1/Mnemosyne-2.6.1.tar.gz" +MD5SUM="2b2f8fd019370af4d107f696f29ee3a2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="python3-PyQt5 PyOpenGL CherryPy matplotlib WebOb" diff --git a/academic/Mnemosyne/README b/academic/Mnemosyne/README index 5961fa5c7d..a4ee7f3e3e 100644 --- a/academic/Mnemosyne/README +++ b/academic/Mnemosyne/README @@ -6,4 +6,5 @@ it is very powerful, and its architecture allows infinite extensibility and customisibility through plugins and a scripting API, for the benefit of power users. -Optional Dependency: texlive (for entering mathematical equations in cards) +Optional Dependency: texlive (for entering mathematical equations in +cards using LaTeX) diff --git a/academic/OpenFOAM/OpenFOAM.SlackBuild b/academic/OpenFOAM/OpenFOAM.SlackBuild index edf0a4763e..14db243780 100644 --- a/academic/OpenFOAM/OpenFOAM.SlackBuild +++ b/academic/OpenFOAM/OpenFOAM.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for OpenFOAM -# Copyright 2017, 2018 Lorenzo Trevisan, Caorle, Venice, Italy +# Copyright 2017, 2018, 2019, 2020 Lorenzo Trevisan, Caorle, Venice, Italy # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=OpenFOAM -VERSION=${VERSION:-6} +VERSION=${VERSION:-8} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/OpenFOAM/OpenFOAM.info b/academic/OpenFOAM/OpenFOAM.info index 67f8c46c63..df75c6f7c1 100644 --- a/academic/OpenFOAM/OpenFOAM.info +++ b/academic/OpenFOAM/OpenFOAM.info @@ -1,10 +1,10 @@ PRGNAM="OpenFOAM" -VERSION="6" +VERSION="8" HOMEPAGE="https://openfoam.org/" -DOWNLOAD="https://github.com/OpenFOAM/OpenFOAM-6/archive/version-6/OpenFOAM-6-version-6.tar.gz \ - https://github.com/OpenFOAM/ThirdParty-6/archive/version-6/ThirdParty-6-version-6.tar.gz" -MD5SUM="f40aa39d4d5dfe7ea8d9a58f2625037a \ - 848652a3eaf8a1a7e17a7ad9655a123c" +DOWNLOAD="https://github.com/OpenFOAM/OpenFOAM-8/archive/version-8/OpenFOAM-8-version-8.tar.gz \ + https://github.com/OpenFOAM/ThirdParty-8/archive/version-8/ThirdParty-8-version-8.tar.gz" +MD5SUM="261dc0d01c4417b737487a60ab4784aa \ + a1beb9f9ce9ca547cd458ec6c1472bcd" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi CGAL" diff --git a/academic/OpenFOAM/OpenFOAM.sh b/academic/OpenFOAM/OpenFOAM.sh index fd91481fb4..a4e69f6d1e 100644 --- a/academic/OpenFOAM/OpenFOAM.sh +++ b/academic/OpenFOAM/OpenFOAM.sh @@ -1 +1 @@ -. /opt/OpenFOAM/OpenFOAM-6/etc/bashrc +. /opt/OpenFOAM/OpenFOAM-8/etc/bashrc diff --git a/academic/OpenFOAM/README b/academic/OpenFOAM/README index fd23aef9b7..d91ec421c8 100644 --- a/academic/OpenFOAM/README +++ b/academic/OpenFOAM/README @@ -9,4 +9,5 @@ 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. +You can build with multiple jobs by setting the MAKEFLAGS environment +variable. diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild index 3685485c5f..893454e123 100644 --- a/academic/PhyML/PhyML.SlackBuild +++ b/academic/PhyML/PhyML.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for PhyML -# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,11 +25,12 @@ # Thanks to Niels Horn for some handy modifications and corrections. PRGNAM=PhyML -SRCNAM=$(echo $PRGNAM | tr A-Z a-z) -VERSION=${VERSION:-3.3.20180621} +VERSION=${VERSION:-3.3.20200621} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +SRCNAM=$(echo $PRGNAM | tr A-Z a-z) + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -86,12 +87,11 @@ find -L . \ --build=$ARCH-slackware-linux # Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" src/Makefile -sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make +# The -mfma flag is needed for building on 14.2. Help is from here: +# https://github.com/horovod/horovod/issues/1832 +CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG # This is PhyML MPI. If you do not want it, comment the lines below. Then you do @@ -108,12 +108,9 @@ make install DESTDIR=$PKG --build=$ARCH-slackware-linux # Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" src/Makefile -sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make +CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG # This is Phyrex @@ -129,12 +126,9 @@ make install DESTDIR=$PKG --build=$ARCH-slackware-linux # Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" src/Makefile -sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make +CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG # This is PhyTime @@ -150,12 +144,9 @@ make install DESTDIR=$PKG --build=$ARCH-slackware-linux # Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" src/Makefile -sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make +CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ @@ -167,7 +158,7 @@ cp -a examples $PKG/usr/share/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - doc/{$SRCNAM-manual.pdf,ref.bib,$SRCNAM-manual.tex,fig} README \ + doc/{$SRCNAM-manual.pdf,ref.bib,$SRCNAM-manual.tex,fig} COPYING 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/PhyML/PhyML.info b/academic/PhyML/PhyML.info index 80d3f34388..ec04310e99 100644 --- a/academic/PhyML/PhyML.info +++ b/academic/PhyML/PhyML.info @@ -1,8 +1,8 @@ PRGNAM="PhyML" -VERSION="3.3.20180621" +VERSION="3.3.20200621" HOMEPAGE="https://github.com/stephaneguindon/phyml/" -DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20180621/phyml-3.3.20180621.tar.gz" -MD5SUM="39f5df7eeb317466ab5724b38efb6915" +DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20200621/phyml-3.3.20200621.tar.gz" +MD5SUM="12622e111c388bcb16696660033143b5" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi" diff --git a/academic/PyAMG/README b/academic/PyAMG/README index c72262fa35..f5a2ac3fe5 100644 --- a/academic/PyAMG/README +++ b/academic/PyAMG/README @@ -1,9 +1,9 @@ -PyAMG is a library of **Algebraic Multigrid (AMG)** solvers with a convenient -Python interface. +PyAMG is a library of **Algebraic Multigrid (AMG)** solvers with a +convenient Python interface. -AMG is a multilevel technique for solving large-scale linear systems with -optimal or near-optimal efficiency. Unlike geometric multigrid, AMG requires -little or no geometric information about the underlying problem and develops a -sequence of coarser grids directly from the input matrix. This feature is -especially important for problems discretized on unstructured meshes and -irregular grids. +AMG is a multilevel technique for solving large-scale linear systems +with optimal or near-optimal efficiency. Unlike geometric multigrid, +AMG requires little or no geometric information about the underlying +problem and develops a sequence of coarser grids directly from the +input matrix. This feature is especially important for problems +discretized on unstructured meshes and irregular grids. diff --git a/academic/R/R.SlackBuild b/academic/R/R.SlackBuild index 6646fb5a21..3f31ad4a38 100644 --- a/academic/R/R.SlackBuild +++ b/academic/R/R.SlackBuild @@ -2,8 +2,8 @@ # SlackBuild script for R -# Copyright 2014-2017 melikamp, Andrew Rowland. (Contributors are -# listed in order of first participation.) +# Copyright 2019-2020 Andrew Payne <phalange@komputermatrix.com> +# Copyright 2014-2017 melikamp, Andrew Rowland # 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 @@ -24,7 +24,7 @@ # <http://www.gnu.org/licenses/>. PRGNAM=R -VERSION=${VERSION:-3.5.1} +VERSION=${VERSION:-4.0.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/R/R.info b/academic/R/R.info index ef0749f60b..04109237e7 100644 --- a/academic/R/R.info +++ b/academic/R/R.info @@ -1,10 +1,10 @@ PRGNAM="R" -VERSION="3.5.1" +VERSION="4.0.0" HOMEPAGE="http://www.r-project.org/" -DOWNLOAD="https://cran.cnr.berkeley.edu/src/base/R-3/R-3.5.1.tar.gz" -MD5SUM="8620686bc237cf80288afff336fcc93c" +DOWNLOAD="https://cran.r-project.org/src/base/R-4/R-4.0.0.tar.gz" +MD5SUM="48c487c68112cb3191f3015c6277a50b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="melikamp" -EMAIL="melikamp@melikamp.net" +REQUIRES="pcre2" +MAINTAINER="Andrew Payne" +EMAIL="phalange@komputermatrix.com" diff --git a/academic/R/README b/academic/R/README index cd6a7109c8..cdd9f7dbd6 100644 --- a/academic/R/README +++ b/academic/R/README @@ -1,21 +1,22 @@ R is an integrated suite of software facilities for data manipulation, -calculation and graphical display. Among other things it has +calculation and graphical display. It includes * an effective data handling and storage facility, * a suite of operators for calculations on arrays, in particular - matrices, +matrices, * a large, coherent, integrated collection of intermediate tools for - data analysis, +data analysis, -* graphical facilities for data analysis and display either directly - at the computer or on hardcopy, and +* graphical facilities for data analysis and display either on-screen +or on hardcopy, and -* a well developed, simple and effective programming language (called - `S') which includes conditionals, loops, user defined recursive - functions and input and output facilities. (Indeed most of the - system supplied functions are themselves written in the S language.) +* a well-developed, simple and effective programming language which +includes conditionals, loops, user-defined recursive functions and +input and output facilities. + +Notes: If you do not need to build the R shared library (which is needed if you would like to call R functions from other applications), execute @@ -24,3 +25,6 @@ the script as R_SHLIB=no ./R.SlackBuild If you do not need to build the BLAS shared library (which is useful for swapping default unaccelerated BLAS for an accelerated one), execute the script as BLAS_SHLIB=no ./R.SlackBuild + +This package builds R from source; example build time (Intel Core +i7-7500U) is < 10 minutes. diff --git a/academic/R/slack-desc b/academic/R/slack-desc index 0d2de38c47..f6e2acfb82 100644 --- a/academic/R/slack-desc +++ b/academic/R/slack-desc @@ -15,5 +15,5 @@ R: by John Chambers and colleagues. R can be considered as a R: different implementation of S. There are some important R: differences, but much code written for S runs unaltered under R. R: -R: +R: Homepage: https://www.r-project.org/ R: diff --git a/academic/RAxML/RAxML.SlackBuild b/academic/RAxML/RAxML.SlackBuild new file mode 100644 index 0000000000..0c4e98a6ce --- /dev/null +++ b/academic/RAxML/RAxML.SlackBuild @@ -0,0 +1,155 @@ +#!/bin/sh + +# Slackware build script for RAxML + +# Copyright 2019 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. + +PRGNAM=RAxML +VERSION=${VERSION:-8.2.12} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 $TMP +rm -rf standard-$PRGNAM-$VERSION +tar xvf $CWD/standard-$PRGNAM-$VERSION.tar.gz +cd standard-$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 {} \; + +# Build executables with the default Slackware compiler flags. + +# Sequential version +cp Makefile.gcc Makefile +sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i "s|raxmlHPC|raxml|g" Makefile +CFLAGS="$SLKCFLAGS" \ +make -f Makefile +install -D -m755 raxml $PKG/usr/bin/raxml + +# Openmpi version +cp Makefile.MPI.gcc Makefile.MPI +sed -i "/^CFLAGS/s/=/+=/" Makefile.MPI +sed -i "s|raxmlHPC-MPI|raxml-MPI|g" Makefile.MPI +CFLAGS="$SLKCFLAGS" \ +make -f Makefile.MPI +install -D -m755 raxml-MPI $PKG/usr/bin/raxml-MPI + +########################################################################## +### You are highly encouraged to try the other optimisations below for ### +### performance enhancements. Just uncomment the corresponding lines. ### +########################################################################## + +## Default sequential version +#make -f Makefile.gcc +#install -D -m755 raxmlHPC $PKG/usr/bin/raxmlHPC + +#make -f Makefile.SSE3.gcc +#install -D -m755 raxmlHPC-SSE3 $PKG/usr/bin/raxmlHPC-SSE3 + +#make -f Makefile.AVX.gcc +#install -D -m755 raxmlHPC-AVX $PKG/usr/bin/raxmlHPC-AVX + +## Pthreads version +#make -f Makefile.PTHREADS.gcc +#install -D -m755 raxmlHPC-PTHREADS $PKG/usr/bin/raxmlHPC-PTHREADS + +#make -f Makefile.SSE3.PTHREADS.gcc +#install -D -m755 raxmlHPC-PTHREADS-SSE3 $PKG/usr/bin/raxmlHPC-PTHREADS-SSE3 + +#make -f Makefile.AVX.PTHREADS.gcc +#install -D -m755 raxmlHPC-PTHREADS-AVX $PKG/usr/bin/raxmlHPC-PTHREADS-AVX + +## Default coarse-grain MPI version +#make -f Makefile.MPI.gcc +#install -D -m755 raxmlHPC-MPI $PKG/usr/bin/raxmlHPC-MPI + +#make -f Makefile.SSE3.MPI.gcc +#install -D -m755 raxmlHPC-MPI-SSE3 $PKG/usr/bin/raxmlHPC-MPI-SSE3 + +#make -f Makefile.AVX.MPI.gcc +#install -D -m755 raxmlHPC-MPI-AVX $PKG/usr/bin/raxmlHPC-MPI-AVX + +## Hybrid MPI/Pthreads version +# Before using this version, please read this paper here: +# http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2010-3.pdf +# and look at these slides: +# http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf +#make -f Makefile.HYBRID.gcc +#install -D -m755 raxmlHPC-HYBRID $PKG/usr/bin/raxmlHPC-HYBRID + +#make -f Makefile.SSE3.HYBRID.gcc +#install -D -m755 raxmlHPC-HYBRID-SSE3 $PKG/usr/bin/raxmlHPC-HYBRID-SSE3 + +#make -f Makefile.AVX.HYBRID.gcc +#install -D -m755 raxmlHPC-HYBRID-AVX $PKG/usr/bin/raxmlHPC-HYBRID-AVX + +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 the useful scripts +mkdir -p $PKG/usr/share/$PRGNAM +cp -a usefulScripts $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README manual $PKG/usr/doc/$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:-tgz} diff --git a/academic/RAxML/RAxML.info b/academic/RAxML/RAxML.info new file mode 100644 index 0000000000..a6ef346e17 --- /dev/null +++ b/academic/RAxML/RAxML.info @@ -0,0 +1,10 @@ +PRGNAM="RAxML" +VERSION="8.2.12" +HOMEPAGE="https://cme.h-its.org/exelixis/web/software/raxml/index.html" +DOWNLOAD="https://github.com/stamatak/standard-RAxML/archive/v8.2.12/standard-RAxML-8.2.12.tar.gz" +MD5SUM="4ac68b0156bc52fe056207ba8ef719d2" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="openmpi" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/RAxML/README b/academic/RAxML/README new file mode 100644 index 0000000000..b03ec92b2e --- /dev/null +++ b/academic/RAxML/README @@ -0,0 +1,16 @@ +RAxML - Randomized Axelerated Maximum Likelihood + +RAxML is a program for sequential and parallel Maximum Likelihood (ML) +based inference of large phylogenetic trees. It can also be used for +postanalyses of sets of phylogenetic trees, analyses of alignments and, +evolutionary placement of short reads. + +NOTE! +The script builds single threaded and mpi versions of the executable +with Slackware's default compiler flags. You are highly encouraged to +check the script for building with other flags and optimisations. This +will dramatically speed up RAxML on modern processors. + +When using RAxML please cite the following paper: A. Stamatakis: +"RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of +Large Phylogenies". In Bioinformatics, 2014 diff --git a/academic/RAxML/References b/academic/RAxML/References new file mode 100644 index 0000000000..971db2e337 --- /dev/null +++ b/academic/RAxML/References @@ -0,0 +1,4 @@ +When using RAxML please cite the following paper: A. Stamatakis: +"RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of +Large Phylogenies". In Bioinformatics, 2014, open access. + diff --git a/academic/RAxML/slack-desc b/academic/RAxML/slack-desc new file mode 100644 index 0000000000..7dbc6b8967 --- /dev/null +++ b/academic/RAxML/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------------------------------------------------------| +RAxML: RAxML (Randomized Axelerated Maximum Likelihood) +RAxML: +RAxML: RAxML is a program for sequential and parallel Maximum Likelihood +RAxML: (ML) based inference of large phylogenetic trees. It can also be +RAxML: used for postanalyses of sets of phylogenetic trees, analyses of +RAxML: alignments and, evolutionary placement of short reads. +RAxML: +RAxML: https://cme.h-its.org/exelixis/web/software/raxml/index.html +RAxML: https://github.com/stamatak/standard-RAxML +RAxML: +RAxML: diff --git a/academic/RepeatMasker/README b/academic/RepeatMasker/README index a62062fa85..536b0897a5 100644 --- a/academic/RepeatMasker/README +++ b/academic/RepeatMasker/README @@ -20,7 +20,7 @@ supports Dfam (profile HMM library derived from Repbase sequences) and Repbase, a service of the Genetic Information Research Institute. WARNING! -Due to the bundled databases, the installed size of this is 1.8 GiB! +Due to the bundled databases, the installed size of this is 2.1 GB! NOTE! The package is installed in /opt. After install go fo /opt/RepeatMasker diff --git a/academic/RepeatMasker/RepeatMasker.SlackBuild b/academic/RepeatMasker/RepeatMasker.SlackBuild index 6e0c876dad..2975550e19 100644 --- a/academic/RepeatMasker/RepeatMasker.SlackBuild +++ b/academic/RepeatMasker/RepeatMasker.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for RepeatMasker -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,11 +23,10 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=RepeatMasker -VERSION=${VERSION:-4.0.8} +VERSION=${VERSION:-4.1.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -SRCVER=${SRCVER:-4-0-8} ARCH=noarch CWD=$(pwd) @@ -42,7 +41,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM -tar xvf $CWD/$PRGNAM-open-$SRCVER.tar.gz +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM chown -R root:root . find -L . \ @@ -67,7 +66,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr # 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 \ + bluegrad.jpg daterepeats.help HTMLAnnotHeader.html INSTALL 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-$VERSION/README.SLACKWARE diff --git a/academic/RepeatMasker/RepeatMasker.info b/academic/RepeatMasker/RepeatMasker.info index 20543128f6..322653dd70 100644 --- a/academic/RepeatMasker/RepeatMasker.info +++ b/academic/RepeatMasker/RepeatMasker.info @@ -1,8 +1,8 @@ PRGNAM="RepeatMasker" -VERSION="4.0.8" +VERSION="4.1.1" HOMEPAGE="http://www.repeatmasker.org/" -DOWNLOAD="http://www.repeatmasker.org/RepeatMasker-open-4-0-8.tar.gz" -MD5SUM="539faa4def9b81b6ede7e9bb8f46f78f" +DOWNLOAD="http://www.repeatmasker.org/RepeatMasker-4.1.1.tar.gz" +MD5SUM="6df7b188757b5ef2d2575320eb0b014e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="perl-Text-Soundex trfind HMMER ncbi-rmblastn" diff --git a/academic/STAR/README b/academic/STAR/README index 24272d0a1f..7d410d628f 100644 --- a/academic/STAR/README +++ b/academic/STAR/README @@ -2,6 +2,9 @@ STAR aligns short and long RNA-seq reads to a reference genome using uncompressed suffix arrays, resulting in fast, accurate mapping. STAR is capable of unbiased de novo detection of canonical splice junctions, can discover non-canonical splices and chimeric (fusion) -transcripts and can map full-length RNA sequences. +transcripts and can map full-length RNA sequences. Comes with +STARsolo for: mapping, demultiplexing and gene quantification for +single cell RNA-seq (See STARmanual). + Reference: https://www.ncbi.nlm.nih.gov/pubmed/23104886 diff --git a/academic/STAR/STAR.SlackBuild b/academic/STAR/STAR.SlackBuild index b5818beaec..d785f46923 100644 --- a/academic/STAR/STAR.SlackBuild +++ b/academic/STAR/STAR.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for STAR -# Copyright 2018 Rob van Nues +# Copyright 2018-2021 Rob van Nues <sborg63@disroot.org> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=STAR -VERSION=${VERSION:-2.6.1d} +VERSION=${VERSION:-2.7.8a} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/STAR/STAR.info b/academic/STAR/STAR.info index 8929bb763d..68740e69a3 100644 --- a/academic/STAR/STAR.info +++ b/academic/STAR/STAR.info @@ -1,10 +1,10 @@ PRGNAM="STAR" -VERSION="2.6.1d" +VERSION="2.7.8a" HOMEPAGE="https://github.com/alexdobin/STAR" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.6.1d/STAR-2.6.1d.tar.gz" -MD5SUM_x86_64="c74965ee85f551641175b63f8a26a6f5" +DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.7.8a/STAR-2.7.8a.tar.gz" +MD5SUM_x86_64="b6482dd380c5c07587166ee240573780" REQUIRES="" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/STAR/slack-desc b/academic/STAR/slack-desc index 433a7dfbb0..ac9ff6cc26 100644 --- a/academic/STAR/slack-desc +++ b/academic/STAR/slack-desc @@ -9,10 +9,10 @@ STAR: STAR (Spliced Transcripts Alignment to a Reference) STAR: STAR: STAR aligns short and long RNA-seq reads to a reference genome using -STAR: uncompressed suffix arrays, resulting in fast, accurate mapping. -STAR: STAR is capable of unbiased de novo detection of canonical junctions, -STAR: can discover non-canonical splices and chimeric (fusion) transcripts -STAR: and can map full-length RNA sequences. +STAR: uncompressed suffix arrays, resulting in fast, accurate mapping. STAR +STAR: is capable of unbiased de novo detection of canonical junctions, can +STAR: discover non-canonical splices and chimeric transcripts, can map full- +STAR: length RNA sequences and can be used for single cell RNA-seq mapping. STAR: STAR: https://github.com/alexdobin/STAR STAR: Reference: https://www.ncbi.nlm.nih.gov/pubmed/23104886 diff --git a/academic/SU2/README b/academic/SU2/README new file mode 100644 index 0000000000..fd4519ee57 --- /dev/null +++ b/academic/SU2/README @@ -0,0 +1,19 @@ +SU2 - Open-Source CFD code + +Open-source suite for Partial Differential Equation (PDE) analysis and +PDE-constrained optimization problems. Designed with Computational +Fluid Dynamics (CFD) and aerodynamic shape optimization in mind, but +extensible to arbitrary sets of governing equations such as potential +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: + +--enable-mpi +--with-cxx=/usr/bin/mpicxx +--with-cc=/usr/bin/mpicc + +and then no need for mpich / openmpi. diff --git a/academic/freechartgeany/freechartgeany.SlackBuild b/academic/SU2/SU2.SlackBuild index 13ac323d36..a32beff5c2 100644 --- a/academic/freechartgeany/freechartgeany.SlackBuild +++ b/academic/SU2/SU2.SlackBuild @@ -1,8 +1,8 @@ #!/bin/sh -# Slackware build script for freechartgeany - -# Copyright 2012-2016 Larry Hajali <larryhaja[at]gmail[dot]com> +# Slackware build script for SU2 +# +# Copyright 2019 Judah Milgram, Washington DC USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,14 +22,15 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=freechartgeany -VERSION=${VERSION:-2.0.3} + +PRGNAM=SU2 +VERSION=${VERSION:-6.2.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -40,8 +41,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -69,30 +70,38 @@ 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 {} \; -qmake QMAKE_CFLAGS+="$SLKCFLAGS" QMAKE_CXXFLAGS+="$SLKCFLAGS" \ - -o Makefile FreeChartGeany.pro +./bootstrap + +# For serial version, delete --enable-mpi, --with-cxx, and --with-cc + +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 make -make install INSTALL_ROOT=$PKG +make install-strip DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# Install .desktop item and icons. -sed -i "/^Icon/s|=.*|=${PRGNAM}|" $PKG/usr/share/applications/$PRGNAM.desktop -rm -rf $PKG/usr/share/pixmaps -for i in 16 32 64 128; do - install -D -m 0644 images/icons/logo${i}.png \ - $PKG/usr/share/icons/hicolor/${i}x${i}/apps/$PRGNAM.png -done - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING images/icons/Readme.rtf licenses/* $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ +COPYING INSTALL 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:-tgz} diff --git a/academic/SU2/SU2.info b/academic/SU2/SU2.info new file mode 100644 index 0000000000..a7fb802ad1 --- /dev/null +++ b/academic/SU2/SU2.info @@ -0,0 +1,10 @@ +PRGNAM="SU2" +VERSION="6.2.0" +HOMEPAGE="https://su2code.github.io/docs/home/" +DOWNLOAD="https://github.com/su2code/SU2/archive/v6.2.0/SU2-6.2.0.tar.gz" +MD5SUM="c74d1dbe52d6239c4f9c75cbd3102a90" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="mpich" +MAINTAINER="Judah Milgram" +EMAIL="milgram@cgpp.com" diff --git a/academic/SU2/slack-desc b/academic/SU2/slack-desc new file mode 100644 index 0000000000..67f9c3b830 --- /dev/null +++ b/academic/SU2/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------------------------------------------------------| +SU2: SU2 (Open Source CFD Code) +SU2: +SU2: Open-source suite for Partial Differential Equation (PDE) analysis and +SU2: PDE-constrained optimization problems. Designed with Computational +SU2: Fluid Dynamics (CFD) and aerodynamic shape optimization in mind, but +SU2: extensible to arbitrary sets of governing equations such as potential +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/ diff --git a/academic/SeqMonk/README b/academic/SeqMonk/README new file mode 100644 index 0000000000..a5d7990f84 --- /dev/null +++ b/academic/SeqMonk/README @@ -0,0 +1,15 @@ +SeqMonk - A Mapped Sequence Analysis tool +----------------------------------------- + +SeqMonk is a tool for viewing and analysing mapped sequence data. It +was initially written to cope with remapping experiment data from +next generation sequencers, but could be applied to any dataset +consisting of a series of mapped genomic regions. The program allows +you to visualise the positions of your mapped regions against an +annotated genome and to quantify the data in order to make comparisons +between data sets. + +If you have any comments about SeqMonk the authors would like to hear +them. You either enter them in the bug tracking system at: + +https://github.com/s-andrews/seqmonk/issues/ diff --git a/academic/SeqMonk/SeqMonk.SlackBuild b/academic/SeqMonk/SeqMonk.SlackBuild new file mode 100644 index 0000000000..e09ee60c9a --- /dev/null +++ b/academic/SeqMonk/SeqMonk.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/sh + +# Slackware build script for SeqMonk + +# Copyright 2020 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. + +PRGNAM=SeqMonk +VERSION=${VERSION:-1.47.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +EXENAM=seqmonk +TARNAM=${EXENAM}_v${VERSION}_linux64 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +if [ "$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 $PRGNAM +tar xvf $CWD/$TARNAM.tar.gz +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 {} \; + +# Make sure SeqMonk finds its own java environment +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 + +mkdir -p $PKG/opt/$PRGNAM +cp -a \ + com edu Help jre net Scripts Templates uk *.jar seqmonk seqmonk_import \ + $PKG/opt/$PRGNAM + +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 \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp -a uk/ac/babraham/SeqMonk/Resources/monk_logo.png $PKG/usr/share/pixmaps/$EXENAM.png +cp -a $EXENAM.desktop $PKG/usr/share/applications + +# Leave the program in /opt and create a symlink to it +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../../opt/$PRGNAM/$EXENAM . +cd - + +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:-tgz} diff --git a/academic/SeqMonk/SeqMonk.info b/academic/SeqMonk/SeqMonk.info new file mode 100644 index 0000000000..af8b37178c --- /dev/null +++ b/academic/SeqMonk/SeqMonk.info @@ -0,0 +1,10 @@ +PRGNAM="SeqMonk" +VERSION="1.47.1" +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" +REQUIRES="R" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/SeqMonk/doinst.sh b/academic/SeqMonk/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/SeqMonk/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/SeqMonk/slack-desc b/academic/SeqMonk/slack-desc new file mode 100644 index 0000000000..632f4c5de1 --- /dev/null +++ b/academic/SeqMonk/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------------------------------------------------------| +SeqMonk: SeqMonk (A Mapped Sequence Analysis tool) +SeqMonk: +SeqMonk: SeqMonk is a tool for viewing and analysing mapped sequence data. +SeqMonk: It was initially written to cope with remapping experiment data +SeqMonk: from next generation sequencers, but could be applied to any +SeqMonk: dataset consisting of a series of mapped genomic regions. The +SeqMonk: program allows you to visualise the positions of your mapped +SeqMonk: regions against an annotated genome and to quantify the data in +SeqMonk: order to make comparisons between data sets. +SeqMonk: +SeqMonk: https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ diff --git a/academic/Shark/Shark.SlackBuild b/academic/Shark/Shark.SlackBuild index d7a328ef6c..e8faee8c7f 100644 --- a/academic/Shark/Shark.SlackBuild +++ b/academic/Shark/Shark.SlackBuild @@ -2,7 +2,7 @@ # SlackBuild script for Shark -# Copyright 2018 Benjamin Trigona-Harany <slackbuilds@jaxartes.net> +# Copyright 2018-2019 Benjamin Trigona-Harany <slackbuilds@jaxartes.net> # All rights reserved. # # Redistribution and use in source and binary forms, with or without @@ -25,7 +25,7 @@ # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=Shark -VERSION=${VERSION:-3.1.4} +VERSION=${VERSION:-4.0.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/Shark/Shark.info b/academic/Shark/Shark.info index 1481221e0a..cae38a7659 100644 --- a/academic/Shark/Shark.info +++ b/academic/Shark/Shark.info @@ -1,8 +1,8 @@ PRGNAM="Shark" -VERSION="3.1.4" +VERSION="4.0.0" HOMEPAGE="http://image.diku.dk/shark" -DOWNLOAD="https://github.com/Shark-ML/Shark/archive/v3.1.4/Shark-3.1.4.tar.gz" -MD5SUM="b6d3859050d7de9500841c7cebec87a3" +DOWNLOAD="https://github.com/Shark-ML/Shark/archive/v4.0.0/Shark-4.0.0.tar.gz" +MD5SUM="a1c240bdbc0e4ad8ed09a855cc8e0444" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/TreeGraph/TreeGraph.SlackBuild b/academic/TreeGraph/TreeGraph.SlackBuild index a3f304b739..1deeb4c780 100644 --- a/academic/TreeGraph/TreeGraph.SlackBuild +++ b/academic/TreeGraph/TreeGraph.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for TreeGraph -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,11 +23,11 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=TreeGraph -VERSION=${VERSION:-2.14.0_771_beta} +VERSION=${VERSION:-2.15.0_887_beta} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -ZIPVER=2.14.0-771_beta +ZIPVER=2.15.0-887_beta ARCH=noarch CWD=$(pwd) diff --git a/academic/TreeGraph/TreeGraph.info b/academic/TreeGraph/TreeGraph.info index 04673ad615..05ab5af79b 100644 --- a/academic/TreeGraph/TreeGraph.info +++ b/academic/TreeGraph/TreeGraph.info @@ -1,8 +1,8 @@ PRGNAM="TreeGraph" -VERSION="2.14.0_771_beta" +VERSION="2.15.0_887_beta" HOMEPAGE="http://treegraph.bioinfweb.info/" -DOWNLOAD="http://treegraph.bioinfweb.info/Download/Complete/TreeGraph_2.14.0-771_beta.zip" -MD5SUM="78dbfd08f946bb46622314457a25a78e" +DOWNLOAD="http://treegraph.bioinfweb.info/Download/Complete/TreeGraph_2.15.0-887_beta.zip" +MD5SUM="4ca90fbb7cb7aae9a37d99ac742bd22f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="jdk" diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README new file mode 100644 index 0000000000..a82c7160b2 --- /dev/null +++ b/academic/ViennaRNA/README @@ -0,0 +1,54 @@ +# ViennaRNA Package + +A C code library and several stand-alone programs for the prediction +and comparison of RNA secondary structures. + +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 + +For those who wish to link the Vienna package to their own C, perl +or python programs (see below), the RNAlib Reference Manual can be +assessed at: + +https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html +(or unpacked from the src: $PRGNAM-$VERSION/doc/html/) +https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/RNAlib-$VERSION.pdf +(or unpacked from the src: $PRGNAM-$VERSION/doc/RNAlib-$VERSION.pdf) + +Amongst other things, the ViennRNA implementations allow you to: + +- predict minimum free energy secondary structures +- calculate the partition function for the ensemble of structures +- compute various equilibrium probabilities +- calculate suboptimal structures in a given energy range +- compute local structures in long sequences +- predict consensus secondary structures from a multiple sequence + alignment +- predict melting curves +- search for sequences folding into a given structure +- compare two secondary structures +- predict hybridization structures of two RNA molecules + +The package includes `Perl 5` 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). + +For further info see: + +https://www.tbi.univie.ac.at/RNA/documentation.html diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild new file mode 100644 index 0000000000..8bc20e2a45 --- /dev/null +++ b/academic/ViennaRNA/ViennaRNA.SlackBuild @@ -0,0 +1,192 @@ +#!/bin/sh + +# Slackware build script for ViennaRNA + +# Copyright 2018 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: +# +# 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. + +PRGNAM=ViennaRNA +VERSION=${VERSION:-2.4.17} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 {} \; + +# You can configure some ViennaRNA features that are (not) compiled by default. +# See the README.md for details. You can enable/disable a these features by +# passing variables to the script (VAR=yes/no ./ViennaRNA.SlackBuild). +# indicated parts can be included/omitted +# not-included by default +# - CLuster Analysis (AnalyseSeqs, AnalyseDists) +# - Kinwalker (co-transcriptional folding) +# included but can be omitted: +# - Kinfold +# - RNAforester +# - RNAlocmin +# - Swig (all scripting interfaces) +# - Perl interface +# - Python interface +# - Python 3 interface +# - Streaming SIMD Extension support +# in the case of run time/ make/ or configure problems try turning off: +# - Link Time Optimization (LTO) +# for concurrent computation: +# - OpenMP support (disabling makes RNAlib not entirely threadsafe) +# - POSIX threads (pthread) support +# in case the following cause problems with your own third-party program that links against RNAlib +# for Z-score filtering via statically linked libsvm: +# - SVM Z-score filter in RNALfold +# - GNU Scientific Library for RNApvmin + +cluster="" ; [ "${CLUSTER:-yes}" != "no" ] && cluster="--with-cluster" +kinwalker="" ; [ "${KINWALKER:-yes}" != "no" ] && kinwalker="--with-kinwalker" +# Default enabled features: +forester="" ; [ "${FORESTER:-yes}" != "yes" ] && forester="--without-forester" +kinfold="" ; [ "${KINFOLD:-yes}" != "yes" ] && kinwalk="--without-kinfold" +rnalocmin="" ; [ "${RNALOCMIN:-yes}" != "yes" ] && rnalocmin="--without-rnalocmin" +perl="" ; [ "${PERL:-yes}" != "yes" ] && perl="--without-perl" + +python3="" ; [ "${PYTHON3:-yes}" != "yes" ] && python3="--without-python3" +swig="" ; [ "${SWIG:-yes}" != "yes" ] && swig="--without-swig" +simd="" ; [ "${SIMD:-yes}" != "yes" ] && simd="--disable-simd" +lto="" ; [ "${LTO:-yes}" != "yes" ] && lto="--disable-lto" +openmp="" ; [ "${OPENMP:-yes}" != "yes" ] && openmp="--disable-openmp" +pthreads="" ; [ "${PTHREADS:-yes}" != "yes" ] && pthreads="--disable-pthreads" +svm="" ; [ "${SVM:-yes}" != "yes" ] && svm="--without-svm" +gsl="" ; [ "${GSL:-yes}" != "yes" ] && gsl="--without-gsl" +# Default to python3 (above) only; +python="" ; [ "${PYTHON:-no}" != "yes" ] && python="--without-python" + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib$LIBDIRSUFFIX \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux \ + $cluster \ + $kinwalker \ + $forester \ + $kinfold \ + $rnalocmin \ + $perl \ + $python \ + $python3 \ + $swig \ + $simd \ + $lto \ + $openmp \ + $pthreads \ + $svm \ + $gsl || exit 1 + +make +make install DESTDIR=$PKG + +##from https://www.tbi.univie.ac.at/RNA/packages/arch/PKGBUILD +cd misc +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 + +# cleanup after dirty install ... +for perlscript in $PKG/usr/share/ViennaRNA/bin/*.pl ; do + mv "$perlscript" "$PKG/usr/bin/" +done +rm -r $PKG/usr/share/ViennaRNA/bin + +# no need for that file it is outdated anyway +rm $PKG/usr/share/info/dir + +#gzip info file +gzip -9 $PKG/usr/share/info/*.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 + +find $PKG -name perllocal.pod \ + -o -name ".packlist" \ + -o -name "*.bs" \ + | xargs rm -f + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION + +#keep help and RNAlib-${VERSION} in src +if [[ -d $PKG/usr/doc/$PRGNAM-$VERSION/html ]]; then + rm -r $PKG/usr/doc/$PRGNAM-$VERSION/html +fi + +if [[ -e $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf ]]; then + rm $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf +fi + +cp -a \ + NEWS README.md AUTHORS COPYING THANKS INSTALL CHANGELOG.md license.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:-tgz} diff --git a/academic/ViennaRNA/ViennaRNA.info b/academic/ViennaRNA/ViennaRNA.info new file mode 100644 index 0000000000..162b17f93a --- /dev/null +++ b/academic/ViennaRNA/ViennaRNA.info @@ -0,0 +1,10 @@ +PRGNAM="ViennaRNA" +VERSION="2.4.17" +HOMEPAGE="https://www.tbi.univie.ac.at/RNA" +DOWNLOAD="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.17.tar.gz" +MD5SUM="16bc4e1889c301b91985a3bac1f21e30" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3" +MAINTAINER="Rob van Nues" +EMAIL="sborg63@disroot.org" diff --git a/academic/ViennaRNA/slack-desc b/academic/ViennaRNA/slack-desc new file mode 100644 index 0000000000..5e5f6be6ea --- /dev/null +++ b/academic/ViennaRNA/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------------------------------------------------------| +ViennaRNA: ViennaRNA (C Library) +ViennaRNA: +ViennaRNA: The ViennaRNA Package consists of a C code library and several +ViennaRNA: stand-alone programs for the prediction and comparison of RNA +ViennaRNA: secondary structures. +ViennaRNA: +ViennaRNA: Reference: Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafe +ViennaRNA: H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0 +ViennaRNA: Algorithms Mol. Biol., 6:1 26, 2011, doi:10.1186/1748-7188-6-26 +ViennaRNA: Home: https://www.tbi.univie.ac.at/RNA +ViennaRNA: diff --git a/academic/WordNet/README b/academic/WordNet/README index ccebc68f64..836afa9950 100644 --- a/academic/WordNet/README +++ b/academic/WordNet/README @@ -1,8 +1,9 @@ -WordNet(r) is a large lexical database of English, developed under the -direction of George A. Miller. Nouns, verbs, adjectives and adverbs are -grouped into sets of cognitive synonyms (synsets), each expressing a -distinct concept. Synsets are interlinked by means of conceptual-semantic -and lexical relations. The resulting network of meaningfully related words -and concepts can be navigated with the browser. WordNet is also freely -and publicly available for download. WordNet's structure makes it a -useful tool for computational linguistics and natural language processing. +WordNet(r) is a large lexical database of English, developed under +the direction of George A. Miller. Nouns, verbs, adjectives and +adverbs are grouped into sets of cognitive synonyms (synsets), each +expressing a distinct concept. Synsets are interlinked by means of +conceptual-semantic and lexical relations. The resulting network of +meaningfully related words and concepts can be navigated with the +browser. WordNet is also freely and publicly available for download. +WordNet's structure makes it a useful tool for computational +linguistics and natural language processing. diff --git a/academic/WordNet/WordNet.info b/academic/WordNet/WordNet.info index e0eaf6769e..96ef4d0f7c 100644 --- a/academic/WordNet/WordNet.info +++ b/academic/WordNet/WordNet.info @@ -6,5 +6,5 @@ MD5SUM="89b4db7c6840ce69a8e315a3f83d996b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Michael Gabilondo" -EMAIL="mgabilo{at}gmail{dot}com" +MAINTAINER="Glenn Becker" +EMAIL="glenn.becker@gmail.com" diff --git a/academic/Xyce/README b/academic/Xyce/README index ff16f7e41f..14d894e3e0 100644 --- a/academic/Xyce/README +++ b/academic/Xyce/README @@ -1,21 +1,22 @@ Xyce is an open source, SPICE-compatible, high-performance analog -circuit simulator, capable of solving extremely large circuit problems -by supporting large-scale parallel computing platforms. It also supports -serial execution on all common desktop platforms, and small-scale parallel -runs on Unix-like systems. In addition to analog electronic simulation, -Xyce has also been used to investigate more general network systems, -such as neural networks and power grids. +circuit simulator, capable of solving extremely large circuit +problems by supporting large-scale parallel computing platforms. It +also supports serial execution on all common desktop platforms, and +small-scale parallel runs on Unix-like systems. In addition to analog +electronic simulation, Xyce has also been used to investigate more +general network systems, such as neural networks and power grids. The Xyce Parallel Electronic Simulator is a SPICE-compatible circuit -simulator, developed internally at Sandia National Laboratories and funded -by the National Nuclear Security Administration's Advanced Simulation and -Computing (ASC) Campaign. In continuous development since 1999, Xyce is -designed to run on large-scale parallel computing platforms, though it -also executes efficiently on a variety of architectures, including single -processor workstations. As a mature platform for large-scale parallel -circuit simulation, Xyce supports standard capabilities available from -commercial simulators, in addition to a variety of devices and models -specific to Sandia's needs. +simulator, developed internally at Sandia National Laboratories +and funded by the National Nuclear Security Administration's +Advanced Simulation and Computing (ASC) Campaign. In continuous +development since 1999, Xyce is designed to run on large-scale +parallel computing platforms, though it also executes efficiently on a +variety of architectures, including single processor workstations. As +a mature platform for large-scale parallel circuit simulation, Xyce +supports standard capabilities available from commercial simulators, +in addition to a variety of devices and models specific to Sandia's +needs. The package is intalled at: /opt/Xyce Remember to set the library and path: diff --git a/academic/abella/README b/academic/abella/README new file mode 100644 index 0000000000..7954d1e751 --- /dev/null +++ b/academic/abella/README @@ -0,0 +1,33 @@ +Abella is an interactive theorem prover based on lambda-tree syntax. + +This means that Abella is well-suited for reasoning about the +meta-theory of programming languages and other logical systems +which manipulate objects with binding. For example, the following +applications are included in the distribution of Abella. + +* Various results on the lambda calculus involving big-step + evaluation, small-step evaluation, and typing judgments +* Cut-admissibility for a sequent calculus +* Part 1a and Part 2a of the POPLmark challenge +* Takahashi's proof of the Church-Rosser theorem +* Tait's logical relations argument for weak normalization of the + simply-typed lambda calculus +* Girard's proof of strong normalization of the simply-typed lambda + calculus +* Some ?-calculus meta-theory +* Relation between ?-reduction and paths in A-calculus + +For Full List: +http://abella-prover.org/examples/index.html + +Abella uses a two-level logic approach to reasoning. Specifications +are made in the logic of second-order hereditary Harrop formulas using +lambda-tree syntax. This logic is executable and is a subset of the +AProlog language (see the Teyjus system for an implementation of this +language). + +The reasoning logic of Abella is the culmination of a series +of extensions to proof theory for the treatment of definitions, +lambda-tree syntax, and generic judgments. The reasoning logic of +Abella is able to encode the semantics of our specification logic as a +definition and thereby reason over specifications in that logic. diff --git a/academic/abella/abella.SlackBuild b/academic/abella/abella.SlackBuild new file mode 100644 index 0000000000..ea575be990 --- /dev/null +++ b/academic/abella/abella.SlackBuild @@ -0,0 +1,78 @@ +#!/bin/sh +# Slackware build script for abella +# Copyright 2019 Jefferson Rocha <root@slackjeff.com.br> +# 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. + +#==========================VARS +PRGNAM=abella +VERSION=${VERSION:-2.0.6} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +ARCH=noarch +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +#Root? +[ "$UID" -ne '0' ] && { echo "Need root."; exit 1 ;} + +#=========================START +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP + +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION + +# Fix Permissions +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -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 {} \; + +# Generate bin +make +strip -s $PRGNAM + +mkdir -p $PKG/usr/bin +cp "$PRGNAM" $PKG/usr/bin + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION + +# Send original Docs and archives +for create in "$PRGNAM.SlackBuild" 'LICENSE' 'CHANGES'; do + if [ "$create" = $PRGNAM.SlackBuild ]; then + cp $CWD/$create $PKG/usr/doc/$PRGNAM-$VERSION/ + else + cp $create $PKG/usr/doc/$PRGNAM-$VERSION/ + fi +done + +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:-tgz} diff --git a/academic/abella/abella.info b/academic/abella/abella.info new file mode 100644 index 0000000000..88abb3f04c --- /dev/null +++ b/academic/abella/abella.info @@ -0,0 +1,10 @@ +PRGNAM="abella" +VERSION="2.0.6" +HOMEPAGE="http://abella-prover.org/" +DOWNLOAD="http://abella-prover.org/distributions/abella-2.0.6.tar.gz" +MD5SUM="077cb3fbbdf35159e4b8860faf431c6a" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="ocamlbuild ocaml-findlib" +MAINTAINER="Jefferson Rocha" +EMAIL="root@slackjeff.com.br" diff --git a/academic/abella/slack-desc b/academic/abella/slack-desc new file mode 100644 index 0000000000..15174390e7 --- /dev/null +++ b/academic/abella/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 ':'. + + |-----handy-ruler------------------------------------------------------| +abella: abella (interactive theorem prover based on lambda-tree syntax) +abella: +abella: Abella is an interactive theorem prover based on lambda-tree syntax. +abella: This means that Abella is well-suited for reasoning about the meta +abella: theory of programming languages and other logical systems which +abella: manipulate objects with binding. +abella: For example, the following applications are included in the +abella: distribution of Abella. +abella: +abella: http://abella-prover.org/ +abella: diff --git a/academic/aenig4/README b/academic/aenig4/README index 3ac2263e9d..ee1505f360 100644 --- a/academic/aenig4/README +++ b/academic/aenig4/README @@ -1,5 +1,5 @@ aenig4 (Enigma M4 Cipher Machine Emulator) -aenig4 emulates the Enigma M4 cipher machine used by the U-boot divsion of -the German Navy during World War II. It can be used as well to emulate the -Enigma I machine (M1, M2, M3). +aenig4 emulates the Enigma M4 cipher machine used by the U-boot +divsion of the German Navy during World War II. It can be used as well +to emulate the Enigma I machine (M1, M2, M3). diff --git a/academic/aliview/aliview.SlackBuild b/academic/aliview/aliview.SlackBuild index 10073a11d0..89b70e0ceb 100644 --- a/academic/aliview/aliview.SlackBuild +++ b/academic/aliview/aliview.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for aliview -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2019 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=aliview -VERSION=${VERSION:-1.25} +VERSION=${VERSION:-1.26} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/aliview/aliview.info b/academic/aliview/aliview.info index e355fba160..6f392759ae 100644 --- a/academic/aliview/aliview.info +++ b/academic/aliview/aliview.info @@ -1,8 +1,8 @@ PRGNAM="aliview" -VERSION="1.25" +VERSION="1.26" HOMEPAGE="http://www.ormbunkar.se/aliview/" -DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-versions-all/linux-version-1.25/aliview.tgz" -MD5SUM="45ddbf6ed113e1b641f601bfdb8f8e45" +DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-versions-all/linux-version-1.26/aliview.tgz" +MD5SUM="9aac430a5f9e1cc465815cea0bf69af8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="jdk" diff --git a/academic/amd/README b/academic/amd/README index 07e4dcafc0..b2ae697056 100644 --- a/academic/amd/README +++ b/academic/amd/README @@ -1,6 +1,7 @@ -AMD is a set of routines for ordering a sparse matrix prior to Cholesky -factorization (or for LU factorization with diagonal pivoting). There are -versions in both C and Fortran. Note that this software has nothing to do -with AMD the company. This package runs on any platform. +AMD is a set of routines for ordering a sparse matrix prior to +Cholesky factorization (or for LU factorization with diagonal +pivoting). There are versions in both C and Fortran. Note that this +software has nothing to do with AMD the company. This package runs on +any platform. This package is part of SuiteSparse. diff --git a/academic/amd/amd.SlackBuild b/academic/amd/amd.SlackBuild index 905dcfb0ec..57645d2d25 100644 --- a/academic/amd/amd.SlackBuild +++ b/academic/amd/amd.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for AMD -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=amd SRCNAM=SuiteSparse SUBDIR=AMD VERSION=${VERSION:-2.4.6} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-5} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/amd/amd.info b/academic/amd/amd.info index 0abec62bee..da6c16b92b 100644 --- a/academic/amd/amd.info +++ b/academic/amd/amd.info @@ -1,8 +1,8 @@ PRGNAM="amd" VERSION="2.4.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/amd/patches/autoconfiscate.diff b/academic/amd/patches/autoconfiscate.diff index 1a954abc55..75b798c93e 100644 --- a/academic/amd/patches/autoconfiscate.diff +++ b/academic/amd/patches/autoconfiscate.diff @@ -176,7 +176,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([AMD],[2.4.6],[DrTimothyAldenDavis@gmail.com],[amd],[http://www.suitesparse.com/]) ++AC_INIT([AMD],[2.4.6],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[amd],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/amd_order.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/amplifx/amplifx.info b/academic/amplifx/amplifx.info index 1ec2301b5b..b8e5894a9f 100644 --- a/academic/amplifx/amplifx.info +++ b/academic/amplifx/amplifx.info @@ -1,7 +1,7 @@ PRGNAM="amplifx" VERSION="1.7.0" -HOMEPAGE="http://crn2m.univ-mrs.fr/AmplifX" -DOWNLOAD="http://crn2m.univ-mrs.fr/IMG/zip/AmplifX_Lin_Latest.zip" +HOMEPAGE="https://inp.univ-amu.fr/en/amplifx-manage-test-and-design-your-primers-for-pcr" +DOWNLOAD="http://jim.inp.univ-amu.fr/IMG/zip/AmplifX_Lin_Latest.zip" MD5SUM="ff84d1c4a800dcb651beaa877ff7b1ca" DOWNLOAD_x86_64="UNSUPPORTED" MD5SUM_x86_64="" diff --git a/academic/amplifx/slack-desc b/academic/amplifx/slack-desc index 2de0b1133a..670bbfccee 100644 --- a/academic/amplifx/slack-desc +++ b/academic/amplifx/slack-desc @@ -14,6 +14,6 @@ amplifx: which can be use to amplify a fragment into a target sequence, amplifx: for example, and particularly, to design strategies to screen amplifx: recombinant clones by PCR. amplifx: -amplifx: Home: http://crn2m.univ-mrs.fr/AmplifX -amplifx: References: /usr/doc/amplifx-1.7.0/References +amplifx: +amplifx: amplifx: diff --git a/academic/antiprism/README b/academic/antiprism/README index e81e3a4e32..6d7cca97a3 100644 --- a/academic/antiprism/README +++ b/academic/antiprism/README @@ -1,2 +1,2 @@ -Antiprism is a set of programs for generating, manipulating, transforming -and visualising polyhedra. +Antiprism is a set of programs for generating, manipulating, +transforming and visualising polyhedra. diff --git a/academic/antiprism/antiprism.info b/academic/antiprism/antiprism.info index 6791fc2ce3..993e85aa85 100644 --- a/academic/antiprism/antiprism.info +++ b/academic/antiprism/antiprism.info @@ -6,5 +6,5 @@ MD5SUM="bf09ffa0b54cb03edece25fbdf233fd3" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Jorge Barros de Abreu" -EMAIL="ficmatin10@gmail.com" +MAINTAINER="Glenn Becker" +EMAIL="glenn.becker@gmail.com" diff --git a/academic/aris/README b/academic/aris/README index 65cf47df47..13f3372b78 100644 --- a/academic/aris/README +++ b/academic/aris/README @@ -1,6 +1,6 @@ -GNU Aris is a sequential proof program, designed to assist anyone interested -in solving logical proofs. Aris supports both propositional and predicate -logic, as well as Boolean algebra and arithmetical logic in the form of -abstract sequences. It uses a predefined set of both inference and equivalence -rules, however gives the user options to use older proofs as lemmas, including -Isabelle's Isar proofs. +GNU Aris is a sequential proof program, designed to assist anyone +interested in solving logical proofs. Aris supports both propositional +and predicate logic, as well as Boolean algebra and arithmetical logic +in the form of abstract sequences. It uses a predefined set of both +inference and equivalence rules, however gives the user options to use +older proofs as lemmas, including Isabelle's Isar proofs. diff --git a/academic/aris/aris.SlackBuild b/academic/aris/aris.SlackBuild index a377d31a7f..4d0f2a04f2 100644 --- a/academic/aris/aris.SlackBuild +++ b/academic/aris/aris.SlackBuild @@ -2,16 +2,34 @@ # Slackware build script for GNU aris -# Written by Juan M. Lasca <juanmlasca@gmail.com> +# Originally written by Juan M. Lasca <juanmlasca at gmail dot com> +# Currently maintained by Philip Lacroix <slackph at posteo dot de> + +# 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. PRGNAM=aris -VERSION=${VERSION:-2.1.1} +VERSION=${VERSION:-2.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -22,18 +40,14 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" 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 @@ -46,26 +60,20 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -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="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --htmldir=/usr/doc/$PRGNAM-$VERSION/html \ + --disable-static \ --build=$ARCH-slackware-linux -# this will allow aris to find its documentation -# in a better place. -patch -p1 < $CWD/html_doc.patch +# Fix path for local manual +patch src/aris.c < $CWD/help_path.diff make make install DESTDIR=$PKG @@ -73,15 +81,13 @@ 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 -# "make install" won't locate the aris.info file in DESTDIR. -# Workaround: -mkdir -p $PKG/usr/info +# 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 - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a README $PKG/usr/doc/$PRGNAM-$VERSION -cp -ar doc/$PRGNAM/ $PKG/usr/doc/$PRGNAM-$VERSION/html +cp -a README AUTHORS ChangeLog NEWS THANKS TODO $PKG/usr/doc/$PRGNAM-$VERSION/ +cp -ar doc/$PRGNAM/ $PKG/usr/doc/$PRGNAM-$VERSION/html/ +cp -ar doc/proofs $PKG/usr/doc/$PRGNAM-$VERSION/ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/aris/aris.info b/academic/aris/aris.info index 35d002b89c..484ce06315 100644 --- a/academic/aris/aris.info +++ b/academic/aris/aris.info @@ -1,10 +1,10 @@ PRGNAM="aris" -VERSION="2.1.1" -HOMEPAGE="http://www.gnu.org/software/aris/" -DOWNLOAD="http://ftp.gnu.org/gnu/aris/aris-2.1.1.tar.bz2" -MD5SUM="ef1b8f3be8edac44305e36493068f745" +VERSION="2.2" +HOMEPAGE="https://www.gnu.org/software/aris/" +DOWNLOAD="https://ftp.gnu.org/gnu/aris/aris-2.2.tar.bz2" +MD5SUM="523e2c40f17e6e857b533c22a26ff4e1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Juan M. Lasca" -EMAIL="juanmlasca@gmail.com" +MAINTAINER="Philip Lacroix" +EMAIL="slackph at posteo dot de" diff --git a/academic/aris/help_path.diff b/academic/aris/help_path.diff new file mode 100644 index 0000000000..0d2853fcbe --- /dev/null +++ b/academic/aris/help_path.diff @@ -0,0 +1,11 @@ +--- a/aris.c 2021-02-10 17:51:33.532759576 +0400 ++++ b/aris.c 2021-02-10 17:52:15.210759108 +0400 +@@ -845,7 +845,7 @@ + if (the_app->working_dir) + { + parent = g_file_get_parent (parent); +- sprintf (the_app->help_file, "file://%s/doc/aris/index.html", g_file_get_path (parent)); ++ sprintf (the_app->help_file, "file:///usr/doc/aris-2.2/html/index.html", g_file_get_path (parent)); + } + + int ret; diff --git a/academic/aris/html_doc.patch b/academic/aris/html_doc.patch deleted file mode 100644 index 1b359b73d6..0000000000 --- a/academic/aris/html_doc.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- aris-2.0/configure 2012-09-25 05:06:22.000000000 -0300 -+++ aris-2.0b/configure 2013-03-23 18:34:59.483719378 -0300 -@@ -4610,3 +4610,1 @@ --cat >>confdefs.h <<_ACEOF --#define HELP_FILE "file://`pwd`/doc/aris/index.html" --_ACEOF -+echo "#define HELP_FILE \"file://"$htmldir"/index.html\"" >>confdefs.h ---- aris-2.0/src/aris.c 2012-09-25 05:06:22.000000000 -0300 -+++ aris-2.0b/src/aris.c 2013-03-23 18:45:25.290749474 -0300 -@@ -1064,0 +1065,6 @@ -+#ifdef HELP_FILE /* Which should be defined in config.h */ -+ -+ strcpy (the_app->help_file, HELP_FILE); -+ -+#else -+ -@@ -1076,0 +1083,2 @@ -+ -+#endif /* HELP FILE */ diff --git a/academic/aris/slack-desc b/academic/aris/slack-desc index 218444d055..c061cf1dc4 100644 --- a/academic/aris/slack-desc +++ b/academic/aris/slack-desc @@ -15,5 +15,5 @@ aris: in the form of abstract sequences. It uses a predefined set of both aris: inference and equivalence rules, however gives the user options to use aris: older proofs as lemmas, including Isabelle's Isar proofs. aris: -aris: Home page: http://www.gnu.org/software/aris/ +aris: Home page: https://www.gnu.org/software/aris/ aris: diff --git a/academic/armadillo/README b/academic/armadillo/README index 17bef8f786..9327750b8d 100644 --- a/academic/armadillo/README +++ b/academic/armadillo/README @@ -2,9 +2,10 @@ Armadillo is a high quality C++ linear algebra library useful for development of algorithms in machine learning, pattern recognition, signal processing, bioinformatics, statistics, etc. -Armadillo makes extensive use of template meta-programming, recursive templates -and template based function overloading. As such, C++ compilers which do not -fully implement the C++ standard may not work correctly. +Armadillo makes extensive use of template meta-programming, recursive +templates and template based function overloading. As such, C++ +compilers which do not fully implement the C++ standard may not work +correctly. The functionality of Armadillo is partly dependent on other libraries: LAPACK, BLAS and ARPACK. The LAPACK and BLAS libraries are used for diff --git a/academic/arpack-ng/README b/academic/arpack-ng/README index e24427e956..596f89a447 100644 --- a/academic/arpack-ng/README +++ b/academic/arpack-ng/README @@ -4,15 +4,18 @@ large scale eigenvalue problems. This is a fork of ARPACK that is actively maintained. As such, this package will conflict with the ARPACK package. Do not install both. -This requires a BLAS/LAPACK implementation. Choose one of these package sets: +This requires a BLAS/LAPACK implementation. Choose one of these +package sets: * OpenBLAS (includes both a BLAS and a LAPACK implementation) * atlas (includes both a BLAS and a LAPACK implementation) * blas, lapack (the Netlib reference implementations) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib +reference implementations; other packages that require a BLAS or +LAPACK implementation may not build if they are not configured to +detect/use alternate implementations. -If the `make check` command fails, try switching to the Netlib reference -implementations, or comment out that command at your own risk. +If the `make check` command fails, try switching to the Netlib +reference implementations, or comment out that command at your own +risk. diff --git a/academic/arpack-ng/arpack-ng.SlackBuild b/academic/arpack-ng/arpack-ng.SlackBuild index b5639de58b..a86140d997 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 2014-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2014-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=arpack-ng -VERSION=${VERSION:-3.7.0} +VERSION=${VERSION:-3.8.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -37,10 +37,10 @@ fi CWD=$(pwd) TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM +PKG=$TMP/package-$PRGNAM-$VERSION OUTPUT=${OUTPUT:-/tmp} -DOCS="CHANGES COPYING PARPACK_CHANGES README.md TODO" +DOCS="CHANGES COPYING README.md TODO" if [ "$ARCH" = "i486" ]; then SLKCFLAGS="-O2 -march=i486 -mtune=i686" @@ -81,8 +81,6 @@ patch -p1 < $CWD/patches/atlas-lib-rename.diff --mandir=/usr/man \ --infodir=/usr/info \ --docdir=/usr/doc/$PRGNAM-$VERSION \ - --enable-shared \ - --disable-static \ --disable-dependency-tracking \ --enable-icb \ --build=$ARCH-slackware-linux \ diff --git a/academic/arpack-ng/arpack-ng.info b/academic/arpack-ng/arpack-ng.info index 9af4707aa5..10dc19bd10 100644 --- a/academic/arpack-ng/arpack-ng.info +++ b/academic/arpack-ng/arpack-ng.info @@ -1,8 +1,8 @@ PRGNAM="arpack-ng" -VERSION="3.7.0" +VERSION="3.8.0" HOMEPAGE="https://github.com/opencollab/arpack-ng" -DOWNLOAD="https://github.com/opencollab/arpack-ng/archive/3.7.0/arpack-ng-3.7.0.tar.gz" -MD5SUM="6fc6c6bf78dbd4f144595ef0675c8430" +DOWNLOAD="https://github.com/opencollab/arpack-ng/archive/3.8.0/arpack-ng-3.8.0.tar.gz" +MD5SUM="bb4cf448f2480a0ffe5517d579f980c3" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="blas lapack" diff --git a/academic/artha/README b/academic/artha/README index dc6d794f61..5e08f3e1fd 100644 --- a/academic/artha/README +++ b/academic/artha/README @@ -4,7 +4,7 @@ off-line and is based on WordNet. The main focus of Artha is high usability, with much simplicity. It has distinct features like: -* hotkey press - word look-up (select text and press a hotkey for look-up) +* hotkey press - word lookup (select text and press a hotkey for lookup) * regex-based search (find words using wild-cards like *, ?, etc.) * passive desktop notifications (of word definitions for uninterrupted workflow) diff --git a/academic/avogadro/README b/academic/avogadro/README index 531f972b75..ef97a2fae0 100644 --- a/academic/avogadro/README +++ b/academic/avogadro/README @@ -1,5 +1,6 @@ -Avogadro is a molecular graphics and modelling system targeted at molecules -and biomolecules. It can visualize properties like molecular orbitals or -electrostatic potentials and features an intuitive molecular builder. +Avogadro is a molecular graphics and modelling system targeted at +molecules and biomolecules. It can visualize properties like molecular +orbitals or electrostatic potentials and features an intuitive +molecular builder. Optionally numpy can be installed for python support. diff --git a/academic/bcftools/README b/academic/bcftools/README index 731b912643..51b0b0b55b 100644 --- a/academic/bcftools/README +++ b/academic/bcftools/README @@ -1,5 +1,9 @@ -Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed in -a single samtools-0.1.x package. -This old version remains available from SBo as samtools-legacy +bcftools (BCF calling tools) contains all the "vcf..." commands which +previously lived in the htslib repository (such as vcfcheck, vcfmerge, +vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory +of the previous samtools. BCFtools are meant as a faster replacement +for most of the perl VCFtools commands. -The BCFtools is now distributed as an individual package. +Prior to the introduction of HTSlib, SAMtools and BCFtools were +distributed in a single samtools-0.1.x package. This old version remains +available from SBo as samtools-legacy. diff --git a/academic/bcftools/bcftools.SlackBuild b/academic/bcftools/bcftools.SlackBuild index 5607ba9d9a..9576a89c84 100644 --- a/academic/bcftools/bcftools.SlackBuild +++ b/academic/bcftools/bcftools.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for samtools -# Copyright 2017-2018 Rob van Nues # All rights reserved. +# Copyright 2017-2021 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: @@ -22,16 +22,15 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=bcftools -VERSION=${VERSION:-1.9} +PRGNAM=bcftools +VERSION=${VERSION:-1.12} BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} +TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; arm*) ARCH=arm ;; - # Unless $ARCH is already set, use uname -m for all other archs: *) ARCH=$( uname -m ) ;; esac fi @@ -69,7 +68,7 @@ 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 {} \; -#force linking to installed htslib +# Force linking to installed htslib rm -r htslib-$VERSION CFLAGS="$SLKCFLAGS" \ @@ -90,7 +89,6 @@ CXXFLAGS="$SLKCFLAGS" \ --build=$ARCH-slackware-linux make -#make test make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ diff --git a/academic/bcftools/bcftools.info b/academic/bcftools/bcftools.info index 12d206a836..ad211ee207 100644 --- a/academic/bcftools/bcftools.info +++ b/academic/bcftools/bcftools.info @@ -1,8 +1,8 @@ PRGNAM="bcftools" -VERSION="1.9" +VERSION="1.12" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2" -MD5SUM="c8fb7bb9c9251342b0ecf1e6f0c98335" +DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.12/bcftools-1.12.tar.bz2" +MD5SUM="d3622cb3e52039055fd91ad65ea5131e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="htslib" diff --git a/academic/bcftools/slack-desc b/academic/bcftools/slack-desc index a5f72be8ed..2f85ffb7dd 100644 --- a/academic/bcftools/slack-desc +++ b/academic/bcftools/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| 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: samtools. BCFtools are meant as a faster replacement for most of the +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: samtools. BCFtools are meant as a faster replacement for most of the bcftools: perl VCFtools commands. Bcftools comes with its own hstlib sources. bcftools: -bcftools: Home: http://www.htslib.org -bcftools: +bcftools: Homepage: http://www.htslib.org +bcftools: bcftools: diff --git a/academic/bedtools/bedtools.SlackBuild b/academic/bedtools/bedtools.SlackBuild index d215030da4..c29f69d3e2 100644 --- a/academic/bedtools/bedtools.SlackBuild +++ b/academic/bedtools/bedtools.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bedtools -# Copyright 2014-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2014-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,7 +24,7 @@ PRGNAM=bedtools DIRNAM=bedtools2 -VERSION=${VERSION:-2.27.1} +VERSION=${VERSION:-2.29.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -70,11 +70,7 @@ 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 {} \; -# Use our CFLAGS -sed -i "/CXXFLAGS/s/=/+=/" Makefile - -CXXFLAGS="$SLKCFLAGS -std=c++11" \ -make +CXXFLAGS="$SLKCFLAGS" make # Install the binary and scripts cd bin @@ -91,7 +87,7 @@ 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 LICENSE README.md RELEASE_HISTORY $PKG/usr/doc/$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 diff --git a/academic/bedtools/bedtools.info b/academic/bedtools/bedtools.info index 37153c5c89..79634be6cb 100644 --- a/academic/bedtools/bedtools.info +++ b/academic/bedtools/bedtools.info @@ -1,8 +1,8 @@ PRGNAM="bedtools" -VERSION="2.27.1" +VERSION="2.29.2" HOMEPAGE="http://bedtools.readthedocs.org/" -DOWNLOAD="https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz" -MD5SUM="ec87cf43735e15c69f13183c6aae00a6" +DOWNLOAD="https://github.com/arq5x/bedtools2/releases/download/v2.29.2/bedtools-2.29.2.tar.gz" +MD5SUM="a600f2cd58768310cb8427eb1ae54c17" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/biblesync/README b/academic/biblesync/README index 6a70d6d96d..d2d91161ca 100644 --- a/academic/biblesync/README +++ b/academic/biblesync/README @@ -9,7 +9,7 @@ Bible program induces the audience's programs to follow along. Some History. Up until and including xiphos 4.0.0 biblesync was included as part of -the xiphos source code. It has been removed from the source in xiphos 4.0.1 -and set to be a general library for any bible software that wants to use -shared navigation. +the xiphos source code. It has been removed from the source in xiphos +4.0.1 and set to be a general library for any bible software that +wants to use shared navigation. biblesync is a requirement for xiphos 4.0.1 or higher. diff --git a/academic/biblesync/biblesync.SlackBuild b/academic/biblesync/biblesync.SlackBuild index dfdd60598a..ffe9300400 100644 --- a/academic/biblesync/biblesync.SlackBuild +++ b/academic/biblesync/biblesync.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for biblesync -# Copyright (c) 2015/2018 Tim Dickson <dickson.tim@googlemail.com> +# Copyright (c) 2015/2020 Tim Dickson <dickson.tim@googlemail.com> # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are @@ -31,7 +31,7 @@ # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=biblesync -VERSION=${VERSION:-2.0.1} +VERSION=${VERSION:-2.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -91,23 +91,18 @@ make install DESTDIR=$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 -# Compress man page -mkdir -p $PKG/usr/man/man7 -mv $PKG/usr/share/man/man7/$PRGNAM.7 $PKG/usr/man/man7/$PRGNAM.7 +mv $PKG/usr/share/man $PKG/usr/ gzip $PKG/usr/man/man7/$PRGNAM.7 #remove old man path rm -r $PKG/usr/share -#copy over docs etc. mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a $DOCS $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh -#now to make the package cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/biblesync/biblesync.info b/academic/biblesync/biblesync.info index 00a1bb56d4..560d81ec74 100644 --- a/academic/biblesync/biblesync.info +++ b/academic/biblesync/biblesync.info @@ -1,8 +1,8 @@ PRGNAM="biblesync" -VERSION="2.0.1" +VERSION="2.1.0" HOMEPAGE="https://github.com/karlkleinpaste/biblesync" -DOWNLOAD="https://github.com/karlkleinpaste/biblesync/releases/download/2.0.1/biblesync-2.0.1.tar.gz" -MD5SUM="b9db8aae61bb0f9a4545c0782968466e" +DOWNLOAD="https://github.com/karlkleinpaste/biblesync/releases/download/2.1.0/biblesync-2.1.0.tar.gz" +MD5SUM="51b0deef468812a1f5b3c87ae5d14fb9" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/biblesync/doinst.sh b/academic/biblesync/doinst.sh deleted file mode 100644 index 682c942551..0000000000 --- a/academic/biblesync/doinst.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/sh -#we installed a library so run ldconfig -/sbin/ldconfig diff --git a/academic/bibletime/README b/academic/bibletime/README index 7c0c672c33..7a44c6d012 100644 --- a/academic/bibletime/README +++ b/academic/bibletime/README @@ -1,5 +1,4 @@ -BibleTime is a Bible study application for Linux. It is based on the K Desktop -Environment and uses the Sword programming library to work with Bible texts, -commentaries, dictionaries, and books provided by the Crosswire Bible Society. - -This version requires sword version 1.7.0 or higher. +BibleTime is a Bible study application for Linux. It is based on the K +Desktop Environment and uses the Sword programming library to work with +Bible texts, commentaries, dictionaries, and books provided by the +Crosswire Bible Society. diff --git a/academic/bibletime/bibletime.SlackBuild b/academic/bibletime/bibletime.SlackBuild index a0c3c992fb..807cf266c2 100644 --- a/academic/bibletime/bibletime.SlackBuild +++ b/academic/bibletime/bibletime.SlackBuild @@ -26,11 +26,12 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # Modified by Robert Delahunt [twinreverb[at]puresimplicity.net -# Modified 2018 by Tim Dickson (dickson.tim@googlemail.com) +# Modified 2018/19/20 by Tim Dickson (dickson.tim@googlemail.com) +# Modified 20200918 by B. Watson <yalhcru@gmail.com> PRGNAM=bibletime -VERSION=${VERSION:-2.11.2} -BUILD=${BUILD:-1} +VERSION=${VERSION:-3.0} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -68,18 +69,15 @@ cd $TMP rm -rf $PRGNAM-$VERSION tar -xJvf $CWD/$PRGNAM-$VERSION.tar.xz 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 build -#patch CMakeLists.txt so it works with version of qt5 -# available on slackbuilds.org -sed -i "s/VERSION 5.9/VERSION 5.7.1/g" CMakeLists.txt + +#we need to patch the cmake file to skip tests as they fail at the moment +#hopefully they will be fixed in 3.0.1 + +sed -i "/BTTests/s/^/#/" cmake/BTApplication.cmake + +mkdir -p build cd build + export "PATH=/opt/cmake-202x/bin:$PATH" cmake \ -Wno-dev \ -DCMAKE_BUILD_TYPE=Release \ @@ -87,7 +85,7 @@ cd build -DCMAKE_SKIP_RPATH:BOOL=ON \ -DCMAKE_C_FLAGS="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS="$SLKCFLAGS" \ - -DLIB_SUFFIX=$LIBDIRSUFFIX .. + -DLIB_SUFFIX=$LIBDIRSUFFIX .. make make install DESTDIR=$PKG cd .. diff --git a/academic/bibletime/bibletime.info b/academic/bibletime/bibletime.info index d3b6e7eb3a..43b5b02595 100644 --- a/academic/bibletime/bibletime.info +++ b/academic/bibletime/bibletime.info @@ -1,10 +1,10 @@ PRGNAM="bibletime" -VERSION="2.11.2" +VERSION="3.0" HOMEPAGE="http://www.bibletime.info/" -DOWNLOAD="https://github.com/bibletime/bibletime/releases/download/v2.11.2/bibletime-2.11.2.tar.xz" -MD5SUM="e0aed5f3b672c89ee5e06ffeb505e1ae" +DOWNLOAD="https://github.com/bibletime/bibletime/releases/download/v3.0/bibletime-3.0.tar.xz" +MD5SUM="c90bcafa7938ff0257a8599c3d9cb024" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="sword qt5" +REQUIRES="cmake-202x sword qt5 po4a fop" MAINTAINER="Tim Dickson" EMAIL="dickson.tim@googlemail.com" diff --git a/academic/bibus/README b/academic/bibus/README index 80e25c8602..4286359d52 100644 --- a/academic/bibus/README +++ b/academic/bibus/README @@ -1,4 +1,5 @@ -Bibus is a bibliographic and reference management software. As with other -such tools, Bibus allows one to search, edit, and sort bibliographic records. -In addition, Bibus contains features that makes it unique among open source -and even commercial bibliographic databases. +Bibus is bibliographic and reference management software. +As with other such tools, Bibus allows one to search, edit, and sort +bibliographic records. In addition, Bibus contains features that +makes it unique among open source and even commercial bibliographic +databases. diff --git a/academic/biopython/README b/academic/biopython/README new file mode 100644 index 0000000000..9c61e5c495 --- /dev/null +++ b/academic/biopython/README @@ -0,0 +1,23 @@ +The Biopython Project is an international association of developers of +freely available Python tools for computational molecular biology. + +The Biopython web site provides an online resource for modules, +scripts, and web links for developers of Python-based software for +bioinformatics use and research. Basically, the goal of Biopython is +to make it as easy as possible to use Python for bioinformatics by +creating high-quality, reusable modules and classes. Biopython +features include parsers for various Bioinformatics file formats +(BLAST, Clustalw, FASTA, Genbank,...), access to online services +(NCBI, Expasy,...), interfaces to common and not-so-common programs +(Clustalw, DSSP, MSMS,...), a standard sequence class, various +clustering modules, a KD tree data structure etc. and even +documentation. + +If you use Biopython in work contributing to a scientific publication, +please cite the application note (below) or one of the module specific +publications (listed on Biopython's website): + +Cock, P.J.A. et al. Biopython: freely available Python tools for +computational molecular biology and bioinformatics. Bioinformatics +2009 Jun 1; 25(11) 1422-3 +http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878 diff --git a/academic/biopython/References b/academic/biopython/References new file mode 100644 index 0000000000..cb4bbf6471 --- /dev/null +++ b/academic/biopython/References @@ -0,0 +1,7 @@ +If you use Biopython in work contributing to a scientific publication, we ask +that you cite our application note (below) or one of the module specific +publications (listed on our website): + +Cock, P.J.A. et al. Biopython: freely available Python tools for computational +molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 +http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878
\ No newline at end of file diff --git a/academic/biopython/biopython.SlackBuild b/academic/biopython/biopython.SlackBuild new file mode 100644 index 0000000000..22bd291d1f --- /dev/null +++ b/academic/biopython/biopython.SlackBuild @@ -0,0 +1,86 @@ +#!/bin/sh + +# Slackware build script for biopython + +# Copyright 2019 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. + +PRGNAM=biopython +VERSION=${VERSION:-1.74} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${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 {} \; + +python 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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a *.rst $PKG/usr/doc/$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:-tgz} diff --git a/academic/biopython/biopython.info b/academic/biopython/biopython.info new file mode 100644 index 0000000000..9906f1df81 --- /dev/null +++ b/academic/biopython/biopython.info @@ -0,0 +1,10 @@ +PRGNAM="biopython" +VERSION="1.74" +HOMEPAGE="https://biopython.org/" +DOWNLOAD="http://biopython.org/DIST/biopython-1.74.tar.gz" +MD5SUM="cead2bfe9e7be45267eba00635f68d5c" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="numpy" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/biopython/slack-desc b/academic/biopython/slack-desc new file mode 100644 index 0000000000..14374d1dfd --- /dev/null +++ b/academic/biopython/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------------------------------------------------------| +biopython: biopython (A set of Python tools for biological computation) +biopython: +biopython: Biopython is a set of freely available tools for biological +biopython: computation written in Python. Biopython features include parsers +biopython: for various Bioinformatics file formats (BLAST, Clustalw, FASTA, +biopython: Genbank), access to online services (NCBI, Expasy), interfaces to +biopython: common and not-so-common programs (Clustalw, DSSP, MSMS), a +biopython: standard sequence class, various clustering modules, a KD tree +biopython: data structure etc. and even documentation. +biopython: +biopython: https://biopython.org/ diff --git a/academic/boinc/README b/academic/boinc/README index d9831302df..f2130e2d19 100644 --- a/academic/boinc/README +++ b/academic/boinc/README @@ -1,15 +1,16 @@ The Berkeley Open Infrastructure for Network Computing (BOINC) -BOINC is an open source middleware system for volunteer and grid computing. -It was originally developed to support the SETI@home project before it became -useful as a platform for other distributed applications in areas as diverse as -mathematics, medicine, molecular biology, climatology, and astrophysics. The -intent of BOINC is to make it possible for researchers to tap into the -enormous processing power of personal computers around the world. +BOINC is an open source middleware system for volunteer and grid +computing. It was originally developed to support the SETI@home +project before it became useful as a platform for other distributed +applications in areas as diverse as mathematics, medicine, molecular +biology, climatology, and astrophysics. The intent of BOINC is to make +it possible for researchers to tap into the enormous processing power +of personal computers around the world. -Use the idle time on your computer (Windows, Mac, or Linux) to cure diseases, -study global warming, discover pulsars, and do many other types of scientific -research. It's safe, secure, and easy. +Use the idle time on your computer (Windows, Mac, or Linux) to cure +diseases, study global warming, discover pulsars, and do many other +types of scientific research. It's safe, secure, and easy. Building @@ -20,7 +21,7 @@ Building (2) Edit DATADIR in the script or run - DATADIR="/home/<user>/.boinc_data" ./boinc.Slackbuild + DATADIR="/home/<user>/.boinc_data" ./boinc.SlackBuild to set the data directory in your user's home and build the package. diff --git a/academic/boinc/boinc.SlackBuild b/academic/boinc/boinc.SlackBuild index f4103b52c1..a35a0cce0f 100644 --- a/academic/boinc/boinc.SlackBuild +++ b/academic/boinc/boinc.SlackBuild @@ -25,10 +25,11 @@ # TODO: add rc.boinc. PRGNAM=boinc -VERSION=${VERSION:-7.14.2} -BRANCH=${BRANCH:-7.14} +VERSION=${VERSION:-7.16.16} +BRANCH=${BRANCH:-7.16} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +NUMJOBS=${NUMJOBS:-1} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -60,7 +61,7 @@ fi set -e # Your default working directory location. Pass with DATADIR=<dir> Boinc.SlackBuild -DATADIR=${DATADIR:-'~/.boinc_data'} +DATADIR=${DATADIR:-'$HOME/.boinc_data'} BOINCMGR=${BOINCMGR:-yes} if [ "$BOINCMGR" = "yes" ]; then @@ -99,7 +100,7 @@ CXXFLAGS="$SLKCFLAGS" \ --with-x \ --build=$ARCH-slackware-linux -make +make -j${NUMJOBS} make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ diff --git a/academic/boinc/boinc.info b/academic/boinc/boinc.info index f995b44462..9d7dbd0162 100644 --- a/academic/boinc/boinc.info +++ b/academic/boinc/boinc.info @@ -1,10 +1,10 @@ PRGNAM="boinc" -VERSION="7.14.2" +VERSION="7.16.16" HOMEPAGE="https://boinc.berkeley.edu/" -DOWNLOAD="https://github.com/BOINC/boinc/archive/client_release/7.14/7.14.2/boinc-client_release-7.14-7.14.2.tar.gz" -MD5SUM="9200c1cbd0bead753fbee06e0ef0368a" +DOWNLOAD="https://github.com/BOINC/boinc/archive/client_release/7.16/7.16.16/boinc-client_release-7.16-7.16.16.tar.gz" +MD5SUM="debf658ed8748c1c434c12f8a8a932a1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="libwebp webkitgtk wxGTK3" +REQUIRES="wxGTK3" MAINTAINER="Edward W. Koenig" EMAIL="kingbeowulf@gmail.com" diff --git a/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild b/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild index db90b9ad1c..882dd6040e 100644 --- a/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild +++ b/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild @@ -22,13 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -SRCNAM=bowtie2 -SUFFIX=legacy -PRGNAM=$SRCNAM-$SUFFIX +PRGNAM=bowtie2-legacy VERSION=${VERSION:-2.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +SRCNAM=bowtie2 + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; diff --git a/academic/bowtie2/bowtie2.SlackBuild b/academic/bowtie2/bowtie2.SlackBuild index f113b58359..fa8d2dfa04 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 Rob van Nues sborg63@disroot.org +# Copyright 2018-2020 Rob van Nues sborg63@disroot.org # # All rights reserved. # @@ -25,7 +25,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=bowtie2 -VERSION=${VERSION:-2.3.4.3} +VERSION=${VERSION:-2.4.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -72,8 +72,6 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; #Use our FLAGS -#sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile - RELEASE_FLAGS+="$SLKCFLAGS" \ make @@ -83,9 +81,9 @@ install -D -m755 $PRGNAM-build-l $PKG/usr/bin/$PRGNAM-build-l install -D -m755 $PRGNAM-align-s $PKG/usr/bin/$PRGNAM-align-s install -D -m755 $PRGNAM-build-s $PKG/usr/bin/$PRGNAM-build-s install -D -m755 $PRGNAM-build $PKG/usr/bin/$PRGNAM-build -install -D -m755 $PRGNAM-inspect-l $PKG/usr/bin/$PRGNAM-inspect-l -install -D -m755 $PRGNAM-inspect-s $PKG/usr/bin/$PRGNAM-inspect-s -install -D -m755 $PRGNAM-inspect $PKG/usr/bin/$PRGNAM-inspect +install -D -m755 $PRGNAM-inspect-l $PKG/usr/bin/$PRGNAM-inspect-l +install -D -m755 $PRGNAM-inspect-s $PKG/usr/bin/$PRGNAM-inspect-s +install -D -m755 $PRGNAM-inspect $PKG/usr/bin/$PRGNAM-inspect # Copy examples and scripts mkdir -p $PKG/usr/share/$PRGNAM @@ -102,7 +100,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS LICENSE MANUAL NEWS TUTORIAL VERSION doc \ + AUTHORS LICENSE MANUAL NEWS TUTORIAL BOWTIE2_VERSION doc \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/bowtie2/bowtie2.info b/academic/bowtie2/bowtie2.info index bb5332d8c3..c57cd185f3 100644 --- a/academic/bowtie2/bowtie2.info +++ b/academic/bowtie2/bowtie2.info @@ -1,10 +1,10 @@ PRGNAM="bowtie2" -VERSION="2.3.4.3" +VERSION="2.4.2" HOMEPAGE="https://github.com/BenLangmead/bowtie2/releases" -DOWNLOAD="https://github.com/BenLangmead/bowtie2/archive/v2.3.4.3/bowtie2-2.3.4.3.tar.gz" -MD5SUM="9f8bb660362813277d12580da551b0c7" +DOWNLOAD="https://github.com/BenLangmead/bowtie2/archive/v2.4.2/bowtie2-2.4.2.tar.gz" +MD5SUM="d5f8674aed8bdbf6b96bd07f3df528ee" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="tbb" +REQUIRES="tbb python3" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" 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..4c23467bad --- /dev/null +++ b/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild @@ -0,0 +1,109 @@ +#!/bin/sh + +# Slackware build script for bpp1.9-utils + +# Copyright 2020 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. + +PRGNAM=bpp1.9-numcalc +SRCNAM=bpp-numcalc +VERSION=${VERSION:-1.8.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${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 Urachlay! +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${LIBDIRSUFFIX}/Bpp1.9/:g" NumCalc.spec + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$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 .. + +rm -f $PKG/usr/lib$LIBDIRSUFFIX/Bpp1.9/libbpp-numcalc.a + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING INSTALL \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} 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..0a1c619ed1 --- /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="http://biopp.univ-montp2.fr/repos/sources/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/freechartgeany/slack-desc b/academic/bpp1.9-numcalc/slack-desc index e59bc3b7d8..0b1db4fe56 100644 --- a/academic/freechartgeany/slack-desc +++ b/academic/bpp1.9-numcalc/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -freechartgeany: freechartgeany (market analysis tool) -freechartgeany: -freechartgeany: Free Chart Geany is a multi platform software solution for market -freechartgeany: technical analysis and charting. -freechartgeany: -freechartgeany: Homepage: http://freechartgeany.sourceforge.net/ -freechartgeany: -freechartgeany: -freechartgeany: -freechartgeany: -freechartgeany: +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..f9caa0030c --- /dev/null +++ b/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/sh + +# Slackware build script for bpp1.9-phyl + +# Copyright 2020 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. + +PRGNAM=bpp1.9-phyl +SRCNAM=bpp-phyl +VERSION=${VERSION:-1.9.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# This is needed for vCAPS to find its libraries at runtime. Thanks Urachlay! +LIBDIRPATH="-Wl,-rpath,/usr/lib${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 + +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 .. + +# Remove static library +rm -f $PKG/usr/lib64/Bpp1.9/libbpp-phyl.a + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING INSTALL \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} 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..26d984b0c4 --- /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="http://biopp.univ-montp2.fr/repos/sources/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..a35ba4e508 --- /dev/null +++ b/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/sh + +# Slackware build script for bpp1.9-seq + +# Copyright 2020 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. + +PRGNAM=bpp1.9-seq +SRCNAM=bpp-seq +VERSION=${VERSION:-1.7.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# This is needed for vCAPS to find its libraries at runtime. Thanks Urachlay! +LIBDIRPATH="-Wl,-rpath,/usr/lib${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${LIBDIRSUFFIX}/Bpp1.9/:g" Seq.spec + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$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 .. + +# Remove static lib +rm -f $PKG/usr/lib64/Bpp1.9/libbpp-seq.a + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING INSTALL \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} 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..35b6d40f95 --- /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="http://biopp.univ-montp2.fr/repos/sources/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..daff8c88bf --- /dev/null +++ b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild @@ -0,0 +1,114 @@ +#!/bin/sh + +# Slackware build script for bpp1.9-utils + +# Copyright 2020 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. + +PRGNAM=bpp1.9-utils +SRCNAM=bpp-utils +VERSION=${VERSION:-1.5.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# This is needed for vCAPS to find its libraries at runtime. Thanks Urachlay! +LIBDIRPATH="-Wl,-rpath,/usr/lib${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${LIBDIRSUFFIX}/Bpp1.9/:g" Utils.spec + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$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 .. + +# static library not needed +rm -f $PKG/usr/lib$LIBDIRSUFFIX/Bpp1.9/libbpp-utils.a + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING INSTALL \ + $PKG/usr/doc/$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:-tgz} 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..8e7863e9f1 --- /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="http://biopp.univ-montp2.fr/repos/sources/bpp-utils-1.5.0.tar.gz" +MD5SUM="4625b7f2146caa1815ed7dc433d5eb78" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +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/btf/README b/academic/btf/README index 3666aedf6b..625663f5fe 100644 --- a/academic/btf/README +++ b/academic/btf/README @@ -1,5 +1,5 @@ -BTF permutes an unsymmetric matrix (square or rectangular) into its block -upper triangular form (more precisely, it computes a Dulmage-Mendelsohn -decomposition). +BTF permutes an unsymmetric matrix (square or rectangular) into +its block upper triangular form (more precisely, it computes a +Dulmage-Mendelsohn decomposition). This package is part of SuiteSparse. diff --git a/academic/btf/btf.SlackBuild b/academic/btf/btf.SlackBuild index 1777ae8faf..619dcb650c 100644 --- a/academic/btf/btf.SlackBuild +++ b/academic/btf/btf.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for BTF -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=btf SRCNAM=SuiteSparse SUBDIR=BTF VERSION=${VERSION:-1.2.6} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-5} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/btf/btf.info b/academic/btf/btf.info index b8d40b92d7..df3056d279 100644 --- a/academic/btf/btf.info +++ b/academic/btf/btf.info @@ -1,8 +1,8 @@ PRGNAM="btf" VERSION="1.2.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/btf/patches/autoconfiscate.diff b/academic/btf/patches/autoconfiscate.diff index 8a621ae66b..a07fc25f30 100644 --- a/academic/btf/patches/autoconfiscate.diff +++ b/academic/btf/patches/autoconfiscate.diff @@ -73,7 +73,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([BTF],[1.2.6],[DrTimothyAldenDavis@gmail.com],[btf],[http://www.suitesparse.com/]) ++AC_INIT([BTF],[1.2.6],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[btf],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/btf_order.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/cadabra2/README b/academic/cadabra2/README index 8fe21c13e8..0533ffcdd3 100644 --- a/academic/cadabra2/README +++ b/academic/cadabra2/README @@ -4,7 +4,30 @@ 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. Programmable -in Python. Both a command-line and a graphical interface are available. +types and many more. The input format is a subset of TeX. Both a +command-line and a graphical interface are available. -Optional runtime dependencies are matplotlib, mpmath, and sympy. +* Designed for field-theory problems, with handling of anti-commuting + and non-commuting objects without special notations for their + products, gamma matrix algebra, Fierz identities, Dirac conjugation, + vielbeine, flat and curved, covariant and contravariant indices, + implicit dependence of tensors on coordinates, partial and covariant + derivatives... + +* Powerful tensor simplification algorithms, not just for mono-term + symmetries but also for multi-terms symmetries like the Bianchi + identity, or dimensionally-dependent symmetries like the Schouten + identity. + +* Allows for both abstract and component computations. + +* 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). diff --git a/academic/cadabra2/cadabra2.SlackBuild b/academic/cadabra2/cadabra2.SlackBuild index 35083bc221..f6a618c3ff 100644 --- a/academic/cadabra2/cadabra2.SlackBuild +++ b/academic/cadabra2/cadabra2.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cadabra2 -# Copyright 2017-2018, Alexander Verbovetsky, Moscow, Russia +# Copyright 2017-2021, Alexander Verbovetsky, Moscow, Russia # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,9 +23,10 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=cadabra2 -VERSION=${VERSION:-2.2.0} +VERSION=${VERSION:-2.3.6.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +MMA=${MMA:-OFF} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -69,12 +70,6 @@ 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 {} \; -# workaround for https://github.com/kpeeters/cadabra2/issues/12 -# (caused by https://github.com/zaphoyd/websocketpp/issues/587) -sed --in-place \ - -e 's/listen(lib::asio::ip::tcp::v6(),/listen(lib::asio::ip::tcp::v4(),/' \ - client_server/websocketpp/websocketpp/transport/asio/endpoint.hpp - sed --in-place \ -e "s/\(DESTINATION lib\)/\1${LIBDIRSUFFIX}/" \ client_server/CMakeLists.txt @@ -91,13 +86,20 @@ sed --in-place \ -e '/^install(CODE\s\+"execute_process(COMMAND \(touch\|gtk-update-icon-cache.*\|chmod go+r\) ${ICON_PREFIX}\/share\/icons\/hicolor\(\|\/icon-theme\.cache\))")$/d' \ frontend/gtkmm/CMakeLists.txt +find ./ -type f -name '*.py' -exec \ + sed -i -e 's|#!/usr/bin/python\>|#!/usr/bin/python3|' \ + -e 's|#!/usr/bin/env python\>|#!/usr/bin/env python3|' {} \; + mkdir -p build cd build + export "PATH=/opt/cmake-202x/bin:$PATH" cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ - -DUSE_PYTHON_3=OFF \ + -DSQLITE3_INCLUDE_DIR=/usr/include \ + -DENABLE_SYSTEM_JSONCPP=ON \ + -DENABLE_MATHEMATICA=${MMA^^} \ -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG @@ -106,8 +108,13 @@ 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 +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 doc examples README.rst $PKG/usr/doc/$PRGNAM-$VERSION +cp -a contrib doc examples paper CONTRIBUTING.md JUPYTER.rst 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/cadabra2/cadabra2.info b/academic/cadabra2/cadabra2.info index 31eeb0a2ed..164ad63867 100644 --- a/academic/cadabra2/cadabra2.info +++ b/academic/cadabra2/cadabra2.info @@ -1,10 +1,10 @@ PRGNAM="cadabra2" -VERSION="2.2.0" +VERSION="2.3.6.3" HOMEPAGE="https://cadabra.science" -DOWNLOAD="https://downloads.sourceforge.net/slackbuildsdirectlinks/cadabra2/cadabra2-2.2.0.tar.gz" -MD5SUM="a6d2d94584a2b917a04df01e64b7a237" +DOWNLOAD="https://downloads.sourceforge.net/slackbuildsdirectlinks/cadabra2/cadabra2-2.3.6.3.tar.gz" +MD5SUM="9e792260d2b6dea2bb7c5d8a0a627662" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="python3-matplotlib python3-gmpy2 python3-sympy jsoncpp cmake-202x" MAINTAINER="Alexander Verbovetsky" EMAIL="alik@ejik.org" diff --git a/academic/cadabra2/slack-desc b/academic/cadabra2/slack-desc index ae9caa674d..913802570b 100644 --- a/academic/cadabra2/slack-desc +++ b/academic/cadabra2/slack-desc @@ -10,7 +10,7 @@ cadabra2: cadabra2 (a field-theory motivated approach to computer algebra) cadabra2: cadabra2: Cadabra is a symbolic computer algebra system designed specifically cadabra2: for the solution of problems encountered in field theory. The input -cadabra2: format is a subset of TeX. Programmable in Python. Both a +cadabra2: format is a subset of TeX. Programmable using Python. Both a cadabra2: command-line and a graphical interface are available. cadabra2: cadabra2: Homepage: https://cadabra.science diff --git a/academic/calc/calc.info b/academic/calc/calc.info index f252d3f5cc..a14bf23ea6 100644 --- a/academic/calc/calc.info +++ b/academic/calc/calc.info @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Dave Woodfall" -EMAIL="dave@tty1.uk" +EMAIL="dave@slackbuilds.org" diff --git a/academic/calcoo/README b/academic/calcoo/README index 5c4e7ef8c3..d9891857aa 100644 --- a/academic/calcoo/README +++ b/academic/calcoo/README @@ -1,4 +1,5 @@ -Calcoo is an RPN and scientific calculator that uses the GTK library. It -features both RPN and algebraic modes, bitmapped button labels and display -glyths, undo/redo options, copy/paste interaction with the X clipboard, two -memory registers with displays, and displays for Y, Z, and T registers. +Calcoo is an RPN and scientific calculator that uses the GTK library. +It features both RPN and algebraic modes, bitmapped button labels and +display glyths, undo/redo options, copy/paste interaction with the X +clipboard, two memory registers with displays, and displays for Y, Z, +and T registers. diff --git a/academic/camd/camd.SlackBuild b/academic/camd/camd.SlackBuild index a996709a40..b7253a1aba 100644 --- a/academic/camd/camd.SlackBuild +++ b/academic/camd/camd.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CAMD -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=camd SRCNAM=SuiteSparse SUBDIR=CAMD VERSION=${VERSION:-2.4.6} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-5} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/camd/camd.info b/academic/camd/camd.info index c805112e1a..a02b5c633d 100644 --- a/academic/camd/camd.info +++ b/academic/camd/camd.info @@ -1,8 +1,8 @@ PRGNAM="camd" VERSION="2.4.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/camd/patches/autoconfiscate.diff b/academic/camd/patches/autoconfiscate.diff index e06c348153..c29c93597e 100644 --- a/academic/camd/patches/autoconfiscate.diff +++ b/academic/camd/patches/autoconfiscate.diff @@ -156,7 +156,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([CAMD],[2.4.6],[DrTimothyAldenDavis@gmail.com],[camd],[http://www.suitesparse.com/]) ++AC_INIT([CAMD],[2.4.6],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[camd],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/camd_order.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/cap3/README b/academic/cap3/README index 62792bb4c7..bd6e1fb491 100644 --- a/academic/cap3/README +++ b/academic/cap3/README @@ -1,11 +1,12 @@ CAP3: A DNA sequence assembly program. CAP3 if the third generation of the CAP sequence assembly program. The -program has a capability to clip 5' and 3' low-quality regions of reads. -It uses base quality values in computation of overlaps between reads, -construction of multiple sequence alignments of reads, and generation -of consensus sequences. The program also uses forward-reverse constraints -to correct assembly errors and link contigs. +program has a capability to clip 5' and 3' low-quality regions +of reads. It uses base quality values in computation of overlaps +between reads, construction of multiple sequence alignments of +reads, and generation of consensus sequences. The program also uses +forward-reverse constraints to correct assembly errors and link +contigs. This just repackages the binaries provided from upstream. diff --git a/academic/cblas/README b/academic/cblas/README index 37cd0e0795..96f920457b 100644 --- a/academic/cblas/README +++ b/academic/cblas/README @@ -1,9 +1,10 @@ -CBLAS is a collection of wrappers that provide a C interface to the FORTRAN -BLAS library. The interface can be consulted by opening /usr/include/cblas.h +CBLAS is a collection of wrappers that provide a C interface to the +FORTRAN BLAS library. The interface can be consulted by opening +/usr/include/cblas.h -This package is intended for use with the Netlib reference BLAS. It should -also work with other BLAS implementations that do not already provide a CBLAS -implementation. +This package is intended for use with the Netlib reference BLAS. +It should also work with other BLAS implementations that do not +already provide a CBLAS implementation. To build a static library in addition to the shared library, pass STATIC=yes to the script. diff --git a/academic/cblas/cblas.SlackBuild b/academic/cblas/cblas.SlackBuild index c2e125fc17..3a18cc1daa 100644 --- a/academic/cblas/cblas.SlackBuild +++ b/academic/cblas/cblas.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CBLAS -# Copyright 2016-2017 Kyle Guinn <elyk03@gmail.com>, USA +# Copyright 2016-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,7 +24,7 @@ PRGNAM=cblas SRCNAM=lapack -VERSION=${VERSION:-3.8.0} +VERSION=${VERSION:-3.9.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -38,7 +38,7 @@ fi CWD=$(pwd) TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM +PKG=$TMP/package-$PRGNAM-$VERSION OUTPUT=${OUTPUT:-/tmp} DOCS="LICENSE CBLAS/README" diff --git a/academic/cblas/cblas.info b/academic/cblas/cblas.info index e6abee191c..7821e1a648 100644 --- a/academic/cblas/cblas.info +++ b/academic/cblas/cblas.info @@ -1,8 +1,8 @@ PRGNAM="cblas" -VERSION="3.8.0" -HOMEPAGE="http://www.netlib.org/blas/" -DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.8.0/lapack-3.8.0.tar.gz" -MD5SUM="96591affdbf58c450d45c1daa540dbd2" +VERSION="3.9.1" +HOMEPAGE="https://www.netlib.org/blas/" +DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.9.1/lapack-3.9.1.tar.gz" +MD5SUM="47ab2d11652045145df37ddbe2a32d71" 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 8c2ac6c6a3..378acc8769 100644 --- a/academic/cblas/patches/cmake-piecewise.diff +++ b/academic/cblas/patches/cmake-piecewise.diff @@ -5,25 +5,27 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt message(STATUS "CBLAS enable") enable_language(C) --set(LAPACK_INSTALL_EXPORT_NAME cblas-targets) +-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 -@@ -36,50 +34,8 @@ +@@ -45,54 +43,8 @@ add_subdirectory(examples) endif() -if(NOT BLAS_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} blas) +- set(ALL_TARGETS ${ALL_TARGETS} ${BLASLIB}) -endif() - -# Export cblas targets from the -# install tree, if any. -set(_cblas_config_install_guard_target "") -if(ALL_TARGETS) -- install(EXPORT cblas-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION}) +- install(EXPORT ${CBLASLIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${CBLASLIB}-${LAPACK_VERSION} +- COMPONENT Development +- ) - # Choose one of the cblas targets to use as a guard for - # cblas-config.cmake to load targets from the install tree. - list(GET ALL_TARGETS 0 _cblas_config_install_guard_target) @@ -32,7 +34,7 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt -# Export cblas targets from the build tree, if any. -set(_cblas_config_build_guard_target "") -if(ALL_TARGETS) -- export(TARGETS ${ALL_TARGETS} FILE cblas-targets.cmake) +- export(TARGETS ${ALL_TARGETS} FILE ${CBLASLIB}-targets.cmake) - - # Choose one of the cblas targets to use as a guard - # for cblas-config.cmake to load targets from the build tree. @@ -40,27 +42,29 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt -endif() - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-version.cmake.in -- ${LAPACK_BINARY_DIR}/cblas-config-version.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config-version.cmake @ONLY) -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config.cmake @ONLY) - - - configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY) + configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/${CBLASLIB}.pc @ONLY) install(FILES - ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc + ${CMAKE_CURRENT_BINARY_DIR}/${CBLASLIB}.pc DESTINATION ${PKG_CONFIG_DIR} ) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-install.cmake.in -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/cblas-config.cmake @ONLY) +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${CBLASLIB}-config.cmake @ONLY) -install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/cblas-config.cmake -- ${LAPACK_BINARY_DIR}/cblas-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION} +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${CBLASLIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${CBLASLIB}-${LAPACK_VERSION} - ) - --#install(EXPORT cblas-targets --# DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION}) +-#install(EXPORT ${CBLASLIB}-targets +-# DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${CBLASLIB}-${LAPACK_VERSION} +-# COMPONENT Development +-# ) diff --git a/CBLAS/cmake/cblas-config-build.cmake.in b/CBLAS/cmake/cblas-config-build.cmake.in deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-build.cmake.in @@ -72,14 +76,14 @@ deleted file mode 100644 - -# Load lapack targets from the build tree, including lapacke targets. -if(NOT TARGET lapacke) -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() - -# Report cblas header search locations from build tree. -set(CBLAS_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report cblas libraries. --set(CBLAS_LIBRARIES cblas) +-set(CBLAS_LIBRARIES @CBLASLIB@) diff --git a/CBLAS/cmake/cblas-config-install.cmake.in b/CBLAS/cmake/cblas-config-install.cmake.in deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-install.cmake.in @@ -92,19 +96,19 @@ deleted file mode 100644 -get_filename_component(_CBLAS_PREFIX "${_CBLAS_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_CBLAS_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/lapack-@LAPACK_VERSION@") +-set(LAPACK_DIR "${_CBLAS_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. --if(NOT TARGET cblas) -- include(${_CBLAS_SELF_DIR}/cblas-targets.cmake) +-if(NOT TARGET @CBLASLIB@) +- include(${_CBLAS_SELF_DIR}/@CBLASLIB@-targets.cmake) -endif() - -# Report lapacke header search locations. -set(CBLAS_INCLUDE_DIRS ${_CBLAS_PREFIX}/include) - -# Report lapacke libraries. --set(CBLAS_LIBRARIES cblas) +-set(CBLAS_LIBRARIES @CBLASLIB@) - -unset(_CBLAS_PREFIX) -unset(_CBLAS_SELF_DIR) @@ -124,67 +128,75 @@ 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 -@@ -120,9 +120,5 @@ - VERSION ${LAPACK_VERSION} - SOVERSION ${LAPACK_MAJOR_VERSION} - ) --target_include_directories(cblas PUBLIC +@@ -123,9 +123,5 @@ + if(HAS_ATTRIBUTE_WEAK_SUPPORT) + target_compile_definitions(${CBLASLIB} PRIVATE HAS_ATTRIBUTE_WEAK_SUPPORT) + endif() +-target_include_directories(${CBLASLIB} PUBLIC - $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../include> - $<INSTALL_INTERFACE:include> -) - target_link_libraries(cblas PRIVATE ${BLAS_LIBRARIES}) - lapack_install_library(cblas) + target_link_libraries(${CBLASLIB} PRIVATE ${BLAS_LIBRARIES}) + lapack_install_library(${CBLASLIB}) diff --git a/CMAKE/lapack-config-build.cmake.in b/CMAKE/lapack-config-build.cmake.in deleted file mode 100644 --- a/CMAKE/lapack-config-build.cmake.in +++ /dev/null -@@ -1,10 +0,0 @@ +@@ -1,14 +0,0 @@ -# Load lapack targets from the build tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_build_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - +-# Hint for project building against lapack +-set(LAPACK_Fortran_COMPILER_ID "@CMAKE_Fortran_COMPILER_ID@") +- -# Report the blas and lapack raw or imported libraries. -set(LAPACK_blas_LIBRARIES "@BLAS_LIBRARIES@") -set(LAPACK_lapack_LIBRARIES "@LAPACK_LIBRARIES@") +-set(LAPACK_LIBRARIES ${LAPACK_blas_LIBRARIES} ${LAPACK_lapack_LIBRARIES}) diff --git a/CMAKE/lapack-config-install.cmake.in b/CMAKE/lapack-config-install.cmake.in deleted file mode 100644 --- a/CMAKE/lapack-config-install.cmake.in +++ /dev/null -@@ -1,15 +0,0 @@ +@@ -1,19 +0,0 @@ -# Compute locations from <prefix>/lib/cmake/lapack-<v>/<self>.cmake -get_filename_component(_LAPACK_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) - -# Load lapack targets from the install tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_install_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("${_LAPACK_SELF_DIR}/lapack-targets.cmake") +- include("${_LAPACK_SELF_DIR}/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - +-# Hint for project building against lapack +-set(LAPACK_Fortran_COMPILER_ID "@CMAKE_Fortran_COMPILER_ID@") +- -# Report the blas and lapack raw or imported libraries. -set(LAPACK_blas_LIBRARIES "@BLAS_LIBRARIES@") -set(LAPACK_lapack_LIBRARIES "@LAPACK_LIBRARIES@") +-set(LAPACK_LIBRARIES ${LAPACK_blas_LIBRARIES} ${LAPACK_lapack_LIBRARIES}) - -unset(_LAPACK_SELF_DIR) diff --git a/CMakeLists.txt b/CMakeLists.txt --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -106,11 +106,8 @@ - endif() - # -------------------------------------------------- +@@ -160,11 +160,8 @@ --set(LAPACK_INSTALL_EXPORT_NAME lapack-targets) + + # -------------------------------------------------- +-set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKLIB}-targets) - macro(lapack_install_library lib) install(TARGETS ${lib} - EXPORT ${LAPACK_INSTALL_EXPORT_NAME} - ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} -@@ -139,21 +136,6 @@ + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Development + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT RuntimeLibraries + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT RuntimeLibraries +@@ -204,21 +201,6 @@ include(CheckLAPACKCompilerFlags) CheckLAPACKCompilerFlags() @@ -192,7 +204,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -# Check second function - -include(CheckTimeFunction) --set(TIME_FUNC NONE ${TIME_FUNC}) +-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) @@ -206,7 +218,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # deprecated LAPACK and LAPACKE routines option(BUILD_DEPRECATED "Build deprecated routines" OFF) message(STATUS "Build deprecated routines: ${BUILD_DEPRECATED}") -@@ -177,8 +159,9 @@ +@@ -242,8 +224,9 @@ endif() # -------------------------------------------------- @@ -217,7 +229,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided BLAS libraries if(BLAS_LIBRARIES) -@@ -189,213 +172,117 @@ +@@ -254,113 +237,108 @@ if(BLAS_FOUND) message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRARIES}.") else() @@ -238,7 +250,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt - message(STATUS "Using supplied NETLIB BLAS implementation") - add_subdirectory(BLAS) +elseif(BUILD_BLAS) - set(BLAS_LIBRARIES blas) + set(BLAS_LIBRARIES ${BLASLIB}) -else() - set(CMAKE_EXE_LINKER_FLAGS - "${CMAKE_EXE_LINKER_FLAGS} ${BLAS_LINKER_FLAGS}" @@ -314,14 +326,14 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + find_package(LAPACK) + +elseif(BUILD_LAPACK) - set(LAPACK_LIBRARIES lapack) + set(LAPACK_LIBRARIES ${LAPACKLIB}) + set(LAPACK_FOUND TRUE) + + set(NEED_BLAS TRUE) + + # Check second function + include(CheckTimeFunction) -+ set(TIME_FUNC NONE ${TIME_FUNC}) ++ set(NONE ${TIME_FUNC}) + CHECK_TIME_FUNCTION(NONE TIME_FUNC) + CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) + CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) @@ -351,10 +363,11 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + add_subdirectory(TESTING) + endif() + -+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) ++ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc @ONLY) + install(FILES -+ ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc ++ ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc + DESTINATION ${PKG_CONFIG_DIR} ++ COMPONENT Development + ) endif() @@ -380,16 +393,21 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt add_subdirectory(LAPACKE) endif() +@@ -414,111 +392,16 @@ + ExternalProject_Add_StepDependencies(lapackpp build blaspp ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) + endif() + -# -------------------------------------------------- -# CPACK Packaging - -set(CPACK_PACKAGE_NAME "LAPACK") -set(CPACK_PACKAGE_VENDOR "University of Tennessee, Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd") -set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "LAPACK- Linear Algebra Package") --set(CPACK_PACKAGE_VERSION_MAJOR 3) --set(CPACK_PACKAGE_VERSION_MINOR 5) --set(CPACK_PACKAGE_VERSION_PATCH 0) +-set(CPACK_PACKAGE_VERSION_MAJOR ${LAPACK_MAJOR_VERSION}) +-set(CPACK_PACKAGE_VERSION_MINOR ${LAPACK_MINOR_VERSION}) +-set(CPACK_PACKAGE_VERSION_PATCH ${LAPACK_PATCH_VERSION}) -set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE") +-set(CPACK_MONOLITHIC_INSTALL ON) -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 @@ -412,24 +430,26 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -# -------------------------------------------------- - -if(NOT BLAS_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} blas) +- set(ALL_TARGETS ${ALL_TARGETS} ${BLASLIB}) -endif() - -if(NOT LATESTLAPACK_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} lapack) +- set(ALL_TARGETS ${ALL_TARGETS} ${LAPACKLIB}) -endif() - -if(BUILD_TESTING OR LAPACKE_WITH_TMG) -- set(ALL_TARGETS ${ALL_TARGETS} tmglib) +- set(ALL_TARGETS ${ALL_TARGETS} ${TMGLIB}) -endif() - -# Export lapack targets, not including lapacke, from the -# install tree, if any. -set(_lapack_config_install_guard_target "") -if(ALL_TARGETS) -- install(EXPORT lapack-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapack-${LAPACK_VERSION}) - +- install(EXPORT ${LAPACKLIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKLIB}-${LAPACK_VERSION} +- COMPONENT Development +- ) +- - # Choose one of the lapack targets to use as a guard for - # lapack-config.cmake to load targets from the install tree. - list(GET ALL_TARGETS 0 _lapack_config_install_guard_target) @@ -437,12 +457,12 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt - -# Include cblas in targets exported from the build tree. -if(CBLAS) -- set(ALL_TARGETS ${ALL_TARGETS} cblas) +- set(ALL_TARGETS ${ALL_TARGETS} ${CBLASLIB}) -endif() - -# Include lapacke in targets exported from the build tree. -if(LAPACKE) -- set(ALL_TARGETS ${ALL_TARGETS} lapacke) +- set(ALL_TARGETS ${ALL_TARGETS} ${LAPACKELIB}) +# Neither user specified or optimized BLAS libraries can be used +if(NEED_BLAS AND NOT BLAS_FOUND) + message(FATAL_ERROR "--> No BLAS library found. Specify BLAS_LIBRARIES or enable USE_OPTIMIZED_BLAS or BUILD_BLAS.") @@ -451,7 +471,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -# Export lapack and lapacke targets from the build tree, if any. -set(_lapack_config_build_guard_target "") -if(ALL_TARGETS) -- export(TARGETS ${ALL_TARGETS} FILE lapack-targets.cmake) +- export(TARGETS ${ALL_TARGETS} FILE ${LAPACKLIB}-targets.cmake) - - # Choose one of the lapack or lapacke targets to use as a guard - # for lapack-config.cmake to load targets from the build tree. @@ -460,32 +480,37 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt +if(NEED_LAPACK AND NOT LAPACK_FOUND) + message(FATAL_ERROR "--> No LAPACK library found. Specify LAPACK_LIBRARIES or enable USE_OPTIMIZED_LAPACK or BUILD_LAPACK.") endif() -- + -configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config.cmake @ONLY) - - --configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc @ONLY) - install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc +- ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc - DESTINATION ${PKG_CONFIG_DIR} +- COMPONENT Development - ) - -configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-install.cmake.in -- ${LAPACK_BINARY_DIR}/CMakeFiles/lapack-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/CMakeFiles/${LAPACKLIB}-config.cmake @ONLY) - -include(CMakePackageConfigHelpers) -write_basic_package_version_file( -- ${LAPACK_BINARY_DIR}/lapack-config-version.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config-version.cmake - VERSION ${LAPACK_VERSION} - COMPATIBILITY SameMajorVersion - ) - -install(FILES -- ${LAPACK_BINARY_DIR}/CMakeFiles/lapack-config.cmake -- ${LAPACK_BINARY_DIR}/lapack-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapack-${LAPACK_VERSION} +- ${LAPACK_BINARY_DIR}/CMakeFiles/${LAPACKLIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKLIB}-${LAPACK_VERSION} +- COMPONENT Development - ) + if (LAPACK++) + install( + DIRECTORY "${LAPACK_BINARY_DIR}/lib/" diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt --- a/LAPACKE/CMakeLists.txt +++ b/LAPACKE/CMakeLists.txt @@ -493,66 +518,76 @@ diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt message(STATUS "LAPACKE enable") enable_language(C) --set(LAPACK_INSTALL_EXPORT_NAME lapacke-targets) +-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 -@@ -60,10 +58,6 @@ +@@ -79,14 +77,6 @@ VERSION ${LAPACK_VERSION} SOVERSION ${LAPACK_MAJOR_VERSION} ) --target_include_directories(lapacke PUBLIC -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../include> +-target_include_directories(${LAPACKELIB} PUBLIC +- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> - $<INSTALL_INTERFACE:include> -) +-if(WIN32 AND NOT UNIX) +- target_compile_definitions(${LAPACKELIB} PUBLIC HAVE_LAPACK_CONFIG_H LAPACK_COMPLEX_STRUCTURE) +- message(STATUS "Windows BUILD") +-endif() if(LAPACKE_WITH_TMG) - target_link_libraries(lapacke PRIVATE tmglib) -@@ -83,19 +77,3 @@ - ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc + target_link_libraries(${LAPACKELIB} PRIVATE ${TMGLIB}) +@@ -111,22 +101,3 @@ DESTINATION ${PKG_CONFIG_DIR} + COMPONENT Development ) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-version.cmake.in -- ${LAPACK_BINARY_DIR}/lapacke-config-version.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config-version.cmake @ONLY) -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/lapacke-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config.cmake @ONLY) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-install.cmake.in -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/lapacke-config.cmake @ONLY) +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LAPACKELIB}-config.cmake @ONLY) -install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/lapacke-config.cmake -- ${LAPACK_BINARY_DIR}/lapacke-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapacke-${LAPACK_VERSION} +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LAPACKELIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKELIB}-${LAPACK_VERSION} +- COMPONENT Development - ) - --install(EXPORT lapacke-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapacke-${LAPACK_VERSION}) +-install(EXPORT ${LAPACKELIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKELIB}-${LAPACK_VERSION} +- COMPONENT Development +- ) diff --git a/LAPACKE/cmake/lapacke-config-build.cmake.in b/LAPACKE/cmake/lapacke-config-build.cmake.in deleted file mode 100644 --- a/LAPACKE/cmake/lapacke-config-build.cmake.in +++ /dev/null -@@ -1,14 +0,0 @@ +@@ -1,17 +0,0 @@ -# Load the LAPACK package with which we were built. -set(LAPACK_DIR "@LAPACK_BINARY_DIR@") -find_package(LAPACK NO_MODULE) - -# Load lapack targets from the build tree, including lapacke targets. --if(NOT TARGET lapacke) -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +-if(NOT TARGET @LAPACKELIB@) +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() - +-# Hint for project building against lapack +-set(LAPACKE_Fortran_COMPILER_ID ${LAPACK_Fortran_COMPILER_ID}) +- -# Report lapacke header search locations from build tree. -set(LAPACKE_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) diff --git a/LAPACKE/cmake/lapacke-config-install.cmake.in b/LAPACKE/cmake/lapacke-config-install.cmake.in deleted file mode 100644 --- a/LAPACKE/cmake/lapacke-config-install.cmake.in +++ /dev/null -@@ -1,23 +0,0 @@ +@@ -1,26 +0,0 @@ -# Compute locations from <prefix>/@{LIBRARY_DIR@/cmake/lapacke-<v>/<self>.cmake -get_filename_component(_LAPACKE_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) -get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_SELF_DIR}" PATH) @@ -560,19 +595,22 @@ deleted file mode 100644 -get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_LAPACKE_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/lapack-@LAPACK_VERSION@") +-set(LAPACK_DIR "${_LAPACKE_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/@LAPACK@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. --if(NOT TARGET lapacke) -- include(${_LAPACKE_SELF_DIR}/lapacke-targets.cmake) +-if(NOT TARGET @LAPACKELIB@) +- include(${_LAPACKE_SELF_DIR}/@LAPACKELIB@-targets.cmake) -endif() - +-# Hint for project building against lapack +-set(LAPACKE_Fortran_COMPILER_ID ${LAPACK_Fortran_COMPILER_ID}) +- -# Report lapacke header search locations. -set(LAPACKE_INCLUDE_DIRS ${_LAPACKE_PREFIX}/include) - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) - -unset(_LAPACKE_PREFIX) -unset(_LAPACKE_SELF_DIR) diff --git a/academic/ccolamd/ccolamd.SlackBuild b/academic/ccolamd/ccolamd.SlackBuild index 0a8c854d2a..7a76de236b 100644 --- a/academic/ccolamd/ccolamd.SlackBuild +++ b/academic/ccolamd/ccolamd.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CCOLAMD -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=ccolamd SRCNAM=SuiteSparse SUBDIR=CCOLAMD VERSION=${VERSION:-2.9.6} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-5} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/ccolamd/ccolamd.info b/academic/ccolamd/ccolamd.info index da03a91af2..a7d008e0e5 100644 --- a/academic/ccolamd/ccolamd.info +++ b/academic/ccolamd/ccolamd.info @@ -1,8 +1,8 @@ PRGNAM="ccolamd" VERSION="2.9.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/ccolamd/patches/autoconfiscate.diff b/academic/ccolamd/patches/autoconfiscate.diff index d9cb98c357..54113bd55b 100644 --- a/academic/ccolamd/patches/autoconfiscate.diff +++ b/academic/ccolamd/patches/autoconfiscate.diff @@ -106,7 +106,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([CCOLAMD],[2.9.6],[DrTimothyAldenDavis@gmail.com],[ccolamd],[http://www.suitesparse.com/]) ++AC_INIT([CCOLAMD],[2.9.6],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[ccolamd],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/ccolamd.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/cdo/README b/academic/cdo/README new file mode 100644 index 0000000000..e767d4ea31 --- /dev/null +++ b/academic/cdo/README @@ -0,0 +1,7 @@ +CDO (Climate Data Operators) + +CDO is a collection of command line Operators to manipulate and analyse +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. diff --git a/academic/cdo/cdo.SlackBuild b/academic/cdo/cdo.SlackBuild new file mode 100644 index 0000000000..9aef1c9fdb --- /dev/null +++ b/academic/cdo/cdo.SlackBuild @@ -0,0 +1,108 @@ +#!/bin/sh + +# Slackware build script for cdo + +# Copyright 2020 Gregory J. L. Tourte <artourter@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. + +PRGNAM=cdo +VERSION=${VERSION:-1.9.10} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 {} \; + +# static. +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --with-szlib=yes \ + --with-netcdf=yes \ + --with-hdf5=yes \ + --with-udunits2 \ + --with-threads=yes \ + --disable-static \ + --with-fftw3 \ + --with-proj \ + --with-curl \ + --with-libxml2 \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS COPYING ChangeLog INSTALL NEWS OPERATORS README \ + doc/*.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 + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/cdo/cdo.info b/academic/cdo/cdo.info new file mode 100644 index 0000000000..74453e1a40 --- /dev/null +++ b/academic/cdo/cdo.info @@ -0,0 +1,10 @@ +PRGNAM="cdo" +VERSION="1.9.10" +HOMEPAGE="https://code.mpimet.mpg.de/projects/cdo" +DOWNLOAD="https://code.mpimet.mpg.de/attachments/download/24638/cdo-1.9.10.tar.gz" +MD5SUM="dc2bd3f30ae923bac367e370270051d9" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="proj udunits netcdf" +MAINTAINER="Greg Tourte" +EMAIL="artourter@gmail.com" diff --git a/academic/cdo/slack-desc b/academic/cdo/slack-desc new file mode 100644 index 0000000000..49f7b868c9 --- /dev/null +++ b/academic/cdo/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------------------------------------------------------| +cdo: cdo (Climate Data Operators) +cdo: +cdo: CDO is a collection of command line Operators to manipulate and +cdo: analyse Climate and NWP model Data. +cdo: +cdo: Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and +cdo: IEG. There are more than 600 operators available. +cdo: +cdo: +cdo: +cdo: diff --git a/academic/chartgeany/README b/academic/chartgeany/README new file mode 100644 index 0000000000..0b49fa40f0 --- /dev/null +++ b/academic/chartgeany/README @@ -0,0 +1,6 @@ +Chart Geany is a cross platform software solution for market technical +analysis and charting. + +Optional: qt5 + +QT5GUI=yes ./chartgeany.SlackBuild diff --git a/academic/chartgeany/chartgeany.SlackBuild b/academic/chartgeany/chartgeany.SlackBuild new file mode 100644 index 0000000000..7c9da765d8 --- /dev/null +++ b/academic/chartgeany/chartgeany.SlackBuild @@ -0,0 +1,106 @@ +#!/bin/sh + +# Slackware build script for chartgeany + +# Copyright 2020 Larry Hajali <larryhaja[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. + +PRGNAM=chartgeany +VERSION=${VERSION:-6.1.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 file locaations. +sed -i '/^target.path/s|= /opt/$$PKG_NAME|= /usr/bin|' \ + ChartGeany/ChartGeany.pro cgtool/cgtool.pro +sed -i '/^images.path/s|= /opt/$$PKG_NAME|= /usr/share/pixmaps|' \ + ChartGeany/ChartGeany.pro +sed -i "s|/opt/$PRGNAM/||" ChartGeany/chartgeany.desktop + +if [ "${QT5GUI:-no}" == "yes" ]; then + qmake-qt5 PREFIX="/usr" QMAKE_CFLAGS+="$SLKCFLAGS" QMAKE_CXXFLAGS+="$SLKCFLAGS" \ + -o Makefile $PRGNAM.pro +else + qmake PREFIX="/usr" QMAKE_CFLAGS+="$SLKCFLAGS" QMAKE_CXXFLAGS+="$SLKCFLAGS" \ + -o Makefile $PRGNAM.pro +fi + +make +make install INSTALL_ROOT=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +chmod 0644 $PKG/usr/share/applications/$PRGNAM.desktop + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + COPYING Changelog \ + $PKG/usr/doc/$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:-tgz} diff --git a/academic/chartgeany/chartgeany.info b/academic/chartgeany/chartgeany.info new file mode 100644 index 0000000000..83d6be57c8 --- /dev/null +++ b/academic/chartgeany/chartgeany.info @@ -0,0 +1,10 @@ +PRGNAM="chartgeany" +VERSION="6.1.5" +HOMEPAGE="https://sourceforge.net/projects/chart-geany/" +DOWNLOAD="https://downloads.sourceforge.net/chart-geany/chartgeany-6.1.5.tar.gz" +MD5SUM="c2f0acdc7025de66ff6cbcba65212751" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="libxls" +MAINTAINER="Larry Hajali" +EMAIL="larryhaja[at]gmail[dot]com" diff --git a/academic/chartgeany/doinst.sh b/academic/chartgeany/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/chartgeany/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/chartgeany/slack-desc b/academic/chartgeany/slack-desc new file mode 100644 index 0000000000..cb4c4a3b5c --- /dev/null +++ b/academic/chartgeany/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------------------------------------------------------| +chartgeany: chartgeany (market analysis tool) +chartgeany: +chartgeany: Chart Geany is a cross platform software solution for market technical +chartgeany: analysis and charting. +chartgeany: +chartgeany: Homepage: https://sourceforge.net/projects/chart-geany/ +chartgeany: +chartgeany: +chartgeany: +chartgeany: +chartgeany: diff --git a/academic/cholmod/README b/academic/cholmod/README index 46350dc390..f91a13d263 100644 --- a/academic/cholmod/README +++ b/academic/cholmod/README @@ -1,16 +1,18 @@ -CHOLMOD is a set of ANSI C routines for sparse Cholesky factorization and -update/downdate. +CHOLMOD is a set of ANSI C routines for sparse Cholesky factorization +and update/downdate. This package is part of SuiteSparse. -This requires a BLAS/LAPACK implementation. Choose one of these package sets: +This requires a BLAS/LAPACK implementation. Choose one of these +package sets: * OpenBLAS (includes both a BLAS and a LAPACK implementation) * atlas (includes both a BLAS and a LAPACK implementation) * blas, lapack (the Netlib reference implementations) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib +reference implementations; other packages that require a BLAS or +LAPACK implementation may not build if they are not configured to +detect/use alternate implementations. metis is an optional dependency and will be used if found. diff --git a/academic/cholmod/cholmod.SlackBuild b/academic/cholmod/cholmod.SlackBuild index 2116fba3e4..5ac8ce8cf7 100644 --- a/academic/cholmod/cholmod.SlackBuild +++ b/academic/cholmod/cholmod.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CHOLMOD -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,8 +25,8 @@ PRGNAM=cholmod SRCNAM=SuiteSparse SUBDIR=CHOLMOD -VERSION=${VERSION:-3.0.13} -SRCVER=${SRCVER:-5.4.0} +VERSION=${VERSION:-3.0.14} +SRCVER=${SRCVER:-5.8.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/cholmod/cholmod.info b/academic/cholmod/cholmod.info index 954e244269..ddaabdec00 100644 --- a/academic/cholmod/cholmod.info +++ b/academic/cholmod/cholmod.info @@ -1,8 +1,8 @@ PRGNAM="cholmod" -VERSION="3.0.13" +VERSION="3.0.14" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="blas lapack suitesparseconfig amd camd colamd ccolamd" diff --git a/academic/cholmod/patches/autoconfiscate.diff b/academic/cholmod/patches/autoconfiscate.diff index 66a831b846..36736536c4 100644 --- a/academic/cholmod/patches/autoconfiscate.diff +++ b/academic/cholmod/patches/autoconfiscate.diff @@ -1469,7 +1469,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([CHOLMOD],[3.0.13],[DrTimothyAldenDavis@gmail.com],[cholmod],[http://www.suitesparse.com/]) ++AC_INIT([CHOLMOD],[3.0.14],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[cholmod],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Core/cholmod_common.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) @@ -1690,7 +1690,7 @@ diff --git a/m4/ax_blas.m4 b/m4/ax_blas.m4 new file mode 100644 --- /dev/null +++ b/m4/ax_blas.m4 -@@ -0,0 +1,238 @@ +@@ -0,0 +1,241 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_blas.html +# =========================================================================== @@ -1729,6 +1729,7 @@ new file mode 100644 +# LICENSE +# +# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2019 Geoffrey M. Oxberry <goxberry@gmail.com> +# +# 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 @@ -1756,7 +1757,7 @@ new file mode 100644 +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + -+#serial 16 ++#serial 17 + +AU_ALIAS([ACX_BLAS], [AX_BLAS]) +AC_DEFUN([AX_BLAS], [ @@ -1770,7 +1771,9 @@ new file mode 100644 +case $with_blas in + yes | "") ;; + no) ax_blas_ok=disable ;; -+ -* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;; ++ -* | */* | *.a | *.so | *.so.* | *.dylib | *.dylib.* | *.o) ++ BLAS_LIBS="$with_blas" ++ ;; + *) BLAS_LIBS="-l$with_blas" ;; +esac + @@ -2209,7 +2212,7 @@ diff --git a/m4/ax_lapack.m4 b/m4/ax_lapack.m4 new file mode 100644 --- /dev/null +++ b/m4/ax_lapack.m4 -@@ -0,0 +1,131 @@ +@@ -0,0 +1,134 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_lapack.html +# =========================================================================== @@ -2249,6 +2252,7 @@ new file mode 100644 +# LICENSE +# +# Copyright (c) 2009 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2019 Geoffrey M. Oxberry <goxberry@gmail.com> +# +# 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 @@ -2276,7 +2280,7 @@ new file mode 100644 +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + -+#serial 9 ++#serial 10 + +AU_ALIAS([ACX_LAPACK], [AX_LAPACK]) +AC_DEFUN([AX_LAPACK], [ @@ -2288,7 +2292,9 @@ new file mode 100644 +case $with_lapack in + yes | "") ;; + no) ax_lapack_ok=disable ;; -+ -* | */* | *.a | *.so | *.so.* | *.o) LAPACK_LIBS="$with_lapack" ;; ++ -* | */* | *.a | *.so | *.so.* | *.dylib | *.dylib.* | *.o) ++ LAPACK_LIBS="$with_lapack" ++ ;; + *) LAPACK_LIBS="-l$with_lapack" ;; +esac + diff --git a/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild b/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild index b4bafb5928..3e0270e266 100644 --- a/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild +++ b/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cistrome-CEAS -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,14 +24,14 @@ PRGNAM=cistrome-CEAS VERSION=${VERSION:-1.0.2} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} SRCNAM=CEAS-Package if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -42,8 +42,8 @@ TMP=${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/cistrome-CEAS/cistrome-CEAS.info b/academic/cistrome-CEAS/cistrome-CEAS.info index cb11446bc0..0a2f1c8ced 100644 --- a/academic/cistrome-CEAS/cistrome-CEAS.info +++ b/academic/cistrome-CEAS/cistrome-CEAS.info @@ -1,7 +1,7 @@ PRGNAM="cistrome-CEAS" VERSION="1.0.2" -HOMEPAGE="http://liulab.dfci.harvard.edu/CEAS/" -DOWNLOAD="http://liulab.dfci.harvard.edu/CEAS/src/CEAS-Package-1.0.2.tar.gz" +HOMEPAGE="https://github.com/taoliu/" +DOWNLOAD="http://slackware.uk/sbosrcarch/by-name/academic/cistrome-CEAS/CEAS-Package-1.0.2.tar.gz" MD5SUM="faf202ff613794ab9cd07f282c6e2663" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/cistrome-MACS/cistrome-MACS.SlackBuild b/academic/cistrome-MACS/cistrome-MACS.SlackBuild index 9711808365..ad93aefcdf 100644 --- a/academic/cistrome-MACS/cistrome-MACS.SlackBuild +++ b/academic/cistrome-MACS/cistrome-MACS.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cistrome-MACS -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,7 +24,7 @@ PRGNAM=cistrome-MACS VERSION=${VERSION:-1.4.2} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} SRCNAM=MACS @@ -32,7 +32,7 @@ SRCVER=1.4.2-1 if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -43,8 +43,8 @@ TMP=${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/cistrome-MACS/cistrome-MACS.info b/academic/cistrome-MACS/cistrome-MACS.info index e5f0b603c3..02eb7b8547 100644 --- a/academic/cistrome-MACS/cistrome-MACS.info +++ b/academic/cistrome-MACS/cistrome-MACS.info @@ -1,6 +1,6 @@ PRGNAM="cistrome-MACS" VERSION="1.4.2" -HOMEPAGE="http://liulab.dfci.harvard.edu/MACS/" +HOMEPAGE="https://github.com/taoliu/MACS/" DOWNLOAD="https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz" MD5SUM="950dab09fe1335c8bbb34a896c21e3e2" DOWNLOAD_x86_64="" diff --git a/academic/clark-ugene/clark-ugene.SlackBuild b/academic/clark-ugene/clark-ugene.SlackBuild index bd2a8e55c1..6fd7166595 100644 --- a/academic/clark-ugene/clark-ugene.SlackBuild +++ b/academic/clark-ugene/clark-ugene.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for clark-ugene -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2019 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -SRCNAM=clark -PRGNAM=${SRCNAM}-ugene -VERSION=${VERSION:-git_23801a2} -COMMIT=${COMMIT:-23801a2738b7c104c8a7a1402d50d94fb5b4036b} +PRGNAM=clark-ugene +VERSION=${VERSION:-git_6917bf9} +COMMIT=${COMMIT:-6917bf93df9a8c2b80155db367f6672c1b143d9b} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +SRCNAM=clark + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; diff --git a/academic/clark-ugene/clark-ugene.info b/academic/clark-ugene/clark-ugene.info index 3e139342eb..3062990673 100644 --- a/academic/clark-ugene/clark-ugene.info +++ b/academic/clark-ugene/clark-ugene.info @@ -1,10 +1,10 @@ PRGNAM="clark-ugene" -VERSION="git_23801a2" +VERSION="git_6917bf9" HOMEPAGE="https://github.com/ugeneunipro/clark" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://github.com/ugeneunipro/clark/archive/23801a2/clark-23801a2738b7c104c8a7a1402d50d94fb5b4036b.tar.gz" -MD5SUM_x86_64="f73ffa62e4ae6241f07d4d9fc814b455" +DOWNLOAD_x86_64="https://github.com/ugeneunipro/clark/archive/6917bf9/clark-6917bf93df9a8c2b80155db367f6672c1b143d9b.tar.gz" +MD5SUM_x86_64="c777c1ec34816c145bcd0a40b72cb69b" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/cld2/README b/academic/cld2/README index 164357bf4f..d7d86bd3d4 100644 --- a/academic/cld2/README +++ b/academic/cld2/README @@ -1,9 +1,11 @@ -The Compact Language Detection library can detect the language of UTF8-encoded -text. CLD2 supports over 160 languages and can parse both plain text and HTML. +The Compact Language Detection library can detect the language of +UTF8-encoded text. CLD2 supports over 160 languages and can parse both +plain text and HTML. -The Slackware script builds two shared libraries, libcld2 and libcld2_full. The -libcld2 library can recognise the core 83 languages while the libcld2_full -library has support for the entire set of 160+ language tables. +The Slackware script builds two shared libraries, libcld2 and +libcld2_full. The libcld2 library can recognise the core 83 languages +while the libcld2_full library has support for the entire set of 160+ +language tables. -The script also builds a commandline tool, cld2, which is compiled against the -libcld2_full library. +The script also builds a commandline tool, cld2, which is compiled +against the libcld2_full library. diff --git a/academic/colamd/colamd.SlackBuild b/academic/colamd/colamd.SlackBuild index cc655f2cbf..3d2ceacd5a 100644 --- a/academic/colamd/colamd.SlackBuild +++ b/academic/colamd/colamd.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for COLAMD -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=colamd SRCNAM=SuiteSparse SUBDIR=COLAMD VERSION=${VERSION:-2.9.6} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-5} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/colamd/colamd.info b/academic/colamd/colamd.info index a948c27527..132c96f5d0 100644 --- a/academic/colamd/colamd.info +++ b/academic/colamd/colamd.info @@ -1,8 +1,8 @@ PRGNAM="colamd" VERSION="2.9.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/colamd/patches/autoconfiscate.diff b/academic/colamd/patches/autoconfiscate.diff index 92149cb951..3db5efd492 100644 --- a/academic/colamd/patches/autoconfiscate.diff +++ b/academic/colamd/patches/autoconfiscate.diff @@ -106,7 +106,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([COLAMD],[2.9.6],[DrTimothyAldenDavis@gmail.com],[colamd],[http://www.suitesparse.com/]) ++AC_INIT([COLAMD],[2.9.6],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[colamd],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/colamd.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/colin/README b/academic/colin/README new file mode 100644 index 0000000000..7b913061cc --- /dev/null +++ b/academic/colin/README @@ -0,0 +1,5 @@ +colin (a structural analysis application) + +Colin is a structural analysis application with a lightweight +interface. This software for civil engineering students provides an +easier way to learn civil engineering. diff --git a/academic/colin/colin.SlackBuild b/academic/colin/colin.SlackBuild new file mode 100644 index 0000000000..487197cf4d --- /dev/null +++ b/academic/colin/colin.SlackBuild @@ -0,0 +1,93 @@ +#!/bin/sh + +# SlackBuild build script for colin + +# Copyright (c) 2000-2020 Prof. Horstmann <wmh (at) eipg.fr> +# 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. + +PRGNAM=colin +VERSION=${VERSION:-1.8.2} +BUILD=${BUILD:-2} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ "$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 + +CWD=$(pwd) +TMP=${TMP:-/tmp} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.?z* +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -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 {} \; + +qmake +make + +# make install DESTDIR not implemented so go manual ! +install -Dm 0644 xdg/colin.desktop $PKG/usr/share/applications/colin.desktop +install -Dm 0644 xdg/colin.xpm $PKG/usr/share/colin/pixmaps/colin.xpm +install -Dm 0644 xdg/colin.png $PKG/usr/share/colin/pixmaps/colin.png +cp -a icons $PKG/usr/share/colin/ +install -Dm 0755 colin $PKG/usr/bin/colin + +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 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:-tgz} diff --git a/academic/colin/colin.info b/academic/colin/colin.info new file mode 100644 index 0000000000..39bcb740ad --- /dev/null +++ b/academic/colin/colin.info @@ -0,0 +1,10 @@ +PRGNAM="colin" +VERSION="1.8.2" +HOMEPAGE="https://sourceforge.net/projects/colin2" +DOWNLOAD="https://sourceforge.net/projects/colin2/files/colin-1.8.2.tar.xz" +MD5SUM="e7260f262dbc563b40b6de529d6aa519" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="brotli graphite2" +MAINTAINER="Prof. HORSTMANN" +EMAIL="wmh@eipg.fr" diff --git a/academic/colin/slack-desc b/academic/colin/slack-desc new file mode 100644 index 0000000000..73ce0befc5 --- /dev/null +++ b/academic/colin/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------------------------------------------------------| +colin: colin (a structural analysis application) +colin: +colin: Colin is a structural analysis application with a lightweight +colin: interface. This structural analysis software for civil engineering +colin: students, provide an easier way to learn civil engineering. +colin: +colin: Some tutorials (in German) can be found on youtube.com: +colin: http://www.youtube.com/user/ognop42 +colin: +colin: By Prof. Horstmann www.eipg.fr <wmh (at) eipg.fr> +colin: diff --git a/academic/convertall/README b/academic/convertall/README index f0cf40819c..9739c0472c 100644 --- a/academic/convertall/README +++ b/academic/convertall/README @@ -1,7 +1,6 @@ ConvertAll (unit conversion) -With ConvertAll, you can convert units as necessary, or combine any units any -way you want. If you want to convert from inches per decade, that's fine. Or -from meter-pounds. Or from cubic nautical miles. The units don't have to make -sense to anyone else. - +With ConvertAll, you can convert units as necessary, or combine any +units any way you want. If you want to convert from inches per decade, +that's fine. Or from meter-pounds. Or from cubic nautical miles. The +units don't have to make sense to anyone else. diff --git a/academic/convertall/convertall.SlackBuild b/academic/convertall/convertall.SlackBuild index 796ea42d07..fdb395cf6c 100644 --- a/academic/convertall/convertall.SlackBuild +++ b/academic/convertall/convertall.SlackBuild @@ -2,10 +2,12 @@ # # Slackware build script for convertall # -# Copyright 2012 John Berger <irgunii ampersand gmail . com>, TN, USA +# Copyright 2012-2021 John Berger <irgunii ampersand gmail . com>, TN, USA # I couldn't have made this script work without the help of -# Willy Sudiarto Raharjo <willysr@slackware-id.org>, so -# all thanks go to him. +# Willy Sudiarto Raharjo <willysr@slackware-id.org>, so big thanks to him. +# Also a big thank you to Kevin McCormick for helping with a python 3 +# problem I'd missed. +# # # All rights reserved. # @@ -28,13 +30,13 @@ PRGNAM=convertall SRCNAM=ConvertAll -VERSION=${VERSION:-0.5.2} +VERSION=${VERSION:-0.8.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -45,8 +47,8 @@ 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 [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -77,7 +79,7 @@ find -L . \ # Change installation directory to /usr and use LIBDIRSUFFIX sed -i -e "s/usr\/local/usr/" -e "s/'lib'/'lib$LIBDIRSUFFIX'/" install.py -python install.py -b $PKG +python3 install.py -b $PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/convertall/convertall.info b/academic/convertall/convertall.info index 38fc747b7f..181b2b33f8 100644 --- a/academic/convertall/convertall.info +++ b/academic/convertall/convertall.info @@ -1,10 +1,10 @@ PRGNAM="convertall" -VERSION="0.5.2" -HOMEPAGE="http://www.convertall.bellz.org/index.html" -DOWNLOAD="http://downloads.sourceforge.net/convertall/convertall-0.5.2.tar.gz" -MD5SUM="9378cb3ab40cf944570d53bcc5718ee8" +VERSION="0.8.0" +HOMEPAGE="https://www.convertall.bellz.org/index.html" +DOWNLOAD="https://github.com/doug-101/ConvertAll/releases/download/v0.8.0/convertall-0.8.0.tar.gz" +MD5SUM="6e2513d056bc10e2f037591bc08a8e21" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="python3 qt5 python3-PyQt5" MAINTAINER="John Berger" EMAIL="irgunii ampersand gmail . com" diff --git a/academic/convertall/doinst.sh b/academic/convertall/doinst.sh index 4f83cde390..7443749d1c 100644 --- a/academic/convertall/doinst.sh +++ b/academic/convertall/doinst.sh @@ -9,6 +9,6 @@ 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 + /usr/bin/gtk-update-icon-cache usr/share/icons/hicolor >/dev/null 2>&1 fi fi diff --git a/academic/convertall/slack-desc b/academic/convertall/slack-desc index 7f4ae4d1c2..59999208c7 100644 --- a/academic/convertall/slack-desc +++ b/academic/convertall/slack-desc @@ -1,9 +1,9 @@ # 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. +# The "handy ruler" below makes it easier to edit a package description. Line +# up the first '|' above the ':' following the base package name, and the '|' +# on the right side marks the last column you can put a character in. You must +# make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':'. |-----handy-ruler------------------------------------------------------| convertall: convertall (unit conversion) @@ -14,6 +14,6 @@ convertall: decade, that's fine. Or from meter-pounds. Or from cubic convertall: nautical miles. The units don't have to make sense to convertall: anyone but you. convertall: -convertall: Project website: http://www.convertall.bellz.org +convertall: Project website: https://www.convertall.bellz.org convertall: convertall: diff --git a/academic/copasi/README b/academic/copasi/README index 4da8b74120..c640a01c87 100644 --- a/academic/copasi/README +++ b/academic/copasi/README @@ -12,6 +12,6 @@ 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 at Virginia Tech, University of Heidelberg, University of -Connecticut, and previously the University of Manchester and the -EML-Research. +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 7eba36c7fe..ea41da828c 100644 --- a/academic/copasi/copasi.SlackBuild +++ b/academic/copasi/copasi.SlackBuild @@ -23,14 +23,25 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=copasi -VERSION=${VERSION:-4.24.197} +VERSION=${VERSION:-4.28.226} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -case "$(uname -m)" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$(uname -m) ;; +if [ -z "$ARCH" ]; then + ARCH="$(uname -m)" +fi + +case "$ARCH" in + i?86) + BINNAME="Linux-32bit" + ;; + x86_64) + BINNAME="Linux-64bit" + ;; + *) + echo "$ARCH is not supported by the $PRGNAM build script..." + exit 1 + ;; esac CWD=$(pwd) @@ -38,15 +49,6 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i586" ]; then - BINNAME="Linux-32bit" -elif [ "$ARCH" = "x86_64" ]; then - BINNAME="Linux-64bit" -else - echo "$ARCH is not supported by the $PRGNAM build script..." - exit 1 -fi - # This is a repackage of a binary distribution # CFLAGS are not required diff --git a/academic/copasi/copasi.info b/academic/copasi/copasi.info index d11dd46eb0..93b7729f70 100644 --- a/academic/copasi/copasi.info +++ b/academic/copasi/copasi.info @@ -1,10 +1,10 @@ PRGNAM="copasi" -VERSION="4.24.197" -HOMEPAGE="http://www.copasi.org" -DOWNLOAD="https://github.com/copasi/COPASI/releases/download/Build-197/COPASI-4.24.197-Linux-32bit.tar.gz" -MD5SUM="5169246bbcf0d143d56e758ccc8583bc" -DOWNLOAD_x86_64="https://github.com/copasi/COPASI/releases/download/Build-197/COPASI-4.24.197-Linux-64bit.tar.gz" -MD5SUM_x86_64="1ff24812793b94240fe1ae24dd20fad1" +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" REQUIRES="" MAINTAINER="Pedro Mendes" EMAIL="pedro@gepasi.org" diff --git a/academic/coq/README b/academic/coq/README index 81ec48f0d6..e21de9a5fa 100644 --- a/academic/coq/README +++ b/academic/coq/README @@ -1,14 +1,7 @@ -Coq implements a program specification and mathematical higher-level -language called Gallina that is based on an expressive formal language -called the Calculus of Inductive Constructions that itself combines both -a higher-order logic and a richly-typed functional programming language. +coq is a formal proof management system. It provides a formal language +to write mathematical definitions, executable algorithms and theorems +together with an environment for semi-interactive development of +machine-checked proofs. -If you have ocamlopt, Coq will be compiled to native code, which runs 4-10 -times faster. For best performance, OCaml should have support for pthreads. - -If you want CoqIDE, you need LablGTK2 (>= 2.10.0) with development -files, and GTK2+ (>= 2.10.0). This also REQUIRES OCaml to have support -for pthreads. - -If you have emacs installed, emacs files for Coq will be installed. -Otherwise, they will be omitted. +To build CoqIDE, add COQIDE=yes, e.g.: COQIDE=yes ./coq.SlackBuild. +You will need the lablgtk package built with gtksourceview support. diff --git a/academic/coq/coq.SlackBuild b/academic/coq/coq.SlackBuild index c0aca0054a..afa9d5f58f 100644 --- a/academic/coq/coq.SlackBuild +++ b/academic/coq/coq.SlackBuild @@ -1,30 +1,35 @@ #!/bin/sh + +# Slackware build script for coq + +# Copyright 2020 Nick Smallbone <nick@smallbone.se>, Gothenburg, Sweden +# All rights reserved. # -# 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. +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: # -# You should have received a copy of the GNU General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. # -# Slackware build script for coq - -# Written by William Bowman (wilbowma@indiana.edu) +# 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. PRGNAM=coq -VERSION=${VERSION:-8.5pl1} +VERSION=${VERSION:-8.9.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -35,9 +40,7 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -# This is built using the ocaml compiler, not GCC, so SLKCFLAGS are -# not used. -if [ "$ARCH" = "i486" ]; then +if [ "$ARCH" = "i586" ]; then LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then LIBDIRSUFFIX="" @@ -57,30 +60,36 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - - -if hash ocamlopt || hash ocamlopt.opt ; then - OPT="-opt" + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Configure findlib so it can find camlp5. +cp /etc/findlib.conf . +sed -i "s@path=\"@path=\"/usr/lib${LIBDIRSUFFIX}/ocaml:@" findlib.conf +export OCAMLFIND_CONF=$(pwd)/findlib.conf + +CONFIG_ARGS= +if [ z$COQIDE = zyes ];then + CONFIG_ARGS+=" -coqide opt" else - OPT="" + CONFIG_ARGS+=" -coqide no" fi ./configure \ -prefix /usr \ - -libdir /usr/lib${LIBDIRSUFFIX}/coq \ + -libdir /usr/lib${LIBDIRSUFFIX}/$PRGNAM \ + -configdir /etc/xdg/$PRGNAM \ -mandir /usr/man \ + -docdir /usr/doc/$PRGNAM-$VERSION \ -arch $ARCH \ - $OPT + $CONFIG_ARGS -make world -umask 022 -COQINSTALLPREFIX=$PKG make install +make +make install COQINSTALLPREFIX=$PKG -find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ +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 {} \; @@ -88,18 +97,12 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - CHANGES COMPATIBILITY COPYRIGHT CREDITS INSTALL* LICENSE README* \ + CHANGES.md CONTRIBUTING.md CREDITS INSTALL LICENSE README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -zcat $CWD/gpl.txt.gz > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM-SlackBuild-license mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -# Delete this if they don't have emacs. I don't like needless things -if [ `which emacs | grep "no emacs"` ]; then - rm -rf $PKG/usr/lib${LIBDIRSUFFIX}/emacs -fi - cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/coq/coq.info b/academic/coq/coq.info index 9cd9d5bb91..93554ae125 100644 --- a/academic/coq/coq.info +++ b/academic/coq/coq.info @@ -1,10 +1,10 @@ PRGNAM="coq" -VERSION="8.5pl1" +VERSION="8.9.0" HOMEPAGE="http://coq.inria.fr/" -DOWNLOAD="https://coq.inria.fr/distrib/V8.5pl1/files/coq-8.5pl1.tar.gz" -MD5SUM="1faa8a237c3e81905dc938b6b727b807" +DOWNLOAD="https://github.com/coq/coq/archive/V8.9.0/coq-8.9.0.tar.gz" +MD5SUM="490c89609c1271fe7f20e6ea1bd107b5" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="camlp5" -MAINTAINER="William Bowman" -EMAIL="wilbowma@indiana.edu" +REQUIRES="camlp5 ocaml-findlib" +MAINTAINER="Nick Smallbone" +EMAIL="nick@smallbone.se" diff --git a/academic/coq/slack-desc b/academic/coq/slack-desc index badd05cb0b..a5c16bf092 100644 --- a/academic/coq/slack-desc +++ b/academic/coq/slack-desc @@ -13,7 +13,7 @@ coq: to write mathematical definitions, executable algorithms and theorems coq: together with an environment for semi-interactive development of coq: machine-checked proofs. coq: +coq: Homepage: https://coq.inria.fr/ coq: -coq: Homepage: http://coq.inria.fr/ coq: coq: diff --git a/academic/cryptominisat/cryptominisat.SlackBuild b/academic/cryptominisat/cryptominisat.SlackBuild index 61178b83d1..f8f0deea19 100644 --- a/academic/cryptominisat/cryptominisat.SlackBuild +++ b/academic/cryptominisat/cryptominisat.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cryptominisat -# Copyright 2018 Alan Aversa USA +# Copyright 2019 Alan Aversa USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=cryptominisat -VERSION=${VERSION:-5.6.6} +VERSION=${VERSION:-5.7.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/cryptominisat/cryptominisat.info b/academic/cryptominisat/cryptominisat.info index ffaa550c77..ecbc9f24ff 100644 --- a/academic/cryptominisat/cryptominisat.info +++ b/academic/cryptominisat/cryptominisat.info @@ -1,8 +1,8 @@ PRGNAM="cryptominisat" -VERSION="5.6.6" +VERSION="5.7.1" HOMEPAGE="https://www.msoos.org/cryptominisat5/" -DOWNLOAD="https://github.com/msoos/cryptominisat/archive/5.6.6/cryptominisat-5.6.6.tar.gz" -MD5SUM="cce64bfd256700e96baee90b7bdfe770" +DOWNLOAD="https://github.com/msoos/cryptominisat/archive/5.7.1/cryptominisat-5.7.1.tar.gz" +MD5SUM="e4ff835bbfe1995cc5e62a6e464dfd98" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/csparse/README b/academic/csparse/README index 7119c1bf65..2726898d3c 100644 --- a/academic/csparse/README +++ b/academic/csparse/README @@ -1,5 +1,5 @@ -CSparse is a small yet feature-rich sparse matrix package. Its purpose is -to demonstrate a wide range of sparse matrix algorithms in as concise a -code as possible. +CSparse is a small yet feature-rich sparse matrix package. Its +purpose is to demonstrate a wide range of sparse matrix algorithms in +as concise a code as possible. This package is part of SuiteSparse. diff --git a/academic/csparse/csparse.SlackBuild b/academic/csparse/csparse.SlackBuild index f6f3dd53b5..4aa1aa9612 100644 --- a/academic/csparse/csparse.SlackBuild +++ b/academic/csparse/csparse.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CSparse -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=csparse SRCNAM=SuiteSparse SUBDIR=CSparse VERSION=${VERSION:-3.2.0} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-3} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-5} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/csparse/csparse.info b/academic/csparse/csparse.info index ed0b7605cd..861a2ed4c5 100644 --- a/academic/csparse/csparse.info +++ b/academic/csparse/csparse.info @@ -1,8 +1,8 @@ PRGNAM="csparse" VERSION="3.2.0" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/csparse/patches/autoconfiscate.diff b/academic/csparse/patches/autoconfiscate.diff index 45e89ff5b2..e768036abd 100644 --- a/academic/csparse/patches/autoconfiscate.diff +++ b/academic/csparse/patches/autoconfiscate.diff @@ -258,7 +258,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([CSparse],[3.2.0],[DrTimothyAldenDavis@gmail.com],[csparse],[http://www.suitesparse.com/]) ++AC_INIT([CSparse],[3.2.0],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[csparse],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/cs_print.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/cvc4/README b/academic/cvc4/README new file mode 100644 index 0000000000..ed00fa62b8 --- /dev/null +++ b/academic/cvc4/README @@ -0,0 +1,11 @@ +CVC4 is an automated theorem prover and satisfiability modulo theories +(SMT) solver. Given a formula in first-order logic, it attempts to +either prove the formula or find a counterexample. CVC4 supports +arithmetic, reasoning about arrays, and several other built-in +theories. Input problems are written in SMT-LIB format. + +This package includes the cvc4 program, libraries, and Python 2 +bindings. + +Note that this SlackBuild builds CVC4 with readline support, which means +the resulting executable is licensed under the GPLv3. diff --git a/academic/cvc4/cvc4.SlackBuild b/academic/cvc4/cvc4.SlackBuild new file mode 100644 index 0000000000..d3a964cf03 --- /dev/null +++ b/academic/cvc4/cvc4.SlackBuild @@ -0,0 +1,115 @@ +#!/bin/sh + +# Slackware build script for cvc4 + +# Copyright 2019-2020 Nick Smallbone, Gothenburg, Sweden +# 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. + +# TO DO: +# Add new Python bindings (requires a newer version of Cython?) +# Add Java bindings (requires a newer version of CMake?) + +PRGNAM=cvc4 +VERSION=${VERSION:-1.8} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +SRCNAM=CVC4 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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/LIBRARY_INSTALL_DIR lib/&${LIBDIRSUFFIX}/" CMakeLists.txt +install -m 755 $CWD/run-antlr . +cp $CWD/antlr-3.4-complete.jar . + +cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Production \ + -DANTLR_INCLUDE_DIR=/usr/include/antlr3 \ + -DANTLR_BINARY="$TMP/$SRCNAM-$VERSION/run-antlr" \ + -DUSE_READLINE=OFF \ + -DBUILD_BINDINGS_PYTHON=OFF \ + -DBUILD_SWIG_BINDINGS_PYTHON=ON \ + -DBUILD_SWIG_BINDINGS_JAVA=OFF \ + . + +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 + +mv $PKG/usr/share/man $PKG/usr/man + +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 COPYING NEWS README.md THANKS \ + $PKG/usr/doc/$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:-tgz} diff --git a/academic/cvc4/cvc4.info b/academic/cvc4/cvc4.info new file mode 100644 index 0000000000..4fc4ede8c6 --- /dev/null +++ b/academic/cvc4/cvc4.info @@ -0,0 +1,12 @@ +PRGNAM="cvc4" +VERSION="1.8" +HOMEPAGE="https://cvc4.cs.stanford.edu/" +DOWNLOAD="https://github.com/CVC4/CVC4/archive/1.8/CVC4-1.8.tar.gz \ + https://www.antlr3.org/download/antlr-3.4-complete.jar" +MD5SUM="9f7657e21fec3c4042225b0b8f513c34 \ + 1b91dea1c7d480b3223f7c8a9aa0e172" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="jdk libantlr3c python-toml" +MAINTAINER="Nick Smallbone" +EMAIL="nick@smallbone.se" diff --git a/academic/cvc4/run-antlr b/academic/cvc4/run-antlr new file mode 100644 index 0000000000..26f09c7cac --- /dev/null +++ b/academic/cvc4/run-antlr @@ -0,0 +1,2 @@ +#!/bin/bash +exec java -jar $(dirname $0)/antlr-3.4-complete.jar $* diff --git a/academic/cvc4/slack-desc b/academic/cvc4/slack-desc new file mode 100644 index 0000000000..7916878a78 --- /dev/null +++ b/academic/cvc4/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +cvc4: cvc4 (a first-order theorem prover and SMT solver) +cvc4: +cvc4: CVC4 is an automated theorem prover and satisfiability modulo +cvc4: theories (SMT) solver. Given a formula in first-order logic, it +cvc4: attempts to either prove the formula or find a counterexample. CVC4 +cvc4: supports arithmetic, reasoning about arrays, and several other +cvc4: built-in theories. Input problems are written in SMT-LIB format. +cvc4: +cvc4: This package includes the cvc4 program as well as libraries. +cvc4: +cvc4: Homepage: https://cvc4.cs.stanford.edu/ diff --git a/academic/cxsparse/cxsparse.SlackBuild b/academic/cxsparse/cxsparse.SlackBuild index c885e92f68..50237f46a6 100644 --- a/academic/cxsparse/cxsparse.SlackBuild +++ b/academic/cxsparse/cxsparse.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CXSparse -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=cxsparse SRCNAM=SuiteSparse SUBDIR=CXSparse VERSION=${VERSION:-3.2.0} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-3} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-5} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/cxsparse/cxsparse.info b/academic/cxsparse/cxsparse.info index 3eded7da7c..06c815be7c 100644 --- a/academic/cxsparse/cxsparse.info +++ b/academic/cxsparse/cxsparse.info @@ -1,8 +1,8 @@ PRGNAM="cxsparse" VERSION="3.2.0" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/cxsparse/patches/autoconfiscate.diff b/academic/cxsparse/patches/autoconfiscate.diff index 6302da44f3..6ee6d78b45 100644 --- a/academic/cxsparse/patches/autoconfiscate.diff +++ b/academic/cxsparse/patches/autoconfiscate.diff @@ -522,7 +522,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([CXSparse],[3.2.0],[DrTimothyAldenDavis@gmail.com],[cxsparse],[http://www.suitesparse.com/]) ++AC_INIT([CXSparse],[3.2.0],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[cxsparse],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/cs_print.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/dakota/README b/academic/dakota/README index 01d05fcdec..3a0d5dbe15 100644 --- a/academic/dakota/README +++ b/academic/dakota/README @@ -1,12 +1,16 @@ The Dakota toolkit provides a flexible, extensible interface between analysis codes and iteration methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty -quantification with sampling, reliability, stochastic expansion, and -epistemic methods; parameter estimation with nonlinear least squares -methods; and sensitivity/variance analysis with design of experiments -and parameter study capabilities. These capabilities may be used on -their own or as components within advanced strategies such as -surrogate-based optimization, mixed integer nonlinear programming, or -optimization under uncertainty. +quantification with sampling, reliability, stochastic expansion, +and epistemic methods; parameter estimation with nonlinear least +squares methods; and sensitivity/variance analysis with design of +experiments and parameter study capabilities. These capabilities may +be used on their own or as components within advanced strategies such +as surrogate-based optimization, mixed integer nonlinear programming, +or optimization under uncertainty. -Optional dependency: openmpi +Optional dependency: openmpi (for distributed memory parallel +capabilities) + +You can build with multiple jobs by setting the MAKEFLAGS environment +variable. diff --git a/academic/dakota/dakota.SlackBuild b/academic/dakota/dakota.SlackBuild index cc8e00e755..bd119d0e0d 100644 --- a/academic/dakota/dakota.SlackBuild +++ b/academic/dakota/dakota.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for Dakota -# Copyright 2017 Lorenzo Trevisan, Caorle, Venice, Italy +# Copyright 2017, 2018, 2019, 2020 Lorenzo Trevisan, Caorle, Venice, Italy # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=dakota -VERSION=${VERSION:-6.8} +VERSION=${VERSION:-6.11.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/dakota/dakota.info b/academic/dakota/dakota.info index f20e72ed14..80d0d1cd01 100644 --- a/academic/dakota/dakota.info +++ b/academic/dakota/dakota.info @@ -1,8 +1,8 @@ PRGNAM="dakota" -VERSION="6.8" +VERSION="6.11.0" HOMEPAGE="https://dakota.sandia.gov/" -DOWNLOAD="https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.8-release-public.src-UI.tar.gz" -MD5SUM="85375e8c4df406fe017beda63ab28215" +DOWNLOAD="https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.11.0-release-public.src-UI.tar.gz" +MD5SUM="3a81ce3f6b0c3a9087a0cd8f53e16249" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="blas lapack" diff --git a/academic/datamash/README b/academic/datamash/README new file mode 100644 index 0000000000..01d8fd598d --- /dev/null +++ b/academic/datamash/README @@ -0,0 +1,6 @@ +GNU Datamash is a command-line program which performs basic numeric, +textual and statistical operations on input textual data files. + +It is designed to be portable and reliable, and aid researchers +to easily automate analysis pipelines, without writing code or even +short scripts. diff --git a/academic/datamash/datamash.SlackBuild b/academic/datamash/datamash.SlackBuild new file mode 100644 index 0000000000..4661750499 --- /dev/null +++ b/academic/datamash/datamash.SlackBuild @@ -0,0 +1,107 @@ +#!/bin/sh + +# Slackware build script for datamash + +# Copyright 2020 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. + +PRGNAM=datamash +VERSION=${VERSION:-1.7} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --infodir=/usr/info \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +make +make check +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +rm -f $PKG/usr/info/dir +gzip -9 $PKG/usr/info/*.info* + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING INSTALL NEWS README THANKS 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:-tgz} diff --git a/academic/datamash/datamash.info b/academic/datamash/datamash.info new file mode 100644 index 0000000000..ff23e91fa2 --- /dev/null +++ b/academic/datamash/datamash.info @@ -0,0 +1,10 @@ +PRGNAM="datamash" +VERSION="1.7" +HOMEPAGE="https://www.gnu.org/software/datamash/" +DOWNLOAD="https://ftp.gnu.org/gnu/datamash/datamash-1.7.tar.gz" +MD5SUM="e5474d3bfee13e7ab1c44ebaec497a0d" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/datamash/slack-desc b/academic/datamash/slack-desc new file mode 100644 index 0000000000..86ef966a72 --- /dev/null +++ b/academic/datamash/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------------------------------------------------------| +datamash: datamash (Basic numeric, textual and statistical operations) +datamash: +datamash: GNU Datamash is a command-line program which performs basic +datamash: numeric, textual and statistical operations on input textual +datamash: data files. +datamash: +datamash: https://www.gnu.org/software/datamash/ +datamash: +datamash: +datamash: +datamash: diff --git a/academic/diamond/README b/academic/diamond/README index a5c66d0988..07af60110e 100644 --- a/academic/diamond/README +++ b/academic/diamond/README @@ -11,22 +11,22 @@ features are: as well as taxonomic classification. To now run an alignment task, we assume to have a protein database file -in FASTA format named `nr.faa` and a file of DNA reads that we want to -align named `reads.fna`. +in FASTA format named 'nr.faa' and a file of DNA reads that we want to +align named 'reads.fna'. -In order to set up a reference database for DIAMOND, the `makedb` +In order to set up a reference database for DIAMOND, the 'makedb' command needs to be executed with the following command line: $ diamond makedb --in nr.faa -d nr This will create a binary DIAMOND database file with the specified name -(`nr.dmnd`). The alignment task may then be initiated using the `blastx` +('nr.dmnd'). The alignment task may then be initiated using the 'blastx' command like this: $ diamond blastx -d nr -q reads.fna -o matches.m8 -The output file here is specified with the `–o` option and named -`matches.m8`. By default, it is generated in BLAST tabular format. +The output file here is specified with the '-o' option and named +'matches.m8'. By default, it is generated in BLAST tabular format. Publication: Buchfink B, Xie C, Huson DH, "Fast and sensitive protein alignment using diff --git a/academic/diamond/diamond.SlackBuild b/academic/diamond/diamond.SlackBuild index 934c1e800a..9a59218bbd 100644 --- a/academic/diamond/diamond.SlackBuild +++ b/academic/diamond/diamond.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for diamond -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=diamond -VERSION=${VERSION:-0.9.23} +VERSION=${VERSION:-0.9.36} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -85,7 +85,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - ${PRGNAM}_manual.pdf LICENSE README.md src/ChangeLog \ + LICENSE README.md src/ChangeLog \ $PKG/usr/doc/$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/diamond/diamond.info b/academic/diamond/diamond.info index 5163768da2..e1160377d7 100644 --- a/academic/diamond/diamond.info +++ b/academic/diamond/diamond.info @@ -1,8 +1,8 @@ PRGNAM="diamond" -VERSION="0.9.23" +VERSION="0.9.36" HOMEPAGE="https://github.com/bbuchfink/diamond" -DOWNLOAD="https://github.com/bbuchfink/diamond/archive/v0.9.23/diamond-0.9.23.tar.gz" -MD5SUM="3597695081d4b6fd8978c257cdb5fe4a" +DOWNLOAD="https://github.com/bbuchfink/diamond/archive/v0.9.36/diamond-0.9.36.tar.gz" +MD5SUM="ce6f019e2e5dbc22e1210ba408ccefb4" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/ds9/README b/academic/ds9/README index 5bffb53e7f..bab29ee863 100644 --- a/academic/ds9/README +++ b/academic/ds9/README @@ -1,7 +1,10 @@ -SAOImage DS9 is an application for astronomical imaging and data -visualization. It supports the FITS format and binary tables. As well -as standard imaging manipulation tools, it includes many advanced -features such as multiple frame buffers, 2D, 3D, RGB frame buffers, -region and colormap manipulation, mosaic images and geometric markers. -DS9 supports a variety of coordinate systems and it has a user -configurable interface. +SAOImageDS9 is an astronomical imaging and data visualization application. DS9 +is a stand-alone application which supports FITS images and binary tables, +multiple frame buffers, region manipulation, and many scale algorithms and +colormaps. DS9 supports a consistent set of GUI and functional capabilities, +as well as advanced features such as 2-D, 3-D and RGB frame buffers, mosaic +images, tiling, blinking, geometric markers, colormap manipulation, scaling, +arbitrary zoom, cropping, rotation, pan, and a variety of coordinate systems. +The GUI for DS9 is user configurable. GUI elements such as the coordinate +display, panner, magnifier, horizontal and vertical graphs, button bar, and +color bar can be configured via menus or the command line. diff --git a/academic/ds9/ds9.SlackBuild b/academic/ds9/ds9.SlackBuild index a757a1bed5..6f38b13804 100644 --- a/academic/ds9/ds9.SlackBuild +++ b/academic/ds9/ds9.SlackBuild @@ -1,8 +1,8 @@ #!/bin/sh -# Slackware build script for SAOImage DS9 +# Slackware build script for ds9 (SAOImageDS9) -# Copyright 2017 Nitish Ragoomundun, Mauritius +# Copyright 2021 Nitish Ragoomundun, Mauritius # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=ds9 -VERSION=${VERSION:-7.6} +VERSION=${VERSION:-8.2.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -78,9 +78,12 @@ CXXFLAGS="$SLKCFLAGS" \ --sysconfdir=/etc \ --localstatedir=/var \ --docdir=/usr/doc/$PRGNAM-$VERSION \ - --with-arch=${ARCH}-slackware-linux + --x-includes=/usr/include \ + --x-libraries=/usr/lib$LIBDIRSUFFIX \ + --with-x \ + --with-arch=$ARCH-slackware-linux -make -j1 +make # Install the ds9 executable mkdir -p $PKG/usr/{bin,doc/$PRGNAM-$VERSION} diff --git a/academic/ds9/ds9.desktop b/academic/ds9/ds9.desktop index 318d5d41c2..08b18e0bbd 100644 --- a/academic/ds9/ds9.desktop +++ b/academic/ds9/ds9.desktop @@ -1,7 +1,7 @@ [Desktop Entry] -Name=DS9 -GenericName=SAOImage DS9 -Comment=SAOImage DS9 Astronomical Software +Name=ds9 +GenericName=SAOImageDS9 +Comment=Astronomical Software and FITS viewing program Exec=ds9 Icon=ds9-icon Terminal=false diff --git a/academic/ds9/ds9.info b/academic/ds9/ds9.info index bab590e743..475fe53290 100644 --- a/academic/ds9/ds9.info +++ b/academic/ds9/ds9.info @@ -1,8 +1,8 @@ PRGNAM="ds9" -VERSION="7.6" -HOMEPAGE="http://ds9.si.edu/site/Home.html" -DOWNLOAD="http://ds9.si.edu/archive/source/ds9.7.6.tar.gz" -MD5SUM="b700dd815fe1f7fa93e3e3bba1132ca7" +VERSION="8.2.1" +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_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/ds9/slack-desc b/academic/ds9/slack-desc index b07917b061..b4bd41a641 100644 --- a/academic/ds9/slack-desc +++ b/academic/ds9/slack-desc @@ -15,5 +15,5 @@ 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: Homepage: http://ds9.si.edu/site/Home.html +ds9: Homepage: https://sites.google.com/cfa.harvard.edu/saoimageds9/home ds9: diff --git a/academic/ed-v6/README b/academic/ed-v6/README new file mode 100644 index 0000000000..f116d5fc40 --- /dev/null +++ b/academic/ed-v6/README @@ -0,0 +1,85 @@ +Old UNIX V6 ed, lightly ported to modern systems. + +The old UNIX version of 'ed', the line editor. This is +intended to be for academic interest more than anything and +perhaps shouldn't be used for any serious editing of system +files etc. You have been warned! :) + +The binary is named 'ed-v6' so as not to clobber gnu ed. + +There are some major differences between this and POSIX ed +(see the notes at the end for more info.) + +NOTE: The linked sources are redistributed on github +with no associated license. + +OPTIONS + +Build a 32 bit binary on x86_64 (Multilib needed): + + M32=yes + +Build a static binary (size is ~ 800k vs. ~ 18k for the +dynamic): + + STATIC=yes + + +DEVELOPER'S NOTES + + 1. compile with a K&R compiler (not even ansified); + replacing =+ with += and using "=" for default + assignment + 2. assume 32-bits or better (ldiv and ldivr, increasing the + sbrk to 4096) + 3. use setjmp+longjmp instead of sysexit+reset + 4. use lseek() instead of seek() (although still assumes + 512 bytes) + 5. copies the tempfilename to work on systems without + writable strings + 6. use SIG_IGN instead of the numeric value "1" + 7. remove the goto errlab since that doesn't work in ANSI C + 8. commented out getpid() in favor of a local copy + 9. renamed unix() to run_unix() because some systems (at + least some linux) annoyingly do a -Dunix=1 +10. use sizeof(buf) instead of buf +11. renamed putchar() to putc() because gcc and clang + generate errors if you create a function called putchar() + with a different signature. +12. added a prototype for errfunc() because clang refuses to + honor `-ansi` + +I've tried to keep these modifications as minimal as +possible in an effort to preserve the editor that I learned +unix on. + +`ed.c.orig` is included so you can verify how minimal my +changes were. + + +MAINTAINER'S NOTES + +Compilation: + +Added -D_XOPEN_SOURCE=500 to compile with fcntl.h in +glibc-2.23. + +Manual page: + +If you are unfamiliar with ed then gnu ed has a very good +info page. + +This is the closest I can find to the original man page: + +https://freebsd.org/cgi/man.cgi?query=ed&manpath=Unix+Seventh+Edition + +Among other things, there is no -p option, single , or ; +will throw errors, no G//, and r does not support shell +commands. H and h are also unsupported, so errors will lack +any explanation. + +Using with rlwrap: + +This does work with rlwrap, however it repeats every +command. This doesn't affect the functionality, but it can +look quite confusing to have everything repeated. diff --git a/academic/ed-v6/ed-v6.SlackBuild b/academic/ed-v6/ed-v6.SlackBuild new file mode 100644 index 0000000000..e2da7582a0 --- /dev/null +++ b/academic/ed-v6/ed-v6.SlackBuild @@ -0,0 +1,90 @@ +#!/bin/sh + +# Slackware build script for ed-v6 +# Copyright 2019 Dave Woodfall <dave@slackbuilds.org> +# 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. + +PRGNAM=ed-v6 +VERSION=${VERSION:-c72c0e} +SRCVERSION=${SRCVERSION:-c72c0e9445af26bd9fde2d39da5628e6dabf36dd} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${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 + +STRIP=${STRIP:-yes} +[ "$M32" = "yes" ] && M32="-m32" || unset M32 +[ "$STATIC" = "yes" ] && STATIC="-static" || unset STATIC + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$SRCVERSION +tar xvf $CWD/$SRCVERSION.tar.gz +cd $PRGNAM-$SRCVERSION +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" \ + gcc $M32 $STATIC -Os -ansi -w -D_XOPEN_SOURCE=500 -o ed-v6 ed.c + +install -D -m 0755 ed-v6 $PKG/usr/bin/ed-v6 + +if [ "$STRIP" = "yes" ]; then + strip --strip-unneeded 2>/dev/null $PKG/usr/bin/ed-v6 +fi + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README.md ed.c ed.c.orig \ + $PKG/usr/doc/$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:-tgz} diff --git a/academic/ed-v6/ed-v6.info b/academic/ed-v6/ed-v6.info new file mode 100644 index 0000000000..35e5735a5a --- /dev/null +++ b/academic/ed-v6/ed-v6.info @@ -0,0 +1,10 @@ +PRGNAM="ed-v6" +VERSION="c72c0e" +HOMEPAGE="https://github.com/geocar/ed-v6" +DOWNLOAD="https://github.com/geocar/ed-v6/archive/c72c0e9/c72c0e9445af26bd9fde2d39da5628e6dabf36dd.tar.gz" +MD5SUM="797a81796fdaf0b35bbce721d08d7bd7" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Dave Woodfall" +EMAIL="dave@slackbuilds.org" diff --git a/academic/ed-v6/slack-desc b/academic/ed-v6/slack-desc new file mode 100644 index 0000000000..667b5eb513 --- /dev/null +++ b/academic/ed-v6/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 ':'. + + |-----handy-ruler------------------------------------------------------| +ed-v6: ed-v6 (Old UNIX V6 ed _lightly_ ported to modern systems) +ed-v6: +ed-v6: The old UNIX version of 'ed', the line editor. This is intended to +ed-v6: be for academic interest more than anything and perhaps shouldn't be +ed-v6: used for any serious editing of system files etc. You have been +ed-v6: warned! :) +ed-v6: +ed-v6: https://github.com/geocar/ed-v6 +ed-v6: +ed-v6: +ed-v6: diff --git a/academic/edsim51di/edsim51di.info b/academic/edsim51di/edsim51di.info index 9581b82bd8..ff9f94cec3 100644 --- a/academic/edsim51di/edsim51di.info +++ b/academic/edsim51di/edsim51di.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.edsim51.com/8051simulator/edsim51di.zip" MD5SUM="b97b326e8d74a2f5ade7f30e617d8ce8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="openjdk" +REQUIRES="openjdk7" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/engauge/README b/academic/engauge/README index 8e946775e7..a1c9e75bbf 100644 --- a/academic/engauge/README +++ b/academic/engauge/README @@ -1,7 +1,8 @@ -Engauge digitizing software converts an image file showing a graph or map, -into numbers. The image file can come from a scanner, digital camera or -screenshot. The numbers can be read on the screen, and written or copied -to a spreadsheet. Engauge Digitizer compensates for rotation, scaling -and skew (also known as shearing) in graphs. Engauge recognizes BMP, CUR, -DDS, GIF, ICNS, ICO, JP2, JPG, MNG, PBM, PDF, PGM, PNG, PPM, SVG, SVGZ, -TGA, TIFF, WBMP, WEBP, XBM and XPM image files. +Engauge digitizing software converts an image file showing a graph or +map, into numbers. The image file can come from a scanner, digital +camera or screenshot. The numbers can be read on the screen, and +written or copied to a spreadsheet. Engauge Digitizer compensates for +rotation, scaling and skew (also known as shearing) in graphs. Engauge +recognizes BMP, CUR, DDS, GIF, ICNS, ICO, JP2, JPG, MNG, PBM, PDF, +PGM, PNG, PPM, SVG, SVGZ, TGA, TIFF, WBMP, WEBP, XBM and XPM image +files. diff --git a/academic/eprover/README b/academic/eprover/README new file mode 100644 index 0000000000..f123407313 --- /dev/null +++ b/academic/eprover/README @@ -0,0 +1 @@ +E is an automated theorem prover for first-order and equational logic. diff --git a/academic/eprover/eprover.SlackBuild b/academic/eprover/eprover.SlackBuild new file mode 100644 index 0000000000..5ab9c7485b --- /dev/null +++ b/academic/eprover/eprover.SlackBuild @@ -0,0 +1,101 @@ +#!/bin/sh + +# Slackware build script for eprover + +# Copyright 2019-2020 Nick Smallbone, Gothenburg, Sweden +# 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. + +PRGNAM=eprover +VERSION=${VERSION:-2.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 E +tar xvf $CWD/E.tgz +cd E +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 makefile doesn't support DESTDIR, but luckily it doesn't use the +# configured --bindir and --man-prefix until install time. +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --bindir=$PKG/usr/bin \ + --man-prefix=$PKG/usr/man/man1 + +make +make install +# The picosat binary is not used by E but gets installed anyway. +rm $PKG/usr/bin/picosat + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README COPYING DOC/CONTRIBUTORS DOC/eprover.pdf DOC/NEWS \ + $PKG/usr/doc/$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:-tgz} diff --git a/academic/eprover/eprover.info b/academic/eprover/eprover.info new file mode 100644 index 0000000000..9371d82d3e --- /dev/null +++ b/academic/eprover/eprover.info @@ -0,0 +1,10 @@ +PRGNAM="eprover" +VERSION="2.5" +HOMEPAGE="http://www.eprover.org" +DOWNLOAD="http://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_2.5/E.tgz" +MD5SUM="f73852315dde1071acfa552b9532c7ab" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Nick Smallbone" +EMAIL="nick@smallbone.se" diff --git a/academic/eprover/slack-desc b/academic/eprover/slack-desc new file mode 100644 index 0000000000..fa5448b269 --- /dev/null +++ b/academic/eprover/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------------------------------------------------------| +eprover: eprover (a first-order theorem prover) +eprover: +eprover: E is an automated theorem prover for first-order and equational logic. +eprover: +eprover: Homepage: http://www.eprover.org/ +eprover: +eprover: +eprover: +eprover: +eprover: +eprover: diff --git a/academic/equalx/README b/academic/equalx/README index 831c609278..7f21876c2b 100644 --- a/academic/equalx/README +++ b/academic/equalx/README @@ -1,3 +1,5 @@ +equalx (equation editor) + Equalx is an equation editor and viewer that uses a LaTeX installation to generate LaTeX math code to either eps, png, pdf, jpg, tex, ps, or svg format. diff --git a/academic/equalx/equalx.SlackBuild b/academic/equalx/equalx.SlackBuild index 085144e7d2..900e97e5e6 100644 --- a/academic/equalx/equalx.SlackBuild +++ b/academic/equalx/equalx.SlackBuild @@ -3,6 +3,7 @@ # Slackware build script for equalx # Copyright 2015 Charles E. Kauffman +# Copyright 2020 B. Watson # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,14 +23,25 @@ # 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> + +# 20200101 bkw: +# - take over maintenance +# - BUILD=2 +# - fix default paths for applications (gs, pdflatex, pdftocairo) +# - actually use SLKCFLAGS +# - strip binary +# - use a .desktop file that validates +# - minor cleanups/etc in script, slack-desc, README + PRGNAM=equalx VERSION=${VERSION:-0.7.1} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -40,8 +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" @@ -63,27 +75,36 @@ 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 {} \; +find -L . -perm /111 -a \! -perm 755 -a -exec chmod 755 {} \+ -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} \+ -qmake +# Make sure the application can find the external binaries it runs, +# without defaulting to silly things like .exe files. The patch actually +# makes it look for pdflatex in both places it might be found (/usr/bin +# for texlive, /usr/share/texmf/bin for tetex). +zcat $CWD/externpaths.diff.gz | patch -p1 + +CFLAGS="$SLKCFLAGS" CXXFLAGS="$SLKCFLAGS" qmake +sed -i "s,-O2,$SLKCFLAGS," Makefile make -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION $PKG/usr/bin $PKG/usr/man/man1 $PKG/usr/share/pixmaps $PKG/usr/share/applications +# No install target in .pro file, do it manually. +mkdir -p \ + $PKG/usr/doc/$PRGNAM-$VERSION \ + $PKG/usr/bin \ + $PKG/usr/man/man1 \ + $PKG/usr/share/pixmaps \ + $PKG/usr/share/applications -cp resources/icons/equalx/equalx-64x64.png $PKG/usr/share/pixmaps -cp LICENSE README THANKS changelog $PKG/usr/doc/$PRGNAM-$VERSION +install -s -m0755 -oroot -groot $PRGNAM $PKG/usr/bin +gzip -9c < $PRGNAM.1 > $PKG/usr/man/man1/$PRGNAM.1.gz +cp -a resources/icons/equalx/equalx-64x64.png $PKG/usr/share/pixmaps +cp -a LICENSE README THANKS changelog $PKG/usr/doc/$PRGNAM-$VERSION -cp equalx $PKG/usr/bin -cp equalx.1 $PKG/usr/man/man1 +# Edited version of the .desktop that actually validates. +cat $CWD/$PRGNAM.desktop > $PKG/usr/share/applications/$PRGNAM.desktop cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -sed 's;0\.7\.0;0\.7\.1;' resources/equalx.desktop > $PKG/usr/share/applications/equalx.desktop - -find $PKG/usr/man -type f -exec gzip {} \; mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/equalx/equalx.desktop b/academic/equalx/equalx.desktop new file mode 100644 index 0000000000..580a525edc --- /dev/null +++ b/academic/equalx/equalx.desktop @@ -0,0 +1,16 @@ +[Desktop Entry] +Version=1.0 +Exec=equalx +Terminal=false +Type=Application +StartupNotify=false +MimeType=image/png;image/svg+xml;image/jpg; +Icon=/usr/share/pixmaps/equalx-64x64.png +Categories=Qt;KDE;Math;Science; +X-DBUS-StartupType=Unique +Name=EqualX +Name[ro]=EgalX +GenericName=LaTeX Equation Editor +GenericName[ro]=Editor LaTeX de ecuaČ›ii +Comment=Create equations in LaTeX +Comment[ro]=CreeazÄ ecuaČ›ii folosind LaTeX diff --git a/academic/equalx/equalx.info b/academic/equalx/equalx.info index 2c65a9106d..c99a016018 100644 --- a/academic/equalx/equalx.info +++ b/academic/equalx/equalx.info @@ -6,5 +6,5 @@ MD5SUM="f7164b254f25fb265388b46e3fb8e464" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="exempi" -MAINTAINER="Charles E. Kauffman" -EMAIL="molbolom@gmail.com" +MAINTAINER="B. Watson" +EMAIL="yalhcru@gmail.com" diff --git a/academic/equalx/externpaths.diff.gz b/academic/equalx/externpaths.diff.gz Binary files differnew file mode 100644 index 0000000000..af90a2c20e --- /dev/null +++ b/academic/equalx/externpaths.diff.gz diff --git a/academic/ess/README b/academic/ess/README index 75a031fca0..79cd22990b 100644 --- a/academic/ess/README +++ b/academic/ess/README @@ -1,4 +1,4 @@ -Emacs Speaks Statistics is an add-on package for emacs-based text editors -such as GNU Emacs and XEmacs. It is designed to support editing of scripts -and interaction with various statistical analysis programs such S-Plus, R, -SAS, Stata, and others. +Emacs Speaks Statistics is an add-on package for emacs-based text +editors such as GNU Emacs and XEmacs. It is designed to support +editing of scripts and interaction with various statistical analysis +programs such S-Plus, R, SAS, Stata, and others. diff --git a/academic/evopedia_qt/evopedia_qt.info b/academic/evopedia_qt/evopedia_qt.info index bb2828094f..a918ec4dd3 100644 --- a/academic/evopedia_qt/evopedia_qt.info +++ b/academic/evopedia_qt/evopedia_qt.info @@ -1,7 +1,7 @@ PRGNAM="evopedia_qt" VERSION="0.4.4" HOMEPAGE="http://evopedia.info" -DOWNLOAD="https://github.com/evopedia/evopedia_qt/archive/v0.4.4.zip" +DOWNLOAD="https://github.com/evopedia/evopedia_qt/archive/v0.4.4/evopedia_qt-0.4.4.zip" MD5SUM="3418c22e5d69baa06fe0de7de7c57110" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/fann/README b/academic/fann/README index 8fd6161fd4..936d077cc7 100644 --- a/academic/fann/README +++ b/academic/fann/README @@ -1,7 +1,8 @@ -Fast Artificial Neural Network Library is a free open source neural network -library, which implements multilayer artificial neural networks in C with -support for both fully connected and sparsely connected networks. -Cross-platform execution in both fixed and floating point are supported. It -includes a framework for easy handling of training data sets. It is easy to -use, versatile, well documented, and fast. Bindings to more than 15 programming -languages are available. +Fast Artificial Neural Network Library is a free open source neural +network library, which implements multilayer artificial neural +networks in C with support for both fully connected and sparsely +connected networks. Cross-platform execution in both fixed and +floating point are supported. It includes a framework for easy +handling of training data sets. It is easy to use, versatile, well +documented, and fast. Bindings to more than 15 programming languages +are available. diff --git a/academic/fastqc/fastqc.SlackBuild b/academic/fastqc/fastqc.SlackBuild index 72021c6af6..d0add9f9cd 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 Rob van Nues sborg63.org +# Copyright 2015-2018 Petar Petrov slackalaxy@gmail.com; 2018-2020 Rob van Nues sborg63.org # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,8 +24,8 @@ PRGNAM=fastqc SRCNAM=FastQC -VERSION=${VERSION:-0.11.8} -SRCVER=${SRCVER:-v0.11.8} +VERSION=${VERSION:-0.11.9} +SRCVER=${SRCVER:-v0.11.9} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/fastqc/fastqc.info b/academic/fastqc/fastqc.info index 39ebe38dbe..a84ec6f99d 100644 --- a/academic/fastqc/fastqc.info +++ b/academic/fastqc/fastqc.info @@ -1,8 +1,8 @@ PRGNAM="fastqc" -VERSION="0.11.8" +VERSION="0.11.9" HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" -DOWNLOAD="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip" -MD5SUM="bdaf3b9fe957681b3a12349fdfa1c6c0" +DOWNLOAD="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip" +MD5SUM="ee7901b681bb2762d75d5a56c7ec6958" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="jdk" diff --git a/academic/fet/fet.SlackBuild b/academic/fet/fet.SlackBuild index c4a0ce9f74..16d49c2420 100644 --- a/academic/fet/fet.SlackBuild +++ b/academic/fet/fet.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=fet -VERSION=${VERSION:-5.36.1} +VERSION=${VERSION:-5.49.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -60,7 +60,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 +tar jxvf $CWD/$PRGNAM-$VERSION.tar.bz2 cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -71,7 +71,7 @@ find -L . \ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ -qmake fet.pro +qmake-qt5 fet.pro "DEFINES+=USE_SYSTEM_LOCALE" make mkdir -p $PKG/usr/bin diff --git a/academic/fet/fet.info b/academic/fet/fet.info index e4bb3c5e07..81c5073643 100644 --- a/academic/fet/fet.info +++ b/academic/fet/fet.info @@ -1,10 +1,10 @@ PRGNAM="fet" -VERSION="5.36.1" +VERSION="5.49.1" HOMEPAGE="https://www.lalescu.ro/liviu/fet/" -DOWNLOAD="https://www.lalescu.ro/liviu/fet/download/fet-5.36.1.tar.bz2" -MD5SUM="3679e8ad29b0474726a2e28b7c8dd027" +DOWNLOAD="https://www.lalescu.ro/liviu/fet/download/fet-5.49.1.tar.bz2" +MD5SUM="063d3e4fa30c93820737fe8dbb28f55c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="qt5" MAINTAINER="R.S.Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/fet/slack-desc b/academic/fet/slack-desc index 9a8953386d..7d6260d777 100644 --- a/academic/fet/slack-desc +++ b/academic/fet/slack-desc @@ -13,7 +13,7 @@ fet: the timetable of a school, high-school or university. fet: It uses a fast and efficient timetabling algorithm. fet: It is licensed under GNU GPL. fet: -fet: +fet: https://www.lalescu.ro/liviu/fet/ fet: fet: fet: diff --git a/academic/fiji/ImageJ2.desktop b/academic/fiji/ImageJ2.desktop index 87d25dddda..6ea0bc5041 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=Education;Graphics; +Categories=Graphics; Exec=fiji Terminal=false Icon=fiji diff --git a/academic/fiji/README b/academic/fiji/README index 525d5bb3de..873045e097 100644 --- a/academic/fiji/README +++ b/academic/fiji/README @@ -32,11 +32,6 @@ Fiji is Just ImageJ, with extras. It is a distribution of ImageJ with many plugins useful for scientific image analysis in fields such as life sciences. It is actively maintained, with updates released often. -NOTE! -The download link points to an unversioned archive. This means that -he MD5SUM will change when the tarball is updated from upstream. When -this happens, please notify the maintainer. - Citing Schindelin, J.; Arganda-Carreras, I. & Frise, E. et al. (2012) "Fiji: an open-source platform for biological-image analysis" diff --git a/academic/fiji/fiji.SlackBuild b/academic/fiji/fiji.SlackBuild index be3ff27eb1..68c84ec4a6 100644 --- a/academic/fiji/fiji.SlackBuild +++ b/academic/fiji/fiji.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for fiji -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,14 +23,15 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=fiji -DIRNAM=Fiji.app -VERSION=${VERSION:-20181207} +VERSION=${VERSION:-20200902_2101} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +DIRNAM=Fiji.app + if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -41,12 +42,10 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -UPDATER=imagej-updater-0.9.3.jar - set -e # Stop if arch is not supported -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then +if [ "$ARCH" != "x86_64" ]; then printf "\n\n$ARCH is not supported... \n" exit 1 fi @@ -65,26 +64,22 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Rename the binary we need -if [ "$ARCH" = "x86_64" ]; then - mv ImageJ-linux64 $PRGNAM -else - mv ImageJ-linux32 $PRGNAM -fi +mv ImageJ-linux64 $PRGNAM # We will put here two tools, so they are not run at startup. mkdir -p unused cd unused # Remove the check for required updates. If you want it, comment out -# the next lines. You can "enable" it any time by just placing it in the +# the next line. You can "enable" it any time by just placing it in the # plugins/Scripts/Plugins/AutoRun/ folder. mv ../plugins/Scripts/Plugins/AutoRun/Check_Required_Update_Sites.js . # We do not want updates when the program is installed. As above, it # is your system, so if you want this functionality, then comment out -# the line below. You can always "enable it, by placing it in the jars +# the line below. You can always "enable" it, by placing it in the jars # folder. -mv ../jars/$UPDATER . +mv ../jars/imagej-updater-* . cd .. diff --git a/academic/fiji/fiji.info b/academic/fiji/fiji.info index 81d6d231b8..20c501e557 100644 --- a/academic/fiji/fiji.info +++ b/academic/fiji/fiji.info @@ -1,10 +1,10 @@ PRGNAM="fiji" -VERSION="20181207" +VERSION="20200902_2101" HOMEPAGE="https://fiji.sc/" -DOWNLOAD="https://downloads.imagej.net/fiji/latest/fiji-nojre.tar.gz" -MD5SUM="53d7ebea5cc9e0310b32ef42e5894590" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://downloads.imagej.net/fiji/archive/20200902-2101/fiji-nojre.tar.gz" +MD5SUM_x86_64="79c19275017206c662c4381dd43f7dc2" REQUIRES="jdk" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/fityk/README b/academic/fityk/README index c3e6500623..423a6114f5 100644 --- a/academic/fityk/README +++ b/academic/fityk/README @@ -1,6 +1,7 @@ Fityk (program for data processing and nonlinear curve fitting) -Fityk [fi:tik] is a program for data processing and nonlinear curve fitting. +Fityk [fi:tik] is a program for data processing and nonlinear curve +fitting. Primarily used: diff --git a/academic/flann/README b/academic/flann/README index c47071aeab..23c6f4c075 100644 --- a/academic/flann/README +++ b/academic/flann/README @@ -1,7 +1,8 @@ -FLANN is a library for performing fast approximate nearest neighbor searches -in high dimensional spaces. It contains a collection of algorithms we found -to work best for nearest neighbor search and a system for automatically -choosing the best algorithm and optimum parameters depending on the dataset. +FLANN is a library for performing fast approximate nearest neighbor +searches in high dimensional spaces. It contains a collection of +algorithms we found to work best for nearest neighbor search and +a system for automatically choosing the best algorithm and optimum +parameters depending on the dataset. -FLANN is written in C++ and contains bindings for the following languages: -C, MATLAB and Python. +FLANN is written in C++ and contains bindings for the following +languages: C, MATLAB and Python. diff --git a/academic/flexbar/flexbar.SlackBuild b/academic/flexbar/flexbar.SlackBuild index 8d8501a051..f4c28a8ef6 100644 --- a/academic/flexbar/flexbar.SlackBuild +++ b/academic/flexbar/flexbar.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=flexbar -VERSION=${VERSION:-3.4.0} +VERSION=${VERSION:-3.5.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/flexbar/flexbar.info b/academic/flexbar/flexbar.info index d1ec20fc1f..23efa136d8 100644 --- a/academic/flexbar/flexbar.info +++ b/academic/flexbar/flexbar.info @@ -1,9 +1,9 @@ PRGNAM="flexbar" -VERSION="3.4.0" +VERSION="3.5.0" HOMEPAGE="https://github.com/seqan/flexbar" -DOWNLOAD="https://github.com/seqan/flexbar/archive/v3.4.0/flexbar-3.4.0.tar.gz \ +DOWNLOAD="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="ec45e1ca17003a7816b6d2bae61e7f46 \ +MD5SUM="0e07bf4afebfd731c4718b401383224a \ eeadf5544555c1e196537a888d02d09f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/free42/README b/academic/free42/README index 3c30f40e9f..dea3c02b7c 100644 --- a/academic/free42/README +++ b/academic/free42/README @@ -1,6 +1,7 @@ -Free42 is a re-implementation of the HP-42S calculator and the HP-82240 printer. -It is a complete rewrite, not using any HP code, and it does not require an -HP-42S ROM image. Free42 is an Open Source project. The executables and source -code are released under the terms of the GNU General Public License, version 2. -All third-party code used in Free42 is either in the public domain, or licensed -under terms compatible with GPLv2, or used with the authors' permission. +Free42 is a re-implementation of the HP-42S calculator and the +HP-82240 printer. It is a complete rewrite, not using any HP code, +and it does not require an HP-42S ROM image. Free42 is an Open Source +project. The executables and source code are released under the terms +of the GNU General Public License, version 2. All third-party code +used in Free42 is either in the public domain, or licensed under terms +compatible with GPLv2, or used with the authors' permission. diff --git a/academic/freechartgeany/README b/academic/freechartgeany/README deleted file mode 100644 index 82ef887a59..0000000000 --- a/academic/freechartgeany/README +++ /dev/null @@ -1,15 +0,0 @@ -Free Chart Geany is a multi platform software solution for market technical -analysis and charting. - -Key features of Free Chart Geany: - -* Support for major technical analysis indicators like: Simple Moving Average, -Exponential Moving Average, MACD, Relative Strength Index, Bollinger Bands and -Parabolic SAR. -* Support for various Comma Separated Values (CSV) formats like Metastock 7, -Metastock 8, AMI Broker, Yahoo Finance, Google Finance and Standard CSV. -* Support for various drawing and text objects like Labels, Trailing Text, -Horizontal Lines, Vertical Lines, Trend Lines and Fibonacci Retracements. -* Easy download of quotes from Yahoo Finance or Google Finance. -* Free Chart Geany is a tab based application. You can manage the opened charts -the same way you manage the open pages of your web browser. diff --git a/academic/freechartgeany/freechartgeany.info b/academic/freechartgeany/freechartgeany.info deleted file mode 100644 index 265aec66fc..0000000000 --- a/academic/freechartgeany/freechartgeany.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="freechartgeany" -VERSION="2.0.3" -HOMEPAGE="http://freechartgeany.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/freechartgeany/freechartgeany-2.0.3.tar.gz" -MD5SUM="20a084279ea44f99ffb5b18cebbcc217" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Larry Hajali" -EMAIL="larryhaja[at]gmail[dot]com" diff --git a/academic/galculator/galculator.SlackBuild b/academic/galculator/galculator.SlackBuild index 186bf89553..a9bc36534e 100644 --- a/academic/galculator/galculator.SlackBuild +++ b/academic/galculator/galculator.SlackBuild @@ -70,7 +70,7 @@ 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 {} \; -CFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -fcommon" \ CXXFLAGS="$SLKCFLAGS" \ ./autogen.sh \ --prefix=/usr \ diff --git a/academic/gcalctool/README b/academic/gcalctool/README deleted file mode 100644 index 553bf34f98..0000000000 --- a/academic/gcalctool/README +++ /dev/null @@ -1,2 +0,0 @@ -gcalctool is an application that solves mathematical equations and is suitable -as a default application in a Desktop environment. diff --git a/academic/gcalctool/doinst.sh b/academic/gcalctool/doinst.sh deleted file mode 100644 index 401d987795..0000000000 --- a/academic/gcalctool/doinst.sh +++ /dev/null @@ -1,15 +0,0 @@ -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 - -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/gcalctool/gcalctool.info b/academic/gcalctool/gcalctool.info deleted file mode 100644 index 745888e271..0000000000 --- a/academic/gcalctool/gcalctool.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="gcalctool" -VERSION="6.6.2" -HOMEPAGE="https://directory.fsf.org/wiki/Gcalctool" -DOWNLOAD="ftp://ftp.gnome.org/pub/gnome/sources/gcalctool/6.6/gcalctool-6.6.2.tar.xz" -MD5SUM="94b40737ab5d37983826ee558711199f" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="byteframe" -EMAIL="byteframe@gmail.com" diff --git a/academic/gcalctool/slack-desc b/academic/gcalctool/slack-desc deleted file mode 100644 index 366ce33326..0000000000 --- a/academic/gcalctool/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------------------------------------------------------| -gcalctool: gcalctool (a graphical UNIX calculator) -gcalctool: -gcalctool: gcalctool is an application that solves mathematical equations and -gcalctool: is suitable as a default application in a Desktop environment. -gcalctool: -gcalctool: -gcalctool: -gcalctool: -gcalctool: homepage: https://directory.fsf.org/wiki/Gcalctool -gcalctool: -gcalctool: diff --git a/academic/gcompris-qt/README b/academic/gcompris-qt/README new file mode 100644 index 0000000000..72416bbd9c --- /dev/null +++ b/academic/gcompris-qt/README @@ -0,0 +1,18 @@ +GCompris is a high quality educational software suite, including +a large number of activities for children aged 2 to 10. Some of the +activities are game oriented, but nonetheless still educational. + +Currently GCompris offers more than 100 activities, and more are +being developed. + +This is Qt5-based version of gcompris. + +NOTE: +This software runs better on a platform that has OpenGL 2 support. +If you do not have OpenGL 2 support, you have 2 options: +- Add the following parameter "--software-renderer" at the end of + the last line of the script in /opt/gcompris-qt/bin/gcompris-qt.sh + This will affect all users, system-wide. +- Replace "renderer=auto" into "renderer=software" in your local config, + located in ~/.config/gcompris-qt/gcompris-qt.conf + This will affect current user only. diff --git a/academic/qtoctave/doinst.sh b/academic/gcompris-qt/doinst.sh index 65c7e2eeb9..3e5691a052 100644 --- a/academic/qtoctave/doinst.sh +++ b/academic/gcompris-qt/doinst.sh @@ -4,6 +4,6 @@ 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 + /usr/bin/gtk-update-icon-cache usr/share/icons/hicolor >/dev/null 2>&1 fi fi diff --git a/academic/gcompris-qt/gcompris-qt b/academic/gcompris-qt/gcompris-qt new file mode 100644 index 0000000000..f77dbd5de6 --- /dev/null +++ b/academic/gcompris-qt/gcompris-qt @@ -0,0 +1,4 @@ +#!/bin/sh + +cd /opt/gcompris-qt/bin +./gcompris-qt.sh diff --git a/academic/gcompris-qt/gcompris-qt.SlackBuild b/academic/gcompris-qt/gcompris-qt.SlackBuild new file mode 100644 index 0000000000..82f9a43aac --- /dev/null +++ b/academic/gcompris-qt/gcompris-qt.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/sh + +# Slackware build script for gcompris-qt + +# Copyright 2020 Willy Sudiarto Raharjo <willysr@slackbuilds.org> +# All rights reserved. +# +# Redistribution and use in source and binary forms, with or without modification, +# are permitted provided that the following conditions are met: +# +# * Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. +# * Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the distribution. +# +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED +# TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +# 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/>. + +PRGNAM=gcompris-qt +VERSION=${VERSION:-1.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + ARCH="$( uname -m )" +fi + +case "$ARCH" in + i?86) + ARCH=i586 + SRCARCH=32 + ;; + x86_64) + ARCH=x86_64 + SRCARCH=64 + ;; + *) + echo "Unsupported architecture" + exit 1 + ;; +esac + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $PKG/opt/gcompris-qt $OUTPUT +cd $PKG/opt/gcompris-qt + +sh $CWD/$PRGNAM-$VERSION-Linux${SRCARCH}.sh \ + --prefix=$PKG/opt/gcompris-qt \ + --exclude-subdir \ + --skip-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 + +find -L $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 {} \; + +install -D -m644 $CWD/gcompris-qt.desktop \ + $PKG/usr/share/applications/gcompris-qt.desktop + +install -D -m644 $CWD/gcompris-qt.png \ + $PKG/usr/share/icons/hicolor/256x256/apps/gcompris-qt.png + +install -D -m755 $CWD/gcompris-qt $PKG/usr/bin/gcompris-qt + +# move this here to catch anything that may not have proper ownership +chown -R root:root $PKG + +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:-tgz} diff --git a/academic/gcompris-qt/gcompris-qt.desktop b/academic/gcompris-qt/gcompris-qt.desktop new file mode 100644 index 0000000000..6940f39c97 --- /dev/null +++ b/academic/gcompris-qt/gcompris-qt.desktop @@ -0,0 +1,88 @@ +[Desktop Entry] +Name=GCompris +Name[ca]=GCompris +Name[cs]=GCompris +Name[el]=GCompris +Name[en_GB]=GCompris +Name[es]=GCompris +Name[et]=GCompris +Name[eu]=GCompris +Name[fr]=GCompris +Name[gl]=GCompris +Name[it]=GCompris +Name[ml]=ജികോംപ്രി +Name[nl]=GCompris +Name[nn]=GCompris +Name[pl]=GCompris +Name[pt]=GCompris +Name[pt_BR]=GCompris +Name[ro]=GCompris +Name[sk]=GCompris +Name[sv]=GCompris +Name[uk]=GCompris +Name[x-test]=xxGComprisxx +Name[zh_TW]=GCompris +GenericName=Educational Game +GenericName[ca]=Joc educatiu +GenericName[cs]=VĂ˝uková hra +GenericName[el]=Εκπαιδευτικό παιχνίδι +GenericName[en_GB]=Educational Game +GenericName[es]=Juego educativo +GenericName[et]=Hariv mäng +GenericName[eu]=Hezkuntza-jokoa +GenericName[fr]=Jeu Ă©ducatif +GenericName[gl]=Xogo educativo +GenericName[it]=Gioco didattico +GenericName[ml]=വിദ്യാŕ´ŕµŤŕ´Żŕ´ľŕ´¸ŕ´Şŕ´°ŕ´®ŕ´ľŕ´Ż ŕ´•ŕ´łŕ´ż +GenericName[nl]=Educatief spel +GenericName[nn]=Leik-og-lær-spel +GenericName[pl]=Gra edukacyjna +GenericName[pt]=Jogo Educativo +GenericName[pt_BR]=Jogo educacional +GenericName[ro]=Joc educaČ›ional +GenericName[sk]=VĂ˝uková hra +GenericName[sv]=Pedagogiskt spel +GenericName[uk]=ĐžŃвітня гра +GenericName[x-test]=xxEducational Gamexx +GenericName[zh_CN]=ć•™č‚˛ć¸¸ćŹ +GenericName[zh_TW]=教育éŠć˛ +Comment=Multi-Activity Educational game for children 2 to 10 +Comment[br]=C'hoari kelennadel gant oberezhioĂą a bep seurt evit ar vugale etre 2 ha 10 vloaz +Comment[ca]=Joc educatiu amb mĂşltiples activitats per a infants de 2 a 10 anys +Comment[ca@valencia]=Joc educatiu amb mĂşltiples activitats per a infants de 2 a 10 anys +Comment[de]=Lernspiel mit vielen Aktivitäten fĂĽr Kinder von 2 bis 10 Jahren +Comment[el]=Εκπαιδευτικό παιχνίδι πολλαπλών δĎαĎτηĎιοτήτων για ηλικίες 2 Îως 10 ετών +Comment[en_GB]=Multi-Activity Educational game for children 2 to 10 +Comment[es]=Juego educativo multiactividad para niños de 2 a 10 años +Comment[et]=Rohkete tegevustega hariv mäng lastele vanuses 2-10 +Comment[eu]=Jarduera anitzeko Hezkuntza-jokoa 2 eta 10 urte arteko haurrentzat +Comment[fi]=Useampitoimintoinen opettavainen peli 2–10-vuotiaille lapsille +Comment[fr]=Jeu Ă©ducatif multi-activitĂ©s pour les enfants de 2 Ă 10 ans +Comment[gl]=Xogo educativo con varias actividades para nenos entre 2 e 10 anos +Comment[hi]=२ से १० वर्ष के बच्चों के लिए विŕ¤ŕ¤żŕ¤¨ŕĄŤŕ¤¨ क्रियाएं वाला शेक्षणिक खेल +Comment[id]=GCompris adalah kumpulan permainan kegiatan pendidikan untuk anak umur 2 sampai 10 tahun +Comment[it]=Gioco didattico multi-attivitĂ per bambini da 2 a 10 anni +Comment[ko]=2-10세 어린이를 ěś„í•ś 다양한 활동이 ěžëŠ” ęµěśˇěš© 게임 +Comment[ml]=2 ŕ´®ŕµŕ´¤ŕµ˝ 10 വയസ്സŕµŕ´µŕ´°ŕµ†ŕ´Żŕµŕ´łŕµŤŕ´ł ŕ´•ŕµŕ´źŕµŤŕ´źŕ´żŕ´•ŕµľŕ´•ŕµŤŕ´•ŕµŤ വിവിധ പ്രവർത്തനങ്ങളിലൂടെ പഠിക്കാനായŕµŕ´łŕµŤŕ´ł ŕ´•ŕ´łŕ´ż. +Comment[nl]=Educatief spel met meerdere activiteiten voor kinderen van 2 tot 10 +Comment[nn]=Leik-og-lærspel med mange aktivitetar – for barn frĂĄ 2 til 10 ĂĄr +Comment[pl]=Gra edukacyjna z wieloma aktywnoĹ›ciami dla dzieci w wieku od 2 do 10 lat +Comment[pt]=Jogo educativo multi-actividades para crianças dos 2 aos 10 anos +Comment[pt_BR]=Jogo educacional com várias atividades para crianças de 2 a 10 anos +Comment[ro]=Joc educaČ›ional cu activitÄČ›i multiple pentru copii Ă®ntre 2 Č™i 10 ani +Comment[ru]=ОбŃчающие игры для детей от 2 Đ´Đľ 10 лет +Comment[sk]=Viac-aktivitová vĂ˝uková hra pre deti od 2 do 10 rokov +Comment[sl]=IzobraĹľevalna igra z veÄŤ dejavnostmi za otroke med drugim in desetim letom starosti +Comment[sv]=Pedagogiskt multiaktivitetsspel för barn frĂĄn 2 till 10 ĂĄr +Comment[tr]=2-10 yaĹź arası çocuklar için Çoklu EtkileĹźimli EÄźitici oyun +Comment[uk]=Набір ĐľŃвітніх ігор для дітей від 2 Đ´Đľ 10 років +Comment[x-test]=xxMulti-Activity Educational game for children 2 to 10xx +Comment[zh_CN]=为 2 ĺ° 10 ĺ˛ĺ„żç«Ąĺ‡†ĺ¤‡çš„多功č˝ć•™č‚˛ć¸¸ćŹ +Comment[zh_TW]=ç‚ş 2-10 ć˛ĺ©ĺč¨č¨çš„教育éŠć˛ +Exec=gcompris-qt +Icon=gcompris-qt +Terminal=false +Type=Application +Categories=Education;Game;KidsGame; +StartupNotify=true +X-DocPath=gcompris/index.html diff --git a/academic/gcompris-qt/gcompris-qt.info b/academic/gcompris-qt/gcompris-qt.info new file mode 100644 index 0000000000..91ca5b1c07 --- /dev/null +++ b/academic/gcompris-qt/gcompris-qt.info @@ -0,0 +1,10 @@ +PRGNAM="gcompris-qt" +VERSION="1.1" +HOMEPAGE="http://gcompris.net/" +DOWNLOAD="http://gcompris.net/download/qt/linux/gcompris-qt-1.1-Linux32.sh" +MD5SUM="381f16e7f476a479e663e55c0f386c13" +DOWNLOAD_x86_64="http://gcompris.net/download/qt/linux/gcompris-qt-1.1-Linux64.sh" +MD5SUM_x86_64="06e571bb48a1fb30edeb00c5e6295cd9" +REQUIRES="krb5" +MAINTAINER="Willy Sudiarto Raharjo" +EMAIL="willysr@slackbuilds.org" diff --git a/academic/gcompris-qt/gcompris-qt.png b/academic/gcompris-qt/gcompris-qt.png Binary files differnew file mode 100644 index 0000000000..40cec079f4 --- /dev/null +++ b/academic/gcompris-qt/gcompris-qt.png diff --git a/academic/gcompris-qt/slack-desc b/academic/gcompris-qt/slack-desc new file mode 100644 index 0000000000..995c085f2f --- /dev/null +++ b/academic/gcompris-qt/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------------------------------------------------------| +gcompris-qt: gcompris-qt (an educational software suite) +gcompris-qt: +gcompris-qt: GCompris is a high quality educational software suite, including +gcompris-qt: a large number of activities for children aged 2 to 10. Some of the +gcompris-qt: activities are game orientated, but nonetheless still educational. +gcompris-qt: +gcompris-qt: Currently GCompris offers more than 100 activities, and more are +gcompris-qt: being developed. +gcompris-qt: +gcompris-qt: Homepage: http://gcompris.net/ +gcompris-qt: diff --git a/academic/gcompris/README b/academic/gcompris/README index ec155c2ea3..63345e597b 100644 --- a/academic/gcompris/README +++ b/academic/gcompris/README @@ -1,5 +1,5 @@ -GCompris is an educational software suite comprising of numerous activities -for children aged 2 to 10. Some of the activities are game oriented, but -nonetheless still educational. Currently GCompris offers in excess of 140 -activities and more are being developed. GCompris currently is translated -in more than 40 languages. +GCompris is an educational software suite comprising of numerous +activities for children aged 2 to 10. Some of the activities are game +oriented, but nonetheless still educational. Currently GCompris offers +in excess of 140 activities and more are being developed. GCompris +currently is translated into more than 40 languages. diff --git a/academic/geda-gaf/README b/academic/geda-gaf/README index 58eabd38cd..d5484fbf37 100644 --- a/academic/geda-gaf/README +++ b/academic/geda-gaf/README @@ -1,8 +1,8 @@ -The gEDA project has produced and continues working on a full GPL'd suite -and toolkit of Electronic Design Automation tools. These tools are used for -electrical circuit design, schematic capture, simulation, prototyping, and -production. Currently, the gEDA project offers a mature suite of free -software applications for electronics design, including schematic capture, -attribute management, bill of materials (BOM) generation, netlisting into -over 20 netlist formats, analog and digital simulation, and printed circuit -board (PCB) layout. +The gEDA project has produced and continues working on a full GPL'd +suite and toolkit of Electronic Design Automation tools. These tools +are used for electrical circuit design, schematic capture, simulation, +prototyping, and production. Currently, the gEDA project offers a +mature suite of free software applications for electronics design, +including schematic capture, attribute management, bill of materials +(BOM) generation, netlisting into over 20 netlist formats, analog and +digital simulation, and printed circuit board (PCB) layout. diff --git a/academic/gelemental/gelemental-1.2.0-gcc43.patch b/academic/gelemental/gelemental-1.2.0-gcc43.patch deleted file mode 100644 index 87cfbcc5fd..0000000000 --- a/academic/gelemental/gelemental-1.2.0-gcc43.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- gelemental-1.2.0.org/libelemental/value.hh 2007-09-25 09:10:16.000000000 +0400 -+++ gelemental-1.2.0/libelemental/value.hh 2008-06-29 12:36:30.000000000 +0400 -@@ -27,6 +27,7 @@ - #include <libelemental/misc/ucompose.hh> - #include <libelemental/misc/extras.hh> - -+#include <limits> - #include <iomanip> - #include <ostream> - #include <vector> diff --git a/academic/gelemental/gelemental.SlackBuild b/academic/gelemental/gelemental.SlackBuild index 22beaf7d9c..e4b332e18a 100644 --- a/academic/gelemental/gelemental.SlackBuild +++ b/academic/gelemental/gelemental.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for gelemental -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2019 Petar Petrov slackalaxy@gmail.com # 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. -# The patch is from openSUSE (IIRC) and source tarball is from Debian. Thank you! - PRGNAM=gelemental -VERSION=${VERSION:-1.2.0} -BUILD=${BUILD:-3} +VERSION=${VERSION:-2.0.0} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) export ARCH=i486 ;; + i?86) export ARCH=i586 ;; arm*) export ARCH=arm ;; *) export ARCH=$( uname -m ) ;; esac @@ -42,8 +40,8 @@ TMP=${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" @@ -62,27 +60,15 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar -xvf $CWD/${PRGNAM}_${VERSION}.orig.tar.gz - -patch -p0 -s < $CWD/$PRGNAM-$VERSION-gcc43.patch +tar -xvf $CWD/${PRGNAM}-${VERSION}.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -# Change the menu category to "Education" -sed -i "s:Categories=GTK;Utility;Science;Chemistry;:Categories=Education;:" data/gelemental.desktop.in - -# Increase the info button size -sed -i "s:set_size_request (50, 50):set_size_request (64, 64):" src/buttons.cc - -# Starting with glib 2.32 it is now mandatory to -# include glib.h instead of individual headers. -patch -p1 -i $CWD/glib-single-include.patch + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -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 -std=c++11" \ diff --git a/academic/gelemental/gelemental.info b/academic/gelemental/gelemental.info index 26ae0cb79e..17d587816a 100644 --- a/academic/gelemental/gelemental.info +++ b/academic/gelemental/gelemental.info @@ -1,8 +1,8 @@ PRGNAM="gelemental" -VERSION="1.2.0" +VERSION="2.0.0" HOMEPAGE="http://freecode.com/projects/gelemental" -DOWNLOAD="https://sourceforge.net/projects/sboppetrov/files/gelemental/gelemental_1.2.0.orig.tar.gz" -MD5SUM="94cc73c76a02f75598f579ff57696805" +DOWNLOAD="https://github.com/ginggs/gelemental/archive/v2.0.0/gelemental-2.0.0.tar.gz" +MD5SUM="8d38d7599b0f2fc96e2bd622cd762b9a" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/gelemental/glib-single-include.patch b/academic/gelemental/glib-single-include.patch deleted file mode 100644 index da0c6b4bcf..0000000000 --- a/academic/gelemental/glib-single-include.patch +++ /dev/null @@ -1,40 +0,0 @@ -Index: gelemental-1.2.0/libelemental/misc/extras.cc -=================================================================== ---- gelemental-1.2.0.orig/libelemental/misc/extras.cc -+++ gelemental-1.2.0/libelemental/misc/extras.cc -@@ -21,7 +21,7 @@ - - #include <algorithm> - #include <stdexcept> --#include <glib/gmem.h> -+#include <glib.h> - #include <glibmm/utility.h> - - namespace misc { -Index: gelemental-1.2.0/libelemental/misc/widgets.cc -=================================================================== ---- gelemental-1.2.0.orig/libelemental/misc/widgets.cc -+++ gelemental-1.2.0/libelemental/misc/widgets.cc -@@ -20,7 +20,7 @@ - #include "macros.hh" - #include "widgets.hh" - --#include <glib/gmessages.h> -+#include <glib.h> - #include <gtkmm/alignment.h> - #include <gtkmm/image.h> - #include <gtkmm/label.h> -Index: gelemental-1.2.0/src/main.cc -=================================================================== ---- gelemental-1.2.0.orig/src/main.cc -+++ gelemental-1.2.0/src/main.cc -@@ -26,8 +26,7 @@ - #include <clocale> - #include <iostream> - #include <locale> --#include <glib/goption.h> --#include <glib/gutils.h> -+#include <glib.h> - #include <glibmm/optionentry.h> - #include <gtk/gtkaboutdialog.h> - #include <gtk/gtkversion.h> diff --git a/academic/genometools/genometools.SlackBuild b/academic/genometools/genometools.SlackBuild index f4af4db0f9..0814b7dc9e 100644 --- a/academic/genometools/genometools.SlackBuild +++ b/academic/genometools/genometools.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for genometools -# Copyright 2014-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2014-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=genometools -VERSION=${VERSION:-1.5.10} +VERSION=${VERSION:-1.6.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -72,9 +72,10 @@ 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 {} \; -# Fix library path +# 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 +sed -i "s:/share/man/:/man/:g" Makefile CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -90,10 +91,6 @@ cd gtpython python setup.py install --root=$PKG cd .. -# We don't need this -rm -rf $PKG/usr/bin/genometools-config -rm -rf $PKG/usr/lib${LIBDIRSUFFIX}/libgenometools.a - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/genometools/genometools.info b/academic/genometools/genometools.info index 5026cd2a29..7692e762e8 100644 --- a/academic/genometools/genometools.info +++ b/academic/genometools/genometools.info @@ -1,8 +1,8 @@ PRGNAM="genometools" -VERSION="1.5.10" +VERSION="1.6.1" HOMEPAGE="http://genometools.org/" -DOWNLOAD="http://genometools.org/pub/genometools-1.5.10.tar.gz" -MD5SUM="2c654825746692b968e1c58873b6a3d2" +DOWNLOAD="http://genometools.org/pub/genometools-1.6.1.tar.gz" +MD5SUM="1dc80df17be32973266f5a3601fc64b8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/geomview/geomview.info b/academic/geomview/geomview.info index 9254668ba4..012d830954 100644 --- a/academic/geomview/geomview.info +++ b/academic/geomview/geomview.info @@ -6,5 +6,5 @@ MD5SUM="29c7e6d678af7b9968980f92954419bb" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Jorge Barros de Abreu" -EMAIL="ficmatin10@gmail.com" +MAINTAINER="Philip Lacroix" +EMAIL="slackph at posteo dot de" diff --git a/academic/gerbv/README b/academic/gerbv/README index df4a71fc61..9cd537e588 100644 --- a/academic/gerbv/README +++ b/academic/gerbv/README @@ -2,9 +2,9 @@ Gerbv is one of the utilities affiliated with the gEDA project, an umbrella organization dedicated to producing free software tools for electronic design. -Gerbv is a viewer for Gerber RS-274X files, Excellon drill files, and -CSV pick-and-place files. It is a native Linux application, and it runs -on many common unix platforms. Gerbv is free / open-source software. The -core functionality of gerbv is located in a separate library (libgerbv), -allowing developers to include Gerber parsing/editing/exporting/rendering -into other programs. +Gerbv is a viewer for Gerber RS-274X files, Excellon drill files, +and CSV pick-and-place files. It is a native Linux application, and +it runs on many common unix platforms. Gerbv is free / open-source +software. The core functionality of gerbv is located in a separate +library (libgerbv), allowing developers to include Gerber parsing, +editing, exporting, rendering into other programs. diff --git a/academic/getdp/Kernel_Operation__Broadcast.patch b/academic/getdp/Kernel_Operation__Broadcast.patch new file mode 100644 index 0000000000..621e3e25aa --- /dev/null +++ b/academic/getdp/Kernel_Operation__Broadcast.patch @@ -0,0 +1,11 @@ +#diff a/Kernel/Operation_Broadcast.cpp b/Kernel/Operation_Broadcast.cpp +#--- a/Kernel/Operation_Broadcast.cpp +#+++ b/Kernel/Operation_Broadcast.cpp +@@ -5,6 +5,7 @@ + + #include <vector> + #include <string> ++#include <cstring> // for strncpy() + #include <sstream> + #include <stdio.h> + #include <stdlib.h> diff --git a/academic/getdp/README b/academic/getdp/README new file mode 100644 index 0000000000..3dab37d132 --- /dev/null +++ b/academic/getdp/README @@ -0,0 +1,8 @@ +GetDP (A General Environment for the Treatment of Discrete Problems) + +GetDP is a free finite element solver using mixed elements +to discretize de Rham-type complexes in one, two and three +dimensions. The main feature of GetDP is the closeness between +the input data defining discrete problems (written by the user in +ASCII data files) and the symbolic mathematical expressions of these +problems. diff --git a/academic/gcalctool/gcalctool.SlackBuild b/academic/getdp/getdp.SlackBuild index 4be2cdff1e..240d073028 100644 --- a/academic/gcalctool/gcalctool.SlackBuild +++ b/academic/getdp/getdp.SlackBuild @@ -1,10 +1,7 @@ #!/bin/sh -# Slackware build script for gcalctool - -# Copyright 2010,2011 Robby Workman, Northport, Alabama, USA -# Copyright 2011 byteframe -# All rights reserved. +# Slackware build script for getdp +# Copyright 2020 Fellype do Nascimento, Campinas, Brazil # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -23,8 +20,8 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=gcalctool -VERSION=${VERSION:-6.6.2} +PRGNAM=getdp +VERSION=${VERSION:-3.3.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -48,7 +45,7 @@ elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" + SLKCFLAGS="-O3 -fPIC" LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" @@ -60,43 +57,53 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.xz -cd $PRGNAM-$VERSION +rm -rf $PRGNAM-$VERSION-source +tar -xzvf $CWD/$PRGNAM-$VERSION-source.tgz +cd $PRGNAM-$VERSION-source 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 {} \; - -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 + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -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 that allow compilation without a fail (credits to: DragonFlyBSD/DPorts) +patch -p1 < $CWD/Kernel_Operation__Broadcast.patch Kernel/Operation_Broadcast.cpp + +mkdir build +cd build +cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr \ + -DCMAKE_INSTALL_DOCDIR:PATH=/usr/share/getdp \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DENABLE_BUILD_SHARED=ON \ + -DENABLE_PETSC=OFF \ + -DENABLE_SLEPC=OFF \ + .. +# only demos/ and templates/ folders will be leaved in the /usr/share/getdp dir make make install DESTDIR=$PKG +cd - -find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ +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/man/man1 +mv $PKG/usr/share/man/man1/getdp.1 $PKG/usr/man/man1/ +rm -Rf $PKG/usr/share/man/ + 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 COPYING NEWS README $PKG/usr/doc/$PRGNAM-$VERSION +cp -a CHANGELOG.txt CREDITS.txt LICENSE.txt README.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm $PKG/usr/share/getdp/*.txt +rm -Rf $PKG/tmp 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:-tgz} diff --git a/academic/getdp/getdp.info b/academic/getdp/getdp.info new file mode 100644 index 0000000000..8b5b964589 --- /dev/null +++ b/academic/getdp/getdp.info @@ -0,0 +1,10 @@ +PRGNAM="getdp" +VERSION="3.3.0" +HOMEPAGE="http://getdp.info/" +DOWNLOAD="http://getdp.info/src/getdp-3.3.0-source.tgz" +MD5SUM="0f3e4388bcecd454ff1a19fcfa5979ef" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="arpack-ng OpenBLAS" +MAINTAINER="Fellype do Nascimento" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/getdp/slack-desc b/academic/getdp/slack-desc new file mode 100644 index 0000000000..bed2d36f97 --- /dev/null +++ b/academic/getdp/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 ':'. + + |-----handy-ruler------------------------------------------------------| +getdp: getdp (Finite Element Solver) +getdp: +getdp: GetDP a free finite element solver using mixed elements +getdp: to discretize de Rham-type complexes in one, two and three +getdp: dimensions. The main feature of GetDP is the closeness between +getdp: the input data defining discrete problems (written by the user +getdp: in ASCII data files) and the symbolic mathematical expressions +getdp: of these problems. +getdp: +getdp: GetDP is distributed under the terms of the GNU General Public +getdp: License. diff --git a/academic/ggobi/README b/academic/ggobi/README index 2a325c43df..1bb21d26b4 100644 --- a/academic/ggobi/README +++ b/academic/ggobi/README @@ -1,7 +1,8 @@ -GGobi is an interactive, direct manipulation tool for visualizing high -dimensional data across linked plots. It provides highly dynamic and -interactive graphics such as tours, as well as familiar graphics such -as the scatterplot, barchart and parallel coordinates plots. Plots are -interactive and linked with brushing and identification. The GUI is built -using Gtk+. It reads data in regular ASCII format and more richly using -an XML format. Plugins for other formats are also available. +GGobi is an interactive, direct manipulation tool for visualizing +high dimensional data across linked plots. It provides highly dynamic +and interactive graphics such as tours, as well as familiar graphics +such as the scatterplot, barchart and parallel coordinates plots. +Plots are interactive and linked with brushing and identification. The +GUI is built using Gtk+. It reads data in regular ASCII format and +more richly using an XML format. Plugins for other formats are also +available. diff --git a/academic/gmsh/README b/academic/gmsh/README new file mode 100644 index 0000000000..e2980522f6 --- /dev/null +++ b/academic/gmsh/README @@ -0,0 +1,22 @@ +Gmsh (A three-dimensional finite element mesh generator with built-in +pre- and post-processing facilities) + +Gmsh is an open source 3D finite element mesh generator with a +built-in CAD engine and post-processor. Its design goal is to provide +a fast, light and user-friendly meshing tool with parametric input +and advanced visualization capabilities. Gmsh is built around four +modules: geometry, mesh, solver and post-processing. The specification +of any input to these modules is done either interactively using +the graphical user interface, in ASCII text files using Gmsh's own +scripting language (.geo files), or using the C++, C, Python or Julia +Application Programming Interface (API). + +See this general presentation for a high-level overview of Gmsh +and recent developments, the screencasts for a quick tour of Gmsh's +graphical user interface, and the reference manual for a more thorough +overview of Gmsh's capabilities, some frequently asked questions and +the documentation of the C++, C, Python and Julia API. + +The source code repository contains many examples written using both +the built-in script language (see e.g. the tutorials and demos) and +the API. diff --git a/academic/gmsh/gmsh.SlackBuild b/academic/gmsh/gmsh.SlackBuild new file mode 100644 index 0000000000..3632982bf4 --- /dev/null +++ b/academic/gmsh/gmsh.SlackBuild @@ -0,0 +1,115 @@ +#!/bin/sh + +# Slackware build script for gmsh +# Copyright 2020 Fellype do Nascimento, Campinas, Brazil +# +# Based on SlackBuild by Loris Vincenzi and PKGBUILD for gmsh at AUR +# +# 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. + +PRGNAM=gmsh +VERSION=${VERSION:-4.5.4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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="-O3 -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 -xzvf $CWD/$PRGNAM-$VERSION-source.tgz +cd $PRGNAM-$VERSION-source +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 build +cd build +cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr \ + -DCMAKE_INSTALL_DOCDIR:PATH=/usr/share/gmsh \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DENABLE_BUILD_SHARED=ON \ + -DENABLE_PETSC=OFF \ + -DENABLE_SLEPC=OFF \ + .. +# only demos/ and tutorial/ folders will be leaved in the /usr/share/gmsh dir + +make +make install DESTDIR=$PKG +cd - + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +install -d "$PKG/usr/share/pixmaps/$PRGNAM" +install -m644 utils/icons/*.png "$PKG/usr/share/pixmaps/$PRGNAM" +install -D -m644 utils/icons/solid_32x32.png "$PKG/usr/share/icons/$PRGNAM.png" +install -D -m644 utils/icons/$PRGNAM.svg "$PKG/usr/share/icons/hicolor/scalable/apps/$PRGNAM.svg" + +desktop-file-install --dir="$PKG/usr/share/applications" "$CWD/$PRGNAM.desktop" + +mkdir -p $PKG/usr/man/man1 +mv $PKG/usr/share/man/man1/gmsh.1 $PKG/usr/man/man1/ +rm -Rf $PKG/usr/share/man/ + +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 CHANGELOG.txt CREDITS.txt LICENSE.txt README.txt $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm $PKG/usr/share/gmsh/*.txt +rm -Rf $PKG/tmp + +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:-tgz} diff --git a/academic/gmsh/gmsh.desktop b/academic/gmsh/gmsh.desktop new file mode 100644 index 0000000000..ad08eb309c --- /dev/null +++ b/academic/gmsh/gmsh.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Version=1.0 +Name=Gmsh +Comment=Automatic 3D finite element mesh generator +Icon=gmsh +Exec=gmsh +Encoding=UTF-8 +Terminal=false +Type=Application +Categories=Education;Science;Math; diff --git a/academic/gmsh/gmsh.info b/academic/gmsh/gmsh.info new file mode 100644 index 0000000000..f628e2a4c5 --- /dev/null +++ b/academic/gmsh/gmsh.info @@ -0,0 +1,10 @@ +PRGNAM="gmsh" +VERSION="4.5.4" +HOMEPAGE="http://gmsh.info/" +DOWNLOAD="http://gmsh.info/src/gmsh-4.5.4-source.tgz" +MD5SUM="dc225d64508468107eda763915d9c959" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="fltk lapack med OpenCASCADE" +MAINTAINER="Fellype do Nascimento" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/gmsh/slack-desc b/academic/gmsh/slack-desc new file mode 100644 index 0000000000..35305eed9d --- /dev/null +++ b/academic/gmsh/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 ':'. + + |-----handy-ruler------------------------------------------------------| +gmsh: gmsh (finite element mesh generator) +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: 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. +gmsh: +gmsh: diff --git a/academic/gnucap/README b/academic/gnucap/README index a13ef46e8f..c03f05979f 100644 --- a/academic/gnucap/README +++ b/academic/gnucap/README @@ -1,5 +1,5 @@ -Gnucap is a modern "post-spice" analog and mixed signal circuit simulator. -Gnucap is designed so it can eventually replace Spice. Today, it can -replace Spice in some applications. There are some significant technical -advantages. It is a work in progress. New features are added regularly -as time and demand permits. +Gnucap is a modern "post-spice" analog and mixed signal circuit +simulator. Gnucap is designed so it can eventually replace +Spice. Today, it can replace Spice in some applications. There are +some significant technical advantages. It is a work in progress. New +features are added regularly as time and demand permits. diff --git a/academic/gnucap/gnucap.SlackBuild b/academic/gnucap/gnucap.SlackBuild index 24b68142d7..a350ac9121 100644 --- a/academic/gnucap/gnucap.SlackBuild +++ b/academic/gnucap/gnucap.SlackBuild @@ -23,14 +23,15 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=gnucap -VERSION=${VERSION:-2009-12-07} -PKGVER=20091207 +VERSION=${VERSION:-20091207} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +SRCVER="$( echo $VERSION | sed 's|\(....\)\(..\)\(..\)|\1-\2-\3|' )" + if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -41,8 +42,8 @@ TMP=${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" @@ -60,9 +61,9 @@ 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 $PRGNAM-$SRCVER +tar xvf $CWD/$PRGNAM-$SRCVER.tar.gz +cd $PRGNAM-$SRCVER chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -78,7 +79,7 @@ CXXFLAGS="$SLKCFLAGS" \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PKGVER \ + --docdir=/usr/doc/$VERSION \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG @@ -93,12 +94,12 @@ 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 -mkdir -p $PKG/usr/doc/$PRGNAM-$PKGVER -cp -a AUTHORS COPYING README INSTALL $PKG/usr/doc/$PRGNAM-$PKGVER -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$PKGVER/$PRGNAM.SlackBuild -cp $CWD/$PRGNAM.png $PKG/usr/doc/$PRGNAM-$PKGVER/$PRGNAM.png -cp $PKG/usr/share/gnucap/doc/acs-tutorial $PKG/usr/doc/$PRGNAM-$PKGVER/acs-tutorial -mv $PKG/usr/share/gnucap/examples $PKG/usr/doc/$PRGNAM-$PKGVER/examples +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS COPYING README INSTALL $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cp $CWD/$PRGNAM.png $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.png +cp $PKG/usr/share/gnucap/doc/acs-tutorial $PKG/usr/doc/$PRGNAM-$VERSION/acs-tutorial +mv $PKG/usr/share/gnucap/examples $PKG/usr/doc/$PRGNAM-$VERSION/examples rm -rf $PKG/usr/share/gnucap mkdir -p $PKG/install @@ -120,4 +121,4 @@ StartupNotify=true EOF cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$PKGVER-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/grace/README b/academic/grace/README index 0e60c72cf5..8d1c5d7724 100644 --- a/academic/grace/README +++ b/academic/grace/README @@ -2,10 +2,11 @@ Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. It runs under various (if not all) flavors of Unix with X11 and M*tif (LessTif or Motif). It also runs under VMS, OS/2, and Windows (95/98/NT/2000/XP). Its capabilities are roughly similar to GUI-based -programs like Sigmaplot or Microcal Origin plus script-based tools -like Gnuplot or Genplot. Its strength lies in the fact that it -combines the convenience of a graphical user interface with the power -of a scripting language which enables it to do sophisticated -calculations or perform automated tasks. +programs like Sigmaplot or Microcal Origin plus script-based tools like +Gnuplot or Genplot. Its strength lies in the fact that it combines the +convenience of a graphical user interface with the power of a scripting +language which enables it to do sophisticated calculations or perform +automated tasks. -Grace is derived from Xmgr (a.k.a. ACE/gr), originally written by Paul Turner. +Grace is derived from Xmgr (a.k.a. ACE/gr), originally written by Paul +Turner. diff --git a/academic/grace/grace.SlackBuild b/academic/grace/grace.SlackBuild index 67ea658611..a4005d50b9 100644 --- a/academic/grace/grace.SlackBuild +++ b/academic/grace/grace.SlackBuild @@ -1,11 +1,30 @@ #!/bin/sh # Slackware build script for grace + # Written by B. Jogai <jogaib {at} comcast [dot] net> # Substantially modified by Robby Workman <rworkman@slackware.com> +# Updated by Fellype do Nascimento <fellype (at) gmail (dot) com +# +# 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. PRGNAM=grace -VERSION=${VERSION:-5.1.23} +VERSION=${VERSION:-5.1.25} BUILD=${BUILD:-1} TAG=${TAG:-"_SBo"} @@ -51,18 +70,6 @@ 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 {} \; -# Apply some miscellaneous fixup patches -patch -p0 < $CWD/patches/xmgrace-null.patch -patch -p0 < $CWD/patches/xmgrace-help.patch -patch -p0 < $CWD/patches/xmgrace-strip.patch - -# The invocation of nc_inq_libvers() has changed with the newer netcdf -patch -p1 < $CWD/patches/xmgrace-netcdf.patch - -# The header and library files of package fftw2 have been split -# up into single and double. grace uses double. -patch -p1 < $CWD/patches/xmgrace-fftw.patch - # Fix paths to docs in src/xmgrace.c sed -i "s%/usr/share/doc/packages/%/usr/lib${LIBDIRSUFFIX}/%g" src/xmgrace.c @@ -107,9 +114,9 @@ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild ln -s ../../doc/$PRGNAM-$VERSION doc ) -# We're going to leave the man pages where they are, since grace (might|does) -# look for them in its docs dir. Since grace might still use them directly, -# we're going to leave them uncompressed. Don't fuss - disk space is cheap :-) +rm -f $PKG/usr/man/man1/* +cp -a $PKG/usr/doc/$PRGNAM-$VERSION/*.1 $PKG/usr/man/man1 +gzip -9 $PKG/usr/man/man1/*.? mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/grace/grace.info b/academic/grace/grace.info index 95e4e4f1ea..2ba34f78e3 100644 --- a/academic/grace/grace.info +++ b/academic/grace/grace.info @@ -1,10 +1,10 @@ PRGNAM="grace" -VERSION="5.1.23" +VERSION="5.1.25" HOMEPAGE="http://plasma-gate.weizmann.ac.il/Grace/" -DOWNLOAD="ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/grace-5.1.23.tar.gz" -MD5SUM="e2b28ebe31288952d899fbb5c97858ae" +DOWNLOAD="ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/grace-5.1.25.tar.gz" +MD5SUM="c0482b1f18b113192946a96f5ff35a4d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="netcdf" -MAINTAINER="B. Jogai" -EMAIL="jogaib <at> comcast {dot} net" +MAINTAINER="Fellype do Nascimento" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/grace/patches/xmgrace-fftw.patch b/academic/grace/patches/xmgrace-fftw.patch deleted file mode 100644 index e4dac78592..0000000000 --- a/academic/grace/patches/xmgrace-fftw.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff -Naur grace-5.1.22.orig/configure grace-5.1.22/configure ---- grace-5.1.22.orig/configure 2008-05-21 16:52:09.000000000 -0400 -+++ grace-5.1.22/configure 2009-10-01 12:40:20.976239041 -0400 -@@ -15690,7 +15690,7 @@ - - if test "x$fftw_library" = "x" - then -- fftw_library=-lfftw -+ fftw_library=-ldfftw - fi - - { echo "$as_me:$LINENO: checking for FFTW library >= 2.1.3" >&5 -@@ -15722,7 +15722,7 @@ - cat >>conftest.$ac_ext <<_ACEOF - /* end confdefs.h. */ - --#include <fftw.h> -+#include <dfftw.h> - #include <string.h> - int main(void) { - char *vlib = (char *) fftw_version; -diff -Naur grace-5.1.22.orig/src/fourier.c grace-5.1.22/src/fourier.c ---- grace-5.1.22.orig/src/fourier.c 2004-07-03 16:47:45.000000000 -0400 -+++ grace-5.1.22/src/fourier.c 2009-10-01 12:41:14.567703801 -0400 -@@ -230,7 +230,7 @@ - #else - /* Start of new FFTW-based transforms by Marcus H. Mendenhall */ - --#include <fftw.h> -+#include <dfftw.h> - #include <string.h> - - static char *wisdom_file=0; diff --git a/academic/grace/patches/xmgrace-help.patch b/academic/grace/patches/xmgrace-help.patch deleted file mode 100644 index d8e2780c3c..0000000000 --- a/academic/grace/patches/xmgrace-help.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- src/xmgrace.c 2007/04/26 09:39:20 1.1 -+++ src/xmgrace.c 2007/04/26 09:40:26 -@@ -864,10 +864,10 @@ - - menupane = CreateMenu(menubar, "Help", 'H', TRUE); - -- CreateMenuButton(menupane, "User's Guide", 'G', HelpCB, "doc/UsersGuide.html"); -- CreateMenuButton(menupane, "Tutorial", 'T', HelpCB, "doc/Tutorial.html"); -- CreateMenuButton(menupane, "FAQ", 'Q', HelpCB, "doc/FAQ.html"); -- CreateMenuButton(menupane, "Changes", 'C', HelpCB, "doc/CHANGES.html"); -+ CreateMenuButton(menupane, "User's Guide", 'G', HelpCB, "/usr/share/doc/packages/xmgrace/doc/UsersGuide.html"); -+ CreateMenuButton(menupane, "Tutorial", 'T', HelpCB, "/usr/share/doc/packages/xmgrace/doc/Tutorial.html"); -+ CreateMenuButton(menupane, "FAQ", 'Q', HelpCB, "/usr/share/doc/packages/xmgrace/doc/FAQ.html"); -+ CreateMenuButton(menupane, "Changes", 'C', HelpCB, "/usr/share/doc/packages/xmgrace/doc/CHANGES.html"); - - CreateMenuSeparator(menupane); - diff --git a/academic/grace/patches/xmgrace-netcdf.patch b/academic/grace/patches/xmgrace-netcdf.patch deleted file mode 100644 index f18fbb6fe1..0000000000 --- a/academic/grace/patches/xmgrace-netcdf.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff -Naur grace-5.1.21.orig/configure grace-5.1.21/configure ---- grace-5.1.21.orig/configure 2007-02-16 17:44:49.000000000 -0500 -+++ grace-5.1.21/configure 2008-04-03 08:54:45.000000000 -0400 -@@ -15181,7 +15181,11 @@ - int main(void) { - char *vlib; - vlib = nc_inq_libvers(); -- if (strcmp(vlib, "3.0") < 0) { -+ /* nc_inq_libvers() has changed. It now returns a long string, -+ a portion of which is in quotes. Advance the pointer to -+ eliminate the first quote, then compare. But also need -+ to ensure backward compatibility. */ -+ if ((strcmp(vlib, "3.0") || strcmp(++vlib, "3.0")) < 0) { - exit(1); - } - exit(0); diff --git a/academic/grace/patches/xmgrace-null.patch b/academic/grace/patches/xmgrace-null.patch deleted file mode 100644 index 5a8eb77057..0000000000 --- a/academic/grace/patches/xmgrace-null.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- src/fontwin.c -+++ src/fontwin.c 2006/01/17 09:08:26 -@@ -126,7 +126,7 @@ - fonttool_frame = XmCreateDialogShell(app_shell, "Font tool", NULL, 0); - handle_close(fonttool_frame); - fonttool_panel = XtCreateWidget("fonttool_panel", xmFormWidgetClass, -- fonttool_frame, NULL, 0); -+ fonttool_frame, NULL, NULL); - - font_select_item = CreateFontChoice(fonttool_panel, "Font:"); - XtVaSetValues(font_select_item->menu, diff --git a/academic/grace/patches/xmgrace-strip.patch b/academic/grace/patches/xmgrace-strip.patch deleted file mode 100644 index 5ac62995cc..0000000000 --- a/academic/grace/patches/xmgrace-strip.patch +++ /dev/null @@ -1,33 +0,0 @@ ---- auxiliary/Makefile -+++ auxiliary/Makefile -@@ -27,7 +27,7 @@ - install : $(AUXILIARIES) $(PROGRAMS) $(SCRIPTS) - $(MKINSTALLDIRS) $(DESTDIR)$(GRACE_HOME)/auxiliary - for i in $(AUXILIARIES); do $(INSTALL_DATA) $$i $(DESTDIR)$(GRACE_HOME)/auxiliary; done -- for i in $(PROGRAMS); do $(INSTALL_PROGRAM) -s $$i $(DESTDIR)$(GRACE_HOME)/bin; done -+ for i in $(PROGRAMS); do $(INSTALL_PROGRAM) $$i $(DESTDIR)$(GRACE_HOME)/bin; done - for i in $(SCRIPTS); do $(INSTALL_PROGRAM) $$i $(DESTDIR)$(GRACE_HOME)/bin; done - - tests : dummy ---- grconvert/Makefile -+++ grconvert/Makefile -@@ -42,7 +42,7 @@ - - install : $(PROG) - $(MKINSTALLDIRS) $(DESTDIR)$(GRACE_HOME)/bin -- $(INSTALL_PROGRAM) -s $(PROG) $(DESTDIR)$(GRACE_HOME)/bin/$(PROG) -+ $(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(GRACE_HOME)/bin/$(PROG) - - dummy : - ---- src/Makefile -+++ src/Makefile -@@ -60,7 +60,7 @@ - - install : $(GRACE) - $(MKINSTALLDIRS) $(DESTDIR)$(GRACE_HOME)/bin -- $(INSTALL_PROGRAM) -s $(GRACE) $(DESTDIR)$(GRACE_HOME)/bin/$(GRACE) -+ $(INSTALL_PROGRAM) $(GRACE) $(DESTDIR)$(GRACE_HOME)/bin/$(GRACE) - cd $(DESTDIR)$(GRACE_HOME)/bin; $(RM) $(GRBATCH); $(LN_S) $(GRACE) $(GRBATCH) - - tests : dummy diff --git a/academic/grace/xmgrace.desktop b/academic/grace/xmgrace.desktop index 183f364c08..08273f63e3 100644 --- a/academic/grace/xmgrace.desktop +++ b/academic/grace/xmgrace.desktop @@ -5,4 +5,4 @@ Name=xmgrace Terminal=false Comment=Scientific Plotting Application Icon=/usr/share/pixmaps/xmgrace.png -Categories=Qt;KDE;Graphics;Development; +Categories=Education;Science; diff --git a/academic/gri/README b/academic/gri/README new file mode 100644 index 0000000000..083bd2d993 --- /dev/null +++ b/academic/gri/README @@ -0,0 +1,13 @@ +Gri is a language for scientific graphics applications. By 'language' +I mean that it is a command-driven application, as opposed to a +click/point application. It is analogous to latex or tex, and shares +the property that extensive power is the reward for tolerating a +learning curve. Gri output is in PostScript, suitable for +incorporation in documents prepared by various text processors. + +Gri can make x-y graphs, contour-graphs, and image graphs. In +addition to high-level capabilities, it has enough low-level +capabilities to allow users to achieve a high degree of customization. +Control is extended to all aspects of drawing, including +line widths, colors, and fonts. Text includes a subset of the tex +language for letters and mathematical symbols in labels. diff --git a/academic/gri/UTF8patch.README b/academic/gri/UTF8patch.README new file mode 100644 index 0000000000..f30c7c969b --- /dev/null +++ b/academic/gri/UTF8patch.README @@ -0,0 +1,19 @@ +Compilation of gri breaks on doc/gri.texi with current tex-info. + +"It is because Texinfo 6.7 changed the default input encoding to UTF-8 +and the input is in ISO-8859-1. The easiest way to fix this would be to +convert the input file to UTF-8, but you could also add +"@documentencoding ISO-8859-1" to the file." +(from email correspondence with texinfo developers) + +The patchfile 'gri-texinfo-6.7patch.txt' set the whole file to ISO-8859-1 +and does not alter the contributor's name. + + +The other patchfile, 'texinfo-utf8.patch', was generated by Matteo Bernardini +(http://cgit.ponce.cc/slackbuilds/commit/?h=gri), and changes the accented o in the name. + +Either patch allows compilation of gri. + +see: +https://www.linuxquestions.org/questions/slackware-14/sbo-scripts-not-building-on-current-read-1st-post-pls-4175561999/page142.html#post6049662
\ No newline at end of file diff --git a/academic/gri/gri-texinfo-6.7patch.txt b/academic/gri/gri-texinfo-6.7patch.txt new file mode 100644 index 0000000000..f9b2dedf91 --- /dev/null +++ b/academic/gri/gri-texinfo-6.7patch.txt @@ -0,0 +1,10 @@ +diff -Naur gri-2.12.23/doc/gri.texi gri-2.12.23-new/doc/gri.texi +--- gri-2.12.23/doc/gri.texi 2017-08-24 15:31:52.000000000 +0100 ++++ gri-2.12.23-new/doc/gri.texi 2019-10-22 16:13:33.476840964 +0100 +@@ -1,5 +1,5 @@ + \input texinfo +- ++@documentencoding ISO-8859-1 + @c + @comment *** Start of HTML stuff *** + @comment # HTML support, via comments in texinfo: diff --git a/academic/gri/gri.SlackBuild b/academic/gri/gri.SlackBuild new file mode 100644 index 0000000000..965946ecd2 --- /dev/null +++ b/academic/gri/gri.SlackBuild @@ -0,0 +1,117 @@ +#!/bin/sh + +# Slackware build script for gri + +# Copyright 2018-2019 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: +# +# 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. + +PRGNAM=gri +VERSION=${VERSION:-2.12.23} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 {} \; + +#with thanks to Gavin Smith +patch -p1 < $CWD/gri-texinfo-6.7patch.txt +#with thanks to Matteo Bernardini +#patch -p1 < $CWD/texinfo-utf8.patch + +aclocal +autoconf +automake --add-missing + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +#with thanks to Matteo Bernardini +#see: https://www.linuxquestions.org/questions/slackware-14/sbo-scripts-not-building-on-current-read-1st-post-pls-4175561999/page142.html#post6049662 +make -j1 +make -j1 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 + +mv $PKG/usr/share/man $PKG/usr/man +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +rm -f $PKG/usr/share/info/dir +mv $PKG/usr/share/info $PKG/usr/info +# info is already gzipped +rm $PKG/usr/info/*.info +rm $PKG/usr/info/*.info-[1-3] + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS AUTHOR-NOTES ChangeLog THANKS README NEWS INSTALL DISCUSSION-error-levels COPYING copyright.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:-tgz} diff --git a/academic/gri/gri.info b/academic/gri/gri.info new file mode 100644 index 0000000000..6e4ee42dde --- /dev/null +++ b/academic/gri/gri.info @@ -0,0 +1,10 @@ +PRGNAM="gri" +VERSION="2.12.23" +HOMEPAGE="https://sourceforge.net/p/gri/wiki/Home/" +DOWNLOAD="https://github.com/dankelley/gri/archive/v2.12.23/gri-2.12.23.tar.gz" +MD5SUM="7594140fdd1ea1ccf890c2d7ede0e1e9" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Rob van Nues" +EMAIL="sborg63@disroot.org" diff --git a/academic/gri/slack-desc b/academic/gri/slack-desc new file mode 100644 index 0000000000..ae076aa356 --- /dev/null +++ b/academic/gri/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------------------------------------------------------| +gri: gri (graphics language) +gri: +gri: Gri is a language for scientific graphics applications. +gri: It is a command-driven application and analogous to latex or tex, and +gri: shares the property that extensive power is the reward for tolerating +gri: a learning curve. Gri output is in PostScript, suitable for +gri: incorporation in documents prepared by various text processors. +gri: +gri: Home: https://github.com/dankelley/gri +gri: or http://gri.sourceforge.net/ +gri: diff --git a/academic/gri/texinfo-utf8.patch b/academic/gri/texinfo-utf8.patch new file mode 100644 index 0000000000..b63573de33 --- /dev/null +++ b/academic/gri/texinfo-utf8.patch @@ -0,0 +1,12 @@ +diff -Naur gri-2.12.23.orig/doc/gri.texi gri-2.12.23/doc/gri.texi +--- gri-2.12.23.orig/doc/gri.texi 2017-08-24 16:31:52.000000000 +0200 ++++ gri-2.12.23/doc/gri.texi 2019-10-22 15:39:51.666151000 +0200 +@@ -19277,7 +19277,7 @@ + Thomas Larsen, + @cindex Thomas Larsen (contributor) + @cindex contributor, Thomas Larsen +-Alejandro L�pez-Valencia, ++Alejandro Lopez-Valencia, + @cindex Alejandro Lopez-Valencia (contributor) + @cindex contributor, Alejandro Lopez-Valencia + Kawamura Masao,
\ No newline at end of file diff --git a/academic/grpn/README b/academic/grpn/README index af0f57f7b3..ebe90d81ce 100644 --- a/academic/grpn/README +++ b/academic/grpn/README @@ -1,9 +1,10 @@ -GRPN is a graphical reverse polish notation (RPN) calculator. -GRPN is written in C and uses the GIMP Toolkit (GTK) on top of X11. GRPN -was developed under Linux but has also been tested under SunOS and Solaris. -It should work with almost any UNIX, though. GRPN works with real numbers -and complex numbers. Numbers can be displayed in 4 different radix modes, -and complex numbers can be displayed in either Cartesian or polar form. +GRPN is a graphical reverse polish notation (RPN) calculator. GRPN is +written in C and uses the GIMP Toolkit (GTK) on top of X11. GRPN was +developed under Linux but has also been tested under SunOS and Solaris. +It should work with almost any UNIX, though. GRPN works with real +numbers and complex numbers. Numbers can be displayed in 4 different +radix modes, and complex numbers can be displayed in either Cartesian +or polar form. -GRPN uses a stack and reverse polish notation to evaluate expressions. The -stack in GRPN is infinite and limited only by available memory. +GRPN uses a stack and reverse polish notation to evaluate expressions. +The stack in GRPN is infinite and limited only by available memory. diff --git a/academic/gspiceui/gspiceui.SlackBuild b/academic/gspiceui/gspiceui.SlackBuild index 8375227722..5855a4a05e 100644 --- a/academic/gspiceui/gspiceui.SlackBuild +++ b/academic/gspiceui/gspiceui.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=gspiceui -VERSION=${VERSION:-1.1.00} +VERSION=${VERSION:-1.2.36} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/gspiceui/gspiceui.info b/academic/gspiceui/gspiceui.info index 0b1417a2f4..a46c540959 100644 --- a/academic/gspiceui/gspiceui.info +++ b/academic/gspiceui/gspiceui.info @@ -1,8 +1,8 @@ PRGNAM="gspiceui" -VERSION="1.1.00" +VERSION="1.2.36" HOMEPAGE="http://users.tpg.com.au/micksw012/gspiceui.html" -DOWNLOAD="https://sourceforge.net/projects/gspiceui/files/gSpiceUI/gspiceui-v1.1.00/gspiceui-v1.1.00.tar.gz" -MD5SUM="f159b2c65ab1ee3eaeb61414e919392e" +DOWNLOAD="https://sourceforge.net/projects/gspiceui/files/gSpiceUI/gspiceui-v1.2.36/gspiceui-v1.2.36.tar.gz" +MD5SUM="a385028952ada5aa69acdb7298332c8c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="pangox-compat wxPython3" diff --git a/academic/gtkwave/README b/academic/gtkwave/README index fa42f8d4de..6c030894b0 100644 --- a/academic/gtkwave/README +++ b/academic/gtkwave/README @@ -1,2 +1,2 @@ -GTKWave is a fully featured GTK+ based wave viewer which reads LXT, LXT2, -VZT, and GHW files as well as standard Verilog VCD EVCD files. +GTKWave is a fully featured GTK+ based wave viewer which reads LXT, +LXT2, VZT, and GHW files as well as standard Verilog VCD EVCD files. diff --git a/academic/gwyddion/README b/academic/gwyddion/README index 3b8a4dee6f..6821f7110c 100644 --- a/academic/gwyddion/README +++ b/academic/gwyddion/README @@ -1,7 +1,7 @@ Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for analysis of height fields obtained by means of scanning probe microscopy techniques -(AFM, MFM, STM, SNOM/NSOM), however it can be generally used for any other -height field and image analysis. +(AFM, MFM, STM, SNOM/NSOM), however it can be generally used for any +other height field and image analysis. libminizip, libwebp and cfitsio are the optional dependencies. diff --git a/academic/gwyddion/doinst.sh b/academic/gwyddion/doinst.sh index 36863cab7d..8a5ffa8af5 100644 --- a/academic/gwyddion/doinst.sh +++ b/academic/gwyddion/doinst.sh @@ -1,12 +1,3 @@ -schema_install() { - SCHEMA="$1" - GCONF_CONFIG_SOURCE="xml::etc/gconf/gconf.xml.defaults" \ - chroot . gconftool-2 --makefile-install-rule \ - /etc/gconf/schemas/$SCHEMA \ - 1>/dev/null -} - -schema_install gwyddion-thumbnailer.schemas if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 diff --git a/academic/gwyddion/gwyddion.SlackBuild b/academic/gwyddion/gwyddion.SlackBuild index 226ad86ecb..0af5356e82 100644 --- a/academic/gwyddion/gwyddion.SlackBuild +++ b/academic/gwyddion/gwyddion.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=gwyddion -VERSION=${VERSION:-2.52} +VERSION=${VERSION:-2.58} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/gwyddion/gwyddion.info b/academic/gwyddion/gwyddion.info index 823159876d..13e0741611 100644 --- a/academic/gwyddion/gwyddion.info +++ b/academic/gwyddion/gwyddion.info @@ -1,8 +1,8 @@ PRGNAM="gwyddion" -VERSION="2.52" +VERSION="2.58" HOMEPAGE="http://gwyddion.net" -DOWNLOAD="http://downloads.sourceforge.net/gwyddion/gwyddion-2.52.tar.xz" -MD5SUM="0c7818ecb5618bbaaa16a35c0da7cdf2" +DOWNLOAD="http://downloads.sourceforge.net/gwyddion/gwyddion-2.58.tar.xz" +MD5SUM="a1157cd107049fdc141aec268f9b0032" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="gtkglext" diff --git a/academic/h5utils/README b/academic/h5utils/README new file mode 100644 index 0000000000..3b0ed29af6 --- /dev/null +++ b/academic/h5utils/README @@ -0,0 +1,9 @@ +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. diff --git a/academic/h5utils/h5utils.SlackBuild b/academic/h5utils/h5utils.SlackBuild new file mode 100644 index 0000000000..1f85355f30 --- /dev/null +++ b/academic/h5utils/h5utils.SlackBuild @@ -0,0 +1,114 @@ +#!/bin/sh + +# Slackware build script for h5utils + +# Copyright 2019 Paul Kinsler, U.K. +# 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. + +PRGNAM=h5utils +VERSION=${VERSION:-1.13.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${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 + +# 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 +rm -rf $PRGNAM-$SVERSION +tar xvf $CWD/$PRGNAM-$SVERSION.tar.gz +cd $PRGNAM-$SVERSION +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 there is no configure script, try to build one! +if [ ! -f ./configure ] ; then + ./autogen.sh +fi + +LOCALCONFIGS= + +CFLAGS="$SLKCFLAGS" \ +CPPFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --mandir=/usr/man \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$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 + +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 + +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/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/h5utils/h5utils.info b/academic/h5utils/h5utils.info new file mode 100644 index 0000000000..a600f211b9 --- /dev/null +++ b/academic/h5utils/h5utils.info @@ -0,0 +1,10 @@ +PRGNAM="h5utils" +VERSION="1.13.1" +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_x86_64="" +MD5SUM_x86_64="" +REQUIRES="hdf5" +MAINTAINER="PaulKinsler" +EMAIL="dr.paul@kinsler.org" diff --git a/academic/h5utils/slack-desc b/academic/h5utils/slack-desc new file mode 100644 index 0000000000..226340b323 --- /dev/null +++ b/academic/h5utils/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------------------------------------------------------| +h5utils: h5utils (visualization and conversion of HDF5 data) +h5utils: +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. +h5utils: +h5utils: Homepage: https://github.com/NanoComp/h5utils +h5utils: +h5utils: +h5utils: diff --git a/academic/harminv/README b/academic/harminv/README new file mode 100644 index 0000000000..fc3c9c0bc7 --- /dev/null +++ b/academic/harminv/README @@ -0,0 +1,5 @@ +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. diff --git a/academic/harminv/harminv.SlackBuild b/academic/harminv/harminv.SlackBuild new file mode 100644 index 0000000000..34d85f200d --- /dev/null +++ b/academic/harminv/harminv.SlackBuild @@ -0,0 +1,112 @@ +#!/bin/sh + +# Slackware build script for harminv + +# Copyright 2019 Paul Kinsler, U.K. +# 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. + +PRGNAM=harminv +VERSION=${VERSION:-1.4.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# change annoying underscores into hyphens +SVERSION=$(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 +rm -rf $PRGNAM-$SVERSION +tar xvf $CWD/$PRGNAM-$SVERSION.tar.gz +cd $PRGNAM-$SVERSION +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 there is no configure script, try to build one! +if [ ! -f ./configure ] ; then + ./autogen.sh +fi + +LOCALCONFIGS="--enable-shared --with-blas=atlas" + +CFLAGS="$SLKCFLAGS" \ +CPPFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --mandir=/usr/man \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux \ + --enable-static=no \ + $LOCALCONFIGS + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +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 + +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:-tgz} diff --git a/academic/harminv/harminv.info b/academic/harminv/harminv.info new file mode 100644 index 0000000000..4ba38e5070 --- /dev/null +++ b/academic/harminv/harminv.info @@ -0,0 +1,10 @@ +PRGNAM="harminv" +VERSION="1.4.1" +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_x86_64="" +MD5SUM_x86_64="" +REQUIRES="lapack" +MAINTAINER="PaulKinsler" +EMAIL="dr.paul@kinsler.org" diff --git a/academic/harminv/slack-desc b/academic/harminv/slack-desc new file mode 100644 index 0000000000..63773e4878 --- /dev/null +++ b/academic/harminv/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 ':'. + + |-----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: sinusoids, dettermining the frequencies, decay constants, +harminv: amplitudes, and phases of those sinusoids. +harminv: +harminv: Homepage: https://github.com/NanoComp/harminv +harminv: +harminv: diff --git a/academic/io_lib/io_lib.SlackBuild b/academic/io_lib/io_lib.SlackBuild index e99cd2f10f..9a6f5a76d6 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 2011-2017 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=io_lib -VERSION=${VERSION:-1.14.9} +VERSION=${VERSION:-1.14.13} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/io_lib/io_lib.info b/academic/io_lib/io_lib.info index 304808c5bf..246c55cff8 100644 --- a/academic/io_lib/io_lib.info +++ b/academic/io_lib/io_lib.info @@ -1,8 +1,8 @@ PRGNAM="io_lib" -VERSION="1.14.9" -HOMEPAGE="http://staden.sourceforge.net/" -DOWNLOAD="http://sourceforge.net/projects/staden/files/io_lib/1.14.9/io_lib-1.14.9.tar.gz" -MD5SUM="c063ec3124c4a9c1af70b2cad10cd381" +VERSION="1.14.13" +HOMEPAGE="https://github.com/jkbonfield/io_lib" +DOWNLOAD="https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-13/io_lib-1.14.13.tar.gz" +MD5SUM="5b15a68b9dac242a4e5c83900e330d7d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/jalview/jalview b/academic/jalview/jalview index 31813c2c2a..cfdcceef1f 100644 --- a/academic/jalview/jalview +++ b/academic/jalview/jalview @@ -1,16 +1,2 @@ #!/bin/sh - -# This wrapper script is taken from Arch Linux AUR entry of jalview. -# https://aur.archlinux.org/packages/jalview/ -# Maintainer of the PKGBUILD is Stefan Seemayer. - -progname="jalview" -mainclass="jalview.bin.Jalview" -basedir="/usr/share/java/$progname" - -# build classpath: all jars in $basedir -cp=$( ls $basedir/*.jar | xargs echo | sed "s/ /:/g" ); - - -# run jar -"$JAVA_HOME/bin/java" -cp $cp $mainclass +java -jar /opt/jalview/jalview diff --git a/academic/jalview/jalview.SlackBuild b/academic/jalview/jalview.SlackBuild index 1ec9acf47f..30d2cdbe8f 100644 --- a/academic/jalview/jalview.SlackBuild +++ b/academic/jalview/jalview.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for jalview -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# With help from the jalview PKGBUILD at Arch linux AUR: -# https://aur.archlinux.org/packages/jalview/ - PRGNAM=jalview -VERSION=${VERSION:-2.10.0b1} +VERSION=${VERSION:-2.11.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} ARCH=noarch +JAVA=j1.8 + CWD=$(pwd) TMP=${TMP:-/tmp/SBo} @@ -42,27 +41,11 @@ 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 $PKG/usr/share/java/$PRGNAM -cp -a *.jar $PKG/usr/share/java/$PRGNAM -# The wrapper is from Arch. Thank you! +install -D -m755 $CWD/$PRGNAM-all-$VERSION-$JAVA.jar $PKG/opt/$PRGNAM/$PRGNAM install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - building.html exampleFeatures.txt LICENSE README_IA \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/TheJalviewTutorial_screen.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/Tutorial.pdf cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/jalview/jalview.info b/academic/jalview/jalview.info index 928c20cf89..499422a4d6 100644 --- a/academic/jalview/jalview.info +++ b/academic/jalview/jalview.info @@ -1,10 +1,8 @@ PRGNAM="jalview" -VERSION="2.10.0b1" +VERSION="2.11.1.0" HOMEPAGE="http://www.jalview.org/" -DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/JalView/2.10/jalview-2.10.0b1.tar.gz \ - http://sourceforge.net/projects/sboppetrov/files/JalView/TheJalviewTutorial_screen.pdf" -MD5SUM="fb5b30202210e21647ecc7da5242bab3 \ - 5e2f8da8f2528049f055263aecd2f8af" +DOWNLOAD="http://www.jalview.org/getdown/release/jalview-all-2.11.1.0-j1.8.jar" +MD5SUM="7f79b598a5bfd25d89adf6fe8c9b98f7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="jdk" diff --git a/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild b/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild index 4e22588b36..e2f2db0ffa 100644 --- a/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild +++ b/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild @@ -22,12 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -SRCNAM=jellyfish -PRGNAM=${SRCNAM}_k-mer +PRGNAM=jellyfish_k-mer VERSION=${VERSION:-1.1.12} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +SRCNAM=jellyfish + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; diff --git a/academic/jpicedt/README b/academic/jpicedt/README index ddc93e1dee..2c578cf5bc 100644 --- a/academic/jpicedt/README +++ b/academic/jpicedt/README @@ -1,12 +1,14 @@ -jPicEdt is a software aimed at alleviating the burden of using PSTricks, -eepic or LaTeX's picture environment macros in a LaTeX file. It allows the -user to draw graphical objects using graphic primitives (e.g. splines, -arcs, polygons,...), position them easily with the mouse, and add text -using LaTeX/PSTricks box commands (e.g. dashbox, psframebox,...). +jPicEdt is a software aimed at alleviating the burden of using +PSTricks, eepic or LaTeX's picture environment macros in a LaTeX +file. It allows the user to draw graphical objects using graphic +primitives (e.g. splines, arcs, polygons,...), position them easily +with the mouse, and add text using LaTeX/PSTricks box commands +(e.g. dashbox, psframebox,...). This is a repackaging of the JPicEdt distribution jar archive. -There is a required pstricks-add.{sty,tex} available in add-ons/Tex-macros -of the source. The versions supplied with Slackware's tetex package are -newer and seem to work fine by default; however, if you encounter any problems -with it, you might try using the files supplied with JPicEdt. +There is a required pstricks-add.{sty,tex} available in +add-ons/Tex-macros of the source. The versions supplied with +Slackware's tetex package are newer and seem to work fine by default; +however, if you encounter any problems with it, you might try using the +files supplied with JPicEdt. diff --git a/academic/kiwisolver/README b/academic/kiwisolver/README index 7773aa35ea..96743769c0 100644 --- a/academic/kiwisolver/README +++ b/academic/kiwisolver/README @@ -1,7 +1,7 @@ -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. +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/klavaro/klavaro.SlackBuild b/academic/klavaro/klavaro.SlackBuild index e5b970b788..2ad1b51b30 100644 --- a/academic/klavaro/klavaro.SlackBuild +++ b/academic/klavaro/klavaro.SlackBuild @@ -2,7 +2,8 @@ # Slackware build script for Klavaro -# Copyright 2015 Thibaut Notteboom +# Copyright 2015 Thibaut Notteboom +# Copyright 2019 Johannes Schoepfer, Germany # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,13 +24,13 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=klavaro -VERSION=${VERSION:-3.01} +VERSION=${VERSION:-3.03} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -40,8 +41,8 @@ TMP=${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" @@ -81,6 +82,9 @@ CXXFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG +# Don't ship .la files: +#rm -f $PKG/usr/lib${LIBDIRSUFFIX}/*.la + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/klavaro/klavaro.info b/academic/klavaro/klavaro.info index 2804b8c9c2..a7b7be9946 100644 --- a/academic/klavaro/klavaro.info +++ b/academic/klavaro/klavaro.info @@ -1,10 +1,10 @@ PRGNAM="klavaro" -VERSION="3.01" -HOMEPAGE="http://klavaro.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/project/klavaro/klavaro-3.01.tar.bz2" -MD5SUM="53e2824ccc89f70dd7dca4d52ccf9c0e" +VERSION="3.03" +HOMEPAGE="https://klavaro.sourceforge.io/" +DOWNLOAD="https://downloads.sourceforge.net/project/klavaro/klavaro-3.03.tar.bz2" +MD5SUM="0299f185ed8f9aac3441685fbf7177dc" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Thibaut Notteboom" -EMAIL="thibaut.notteboom@gmail.com" +MAINTAINER="Johannes Schoepfer" +EMAIL="slackbuilds@schoepfer.info" diff --git a/academic/klu/README b/academic/klu/README index fe8941f406..e3da56e0c7 100644 --- a/academic/klu/README +++ b/academic/klu/README @@ -1,7 +1,7 @@ -KLU is a sparse LU factorization algorithm well-suited for use in circuit -simulation. +KLU is a sparse LU factorization algorithm well-suited for use in +circuit simulation. This package is part of SuiteSparse. -CHOLMOD is an optional dependency and will be used if found. -It is primarily used for this package's test suite. +CHOLMOD is an optional dependency and will be used if found. It is +primarily used for this package's test suite. diff --git a/academic/klu/klu.SlackBuild b/academic/klu/klu.SlackBuild index 4578b25590..cff38308c6 100644 --- a/academic/klu/klu.SlackBuild +++ b/academic/klu/klu.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for KLU -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=klu SRCNAM=SuiteSparse SUBDIR=KLU VERSION=${VERSION:-1.3.9} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-2} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-4} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/klu/klu.info b/academic/klu/klu.info index a9ccd6a7b7..2a2faab22f 100644 --- a/academic/klu/klu.info +++ b/academic/klu/klu.info @@ -1,8 +1,8 @@ PRGNAM="klu" VERSION="1.3.9" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig amd colamd btf" diff --git a/academic/klu/patches/autoconfiscate.diff b/academic/klu/patches/autoconfiscate.diff index 81f72fe614..9a17f6fcfa 100644 --- a/academic/klu/patches/autoconfiscate.diff +++ b/academic/klu/patches/autoconfiscate.diff @@ -282,7 +282,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([KLU],[1.3.9],[DrTimothyAldenDavis@gmail.com],[klu],[http://www.suitesparse.com/]) ++AC_INIT([KLU],[1.3.9],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[klu],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/klu.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/kraken/kraken.SlackBuild b/academic/kraken/kraken.SlackBuild index 5b1eacebcb..ab71cb0f0c 100644 --- a/academic/kraken/kraken.SlackBuild +++ b/academic/kraken/kraken.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for kraken -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2019 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=kraken -VERSION=${VERSION:-1.1} +VERSION=${VERSION:-1.1.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/kraken/kraken.info b/academic/kraken/kraken.info index 7b78c71755..08f0e2c6c3 100644 --- a/academic/kraken/kraken.info +++ b/academic/kraken/kraken.info @@ -1,8 +1,8 @@ PRGNAM="kraken" -VERSION="1.1" +VERSION="1.1.1" HOMEPAGE="http://ccb.jhu.edu/software/kraken/" -DOWNLOAD="https://github.com/DerrickWood/kraken/archive/v1.1/kraken-1.1.tar.gz" -MD5SUM="da11f520b3ff21228ac0ceff5ad895a4" +DOWNLOAD="https://github.com/DerrickWood/kraken/archive/v1.1.1/kraken-1.1.1.tar.gz" +MD5SUM="91b988e05ffaa128c7bf28816a41a910" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="jellyfish_k-mer" diff --git a/academic/lalnview/README b/academic/lalnview/README index e91c30683f..364d8d0378 100644 --- a/academic/lalnview/README +++ b/academic/lalnview/README @@ -5,6 +5,13 @@ similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between segments. +A suitable alignment tool for protein sequences is SIM at ExPASy: +https://web.expasy.org/sim/ + +SIM finds a user-defined number of best non-intersecting alignments +between two protein sequences or within a sequence. Once the alignment +is computed, you can view it using LalnView. + For details and citation: Duret, L., Gasteiger, E. and Perriere, G. (1996) LalnView: a graphical viewer for pairwise sequence alignments. Comput. Applic. diff --git a/academic/lalnview/lalnview.SlackBuild b/academic/lalnview/lalnview.SlackBuild index cb92a3bcc3..3ba95c44d5 100644 --- a/academic/lalnview/lalnview.SlackBuild +++ b/academic/lalnview/lalnview.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for lalnview -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,12 +26,14 @@ PRGNAM=lalnview VERSION=${VERSION:-3.0} -BUILD=${BUILD:-2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +SRCTAR=sources20050615.tar + if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -42,8 +44,8 @@ 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" @@ -64,24 +66,24 @@ cd $TMP rm -rf $PRGNAM-$VERSION mkdir $PRGNAM-$VERSION cd $PRGNAM-$VERSION -tar xvf $CWD/sources20050615.tar +tar xvf $CWD/$SRCTAR 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 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -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 {} \; # Point to the correct place of lalnview.help -sed -i "s:lalnview.help:/usr/doc/$PRGNAM-$VERSION/lalnview.help:" MF_MainWindow.cxx +sed -i "s:$PRGNAM.help:/usr/doc/$PRGNAM-$VERSION/$PRGNAM.help:" MF_MainWindow.cxx OPT="$SLKCFLAGS" make -install -D -m755 lalnview $PKG/usr/bin/$PRGNAM +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 -# Couldn't find an icon, so i made one myself. I know it sucks. +# Couldn't find an icon, so i made one myself. 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/lalnview/lalnview.png b/academic/lalnview/lalnview.png Binary files differindex f4cc77c61c..f528cc3d46 100644 --- a/academic/lalnview/lalnview.png +++ b/academic/lalnview/lalnview.png diff --git a/academic/lapack95/lapack95.SlackBuild b/academic/lapack95/lapack95.SlackBuild index 6a4a9e7815..92c1139843 100644 --- a/academic/lapack95/lapack95.SlackBuild +++ b/academic/lapack95/lapack95.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for lapack95 -# Written by Pablo Santamaría (pablosantamaria@gmail.com) +# Written by Pablo SantamarĂa (pablosantamaria@gmail.com) # Copyright 2017 Ekin Akoglu, Erdemli, Mersin, Turkey # All rights reserved. # diff --git a/academic/lapacke/README b/academic/lapacke/README index 56e7a29488..118c2449de 100644 --- a/academic/lapacke/README +++ b/academic/lapacke/README @@ -1,10 +1,12 @@ LAPACKE provides a native C interface to LAPACK routines available at -www.netlib.org/lapack to facilitate usage of LAPACK functionality for C -programmers. +www.netlib.org/lapack to facilitate usage of LAPACK functionality for +C programmers. -This package is intended for use with the Netlib reference LAPACK. It should -also work with other LAPACK implementations that do not already provide a -LAPACKE implementation. +This package is intended for use with the Netlib reference LAPACK. +It should also work with other LAPACK implementations that do not +already provide a LAPACKE implementation. -To build a static library in addition to the shared library, -pass STATIC=yes to the script. +xblas is an optional dependency. + +To build a static library in addition to the shared library, pass +STATIC=yes to the script. diff --git a/academic/lapacke/lapacke.SlackBuild b/academic/lapacke/lapacke.SlackBuild index 8e48993487..b7bac2704f 100644 --- a/academic/lapacke/lapacke.SlackBuild +++ b/academic/lapacke/lapacke.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for LAPACKE -# Copyright 2016-2017 Kyle Guinn <elyk03@gmail.com>, USA +# Copyright 2016-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,7 +24,7 @@ PRGNAM=lapacke SRCNAM=lapack -VERSION=${VERSION:-3.8.0} +VERSION=${VERSION:-3.9.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -38,7 +38,7 @@ fi CWD=$(pwd) TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM +PKG=$TMP/package-$PRGNAM-$VERSION OUTPUT=${OUTPUT:-/tmp} DOCS="LAPACKE/LICENSE LAPACKE/README DOCS/lapacke.pdf" @@ -69,6 +69,10 @@ chmod -R u+w,go-w,a+rX-st . # Allow building only the LAPACKE component. patch -p1 < $CWD/patches/cmake-piecewise.diff +if pkg-config --exists xblas; then + use_xblas='-DUSE_XBLAS=ON' +fi + # Avoid adding an RPATH entry to the shared lib. It's unnecessary (except for # running the test suite), and it's broken on 64-bit (needs LIBDIRSUFFIX). mkdir -p shared @@ -81,6 +85,8 @@ cd shared -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DUSE_OPTIMIZED_LAPACK=ON \ -DBUILD_LAPACKE=ON \ + -DBUILD_DEPRECATED=ON \ + $use_xblas \ -DBUILD_SHARED_LIBS=ON \ -DCMAKE_SKIP_RPATH=YES \ .. @@ -102,6 +108,8 @@ if [ "${STATIC:-no}" != "no" ]; then -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DUSE_OPTIMIZED_LAPACK=ON \ -DBUILD_LAPACKE=ON \ + -DBUILD_DEPRECATED=ON \ + $use_xblas \ .. make make install/strip DESTDIR=$PKG diff --git a/academic/lapacke/lapacke.info b/academic/lapacke/lapacke.info index 66c9eeb65a..aa77adac19 100644 --- a/academic/lapacke/lapacke.info +++ b/academic/lapacke/lapacke.info @@ -1,8 +1,8 @@ PRGNAM="lapacke" -VERSION="3.8.0" -HOMEPAGE="http://www.netlib.org/lapack/lapacke.html" -DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.8.0/lapack-3.8.0.tar.gz" -MD5SUM="96591affdbf58c450d45c1daa540dbd2" +VERSION="3.9.1" +HOMEPAGE="https://www.netlib.org/lapack/lapacke.html" +DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.9.1/lapack-3.9.1.tar.gz" +MD5SUM="47ab2d11652045145df37ddbe2a32d71" 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 8c2ac6c6a3..378acc8769 100644 --- a/academic/lapacke/patches/cmake-piecewise.diff +++ b/academic/lapacke/patches/cmake-piecewise.diff @@ -5,25 +5,27 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt message(STATUS "CBLAS enable") enable_language(C) --set(LAPACK_INSTALL_EXPORT_NAME cblas-targets) +-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 -@@ -36,50 +34,8 @@ +@@ -45,54 +43,8 @@ add_subdirectory(examples) endif() -if(NOT BLAS_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} blas) +- set(ALL_TARGETS ${ALL_TARGETS} ${BLASLIB}) -endif() - -# Export cblas targets from the -# install tree, if any. -set(_cblas_config_install_guard_target "") -if(ALL_TARGETS) -- install(EXPORT cblas-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION}) +- install(EXPORT ${CBLASLIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${CBLASLIB}-${LAPACK_VERSION} +- COMPONENT Development +- ) - # Choose one of the cblas targets to use as a guard for - # cblas-config.cmake to load targets from the install tree. - list(GET ALL_TARGETS 0 _cblas_config_install_guard_target) @@ -32,7 +34,7 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt -# Export cblas targets from the build tree, if any. -set(_cblas_config_build_guard_target "") -if(ALL_TARGETS) -- export(TARGETS ${ALL_TARGETS} FILE cblas-targets.cmake) +- export(TARGETS ${ALL_TARGETS} FILE ${CBLASLIB}-targets.cmake) - - # Choose one of the cblas targets to use as a guard - # for cblas-config.cmake to load targets from the build tree. @@ -40,27 +42,29 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt -endif() - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-version.cmake.in -- ${LAPACK_BINARY_DIR}/cblas-config-version.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config-version.cmake @ONLY) -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config.cmake @ONLY) - - - configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY) + configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/${CBLASLIB}.pc @ONLY) install(FILES - ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc + ${CMAKE_CURRENT_BINARY_DIR}/${CBLASLIB}.pc DESTINATION ${PKG_CONFIG_DIR} ) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-install.cmake.in -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/cblas-config.cmake @ONLY) +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${CBLASLIB}-config.cmake @ONLY) -install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/cblas-config.cmake -- ${LAPACK_BINARY_DIR}/cblas-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION} +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${CBLASLIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${CBLASLIB}-${LAPACK_VERSION} - ) - --#install(EXPORT cblas-targets --# DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION}) +-#install(EXPORT ${CBLASLIB}-targets +-# DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${CBLASLIB}-${LAPACK_VERSION} +-# COMPONENT Development +-# ) diff --git a/CBLAS/cmake/cblas-config-build.cmake.in b/CBLAS/cmake/cblas-config-build.cmake.in deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-build.cmake.in @@ -72,14 +76,14 @@ deleted file mode 100644 - -# Load lapack targets from the build tree, including lapacke targets. -if(NOT TARGET lapacke) -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() - -# Report cblas header search locations from build tree. -set(CBLAS_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report cblas libraries. --set(CBLAS_LIBRARIES cblas) +-set(CBLAS_LIBRARIES @CBLASLIB@) diff --git a/CBLAS/cmake/cblas-config-install.cmake.in b/CBLAS/cmake/cblas-config-install.cmake.in deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-install.cmake.in @@ -92,19 +96,19 @@ deleted file mode 100644 -get_filename_component(_CBLAS_PREFIX "${_CBLAS_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_CBLAS_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/lapack-@LAPACK_VERSION@") +-set(LAPACK_DIR "${_CBLAS_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. --if(NOT TARGET cblas) -- include(${_CBLAS_SELF_DIR}/cblas-targets.cmake) +-if(NOT TARGET @CBLASLIB@) +- include(${_CBLAS_SELF_DIR}/@CBLASLIB@-targets.cmake) -endif() - -# Report lapacke header search locations. -set(CBLAS_INCLUDE_DIRS ${_CBLAS_PREFIX}/include) - -# Report lapacke libraries. --set(CBLAS_LIBRARIES cblas) +-set(CBLAS_LIBRARIES @CBLASLIB@) - -unset(_CBLAS_PREFIX) -unset(_CBLAS_SELF_DIR) @@ -124,67 +128,75 @@ 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 -@@ -120,9 +120,5 @@ - VERSION ${LAPACK_VERSION} - SOVERSION ${LAPACK_MAJOR_VERSION} - ) --target_include_directories(cblas PUBLIC +@@ -123,9 +123,5 @@ + if(HAS_ATTRIBUTE_WEAK_SUPPORT) + target_compile_definitions(${CBLASLIB} PRIVATE HAS_ATTRIBUTE_WEAK_SUPPORT) + endif() +-target_include_directories(${CBLASLIB} PUBLIC - $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../include> - $<INSTALL_INTERFACE:include> -) - target_link_libraries(cblas PRIVATE ${BLAS_LIBRARIES}) - lapack_install_library(cblas) + target_link_libraries(${CBLASLIB} PRIVATE ${BLAS_LIBRARIES}) + lapack_install_library(${CBLASLIB}) diff --git a/CMAKE/lapack-config-build.cmake.in b/CMAKE/lapack-config-build.cmake.in deleted file mode 100644 --- a/CMAKE/lapack-config-build.cmake.in +++ /dev/null -@@ -1,10 +0,0 @@ +@@ -1,14 +0,0 @@ -# Load lapack targets from the build tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_build_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - +-# Hint for project building against lapack +-set(LAPACK_Fortran_COMPILER_ID "@CMAKE_Fortran_COMPILER_ID@") +- -# Report the blas and lapack raw or imported libraries. -set(LAPACK_blas_LIBRARIES "@BLAS_LIBRARIES@") -set(LAPACK_lapack_LIBRARIES "@LAPACK_LIBRARIES@") +-set(LAPACK_LIBRARIES ${LAPACK_blas_LIBRARIES} ${LAPACK_lapack_LIBRARIES}) diff --git a/CMAKE/lapack-config-install.cmake.in b/CMAKE/lapack-config-install.cmake.in deleted file mode 100644 --- a/CMAKE/lapack-config-install.cmake.in +++ /dev/null -@@ -1,15 +0,0 @@ +@@ -1,19 +0,0 @@ -# Compute locations from <prefix>/lib/cmake/lapack-<v>/<self>.cmake -get_filename_component(_LAPACK_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) - -# Load lapack targets from the install tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_install_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("${_LAPACK_SELF_DIR}/lapack-targets.cmake") +- include("${_LAPACK_SELF_DIR}/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - +-# Hint for project building against lapack +-set(LAPACK_Fortran_COMPILER_ID "@CMAKE_Fortran_COMPILER_ID@") +- -# Report the blas and lapack raw or imported libraries. -set(LAPACK_blas_LIBRARIES "@BLAS_LIBRARIES@") -set(LAPACK_lapack_LIBRARIES "@LAPACK_LIBRARIES@") +-set(LAPACK_LIBRARIES ${LAPACK_blas_LIBRARIES} ${LAPACK_lapack_LIBRARIES}) - -unset(_LAPACK_SELF_DIR) diff --git a/CMakeLists.txt b/CMakeLists.txt --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -106,11 +106,8 @@ - endif() - # -------------------------------------------------- +@@ -160,11 +160,8 @@ --set(LAPACK_INSTALL_EXPORT_NAME lapack-targets) + + # -------------------------------------------------- +-set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKLIB}-targets) - macro(lapack_install_library lib) install(TARGETS ${lib} - EXPORT ${LAPACK_INSTALL_EXPORT_NAME} - ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} -@@ -139,21 +136,6 @@ + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Development + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT RuntimeLibraries + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT RuntimeLibraries +@@ -204,21 +201,6 @@ include(CheckLAPACKCompilerFlags) CheckLAPACKCompilerFlags() @@ -192,7 +204,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -# Check second function - -include(CheckTimeFunction) --set(TIME_FUNC NONE ${TIME_FUNC}) +-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) @@ -206,7 +218,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # deprecated LAPACK and LAPACKE routines option(BUILD_DEPRECATED "Build deprecated routines" OFF) message(STATUS "Build deprecated routines: ${BUILD_DEPRECATED}") -@@ -177,8 +159,9 @@ +@@ -242,8 +224,9 @@ endif() # -------------------------------------------------- @@ -217,7 +229,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided BLAS libraries if(BLAS_LIBRARIES) -@@ -189,213 +172,117 @@ +@@ -254,113 +237,108 @@ if(BLAS_FOUND) message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRARIES}.") else() @@ -238,7 +250,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt - message(STATUS "Using supplied NETLIB BLAS implementation") - add_subdirectory(BLAS) +elseif(BUILD_BLAS) - set(BLAS_LIBRARIES blas) + set(BLAS_LIBRARIES ${BLASLIB}) -else() - set(CMAKE_EXE_LINKER_FLAGS - "${CMAKE_EXE_LINKER_FLAGS} ${BLAS_LINKER_FLAGS}" @@ -314,14 +326,14 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + find_package(LAPACK) + +elseif(BUILD_LAPACK) - set(LAPACK_LIBRARIES lapack) + set(LAPACK_LIBRARIES ${LAPACKLIB}) + set(LAPACK_FOUND TRUE) + + set(NEED_BLAS TRUE) + + # Check second function + include(CheckTimeFunction) -+ set(TIME_FUNC NONE ${TIME_FUNC}) ++ set(NONE ${TIME_FUNC}) + CHECK_TIME_FUNCTION(NONE TIME_FUNC) + CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) + CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) @@ -351,10 +363,11 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + add_subdirectory(TESTING) + endif() + -+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) ++ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc @ONLY) + install(FILES -+ ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc ++ ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc + DESTINATION ${PKG_CONFIG_DIR} ++ COMPONENT Development + ) endif() @@ -380,16 +393,21 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt add_subdirectory(LAPACKE) endif() +@@ -414,111 +392,16 @@ + ExternalProject_Add_StepDependencies(lapackpp build blaspp ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) + endif() + -# -------------------------------------------------- -# CPACK Packaging - -set(CPACK_PACKAGE_NAME "LAPACK") -set(CPACK_PACKAGE_VENDOR "University of Tennessee, Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd") -set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "LAPACK- Linear Algebra Package") --set(CPACK_PACKAGE_VERSION_MAJOR 3) --set(CPACK_PACKAGE_VERSION_MINOR 5) --set(CPACK_PACKAGE_VERSION_PATCH 0) +-set(CPACK_PACKAGE_VERSION_MAJOR ${LAPACK_MAJOR_VERSION}) +-set(CPACK_PACKAGE_VERSION_MINOR ${LAPACK_MINOR_VERSION}) +-set(CPACK_PACKAGE_VERSION_PATCH ${LAPACK_PATCH_VERSION}) -set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE") +-set(CPACK_MONOLITHIC_INSTALL ON) -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 @@ -412,24 +430,26 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -# -------------------------------------------------- - -if(NOT BLAS_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} blas) +- set(ALL_TARGETS ${ALL_TARGETS} ${BLASLIB}) -endif() - -if(NOT LATESTLAPACK_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} lapack) +- set(ALL_TARGETS ${ALL_TARGETS} ${LAPACKLIB}) -endif() - -if(BUILD_TESTING OR LAPACKE_WITH_TMG) -- set(ALL_TARGETS ${ALL_TARGETS} tmglib) +- set(ALL_TARGETS ${ALL_TARGETS} ${TMGLIB}) -endif() - -# Export lapack targets, not including lapacke, from the -# install tree, if any. -set(_lapack_config_install_guard_target "") -if(ALL_TARGETS) -- install(EXPORT lapack-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapack-${LAPACK_VERSION}) - +- install(EXPORT ${LAPACKLIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKLIB}-${LAPACK_VERSION} +- COMPONENT Development +- ) +- - # Choose one of the lapack targets to use as a guard for - # lapack-config.cmake to load targets from the install tree. - list(GET ALL_TARGETS 0 _lapack_config_install_guard_target) @@ -437,12 +457,12 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt - -# Include cblas in targets exported from the build tree. -if(CBLAS) -- set(ALL_TARGETS ${ALL_TARGETS} cblas) +- set(ALL_TARGETS ${ALL_TARGETS} ${CBLASLIB}) -endif() - -# Include lapacke in targets exported from the build tree. -if(LAPACKE) -- set(ALL_TARGETS ${ALL_TARGETS} lapacke) +- set(ALL_TARGETS ${ALL_TARGETS} ${LAPACKELIB}) +# Neither user specified or optimized BLAS libraries can be used +if(NEED_BLAS AND NOT BLAS_FOUND) + message(FATAL_ERROR "--> No BLAS library found. Specify BLAS_LIBRARIES or enable USE_OPTIMIZED_BLAS or BUILD_BLAS.") @@ -451,7 +471,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -# Export lapack and lapacke targets from the build tree, if any. -set(_lapack_config_build_guard_target "") -if(ALL_TARGETS) -- export(TARGETS ${ALL_TARGETS} FILE lapack-targets.cmake) +- export(TARGETS ${ALL_TARGETS} FILE ${LAPACKLIB}-targets.cmake) - - # Choose one of the lapack or lapacke targets to use as a guard - # for lapack-config.cmake to load targets from the build tree. @@ -460,32 +480,37 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt +if(NEED_LAPACK AND NOT LAPACK_FOUND) + message(FATAL_ERROR "--> No LAPACK library found. Specify LAPACK_LIBRARIES or enable USE_OPTIMIZED_LAPACK or BUILD_LAPACK.") endif() -- + -configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config.cmake @ONLY) - - --configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc @ONLY) - install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc +- ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc - DESTINATION ${PKG_CONFIG_DIR} +- COMPONENT Development - ) - -configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-install.cmake.in -- ${LAPACK_BINARY_DIR}/CMakeFiles/lapack-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/CMakeFiles/${LAPACKLIB}-config.cmake @ONLY) - -include(CMakePackageConfigHelpers) -write_basic_package_version_file( -- ${LAPACK_BINARY_DIR}/lapack-config-version.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config-version.cmake - VERSION ${LAPACK_VERSION} - COMPATIBILITY SameMajorVersion - ) - -install(FILES -- ${LAPACK_BINARY_DIR}/CMakeFiles/lapack-config.cmake -- ${LAPACK_BINARY_DIR}/lapack-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapack-${LAPACK_VERSION} +- ${LAPACK_BINARY_DIR}/CMakeFiles/${LAPACKLIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKLIB}-${LAPACK_VERSION} +- COMPONENT Development - ) + if (LAPACK++) + install( + DIRECTORY "${LAPACK_BINARY_DIR}/lib/" diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt --- a/LAPACKE/CMakeLists.txt +++ b/LAPACKE/CMakeLists.txt @@ -493,66 +518,76 @@ diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt message(STATUS "LAPACKE enable") enable_language(C) --set(LAPACK_INSTALL_EXPORT_NAME lapacke-targets) +-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 -@@ -60,10 +58,6 @@ +@@ -79,14 +77,6 @@ VERSION ${LAPACK_VERSION} SOVERSION ${LAPACK_MAJOR_VERSION} ) --target_include_directories(lapacke PUBLIC -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../include> +-target_include_directories(${LAPACKELIB} PUBLIC +- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> - $<INSTALL_INTERFACE:include> -) +-if(WIN32 AND NOT UNIX) +- target_compile_definitions(${LAPACKELIB} PUBLIC HAVE_LAPACK_CONFIG_H LAPACK_COMPLEX_STRUCTURE) +- message(STATUS "Windows BUILD") +-endif() if(LAPACKE_WITH_TMG) - target_link_libraries(lapacke PRIVATE tmglib) -@@ -83,19 +77,3 @@ - ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc + target_link_libraries(${LAPACKELIB} PRIVATE ${TMGLIB}) +@@ -111,22 +101,3 @@ DESTINATION ${PKG_CONFIG_DIR} + COMPONENT Development ) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-version.cmake.in -- ${LAPACK_BINARY_DIR}/lapacke-config-version.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config-version.cmake @ONLY) -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/lapacke-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config.cmake @ONLY) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-install.cmake.in -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/lapacke-config.cmake @ONLY) +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LAPACKELIB}-config.cmake @ONLY) -install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/lapacke-config.cmake -- ${LAPACK_BINARY_DIR}/lapacke-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapacke-${LAPACK_VERSION} +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LAPACKELIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKELIB}-${LAPACK_VERSION} +- COMPONENT Development - ) - --install(EXPORT lapacke-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapacke-${LAPACK_VERSION}) +-install(EXPORT ${LAPACKELIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKELIB}-${LAPACK_VERSION} +- COMPONENT Development +- ) diff --git a/LAPACKE/cmake/lapacke-config-build.cmake.in b/LAPACKE/cmake/lapacke-config-build.cmake.in deleted file mode 100644 --- a/LAPACKE/cmake/lapacke-config-build.cmake.in +++ /dev/null -@@ -1,14 +0,0 @@ +@@ -1,17 +0,0 @@ -# Load the LAPACK package with which we were built. -set(LAPACK_DIR "@LAPACK_BINARY_DIR@") -find_package(LAPACK NO_MODULE) - -# Load lapack targets from the build tree, including lapacke targets. --if(NOT TARGET lapacke) -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +-if(NOT TARGET @LAPACKELIB@) +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() - +-# Hint for project building against lapack +-set(LAPACKE_Fortran_COMPILER_ID ${LAPACK_Fortran_COMPILER_ID}) +- -# Report lapacke header search locations from build tree. -set(LAPACKE_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) diff --git a/LAPACKE/cmake/lapacke-config-install.cmake.in b/LAPACKE/cmake/lapacke-config-install.cmake.in deleted file mode 100644 --- a/LAPACKE/cmake/lapacke-config-install.cmake.in +++ /dev/null -@@ -1,23 +0,0 @@ +@@ -1,26 +0,0 @@ -# Compute locations from <prefix>/@{LIBRARY_DIR@/cmake/lapacke-<v>/<self>.cmake -get_filename_component(_LAPACKE_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) -get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_SELF_DIR}" PATH) @@ -560,19 +595,22 @@ deleted file mode 100644 -get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_LAPACKE_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/lapack-@LAPACK_VERSION@") +-set(LAPACK_DIR "${_LAPACKE_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/@LAPACK@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. --if(NOT TARGET lapacke) -- include(${_LAPACKE_SELF_DIR}/lapacke-targets.cmake) +-if(NOT TARGET @LAPACKELIB@) +- include(${_LAPACKE_SELF_DIR}/@LAPACKELIB@-targets.cmake) -endif() - +-# Hint for project building against lapack +-set(LAPACKE_Fortran_COMPILER_ID ${LAPACK_Fortran_COMPILER_ID}) +- -# Report lapacke header search locations. -set(LAPACKE_INCLUDE_DIRS ${_LAPACKE_PREFIX}/include) - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) - -unset(_LAPACKE_PREFIX) -unset(_LAPACKE_SELF_DIR) diff --git a/academic/latex2html/README b/academic/latex2html/README new file mode 100644 index 0000000000..70e56c1337 --- /dev/null +++ b/academic/latex2html/README @@ -0,0 +1,25 @@ +LaTeX is a high-quality typesetting system; it includes features +designed for the production of technical and scientific +documentation. Latex2html is used for converting Latex files which +have a .tex suffix to html + +a basic latex document looks like this: + +\documentclass{article} +\begin{document} + Hello World! +\end{document} + +if you save such a document say called helloworld.tex +then to convert this document to html form, open a terminal +and cd to where helloworld.tex is. + +Then its a simple as +$latex2html helloworld.tex + +for option flags type: $latex2html --help + +for extensive documentation see manual.pdf + +when package is installed a copy of manual.pdf +will be put in /usr/doc/latex2html-2019.2 diff --git a/academic/latex2html/latex2html.SlackBuild b/academic/latex2html/latex2html.SlackBuild new file mode 100644 index 0000000000..5509805331 --- /dev/null +++ b/academic/latex2html/latex2html.SlackBuild @@ -0,0 +1,106 @@ +#!/bin/sh + +# Slackware build script for latex2html + +# Copyright 2019 andrew brookes North East, UK +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=latex2html +VERSION=${VERSION:-2020} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --with-perl=/usr/bin/perl \ + --enable-eps \ + --enable-gif \ + --enable-svg \ + --enable-pk \ + --enable-pipes \ + --build=$ARCH-slackware-linux \ + --host=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + FAQ INSTALL LICENSE MANIFEST README.md TODO \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cp $CWD/manual.pdf $PKG/usr/doc/$PRGNAM-$VERSION + +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:-tgz} diff --git a/academic/latex2html/latex2html.info b/academic/latex2html/latex2html.info new file mode 100644 index 0000000000..199a5829f2 --- /dev/null +++ b/academic/latex2html/latex2html.info @@ -0,0 +1,10 @@ +PRGNAM="latex2html" +VERSION="2020" +HOMEPAGE="http://www.latex2html.org" +DOWNLOAD="https://github.com/latex2html/latex2html/archive/v2020/latex2html-2020.tar.gz" +MD5SUM="d5e2d765ed2bb4d52bd7331a6420f5be" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="andy brookes" +EMAIL="andybrookestar@gmail.com" diff --git a/academic/latex2html/manual.pdf b/academic/latex2html/manual.pdf Binary files differnew file mode 100644 index 0000000000..699a2ce464 --- /dev/null +++ b/academic/latex2html/manual.pdf diff --git a/academic/latex2html/slack-desc b/academic/latex2html/slack-desc new file mode 100644 index 0000000000..934748e46a --- /dev/null +++ b/academic/latex2html/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------------------------------------------------------| +latex2html: latex2html (convert latex document) +latex2html: +latex2html: latex2html is a useful tool to convert latex documents to +latex2html: html form. +latex2html: +latex2html: +latex2html: +latex2html: +latex2html: +latex2html: +latex2html: diff --git a/academic/ldl/README b/academic/ldl/README index b3628fc188..ce58f1983d 100644 --- a/academic/ldl/README +++ b/academic/ldl/README @@ -1,11 +1,12 @@ LDL is a set of concise routines for factorizing symmetric positive-definite sparse matrices, with some applicability to symmetric -indefinite matrices. Its primary purpose is to illustrate much of the -basic theory of sparse matrix algorithms in as concise a code as possible, -including an elegant new method of sparse symmetric factorization that -computes the factorization row-by-row but stores it column-by-column. +indefinite matrices. Its primary purpose is to illustrate much of +the basic theory of sparse matrix algorithms in as concise a code +as possible, including an elegant new method of sparse symmetric +factorization that computes the factorization row-by-row but stores it +column-by-column. This package is part of SuiteSparse. -AMD is an optional dependency and will be used if found. -It is primarily used for this package's test suite. +AMD is an optional dependency and will be used if found. It is +primarily used for this package's test suite. diff --git a/academic/ldl/ldl.SlackBuild b/academic/ldl/ldl.SlackBuild index 34bd69e6e2..c0b4d98c5e 100644 --- a/academic/ldl/ldl.SlackBuild +++ b/academic/ldl/ldl.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for LDL -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=ldl SRCNAM=SuiteSparse SUBDIR=LDL VERSION=${VERSION:-2.2.6} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-5} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/ldl/ldl.info b/academic/ldl/ldl.info index ed86f2ea3a..9274c84ac9 100644 --- a/academic/ldl/ldl.info +++ b/academic/ldl/ldl.info @@ -1,8 +1,8 @@ PRGNAM="ldl" VERSION="2.2.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/ldl/patches/autoconfiscate.diff b/academic/ldl/patches/autoconfiscate.diff index ea7bcaf561..ae66234a96 100644 --- a/academic/ldl/patches/autoconfiscate.diff +++ b/academic/ldl/patches/autoconfiscate.diff @@ -152,7 +152,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([LDL],[2.2.6],[DrTimothyAldenDavis@gmail.com],[ldl],[http://www.suitesparse.com/]) ++AC_INIT([LDL],[2.2.6],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[ldl],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/ldl.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/libqalculate/README b/academic/libqalculate/README index d67d9a7bd8..aa40e23964 100644 --- a/academic/libqalculate/README +++ b/academic/libqalculate/README @@ -1,4 +1,4 @@ -Qalculate! is a multi-purpose desktop calculator for GNU/Linux (and Mac OS). It -is small and simple to use but with much power and versatility underneath. -Features include customizable functions, units, arbitrary precision, plotting, -and a user-friendly interface (GTK+ and CLI). +Qalculate! is a multi-purpose desktop calculator for GNU/Linux (and Mac +OS). It is small and simple to use but with much power and versatility +underneath. Features include customizable functions, units, arbitrary +precision, plotting, and a user-friendly interface (GTK+ and CLI). diff --git a/academic/libqalculate/libqalculate.SlackBuild b/academic/libqalculate/libqalculate.SlackBuild index 2c3db8cfcf..9d906e36f5 100644 --- a/academic/libqalculate/libqalculate.SlackBuild +++ b/academic/libqalculate/libqalculate.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for libqalculate -# Copyright 2016-2018 Larry Hajali <larryhaja[at]gmail[dot]com> +# Copyright 2016-2020 Larry Hajali <larryhaja[at]gmail[dot]com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=libqalculate -VERSION=${VERSION:-2.8.2} +VERSION=${VERSION:-3.10.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -75,6 +75,7 @@ CXXFLAGS="$SLKCFLAGS" \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --docdir=/usr/doc/$PRGNAM-$VERSION \ + --mandir=/usr/man \ --disable-silent-rules \ --enable-static=no \ --disable-rpath \ @@ -89,6 +90,8 @@ make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +find $PKG/usr/man -type f -exec gzip -9 {} \; + cp -a 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/libqalculate/libqalculate.info b/academic/libqalculate/libqalculate.info index 7ef9962161..a2ac9c6801 100644 --- a/academic/libqalculate/libqalculate.info +++ b/academic/libqalculate/libqalculate.info @@ -1,8 +1,8 @@ PRGNAM="libqalculate" -VERSION="2.8.2" -HOMEPAGE="http://qalculate.github.io/" -DOWNLOAD="https://github.com/Qalculate/libqalculate/releases/download/v2.8.2/libqalculate-2.8.2.tar.gz" -MD5SUM="e6bb2bfb12a9e4253cbcd01bb31f1ea5" +VERSION="3.10.0" +HOMEPAGE="https://qalculate.github.io/" +DOWNLOAD="https://github.com/Qalculate/libqalculate/releases/download/v3.10.0/libqalculate-3.10.0.tar.gz" +MD5SUM="2f68e3dfeb36de2c88fc7078cb86ab4c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/link-grammar/README b/academic/link-grammar/README index f985d7cb61..1250ac3145 100644 --- a/academic/link-grammar/README +++ b/academic/link-grammar/README @@ -1,6 +1,6 @@ -The Link Grammar Parser is a syntactic parser of English, based on link -grammar, an original theory of English syntax. Given a sentence, the system -assigns to it a syntactic structure, which consists of a set of labeled links -connecting pairs of words. The parser also produces a "constituent" (Penn -tree-bank style phrase tree) representation of a sentence (showing noun -phrases, verb phrases, etc.). +The Link Grammar Parser is a syntactic parser of English, based on +link grammar, an original theory of English syntax. Given a sentence, +the system assigns to it a syntactic structure, which consists of a set +of labeled links connecting pairs of words. The parser also produces a +"constituent" (Penn tree-bank style phrase tree) representation of a +sentence (showing noun phrases, verb phrases, etc.). diff --git a/academic/locarna/README b/academic/locarna/README new file mode 100644 index 0000000000..ff32b839d9 --- /dev/null +++ b/academic/locarna/README @@ -0,0 +1,48 @@ +LocARNA: Alignment of RNAs +========================== + +LocARNA is a collection of alignment tools for the structural analysis +of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns +and predicts common structures for your RNAs. In this way, LocARNA +performs Sankoff-like alignment and is in particular suited for +analyzing sets of related RNAs without known common structure. + +LocARNA distinguishes itself from many other Sankoff-style multiple +alignment programs by its performance and low memory complexity, high +accuracy, and richness of features. As unique features, it offers +structure-local alignment, flexible structure and anchor constraints, +and provides efficient computation of reliabilities in +sequence-structure alignment. The package offers a robust core of +features and is used as experimental platform for the incorporation of +new features in RNA sequence-structure alignment. + + +At its core, the package offers global and local multiple alignment of +RNAs. + +Multiple alignment can be performed in one of several different ways: + +* progressive alignment using sequence-structure alignment of profiles + +* progressive alignment after consistency transformation using +T-Coffee + +* progressive alignment using probabilistic consistency transformation + and sequence-structure profile alignments, optionally followed by + iterative refinement. + + +Besides of global alignment, LocARNA supports two kinds of +locality. Local alignment as it is known from sequence alignment, +identifies and aligns the best matching subsequences. This form of +locality is called sequence local to distinguish it from structural +locality. When performing structure local alignment, LocARNA +identifies and aligns the best matching substructures in the RNAs. The +sequences of those substructures can be discontinuous on the sequence +level, but remain connected via structural bonds. + +Alignment Reliabilities (LocARNA-P). In this special, probabilistic +mode of operation LocARNA supports the efficient computation of match +probabilities, probabilistic consistency transformation for more +accurate multiple alignment, and generates reliability profiles of +multiple alignments. diff --git a/academic/locarna/locarna.SlackBuild b/academic/locarna/locarna.SlackBuild new file mode 100644 index 0000000000..fdeaea36f9 --- /dev/null +++ b/academic/locarna/locarna.SlackBuild @@ -0,0 +1,107 @@ +#!/bin/sh + +# Slackware build script for locarna + +# Copyright 2019 Rob van Nues <sborg63@disroot.org> +# 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. + + +PRGNAM=locarna +VERSION=${VERSION:-1.9.2.3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +#from https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=locarna + +install -d $PKG/usr/lib${LIBDIRSUFFIX}/perl5 +# seems to be 'private': https://github.com/s-will/LocARNA/issues/34 +mv $PKG/usr/lib/perl $PKG/usr/lib${LIBDIRSUFFIX}/perl5/vendor_perl + +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 \ + AUTHORS README INSTALL COPYING ChangeLog \ + $PKG/usr/doc/$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:-tgz} diff --git a/academic/locarna/locarna.info b/academic/locarna/locarna.info new file mode 100644 index 0000000000..cbcfcb5adf --- /dev/null +++ b/academic/locarna/locarna.info @@ -0,0 +1,10 @@ +PRGNAM="locarna" +VERSION="1.9.2.3" +HOMEPAGE="http://www.bioinf.uni-freiburg.de/Software/LocARNA/" +DOWNLOAD="https://github.com/s-will/LocARNA/releases/download/v1.9.2.3/locarna-1.9.2.3.tar.gz" +MD5SUM="d6c62b9905293ea77c12af4a43beb551" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="ViennaRNA" +MAINTAINER="Rob van Nues" +EMAIL="sborg63@disroot.org" diff --git a/academic/locarna/slack-desc b/academic/locarna/slack-desc new file mode 100644 index 0000000000..b913a794a6 --- /dev/null +++ b/academic/locarna/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------------------------------------------------------| +locarna: locarna (Local RNA alignment on structural basis) +locarna: +locarna: LocARNA is a collection of alignment tools for the structural +locarna: analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously +locarna: aligns and predicts common structures for your RNAs. In this way, +locarna: LocARNA performs Sankoff-like alignment and is in particular suited +locarna: for analyzing sets of related RNAs without known common structure. +locarna: +locarna: Home:https://www.bioinf.uni-freiburg.de/Software/LocARNA/ +locarna: +locarna: diff --git a/academic/mafft/mafft.SlackBuild b/academic/mafft/mafft.SlackBuild index 2c53e0b6f8..844be72f25 100644 --- a/academic/mafft/mafft.SlackBuild +++ b/academic/mafft/mafft.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for mafft -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=mafft -VERSION=${VERSION:-7.407} +VERSION=${VERSION:-7.471} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/mafft/mafft.info b/academic/mafft/mafft.info index 49ddaf14e3..dcc03b7049 100644 --- a/academic/mafft/mafft.info +++ b/academic/mafft/mafft.info @@ -1,8 +1,8 @@ PRGNAM="mafft" -VERSION="7.407" +VERSION="7.471" HOMEPAGE="https://mafft.cbrc.jp/alignment/software/" -DOWNLOAD="https://mafft.cbrc.jp/alignment/software/mafft-7.407-with-extensions-src.tgz" -MD5SUM="d3f12363096738561b209938d5ea3ddd" +DOWNLOAD="https://mafft.cbrc.jp/alignment/software/mafft-7.471-with-extensions-src.tgz" +MD5SUM="6ac312a0261d99221dc0be437caba132" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/mathomatic/README b/academic/mathomatic/README index 3c01da81e0..7c3e5292c8 100644 --- a/academic/mathomatic/README +++ b/academic/mathomatic/README @@ -4,11 +4,11 @@ subtraction, multiplication, division, modulo division, and all forms of exponentiation. All arithmetic is double precision floating point with up to 14 decimal digits accuracy. -Mathomatic can symbolically combine and solve equations containing many -variables, completely simplify and compare expressions and equations, do -simple calculus transformations and series, perform standard, complex -number, and polynomial arithmetic, generate optimized C, Java, and Python -language code from simplified equations, carry out quick calculations, and -much more. Plotting with gnuplot is also supported. Not implemented in -Mathomatic are named functions, arbitrary-precision arithmetic, and -matrices. +Mathomatic can symbolically combine and solve equations containing many +variables, completely simplify and compare expressions and equations, +do simple calculus transformations and series, perform standard, +complex number, and polynomial arithmetic, generate optimized C, +Java, and Python language code from simplified equations, carry +out quick calculations, and much more. Plotting with gnuplot is +also supported. Not implemented in Mathomatic are named functions, +arbitrary-precision arithmetic, and matrices. diff --git a/academic/maxima/maxima.SlackBuild b/academic/maxima/maxima.SlackBuild index de32fcbf35..a42281aa78 100644 --- a/academic/maxima/maxima.SlackBuild +++ b/academic/maxima/maxima.SlackBuild @@ -2,6 +2,7 @@ # Slackware build script for maxima +# Copyright 2021 Judah Milgram <milgram@cgpp.com> # Copyright 2017 Dhaby Xiloj <slack.dhabyx@gmail.com> # All rights reserved. # Based on work of Robby and others slackers. @@ -30,9 +31,10 @@ # Modified by Ken Milmore 2009 # 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 PRGNAM=maxima -VERSION=${VERSION:-5.39.0} +VERSION=${VERSION:-5.44.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/maxima/maxima.info b/academic/maxima/maxima.info index 676c4f7b56..8235c0ba3c 100644 --- a/academic/maxima/maxima.info +++ b/academic/maxima/maxima.info @@ -1,10 +1,10 @@ PRGNAM="maxima" -VERSION="5.39.0" +VERSION="5.44.0" HOMEPAGE="http://maxima.sourceforge.net/" -DOWNLOAD="https://sourceforge.net/projects/maxima/files/Maxima-source/5.39.0-source/maxima-5.39.0.tar.gz" -MD5SUM="3bccafb512ff1054be700c61601088af" +DOWNLOAD="https://sourceforge.net/projects/maxima/files/Maxima-source/5.44.0-source/maxima-5.44.0.tar.gz" +MD5SUM="75e040745161901968d9c99c7a258e5c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="DhabyX" -EMAIL="slack.dhabyx@gmail.com" +MAINTAINER="Judah Milgram" +EMAIL="milgram@cgpp.com" diff --git a/academic/meep/README b/academic/meep/README new file mode 100644 index 0000000000..a0623df2cc --- /dev/null +++ b/academic/meep/README @@ -0,0 +1,42 @@ +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. + +You probably will also want to preinstall: harminv, openmpi + +You may wish to also install: h5utils + +You very probably want to build a multi-processor version of this +code by adding the "--with-openmp" configure option. Here, mpb is +specified as a prerequisite since at the present time the python +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. + +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 +"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. diff --git a/academic/meep/meep.SlackBuild b/academic/meep/meep.SlackBuild new file mode 100644 index 0000000000..114680d8ec --- /dev/null +++ b/academic/meep/meep.SlackBuild @@ -0,0 +1,127 @@ +#!/bin/sh + +# Slackware build script for meep + +# Copyright 2019 Paul Kinsler, U.K. +# 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. + +PRGNAM=meep +VERSION=${VERSION:-1.17.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# change annoying underscores into hyphens +SVERSION=$(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 +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 there is no configure script, try to build one! +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 "${SBOPTIONS_MEEP}" ] ; then + LOCALCONFIGS=${LOCALCONFIGS}" "${SBOPTIONS_MEEP} + echo Build options selected by environment: LOCALCONFIGS=${LOCALCONFIGS} +fi + +# 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="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --mandir=/usr/man \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux \ + $LOCALCONFIGS + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +install -m 0644 $DOCFILES $PKG/usr/doc/$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:-tgz} diff --git a/academic/meep/meep.info b/academic/meep/meep.info new file mode 100644 index 0000000000..8faea2fd0f --- /dev/null +++ b/academic/meep/meep.info @@ -0,0 +1,10 @@ +PRGNAM="meep" +VERSION="1.17.1" +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_x86_64="" +MD5SUM_x86_64="" +REQUIRES="lapack hdf5 libctl mpb" +MAINTAINER="PaulKinsler" +EMAIL="dr.paul@kinsler.org" diff --git a/academic/meep/slack-desc b/academic/meep/slack-desc new file mode 100644 index 0000000000..8187e87c47 --- /dev/null +++ b/academic/meep/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------------------------------------------------------| +meep: meep (electromagnetics simulation using FDTD) +meep: +meep: Meep is a free and open-source software package for +meep: electromagnetics simulation via the finite-difference +meep: time-domain (FDTD) method spanning a broad range of +meep: applications. +meep: +meep: Homepage: https://github.com/NanoComp/meep +meep: +meep: +meep: diff --git a/academic/megax/megax.SlackBuild b/academic/megax/megax.SlackBuild index 544a941f5c..e7ae3b4e24 100644 --- a/academic/megax/megax.SlackBuild +++ b/academic/megax/megax.SlackBuild @@ -4,7 +4,7 @@ # This takes the place of "megacc" in 2018, as it includes also the GUI # of the program (megax) in addition to megacc. -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,11 +25,12 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=megax -VERSION=${VERSION:-10.0.5_1} -DEBVER=10.0.5-1 +VERSION=${VERSION:-10.1.8_1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +DEBVER=$(echo $VERSION | tr _ -) + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i386 ;; @@ -83,8 +84,8 @@ cp -a usr/local/share/man $PKG/usr 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}/$PRGNAM/megacc + ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/runmega.sh megax cd - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ diff --git a/academic/megax/megax.info b/academic/megax/megax.info index cf60b8de0d..cf1d99f562 100644 --- a/academic/megax/megax.info +++ b/academic/megax/megax.info @@ -1,10 +1,10 @@ PRGNAM="megax" -VERSION="10.0.5_1" +VERSION="10.1.8_1" HOMEPAGE="http://www.megasoftware.net/" -DOWNLOAD="https://www.megasoftware.net/releases/megax_10.0.5-1_i386.deb" -MD5SUM="0c6d46f647d967328f0d36dfeb9faf72" -DOWNLOAD_x86_64="https://www.megasoftware.net/releases/megax_10.0.5-1_amd64.deb" -MD5SUM_x86_64="0a292812ef7f006f9f65a267f0c16df5" +DOWNLOAD="https://www.megasoftware.net/releases/megax_10.1.8-1_i386.deb" +MD5SUM="132278353e321cf8d6097aefb45dc582" +DOWNLOAD_x86_64="https://www.megasoftware.net/releases/megax_10.1.8-1_amd64.deb" +MD5SUM_x86_64="7083d62e933fd482aac50c98a13dd723" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/meme-db-gomo/README b/academic/meme-db-gomo/README new file mode 100644 index 0000000000..34ed28d819 --- /dev/null +++ b/academic/meme-db-gomo/README @@ -0,0 +1,37 @@ +GOMo Databases (updated 17 Feb 2015) to be used with MEME Suite: + +Single Species +Danio rerio (Zebrafish) +Drosophila Melanogaster (Fruit fly) +Gallus Gallus (Chicken) +Rattus norvegicus (Rat) +Schizosaccharomyces pombe + +Multiple Species +Arabidopsis thaliana (Plant) + +Comparative Species +Oryza sativa (Rice) +Populus trichocarpa (Poplar) +Sorghum brachupodium +Brachypodium distachyon (purple false brome) +E.coli K12 +E.coli CTF073 +Salmonella enterica serovar Typhi Ty2 +Yersinia pestis CO92 +Homo sapiens (Human) +Mus musculus (Mouse) +Canis familiaris (Dog) +Equus caballus (Horse) +Mus musculus (Mouse) +Canis familiaris (Dog) +Rattus Norvegicus (Rat) +Equus caballus (Horse) +Homo sapiens (Human) +Saccharomyces cerevisiae (yeast) +S. bayanus +S. mikatae +S. paradoxus + +Note! +The unarchived size of this is ~378 MB diff --git a/academic/meme-db-gomo/meme-db-gomo.SlackBuild b/academic/meme-db-gomo/meme-db-gomo.SlackBuild new file mode 100644 index 0000000000..ab81c7466f --- /dev/null +++ b/academic/meme-db-gomo/meme-db-gomo.SlackBuild @@ -0,0 +1,65 @@ +#!/bin/sh + +# Slackware build script for meme-db-gomo + +# Copyright 2020 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. + +PRGNAM=meme-db-gomo +VERSION=${VERSION:-3.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=gomo_databases + +ARCH=noarch + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $PKG + +# Extract directly in the $PKG folder +mkdir -p var/lib/meme-suite +cd var/lib/meme-suite +tar xvf $CWD/${SRCNAM}.${VERSION}.tgz +cd $SRCNAM + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p $PKG/usr/doc/$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:-tgz} diff --git a/academic/meme-db-gomo/meme-db-gomo.info b/academic/meme-db-gomo/meme-db-gomo.info new file mode 100644 index 0000000000..b70eb8f874 --- /dev/null +++ b/academic/meme-db-gomo/meme-db-gomo.info @@ -0,0 +1,10 @@ +PRGNAM="meme-db-gomo" +VERSION="3.2" +HOMEPAGE="http://meme-suite.org/db/gomo" +DOWNLOAD="http://meme-suite.org/meme-software/Databases/gomo/gomo_databases.3.2.tgz" +MD5SUM="5b8fcf3c541b30e2a66580f289132e97" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/meme-db-gomo/slack-desc b/academic/meme-db-gomo/slack-desc new file mode 100644 index 0000000000..b75eb92870 --- /dev/null +++ b/academic/meme-db-gomo/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------------------------------------------------------| +meme-db-gomo: meme-db-gomo (MEME Suite GOMo databases) +meme-db-gomo: +meme-db-gomo: GOMo Databases to be used with MEME Suite. +meme-db-gomo: +meme-db-gomo: +meme-db-gomo: +meme-db-gomo: +meme-db-gomo: +meme-db-gomo: +meme-db-gomo: +meme-db-gomo: diff --git a/academic/meme-db-motif/README b/academic/meme-db-motif/README new file mode 100644 index 0000000000..8eb4772731 --- /dev/null +++ b/academic/meme-db-motif/README @@ -0,0 +1,28 @@ +Motif Databases (updated 28 Oct 2019) to be used with MEME Suite: + +Eukaryote DNA (13 Databases) +Prokaryote DNA (4 Databases) +Methylcytosine DNA (1 Databases) +JASPAR (NON-REDUNDANT) DNA (21 Databases) +JASPAR (REDUNDANT) DNA (21 Databases) +JASPAR COLLECTIONS DNA (5 Databases) +TFBSshape DNA (3 Databases) +CIS-BP Single Species DNA (321 Databases) +ARABIDOPSIS (Arabidopsis thaliana) DNA (2 Databases) +ECOLI (Escherichia coli) DNA (2 Databases) +FLY (Drosophila melanogaster) DNA (6 Databases) +HUMAN (Homo sapiens) DNA (4 Databases) +MALARIA (Plasmodia falciparum) DNA (1 Databases) +MOUSE (Mus musculus) DNA (5 Databases) +WORM (Caenorhabditis elegans) DNA (1 Databases) +YEAST (Saccharomyces_cerevisiae) DNA (6 Databases) +CISBP-RNA Single Species RNA (268 Databases) +CISBP-RNA Single Species RNA (DNA-encoded) (268 Databases) +RNA (25 Databases) +RNA (DNA-encoded) (25 Databases) +miRBase Single Species microRNA (223 Databases) +miRBase Single Species microRNA (DNA-encoded) (223 Databases) +Protein Motifs (2 Databases) + +Note! +The unarchived size of this is ~140 MB diff --git a/academic/meme-db-motif/meme-db-motif.SlackBuild b/academic/meme-db-motif/meme-db-motif.SlackBuild new file mode 100644 index 0000000000..f0e266d8c8 --- /dev/null +++ b/academic/meme-db-motif/meme-db-motif.SlackBuild @@ -0,0 +1,65 @@ +#!/bin/sh + +# Slackware build script for meme-db-motif + +# Copyright 2020 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. + +PRGNAM=meme-db-motif +VERSION=${VERSION:-12.19} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=motif_databases + +ARCH=noarch + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $PKG + +# Extract directly in the $PKG folder +mkdir -p var/lib/meme-suite +cd var/lib/meme-suite +tar xvf $CWD/${SRCNAM}.${VERSION}.tgz +cd $SRCNAM + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p $PKG/usr/doc/$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:-tgz} diff --git a/academic/meme-db-motif/meme-db-motif.info b/academic/meme-db-motif/meme-db-motif.info new file mode 100644 index 0000000000..549263ca24 --- /dev/null +++ b/academic/meme-db-motif/meme-db-motif.info @@ -0,0 +1,10 @@ +PRGNAM="meme-db-motif" +VERSION="12.19" +HOMEPAGE="http://meme-suite.org/db/motifs" +DOWNLOAD="http://meme-suite.org/meme-software/Databases/motifs/motif_databases.12.19.tgz" +MD5SUM="f5ffcaecc07570ee19dba20b82d7bd73" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/meme-db-motif/slack-desc b/academic/meme-db-motif/slack-desc new file mode 100644 index 0000000000..351fbd8db9 --- /dev/null +++ b/academic/meme-db-motif/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------------------------------------------------------| +meme-db-motif: meme-db-motif (MEME Suite motif databases) +meme-db-motif: +meme-db-motif: Motif Databases to be used with MEME Suite. +meme-db-motif: +meme-db-motif: +meme-db-motif: +meme-db-motif: +meme-db-motif: +meme-db-motif: +meme-db-motif: +meme-db-motif: diff --git a/academic/meme-db-tgene/README b/academic/meme-db-tgene/README new file mode 100644 index 0000000000..57026d4c12 --- /dev/null +++ b/academic/meme-db-tgene/README @@ -0,0 +1,26 @@ +T-Gene Databases (updated 12 Oct 2019) to be used with MEME Suite: + +Genome + Histone/Expression Data +Human hg19 (ENCODE Tissue Panel) +Human hg19 (Epigenomic Roadmap Tissue Panel) +Mouse mm9 (ENCODE Tissue Panel) + +Genomes Only +Arabidopsis thaliana TAIR10 (Ensembl) +Caenorhabditis elegans WBcel235 (Ensembl) +Caenorhabditis elegans ce11 (UCSC) +Danio rerio GRCz11 (Ensembl) +Danio rerio danRer11 (UCSC) +Drosophila melanogaster BDGP6 (Ensembl) +Drosophila melanogaster dm6 (UCSC) +Homo sapiens GRCh38 (Ensembl) +Homo sapiens hg38 (UCSC) +Mus musculus GRCm38 (Ensembl) +Mus musculus mm10 (UCSC) +Rattus norvegicus Rnor_6 (Ensembl) +Rattus norvegicus rn6 (UCSC) +Saccharomyces cerevisiae R64-1-1 (Ensembl) +Saccharomyces cerevisiae sacCer3 (UCSC) + +Note!!! +The unarchived size of this is ~2.6 GB diff --git a/academic/meme-db-tgene/meme-db-tgene.SlackBuild b/academic/meme-db-tgene/meme-db-tgene.SlackBuild new file mode 100644 index 0000000000..95e75e5a5c --- /dev/null +++ b/academic/meme-db-tgene/meme-db-tgene.SlackBuild @@ -0,0 +1,65 @@ +#!/bin/sh + +# Slackware build script for meme-db-tgene + +# Copyright 2020 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. + +PRGNAM=meme-db-tgene +VERSION=${VERSION:-1.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=tgene_databases + +ARCH=noarch + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $PKG + +# Extract directly in the $PKG folder +mkdir -p var/lib/meme-suite +cd var/lib/meme-suite +tar xvf $CWD/${SRCNAM}.${VERSION}.tgz +cd $SRCNAM + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p $PKG/usr/doc/$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:-tgz} diff --git a/academic/meme-db-tgene/meme-db-tgene.info b/academic/meme-db-tgene/meme-db-tgene.info new file mode 100644 index 0000000000..6c90f7f5d3 --- /dev/null +++ b/academic/meme-db-tgene/meme-db-tgene.info @@ -0,0 +1,10 @@ +PRGNAM="meme-db-tgene" +VERSION="1.0" +HOMEPAGE="http://meme-suite.org/db/tgene" +DOWNLOAD="http://meme-suite.org/meme-software/Databases/tgene/tgene_databases.1.0.tgz" +MD5SUM="8a2e467f979a4721e4fb2233bf2b0a04" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/meme-db-tgene/slack-desc b/academic/meme-db-tgene/slack-desc new file mode 100644 index 0000000000..c1a6e06666 --- /dev/null +++ b/academic/meme-db-tgene/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------------------------------------------------------| +meme-db-tgene: meme-db-tgene (MEME Suite T-gene databases) +meme-db-tgene: +meme-db-tgene: T-Gene Databases to be used with MEME Suite: +meme-db-tgene: +meme-db-tgene: Genome + Histone/Expression Data +meme-db-tgene: Genomes Only +meme-db-tgene: +meme-db-tgene: +meme-db-tgene: +meme-db-tgene: +meme-db-tgene: diff --git a/academic/meme-suite/README b/academic/meme-suite/README index f516c7e371..b48cdaf9f7 100644 --- a/academic/meme-suite/README +++ b/academic/meme-suite/README @@ -1,35 +1,31 @@ The MEME suite: motif based sequence analysis tools -The MEME suite provides tools for discovering and using protein and -DNA sequence motifs. A motif is a pattern of nucleotides or amino acids -that appears repeatedly in a group of related DNA or protein sequences. +The MEME Suite allows the biologist to discover novel motifs in +collections of unaligned nucleotide or protein sequences, and to perform +a wide variety of other motif-based analyses. The Suite supports motif- +based analysis of DNA, RNA and protein sequences. It provides motif +discovery algorithms using both probabilistic (MEME) and discrete models +(MEME), which have complementary strengths. It also allows discovery of +motifs with arbitrary insertions and deletions (GLAM2). In addition to +motif discovery, the MEME Suite provides tools for scanning sequences +for matches to motifs (FIMO, MAST and GLAM2Scan), scanning for clusters +of motifs (MCAST), comparing motifs to known motifs (Tomtom), finding +preferred spacings between motifs (SpaMo), predicting the biological +roles of motifs (GOMo), measuring the positional enrichment of sequences +for known motifs (CentriMo), and analyzing ChIP-seq and other large +datasets (MEME-ChIP). -The MEME suite represents motifs as position-dependent scoring matrices. -It consists of programs which allow you to: +Check README.TESTS for runing the recommended tests on the compiled +executables. Here, the tests *FAIL* on a 32bit system! -- meme - discovery of motifs shared by a group of sequences -- mast - search of databases for sequences containing these motifs -- tomtom - searching databases of motifs for similar motifs -- gomo - finding Gene Ontology terms linked to the motifs -- glam2 - discovery of gapped motifs -- glam2scan - scanning sequences with gapped motifs -- fimo - scanning sequences with motifs -- mcast - finding motif clusters -- meme-chip - analysis of large DNA datasets like ChIPseq output -- spamo - finding motif complexes by analysing motif spacing -- dreme - discovery of short regular expression motifs - -Note: building on a 32bit architecture fails at the 'make test' step -(check script). If the step is disabled, the suite builds, however it -may or may NOT work properly. Therefore, 32bit is set as 'UNTESTED'. -The 'make test' step will also fail if you don't build in a proper root -environment. +Check README.DATABASES for more info or if you want to install +meme-suite without the databases present at build time. To cite the full MEME suite: -Timothy L. Bailey, Mikael BodĂ©n, Fabian A. Buske, Martin Frith, -Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, -William S. Noble, "MEME SUITE: tools for motif discovery and searching", -Nucleic Acids Research, 37:W202-W208, 2009. +Timothy L. Bailey, Mikael BodĂ©n, Fabian A. Buske, Martin Frith, Charles +E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, +"MEME SUITE: tools for motif discovery and searching", Nucleic Acids +Research, 37:W202-W208, 2009. To cite individual tools, please check the citation page: http://meme-suite.org/doc/cite.html diff --git a/academic/meme-suite/README.DATABASES b/academic/meme-suite/README.DATABASES new file mode 100644 index 0000000000..3679a2f8f4 --- /dev/null +++ b/academic/meme-suite/README.DATABASES @@ -0,0 +1,15 @@ +At compile time, meme-suite checks if its database folder folder exists: + +/var/lib/meme-suite + +If you have installed any of the meme-db-* packages, this folder will be +present. If you, however, want to install meme-suite first and later set +the databases you need, just make sure that the folder is present before +building meme-suite: + +mkdir -p /var/lib/meme-suite + +If you want to install the databases manually, they can be downloaded +from here: + +http://meme-suite.org/doc/download.html diff --git a/academic/meme-suite/README.TESTS b/academic/meme-suite/README.TESTS new file mode 100644 index 0000000000..9a408ef4d4 --- /dev/null +++ b/academic/meme-suite/README.TESTS @@ -0,0 +1,28 @@ +It is a good practice to run the series of tests provided by the MEME +Suite developers once the executables are built. Unfortunatelly, they +cannot be run properly as root (at least here). + +You can, however, run them once the package is built as a normal user. +Just copy the folder where the meme suite was built as your normal user, +navigate there and run 'make test'. So, do something like this (for meme +version 5.1.0): + +1) cp -a /tmp/SBo/meme-5.1.0/ ~/ +2) cd ~/meme-5.1.0 +3) make test + +You should receive a summary, like this: + +======================================================================== +Testsuite summary for meme 5.1.0 +======================================================================== +# TOTAL: 152 +# PASS: 152 +# SKIP: 0 +# XFAIL: 0 +# FAIL: 0 +# XPASS: 0 +# ERROR: 0 +======================================================================== + +Note that on my 32bit installation of Slackware in a VM, the tests fail. diff --git a/academic/meme-suite/References b/academic/meme-suite/References index 242a70d914..871bc591a7 100644 --- a/academic/meme-suite/References +++ b/academic/meme-suite/References @@ -1,22 +1,4 @@ -Authors - -The MEME Suite was developed by - -Timothy Bailey at the Institute for Molecular Bioscience at the University of Queensland, -William Stafford Noble in the Department of Genome Sciences at the University of Washington and -with input from - -Charles Elkan and -Michael Gribskov. -Development of portions of the MEME Suite have previously been supported by - -Columbia University, -the Computational Biology Research Center at the National Institute of Advanced Industrial Science and Technology, Japan, -the National Biomedical Computation Resource, and -the San Diego Supercomputer Center. - Citing MEME Suite Programs - To cite the full MEME Suite Timothy L. Bailey, Mikael BodĂ©n, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, "MEME SUITE: tools for motif discovery and searching", Nucleic Acids Research, 37:W202-W208, 2009. [full text] To cite individual tools @@ -25,27 +7,31 @@ Fabian A. Buske, Mikael BodĂ©n, Denis C. Bauer and Timothy L. Bailey, "Assigning AME Robert C. McLeay, Timothy L. Bailey, "Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data", BMC Bioinformatics, 11:165, 2010. [full text] CentriMo -Timothy L. Bailey and Philip Machanick, "Inferring direct DNA binding from ChIP-seq", Nucleic Acids Research, 40:e128, 2012. [Abstract and Full Text] +Timothy L. Bailey and Philip Machanick, "Inferring direct DNA binding from ChIP-seq", Nucleic Acids Research, 40:e128, 2012. [Full Text] +T-Gene +Timothy O'Connor, Charles E. Grant, Mikael BodĂ©n, Timothy L. Bailey, "T-Gene: Improved target gene prediction", bioRxiv, preprint, 2019. DREME Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. [full text] FIMO -Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics 27(7):1017–1018, 2011. [full text] +Charles E. Grant, Timothy L. Bailey and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics 27(7):1017–1018, 2011. [full text] GLAM2 and GLAM2SCAN -Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe, Timothy L. Bailey, "Discovering sequence motifs with arbitrary insertions and deletions", PLoS Computational Biology, 4(5):e1000071, 2008. [full text] +Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe and Timothy L. Bailey, "Discovering sequence motifs with arbitrary insertions and deletions", PLoS Computational Biology, 4(5):e1000071, 2008. [full text] GOMO Fabian A. Buske, Mikael BodĂ©n, Denis C. Bauer and Timothy L. Bailey, "Assigning roles to DNA regulatory motifs using comparative genomics", Bioinformatics, 26(7), 860-866, 2010. [full text] MAST Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, 14(1):48-54, 1998. [pdf] +MCAST +Timothy Bailey and William Stafford Noble, "Searching for statistically significant regulatory modules", Bioinformatics (Proceedings of the European Conference on Computational Biology), 19(Suppl. 2):ii16-ii25, 2003. [full text] MEME -Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [postscript] [pdf] +Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [pdf] MEME-ChIP Philip Machanick and Timothy L. Bailey, "MEME-ChIP: motif analysis of large DNA datasets", Bioinformatics 27(12):1696-1697, 2011. [full text] +MoMo +Alice Cheng, Charles Grant, Timothy L. Bailey and William Noble, "MoMo: Discovery of statistically significant post-translational modification motifs", Bioinformatics, 2018. [full text] PSPs -Timothy L. Bailey, Mikael BodĂ©n, Tom Whitington, and Philip Machanick, "The value of position-specific priors in motif discovery using MEME", BMC Bioinformatics, 11(1):179, 2010. [full text] -MCAST -Timothy Bailey and William Stafford Noble, "Searching for statistically significant regulatory modules", Bioinformatics (Proceedings of the European Conference on Computational Biology), 19(Suppl. 2):ii16-ii25, 2003. [full text] +Timothy L. Bailey, Mikael BodĂ©n, Tom Whitington and Philip Machanick, "The value of position-specific priors in motif discovery using MEME", BMC Bioinformatics, 11(1):179, 2010. [full text] SpaMo -Tom Whitington, Martin C. Frith, James Johnson, and Timothy L. Bailey "Inferring transcription factor complexes from ChIP-seq data", Nucl. Acids Res. 39(15):e98, 2011. [full text] +Tom Whitington, Martin C. Frith, James Johnson and Timothy L. Bailey "Inferring transcription factor complexes from ChIP-seq data", Nucl. Acids Res. 39(15):e98, 2011. [full text] Tomtom Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007. [full text] Related papers @@ -55,24 +41,24 @@ MAST related Timothy L. Bailey and Michael Gribskov, "Score distributions for simultaneous matching to multiple motifs" Journal of Computational Biology, Vol. 4, pp. 45-59, 1997. [pdf] Timothy L. Bailey and Michael Gribskov, "Methods and statistics for combining motif match scores" Journal of Computational Biology, Vol. 5, pp. 211-221, 1998. [pdf] MEME related -Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [postscript] [pdf] +Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [pdf] Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", UCSD Technical Report, CS94-351, March, 1994, University of California at San Diego. [pdf] Timothy L. Bailey, "Discovering motifs in DNA and protein sequences: The approximate common substring problem", Ph.D. dissertation, University of California at San Diego, 1995. [pdf] Timothy L. Bailey and Charles Elkan, "Unsupervised Learning of Multiple Motifs in Biopolymers using EM" Machine Learning, 21(1-2):51-80, October, 1995. [pdf] Timothy L. Bailey and Charles Elkan, "The value of prior knowledge in discovering motifs with MEME", Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, pp. 21-29, AAAI Press, Menlo Park, California, 1995. [pdf] Timothy L. Bailey and Michael Gribskov, "The megaprior heuristic for discovering protein sequence patterns"", Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, pp. 15-24 AAAI Press, Menlo Park, California, 1996. [pdf] William N. Grundy, Timothy L. Bailey and Charles P. Elkan, "ParaMEME: A Parallel Implementation and a Web Interface for a DNA and Protein Motif Discovery Tool", Computer Applications in the Biological Sciences (CABIOS), Vol. 12(4), pp. 303-310, 1996. [pdf] -Timothy L. Bailey, Michael E. Baker and Charles P. Elkan, "An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases", Journal of steroid biochemistry and molecular biology, Vol. 62, 1997. +Timothy L. Bailey, Michael E. Baker and Charles P. Elkan, "An artificial intelligence approach to motif discovery in protein sequences: application to steroid dehydrogenases", Journal of steroid biochemistry and molecular biology, Vol. 62, 1997. Martin Tompa, Nan Li, Timothy L. Bailey, George M. Church, Bart De Moor, Eleazar Eskin, Alexander V. Favorov, Martin C. Frith, Yutao Fu, W. James Kent, Vsevolod J. Makeev, Andrei A. Mironov,, William S. Noble, Giulio Pavesi, Graziano Pesole, Mireille Regnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye and Zhou Zhu. "Assessing computational tools for the discovery of transcription factor binding sites." Nature Biotechnology, 23(1), 137-144, 2005. [full text] -Timothy L. Bailey, Nadya Williams, Chris Misleh, and Wilfred W. Li, "MEME: discovering and analyzing DNA and protein sequence motifs" Nucleic Acids Research, Vol. 34, pp. W369-W373, 2006. [html] [pdf] +Timothy L. Bailey, Nadya Williams, Chris Misleh and Wilfred W. Li, "MEME: discovering and analyzing DNA and protein sequence motifs" Nucleic Acids Research, Vol. 34, pp. W369-W373, 2006. [html] [pdf] Wenxiu Ma, William Stafford Noble and Timothy L. Bailey, "Motif-based analysis of large nucleotide datasets using MEME-ChIP" Nature Protocols, 9(6):1428-1450, 2014. [html] Tomtom related -Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William S. Noble, and Uri Keich, "Improved similarity scores for comparing motifs" Bioinformatics 27(12): 1603-1609, 2011. [full text] +Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William S. Noble and Uri Keich, "Improved similarity scores for comparing motifs" Bioinformatics 27(12): 1603-1609, 2011. [full text] Other William N. Grundy, Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Hidden Markov Model Analysis of Motifs in Steroid Dehydrogenases and their Homologs" Biochemical and Biophysical Research Communications, Vol 231, pp. 760-766, 1997. [pdf] William N. Grundy, Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Meta-MEME: Motif-based Hidden Markov Models of Protein Families" Computer Applications in the Biological Sciences (CABIOS), Vol. 13(4), pp. 397-406, 1997. [pdf] -Michael E. Baker, William N. Grundy, and Charles P. Elkan, "Spinach CSP41, an mRNA-binding protein and ribonuclease, is homologous to nucleotide-sugar epimerases and hydroxysteroid dehydrogenases", Biochemical and Biophysical Research Communications 248(2), 250-254, 1998. [pdf] -Michael E. Baker, William N. Grundy, and Charles P. Elkan, "A common ancestor for a subunit in the mitochondrial proton-translocating NADH:ubiquinone oxidoreductase (complex I) and short-chain dehydrogenases/reductases", Cellular and Molecular Life Sciences, Vol. 55(3), 450-455, 1999. -John Hawkins, Charles Grant, William S. Noble, and Timothy L. Bailey, "Assessing phylogenetic motif models for predicting transcription factor binding sites" Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference), 25(12), i339--347, 2009. [full text] -Gabriel Cuellar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, and Timothy L. Bailey, "Epigenetic priors for identifying active transcription factor binding sites", Bioinformatics 28(1): 56-62, 2012 [pdf] -Timothy L. Bailey, James Johnson, Charles E. Grant and William Stafford Noble, "The MEME Suite." Nucleic Acids Resesearch, 43(W1):W39-49, 2015 [full text] +Michael E. Baker, William N. Grundy and Charles P. Elkan, "Spinach CSP41, an mRNA-binding protein and ribonuclease, is homologous to nucleotide-sugar epimerases and hydroxysteroid dehydrogenases", Biochemical and Biophysical Research Communications 248(2), 250-254, 1998. [pdf] +Michael E. Baker, William N. Grundy and Charles P. Elkan, "A common ancestor for a subunit in the mitochondrial proton-translocating NADH:ubiquinone oxidoreductase (complex I) and short-chain dehydrogenases/reductases", Cellular and Molecular Life Sciences, Vol. 55(3), 450-455, 1999. +John Hawkins, Charles Grant, William S. Noble and Timothy L. Bailey, "Assessing phylogenetic motif models for predicting transcription factor binding sites" Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference), 25(12), i339--347, 2009. [full text] +Gabriel Cuellar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble and Timothy L. Bailey, "Epigenetic priors for identifying active transcription factor binding sites", Bioinformatics 28(1): 56-62, 2012 [pdf] +Timothy L. Bailey, James Johnson, Charles E. Grant and William Stafford Noble, "The MEME Suite." Nucleic Acids Research, 43(W1):W39-49, 2015 [full text] diff --git a/academic/meme-suite/meme-suite.SlackBuild b/academic/meme-suite/meme-suite.SlackBuild index a21bb00ea1..558c35ebd6 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 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,11 +23,12 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=meme-suite -SRCNAM=meme -VERSION=${VERSION:-4.12.0} +VERSION=${VERSION:-5.1.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +SRCNAM=meme + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -60,9 +61,9 @@ 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} +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 \ @@ -70,51 +71,49 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Fix a few paths -sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" Makefile.in -sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/Makefile.* -sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/css/Makefile.* -sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/images/Makefile.* -sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/js/Makefile.* -sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/examples/Makefile.* -sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/examples/compute_prior_dist_example_output_files/Makefile.* -sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/examples/sample_opal_scripts/Makefile.* -sed -i "s:\\$(libdir)/perl:&/vendor_perl:g" scripts/Makefile.* -sed -i "s:\\$(libdir)/python:$(libdir)/python2.7/site-packages:g" scripts/Makefile.* +# Change name from "meme" to "meme-suite" +sed -i "s:PACKAGE_NAME='meme':PACKAGE_NAME='meme-suite':" configure + +# Do not append the package version to folder names +find . -name "Makefile.*" -exec \ +sed -i 's:${PACKAGE_NAME}-${PACKAGE_VERSION}:${PACKAGE_NAME}:g' {} \; + +# Sometimes the brackets are not curly +find . -name "Makefile.*" -exec \ +sed -i 's:$(PACKAGE_NAME)-${PACKAGE_VERSION}:$(PACKAGE_NAME):g' {} \; + +# Documentation should go to docdir not datadir +sed -i 's:${datadir}/${PACKAGE_NAME}:${docdir}:g' doc/Makefile.* + +# Make empty folders for the databases +mkdir -p $PKG/var/lib/$PRGNAM/{fasta_databases,gomo_databases,motif_databases,tgene_databases} ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --with-url="http://meme-suite.org" \ - --datarootdir=/usr/share/$PRGNAM/data \ - --sysconfdir=/usr/share/$PRGNAM/etc \ + --datarootdir=/usr/share \ + --libexecdir=/usr/libexec \ --localstatedir=/var \ + --mandir=/usr/man \ --with-db=/var/lib/$PRGNAM \ - --with-logs=/var/log/$PRGNAM \ --with-temp=/tmp -# CFLAGS should be specified here, otherwise they are not accepted make CFLAGS="$SLKCFLAGS -std=gnu89" - -# The tests are recommended, but take quite some time. Be patient or comment out the line below. -# Also, some tests fail on a 32bit system, therefore it is listed as unsupported. If you find a -# fix, let me know. -make test 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 -# The databases directory should contain folders for motif, gomo and fasta databases -mkdir -p $PKG/var/lib/$PRGNAM/{motif_databases,gomo_databases,fasta_databases} - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ AUTHORS COPYING INSTALL README \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +cat $CWD/README.TESTS > $PKG/usr/doc/$PRGNAM-$VERSION/README.TESTS +cat $CWD/README.DATABASES > $PKG/usr/doc/$PRGNAM-$VERSION/README.DATABASES mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/meme-suite/meme-suite.info b/academic/meme-suite/meme-suite.info index 9f67bd2c7e..8c94b67b1f 100644 --- a/academic/meme-suite/meme-suite.info +++ b/academic/meme-suite/meme-suite.info @@ -1,10 +1,10 @@ PRGNAM="meme-suite" -VERSION="4.12.0" +VERSION="5.1.1" HOMEPAGE="http://meme-suite.org/" -DOWNLOAD="UNSUPPORTED" -MD5SUM="" -DOWNLOAD_x86_64="http://meme-suite.org/meme-software/4.12.0/meme_4.12.0.tar.gz" -MD5SUM_x86_64="40d282cc33f7dedb06b24b9f34ac15c1" -REQUIRES="openmpi perl-HTML-Template perl-HTML-Tree perl-File-Which perl-JSON" +DOWNLOAD="http://meme-suite.org/meme-software/5.1.1/meme-5.1.1.tar.gz" +MD5SUM="98ffab29abb95621b947b2b2fa6e5ee7" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="openmpi perl-HTML-Template perl-JSON python3 meme-db-gomo meme-db-motif meme-db-tgene" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/mpb/README b/academic/mpb/README new file mode 100644 index 0000000000..4710eced99 --- /dev/null +++ b/academic/mpb/README @@ -0,0 +1,42 @@ +mpb (computes electromagnetic band structures and modes) + +MPB is a free and open-source software package for computing +electromagnetic band structures and modes. It saves results in hdf5 +format. + +This package requires: hdf5, libctl, lapack + +You may wish to also install: h5utils + +You very probably want to build a multi-processor version of this +code by adding the "--with-openmp" configure option. + +Configuration: + +If the build script can find the ATLAS libraries, it will adapt the +configure options to use them rather than the default lapack. + +You can add additional options to the command line using +the environment variable SBOPTIONS_MPB; e.g. to enable MPI +(multi-processor calculation) using openmp, use: + +SBOPTIONS_MPB="--with-openmp" ./mpb.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 +"mpb:" followed by options, e.g.: + +mpb: --with-openmp + +If you want to use mpich instead of openmp, you will have to recompile +the installed slackware fftw library with two additional configure +options, i.e. not only "--with-mpi" but also "--enable-type-prefix". + +Note: + +This mpb build script does *two* passes. This is so that when +MPI support is enabled, the first compiles the mpb-data utility, +then the second builds the full MPI version. The resulting package +includes both, with any MPI version of the files replacing the non- +MPI version. diff --git a/academic/mpb/mpb.SlackBuild b/academic/mpb/mpb.SlackBuild new file mode 100644 index 0000000000..2191964934 --- /dev/null +++ b/academic/mpb/mpb.SlackBuild @@ -0,0 +1,150 @@ +#!/bin/sh + +# Slackware build script for mpb + +# Copyright 2019,2020 Paul Kinsler, U.K. +# 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. + +PRGNAM=mpb +VERSION=${VERSION:-1.11.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# change annoying underscores into hyphens +SVERSION=$(echo $VERSION | tr '_' '-') +# make a custom list of doc files in advance +DOCFILES="AUTHORS COPYING COPYRIGHT TODO README.md 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 +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 there is no configure script, try to build one! +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 "${SBOPTIONS_MPB}" ] ; then + LOCALCONFIGS=${LOCALCONFIGS}" "${SBOPTIONS_MPB} + echo Build options selected by environment: LOCALCONFIGS=${LOCALCONFIGS} +fi + +# 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=${LOCALCONFIGS}" --with-blas=atlas" + fi +fi + +# LOCALCONFIGS without any mpi requests so I can do a no-mpi compile. +SPLOCALCONFIGS=$(echo $LOCALCONFIGS | sed s/--with-mpi// | sed s/--with-openmp//) + + +# do two passes; first with no mpi (to get mpb-data), +# then a second *with* mpi + +CFLAGS="$SLKCFLAGS" \ +CPPFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --mandir=/usr/man \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux \ + $SPLOCALCONFIGS + +make +make install DESTDIR=$PKG + +CFLAGS="$SLKCFLAGS" \ +CPPFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --mandir=/usr/man \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux \ + $LOCALCONFIGS + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +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 + +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:-tgz} diff --git a/academic/mpb/mpb.info b/academic/mpb/mpb.info new file mode 100644 index 0000000000..bd24b0e499 --- /dev/null +++ b/academic/mpb/mpb.info @@ -0,0 +1,10 @@ +PRGNAM="mpb" +VERSION="1.11.1" +HOMEPAGE="https://github.com/NanoComp/mpb" +DOWNLOAD="https://github.com/NanoComp/mpb/releases/download/v1.11.1/mpb-1.11.1.tar.gz" +MD5SUM="99afe4e8e11427c62a896d8eadd1c205" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="lapack hdf5 libctl" +MAINTAINER="PaulKinsler" +EMAIL="dr.paul@kinsler.org" diff --git a/academic/mpb/slack-desc b/academic/mpb/slack-desc new file mode 100644 index 0000000000..221d698891 --- /dev/null +++ b/academic/mpb/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------------------------------------------------------| +mpb: mpb (computation of electromagnetic band structures and modes) +mpb: +mpb: MPB is a free and open-source software package for +mpb: computing electromagnetic band structures and modes. +mpb: +mpb: Homepage: https://github.com/NanoComp/mpb +mpb: +mpb: +mpb: +mpb: +mpb: diff --git a/academic/mpmath/README b/academic/mpmath/README deleted file mode 100644 index 36d9586af4..0000000000 --- a/academic/mpmath/README +++ /dev/null @@ -1,3 +0,0 @@ -mpmath is a free (BSD licensed) Python library for real and complex -floating-point arithmetic with arbitrary precision. It has been developed -by Fredrik Johansson since 2007, with help from many contributors. diff --git a/academic/mpmath/mpmath.info b/academic/mpmath/mpmath.info deleted file mode 100644 index 5f7cfb360c..0000000000 --- a/academic/mpmath/mpmath.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="mpmath" -VERSION="0.19" -HOMEPAGE="http://mpmath.org/" -DOWNLOAD="http://mpmath.org/files/mpmath-0.19.tar.gz" -MD5SUM="af5cc956b2673b33a25c3e57299bae7b" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="David Melik" -EMAIL="dchmelik@gmail.com" diff --git a/academic/mrbayes/mrbayes.SlackBuild b/academic/mrbayes/mrbayes.SlackBuild index 5154bdee24..2bf1289cb4 100644 --- a/academic/mrbayes/mrbayes.SlackBuild +++ b/academic/mrbayes/mrbayes.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for mrbayes -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2019 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,13 +23,14 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=mrbayes -VERSION=${VERSION:-3.2.6} +SRCNAM=MrBayes +VERSION=${VERSION:-3.2.7a} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -40,8 +41,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -59,9 +60,9 @@ 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 \ @@ -69,11 +70,6 @@ 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 {} \; -cd src -autoconf - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ @@ -84,17 +80,26 @@ CXXFLAGS="$SLKCFLAGS" \ --with-beagle=no \ --build=$ARCH-slackware-linux -make -install -D -m755 mb $PKG/usr/bin/$PRGNAM +# Fix the examples path +sed -i "s:/share:/share/$PRGNAM:" examples/Makefile +sed -i 's:examples/${PACKAGE}:examples:g' examples/Makefile + +# Use our CFLAGS +sed -i "/^CFLAGS/s/=/+=/" Makefile + +make CFLAGS="$SLKCFLAGS" +make install DESTDIR=$PKG + +# Rename the executable +cd $PKG/usr/bin +mv mb $PRGNAM +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 $PKG/usr/share/$PRGNAM -cp -a ../examples $PKG/usr/share/$PRGNAM - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a gpl.txt ../documentation/* $PKG/usr/doc/$PRGNAM-$VERSION +# Add these too to the doc folder +cp -a INSTALL TODO $PKG/usr/doc/$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/mrbayes/mrbayes.info b/academic/mrbayes/mrbayes.info index 547aa09398..f00c0fc95f 100644 --- a/academic/mrbayes/mrbayes.info +++ b/academic/mrbayes/mrbayes.info @@ -1,8 +1,8 @@ PRGNAM="mrbayes" -VERSION="3.2.6" +VERSION="3.2.7a" HOMEPAGE="http://mrbayes.sourceforge.net/" -DOWNLOAD="http://ponce.cc/slackware/sources/repo/mrbayes-3.2.6.tar.gz" -MD5SUM="95f9822f24be47b976bf87540b55d1fe" +DOWNLOAD="https://github.com/NBISweden/MrBayes/archive/v3.2.7a/MrBayes-3.2.7a.tar.gz" +MD5SUM="504236626ce9a2de1066a8520672f0cc" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/muscle/README b/academic/muscle/README index 4db82130b5..2a8b2c538d 100644 --- a/academic/muscle/README +++ b/academic/muscle/README @@ -3,7 +3,29 @@ nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. -For details and citation: -Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high -accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. -doi:10.1093/nar/gkh340 +Fast, accurate and easy to use +MUSCLE is one of the best-performing multiple alignment programs +according to published benchmark tests, with accuracy and speed that +are consistently better than CLUSTALW. MUSCLE can align hundreds of +sequences in seconds. Most users learn everything they need to know +about MUSCLE in a few minutes—only a handful of command-line options +are needed to perform common alignment tasks. + +NOTE about the "-stable" option no longer being supported: +The "-stable" option had a bug, which sometimes resulted in incorrect +alignments to be produced. The author has created a python script to +be used as a workaround. The SlackBuild includes it and its usage is: + + python muscle-stable.py input.fasta aligned.fasta > stable.fasta + +Papers +There are two papers. The first (NAR) introduced the algorithm, and is +the primary citation if you use the program. The second (in BMC Bio- +informatics) gives more technical details, including descriptions of +non-default options. + +Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high +accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797 + +Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with +reduced time and space complexity BMC Bioinformatics, (5) 113 diff --git a/academic/muscle/muscle.1 b/academic/muscle/muscle.1 new file mode 100644 index 0000000000..057c81da47 --- /dev/null +++ b/academic/muscle/muscle.1 @@ -0,0 +1,135 @@ +.\" Title: MUSCLE +.\" Author: Robert Elgar +.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/> +.\" Date: 02/06/2008 +.\" Manual: Muscle Manual +.\" Source: muscle 3.7 +.\" +.TH "MUSCLE" "1" "02/06/2008" "muscle 3.7" "Muscle Manual" +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.SH "NAME" +muscle - Multiple Protein Sequence Alignment +.SH "SYNOPSIS" +.HP 7 +\fBmuscle\fR \fB\-in\ \fR\fB\fIinput\ file\ (fasta)\fR\fR [\fB\-out\ \fR\fB\fIoutput\ file\ (default\ fasta)\fR\fR] [\fB\-diags\fR] [\fB\-log\ \fR\fB\fIlog\ file\fR\fR] [\fB\-maxiters\ \fR\fB\fIn\fR\fR] [\fB\-maxhours\ \fR\fB\fIn\fR\fR] [\fB\-maxmb\ \fR\fB\fIm\fR\fR] [\fB\-html\fR] [\fB\-msf\fR] [\fB\-clw\fR] [\fB\-clwstrict\fR] [\fB\-log[a]\ \fR\fB\fIlogfile\fR\fR] [\fB\-quiet\fR] [\fB\-stable\fR] [\fB\-group\fR] [\fB\-version\fR] +.SH "DESCRIPTION" +.PP +This manual page documents briefly the +\fBmuscle\fR +command\. +.PP +\fBmuscle\fR +aligns protein sequences and is considered superior and faster than Clustal\ W\. +.SH "OPTIONS" +.PP +\fB\-in \fR\fB\fIinput file\fR\fR +.RS 4 +Path to FASTA formatted input file +.RE +.PP +\fB\-out \fR\fB\fIoutput file\fR\fR +.RS 4 +Path to output file, FASTA formatted by default +.RE +.PP +\fB\-diags\fR +.RS 4 +Find diagonals (faster for similar sequences) +.RE +.PP +\fB\-maxiters \fR\fB\fIn\fR\fR +.RS 4 +Maximum number of iterations (integer, default 16) +.RE +.PP +\fB\-maxhours \fR\fB\fIn\fR\fR +.RS 4 +Maximum time to iterate in hours (default no limit) +.RE +.PP +\fB\-maxmb \fR\fB\fIm\fR\fR +.RS 4 +Maximum memory to allocate in Mb (default 80% of RAM) +.RE +.PP +\fB\-html\fR +.RS 4 +Write output in HTML format (default FASTA) +.RE +.PP +\fB\-msf\fR +.RS 4 +Write output in MSF format (default FASTA) +.RE +.PP +\fB\-clw\fR +.RS 4 +Write output in Clustal\ W format (default FASTA) +.RE +.PP +\fB\-clwstrict\fR +.RS 4 +As \-clw, with \'CLUSTAL W (1\.81)\' header +.RE +.PP +\fB\-log[a] \fR\fB\fIlogfile\fR\fR +.RS 4 +Log to file (append if \-loga, overwrite if \-log) +.RE +.PP +\fB\-quiet\fR +.RS 4 +Do not write progress messages to stderr +.RE +.PP +\fB\-stable\fR +.RS 4 +Output sequences in input order (default is \-group) +.RE +.PP +\fB\-group\fR +.RS 4 +Group sequences by similarity (this is the default) +.RE +.PP +\fB\-version\fR +.RS 4 +Display version information and exit +.RE +.SH "SEE ALSO" +.PP + +\fBclustalw\fR(1), +\fBseaview\fR(1), +\fBt_coffee\fR(1)\. +.SH "AUTHORS" +.PP +\fBRobert Elgar\fR +.sp -1n +.IP "" 4 +Wrote Muscle\. +.PP +\fBSteffen Moeller\fR <\&moeller@debian\.org\&> +.sp -1n +.IP "" 4 +Wrote this manpage\. +.PP +\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&> +.sp -1n +.IP "" 4 +Updated this manpage\. +.SH "COPYRIGHT" +Copyright \(co 2003, 2004 Steffen Moeller (manpage) +.br +Copyright \(co 2007, 2008 Charles Plessy (manpage) +.br +.PP +Muscle is in the public domain, and therefore not subjected to copyright\. +.PP +This manual page was written by Steffen Moeller moeller@debian\.org for the +Debian(TM) +system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document as if it were in public domain\. +.sp diff --git a/academic/muscle/muscle.SlackBuild b/academic/muscle/muscle.SlackBuild index 5a73e12824..2258892211 100644 --- a/academic/muscle/muscle.SlackBuild +++ b/academic/muscle/muscle.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for muscle -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,13 +23,15 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=muscle -VERSION=${VERSION:-3.8.31} -BUILD=${BUILD:-1} +VERSION=${VERSION:-3.8.1551} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +MANUAL=muscle_userguide3.8.pdf + if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -40,8 +42,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -59,28 +61,41 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf ${PRGNAM}${VERSION} -tar xvf $CWD/${PRGNAM}${VERSION}_src.tar.gz -cd ${PRGNAM}${VERSION} +rm -rf ${PRGNAM}-${VERSION} +mkdir -p ${PRGNAM}-${VERSION} +cd ${PRGNAM}-${VERSION} +tar xvf $CWD/${PRGNAM}_src_${VERSION}.tar.gz +tar xvf $CWD/stable.tar.gz + chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -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 CFLAGS +sed -i "/^CFLAGS/s/=/+=/" Makefile -ENV_GCC_OPTS="$SLKCFLAGS" \ - make +CFLAGS="$SLKCFLAGS" \ +make -install -D -m755 muscle $PKG/usr/bin/muscle +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m755 stable.py $PKG/usr/bin/$PRGNAM-stable.py + +# Thanks to Debian for the man page +mkdir -p $PKG/usr/man/man1 +cp $CWD/$PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.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 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/$MANUAL > $PKG/usr/doc/$PRGNAM-$VERSION/$MANUAL cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References mkdir -p $PKG/install diff --git a/academic/muscle/muscle.info b/academic/muscle/muscle.info index 1167cc14bf..e747bd6443 100644 --- a/academic/muscle/muscle.info +++ b/academic/muscle/muscle.info @@ -1,8 +1,12 @@ PRGNAM="muscle" -VERSION="3.8.31" +VERSION="3.8.1551" HOMEPAGE="http://www.drive5.com/muscle/" -DOWNLOAD="http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz" -MD5SUM="f767f00fd15f0c5db944d41936779e10" +DOWNLOAD="http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz \ + http://www.drive5.com/muscle/stable.tar.gz \ + http://www.drive5.com/muscle/muscle_userguide3.8.pdf" +MD5SUM="1b7c9661f275a82d3cf708f923736bf8 \ + fceeab190ff13576bfd681a601e7859b \ + 58bb1b7989cf6f2c197dd46552759a40" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/muscle/slack-desc b/academic/muscle/slack-desc index 5e4e7da441..d3d95c0c28 100644 --- a/academic/muscle/slack-desc +++ b/academic/muscle/slack-desc @@ -13,7 +13,7 @@ muscle: or nucleotide sequences. A range of options is provided that give muscle: you the choice of optimizing accuracy, speed, or some compromise muscle: between the two. muscle: -muscle: Home: http://www.drive5.com/muscle/ -muscle: References: /usr/doc/muscle-3.8.31/References +muscle: http://www.drive5.com/muscle/ +muscle: http://www.drive5.com/muscle/stable.html muscle: muscle: diff --git a/academic/ncbi-blast+/ncbi-blast+.SlackBuild b/academic/ncbi-blast+/ncbi-blast+.SlackBuild index 1e6757bc0d..ded8e93c20 100644 --- a/academic/ncbi-blast+/ncbi-blast+.SlackBuild +++ b/academic/ncbi-blast+/ncbi-blast+.SlackBuild @@ -1,10 +1,10 @@ #!/bin/sh # Slackware build script for ncbi-blast+ -# This takes the place of ncbi-blast-plus (2013-2018), which just +# This takes the place of ncbi-blast-plus (2013-2019), which just # repackaged the binaries provided by upstream. -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,11 +25,12 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=ncbi-blast+ -DIRNAM=ncbi-blast -VERSION=${VERSION:-2.7.1} +VERSION=${VERSION:-2.10.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +DIRNAM=ncbi-blast + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -81,24 +82,31 @@ cd c++ # --without-boost \ # do not use Boost # The full list of options is available in c++/src/build-system/configure +# Do not specify the libraries dir by the default way (--libdir=/lib${LIBDIRSUFFIX}), +# because the libs will not be included in the package. CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir='${exec_prefix}'/lib${LIBDIRSUFFIX} \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ - --with-dll \ --with-mt \ + --with-dll \ --without-debug \ --without-downloaded-vdb \ --without-bdb \ --build=$ARCH-slackware-linux +# It does not seem to matter whether to use 'make all' and 'make install-toolkit', +# but let's have them here as a future reminder that these options exist. +#make all +#make prefix=$PKG/usr install-toolkit + make -make prefix=$PKG/usr install +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 diff --git a/academic/ncbi-blast+/ncbi-blast+.info b/academic/ncbi-blast+/ncbi-blast+.info index 78639eac62..e41785d7da 100644 --- a/academic/ncbi-blast+/ncbi-blast+.info +++ b/academic/ncbi-blast+/ncbi-blast+.info @@ -1,10 +1,10 @@ PRGNAM="ncbi-blast+" -VERSION="2.7.1" +VERSION="2.10.1" HOMEPAGE="https://blast.ncbi.nlm.nih.gov/" -DOWNLOAD="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-src.tar.gz" -MD5SUM="48b37565cf5f3d17388daaf0f17b95bc" +DOWNLOAD="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-src.tar.gz" +MD5SUM="216cddf560eedc2b8d88bdd1ada1dfd1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="lmdb" +REQUIRES="lmdb python3" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/nco/README b/academic/nco/README new file mode 100644 index 0000000000..2b1492ef0e --- /dev/null +++ b/academic/nco/README @@ -0,0 +1,10 @@ +NCO (netCDF Operators Software Stack) + +The NCO toolkit manipulates and analyzes data stored in netCDF- +accessible formats, including DAP, HDF4, and HDF5. It exploits the +geophysical expressivity of many CF (Climate & Forecast) metadata +conventions, the flexible description of physical dimensions translated +by UDUnits, the network transparency of OPeNDAP, the storage features +(e.g., compression, chunking, groups) of HDF (the Hierarchical Data +Format), and many powerful mathematical and statistical algorithms of +GSL (the GNU Scientific Library). diff --git a/academic/nco/nco.SlackBuild b/academic/nco/nco.SlackBuild new file mode 100644 index 0000000000..74bd346139 --- /dev/null +++ b/academic/nco/nco.SlackBuild @@ -0,0 +1,108 @@ +#!/bin/sh + +# Slackware build script for nco + +# Copyright 2020 Gregory J. L. Tourte <artourter@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. + + +PRGNAM=nco +VERSION=${VERSION:-4.9.7} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --infodir=/usr/info \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --disable-static \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +rm -f $PKG/usr/info/dir +gzip -9 $PKG/usr/info/*.info* + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS CITATION COPYING COPYRIGHT INSTALL 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:-tgz} diff --git a/academic/nco/nco.info b/academic/nco/nco.info new file mode 100644 index 0000000000..89cf7d6c3e --- /dev/null +++ b/academic/nco/nco.info @@ -0,0 +1,10 @@ +PRGNAM="nco" +VERSION="4.9.7" +HOMEPAGE="http://nco.sf.net" +DOWNLOAD="https://github.com/nco/nco/archive/4.9.7/nco-4.9.7.tar.gz" +MD5SUM="1ce73d3a65bcc7c9388665e57b05188f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="netcdf udunits antlr2" +MAINTAINER="ArTourter" +EMAIL="artourter@gmail.com" diff --git a/academic/nco/slack-desc b/academic/nco/slack-desc new file mode 100644 index 0000000000..a65912dc40 --- /dev/null +++ b/academic/nco/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------------------------------------------------------| +nco: nco (netCDF Operators Software Stack) +nco: +nco: The NCO toolkit manipulates and analyzes data stored in netCDF- +nco: accessible formats, including DAP, HDF4, and HDF5. It exploits the +nco: geophysical expressivity of many CF (Climate & Forecast) metadata +nco: conventions, the flexible description of physical dimensions +nco: translated by UDUnits, the network transparency of OPeNDAP, the +nco: storage features (e.g., compression, chunking, groups) of HDF (the +nco: Hierarchical Data Format), and many powerful mathematical and +nco: statistical algorithms of GSL (the GNU Scientific Library). +nco: diff --git a/academic/ngspice/ngspice.SlackBuild b/academic/ngspice/ngspice.SlackBuild index 6399a4fb87..964f6d0aaf 100644 --- a/academic/ngspice/ngspice.SlackBuild +++ b/academic/ngspice/ngspice.SlackBuild @@ -1,14 +1,14 @@ #!/bin/sh -# Slackware build script for ngspice +# Slackware build script for ngspice and libngspice # Written by B. Jogai <jogaib {at} comcast [dot] net> # Now maintained by R. S. Ananda Murthy (rsamurti@gmail.com) # Set initial variables: PRGNAM=ngspice -VERSION=${VERSION:-30} -BUILD=${BUILD:-2} +VERSION=${VERSION:-34} +BUILD=${BUILD:-5} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -55,32 +55,48 @@ find -L . \ # Fix the lib path to the code modules if [ "$ARCH" = "x86_64" ]; then - sed -i "s%/lib/%/lib${LIBDIRSUFFIX}/%g" src/spinit.in + sed -i "s%/lib/%/lib${LIBDIRSUFFIX}/%g" src/spinit.in fi +mkdir release +cd release + + ../configure \ + --prefix=/usr \ + --mandir=/usr/man \ + --infodir=/usr/info \ + --enable-xspice \ + --enable-cider \ + --enable-openmp \ + --with-x \ + --disable-debug \ + --with-ngshared + +make + CFLAGS="$SLKCFLAGS" \ - ./configure \ - --prefix=/usr \ - --bindir=/usr/bin \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --disable-debug \ - --with-readline=yes \ - --enable-xgraph \ - --enable-xspice \ - --enable-cider \ - --enable-dot-global \ - --enable-intnoise \ - --enable-numparam \ - --enable-shared \ - --disable-static \ - --enable-x \ - --enable-ndev \ - --build=$ARCH-slackware-linux + ../configure --prefix=/usr \ + --bindir=/usr/bin \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --mandir=/usr/man \ + --infodir=/usr/info \ + --disable-debug \ + --enable-xspice \ + --enable-cider \ + --enable-shared \ + --disable-static \ + --enable-ndev \ + --enable-openmp \ + --with-x \ + --build=$ARCH-slackware-linux + make make DESTDIR=$PKG install +# This has installed the configure output file as /usr/include/config.h. + +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 @@ -88,13 +104,29 @@ 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/examples -cp -a ANALYSES AUTHORS BUGS COPYING ChangeLog DEVICES FAQ \ - INSTALL NEWS README* examples/ $PKG/usr/doc/$PRGNAM-$VERSION/ + +cp -a \ + ANALYSES AUTHORS BUGS COPYING ChangeLog DEVICES FAQ \ + INSTALL NEWS README* examples/ \ + $PKG/usr/doc/$PRGNAM-$VERSION/ + cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -cat $CWD/$PRGNAM-$VERSION-manual.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM-$VERSION-manual.pdf +cat $CWD/$PRGNAM-$VERSION-manual.pdf \ + > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM-$VERSION-manual.pdf + +# The shared library enabled by "--with-ngshared" +install -Dm755 ./release/src/.libs/libngspice.so.0.0.0 \ + "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0.0.0" + +ln -s "libngspice.so.0.0.0" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0" +ln -s "libngspice.so.0.0.0" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so" + +# The include file needed to use the shared library enabled by "--with-ngshared" +install -Dm644 ./src/include/ngspice/sharedspice.h $PKG/usr/include/ngspice/sharedspice.h +# Move the configure output file. +mv $PKG/usr/include/config.h $PKG/usr/include/ngspice/ -mkdir -p $PKG/usr/share/icons/hicolor/48x48/apps -install -m644 $CWD/$PRGNAM.png $PKG/usr/share/icons/hicolor/48x48/apps/$PRGNAM.png +install -Dm644 $CWD/$PRGNAM.png $PKG/usr/share/icons/hicolor/48x48/apps/$PRGNAM.png mkdir -p $PKG/usr/share/applications cat $CWD/$PRGNAM.desktop > $PKG/usr/share/applications/$PRGNAM.desktop diff --git a/academic/ngspice/ngspice.info b/academic/ngspice/ngspice.info index 61ded7344a..23f93fdba1 100644 --- a/academic/ngspice/ngspice.info +++ b/academic/ngspice/ngspice.info @@ -1,12 +1,12 @@ PRGNAM="ngspice" -VERSION="30" +VERSION="34" HOMEPAGE="http://ngspice.sourceforge.net/" -DOWNLOAD="https://sourceforge.net/projects/ngspice/files/ng-spice-rework/30/ngspice-30.tar.gz \ - https://sourceforge.net/projects/ngspice/files/ng-spice-rework/30/ngspice-30-manual.pdf" -MD5SUM="272653b01dd4529c3c3a1dbd2e1588f1 \ - cbf628e8585debaefb2ac1dcddd3c759" +DOWNLOAD="https://sourceforge.net/projects/ngspice/files/ng-spice-rework/34/ngspice-34.tar.gz \ + https://sourceforge.net/projects/ngspice/files/ng-spice-rework/34/ngspice-34-manual.pdf" +MD5SUM="e88377ff1e5a466dcd240fa235de7551 \ + ea1bfad9fccd20d58007898bc5f5a15d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="openmpi" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/novocraft/README-manual-download b/academic/novocraft/README-manual-download new file mode 100644 index 0000000000..c66ccd4c18 --- /dev/null +++ b/academic/novocraft/README-manual-download @@ -0,0 +1,10 @@ +The program can only be downloaded from the the novocraft website + +This is the most direct way: +1) browse to http://www.novocraft.com/support/download/ +2) click on the plus-sign next to or on the boldline with the version +as given in the novocraft.info or novocraft.Slackbuild ($VERSION; this will be relatively close to the top) +3) click on the 'Novocraft Programs' for X86-64 Linux 3.1 Kernel +(it will link to http://www.novocraft.com/support/download/download.php?filename=V{$VERSION}/novocraftV{$VERSION}.Linux3.10.0.tar.gz) +download the program to your computer and +move it to the local repository of your Slackbuilding program (e.g. /var/cache/sbopkg/ ) diff --git a/academic/novocraft/novocraft.SlackBuild b/academic/novocraft/novocraft.SlackBuild index f9c5f9562c..0b09df1622 100644 --- a/academic/novocraft/novocraft.SlackBuild +++ b/academic/novocraft/novocraft.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for novocraft -# Copyright 2017 Rob van Nues +# Copyright 2017-19 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=novocraft -VERSION=${VERSION:-3.09.01} +VERSION=${VERSION:-3.09.03} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/novocraft/novocraft.info b/academic/novocraft/novocraft.info index 41fb415edb..e9b6288695 100644 --- a/academic/novocraft/novocraft.info +++ b/academic/novocraft/novocraft.info @@ -1,10 +1,10 @@ PRGNAM="novocraft" -VERSION="3.09.01" +VERSION="3.09.03" HOMEPAGE="http://www.novocraft.com/products/novoalign/" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="http://www.novocraft.com/support/download/download.php?filename=V3.09.00/novocraftV3.09.01.Linux3.10.0.tar.gz" -MD5SUM_x86_64="e387ea9939cd34d83f992d848cca59f9" +DOWNLOAD_x86_64="http://www.novocraft.com/support/download/download.php?filename=V3.09.03/novocraftV3.09.03.Linux3.10.0.tar.gz" +MD5SUM_x86_64="84c2dd55f8b469f4579dcb6951bc4069" REQUIRES="" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/octave/octave.SlackBuild b/academic/octave/octave.SlackBuild index ad2f4c5728..11493d831c 100644 --- a/academic/octave/octave.SlackBuild +++ b/academic/octave/octave.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for octave -# Copyright 2012-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2012-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=octave -VERSION=${VERSION:-4.4.1} +VERSION=${VERSION:-6.2.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -91,7 +91,7 @@ cd $PRGNAM-$VERSION chown -R root:root . chmod -R u+w,go-w,a+rX-st . -patch -p1 < $CWD/patches/imagemagick.diff +patch -p1 < $CWD/patches/imagemagick.diff # https://savannah.gnu.org/bugs/?49653 patch -p1 < $CWD/patches/atlas-lib-rename.diff autoreconf -vif diff --git a/academic/octave/octave.info b/academic/octave/octave.info index 91b44ae74f..d8b41a92ad 100644 --- a/academic/octave/octave.info +++ b/academic/octave/octave.info @@ -1,10 +1,10 @@ PRGNAM="octave" -VERSION="4.4.1" +VERSION="6.2.0" HOMEPAGE="https://www.gnu.org/software/octave/" -DOWNLOAD="https://ftp.gnu.org/gnu/octave/octave-4.4.1.tar.lz" -MD5SUM="e0d9556caafd83e4276af49b06c5c994" +DOWNLOAD="https://ftpmirror.gnu.org/gnu/octave/octave-6.2.0.tar.lz" +MD5SUM="5de14d8561af9799e2ecf6bedfbdb346" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="%README% blas lapack" +REQUIRES="%README% lapack" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/paml/paml.SlackBuild b/academic/paml/paml.SlackBuild index 0a6759536a..8c56506e26 100644 --- a/academic/paml/paml.SlackBuild +++ b/academic/paml/paml.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for paml -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=paml -VERSION=${VERSION:-4.9h} +VERSION=${VERSION:-4.9j} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -97,9 +97,10 @@ install -D -m755 evolverNSbranches $PKG/usr/libexec/$PRGNAM/evolverNSbranches install -D -m755 evolverNSbranchsites $PKG/usr/libexec/$PRGNAM/evolverNSbranchsites install -D -m755 evolverNSsites $PKG/usr/libexec/$PRGNAM/evolverNSsites -# Compile and install TreeTime -cc $SLKCFLAGS -o TreeTimeJeff TreeTimeJeff.c tools.c -lm -install -D -m755 TreeTimeJeff $PKG/usr/libexec/$PRGNAM/TreeTimeJeff +# This does not build at the moment, so let's disable it for now +# # Compile and install TreeTime +# 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 diff --git a/academic/paml/paml.info b/academic/paml/paml.info index 3617cf5097..7c31ba8a04 100644 --- a/academic/paml/paml.info +++ b/academic/paml/paml.info @@ -1,9 +1,9 @@ PRGNAM="paml" -VERSION="4.9h" +VERSION="4.9j" HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" -DOWNLOAD="http://abacus.gene.ucl.ac.uk/software/paml4.9h.tgz \ +DOWNLOAD="http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz \ http://ponce.cc/slackware/sources/repo/MCMCtree.Tutorials.pdf" -MD5SUM="b45d60cc0a82e4835e8dcda6a4c32040 \ +MD5SUM="50c1760512b7a5df50305e5fd26d0ca5 \ 29c851d887eea56b949c01ab42cc48fb" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/pamlX/pamlX.SlackBuild b/academic/pamlX/pamlX.SlackBuild index e25f9f4651..f2e73890c5 100644 --- a/academic/pamlX/pamlX.SlackBuild +++ b/academic/pamlX/pamlX.SlackBuild @@ -74,8 +74,8 @@ 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-4.9h/|g' mainwindow.cpp -sed -i 's|/doc/|/doc/paml-4.9h/|g' pamlhistorydialog.cpp +sed -i 's|/doc/|/doc/paml-4.9j/|g' mainwindow.cpp +sed -i 's|/doc/|/doc/paml-4.9j/|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/pari/README b/academic/pari/README index 6e10ca3d19..b51ae28edf 100644 --- a/academic/pari/README +++ b/academic/pari/README @@ -1,7 +1,7 @@ -PARI/GP is a widely used computer algebra system designed for fast computations -in number theory (factorizations, algebraic number theory, elliptic curves, -modular forms, L functions...), but also contains a large number of other -useful functions to compute with mathematical entities such as matrices, -polynomials, power series, algebraic numbers etc., and a lot of transcendental -functions. PARI is also available as a C library to allow for faster -computations. +PARI/GP is a widely used computer algebra system designed for fast +computations in number theory (factorizations, algebraic number theory, +elliptic curves, modular forms, L functions...), but also contains a +large number of other useful functions to compute with mathematical +entities such as matrices, polynomials, power series, algebraic numbers +etc., and a lot of transcendental functions. PARI is also available as +a C library to allow for faster computations. diff --git a/academic/pari/pari.SlackBuild b/academic/pari/pari.SlackBuild index a71365c927..536e7dd0d4 100644 --- a/academic/pari/pari.SlackBuild +++ b/academic/pari/pari.SlackBuild @@ -28,9 +28,10 @@ # Modified by Joachim Kruth as needed to build pari/gp instead of maxima # Joachim Kruth -> update to version 2.11.0 # Joachim Kruth -> update to version 2.11.1 +# Joachim Kruth -> update to version 2.11.2 PRGNAM=pari -VERSION=${VERSION:-2.11.1} +VERSION=${VERSION:-2.13.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -93,8 +94,11 @@ 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 +mkdir -p $PKG/usr/man/man1 +mv $PKG/usr/man/*gz $PKG/usr/man/man1 + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS COPYING CHANGES* INSTALL* NEW README* \ +cp -a AUTHORS COPYING CHANGES* NEW README* \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/pari/pari.info b/academic/pari/pari.info index fde05c4be5..1da54f9b76 100644 --- a/academic/pari/pari.info +++ b/academic/pari/pari.info @@ -1,8 +1,8 @@ PRGNAM="pari" -VERSION="2.11.1" +VERSION="2.13.1" HOMEPAGE="https://pari.math.u-bordeaux.fr/" -DOWNLOAD="https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-2.11.1.tar.gz" -MD5SUM="474d5ec6b2fca8f3ef4f747b3dca1ffd" +DOWNLOAD="https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-2.13.1.tar.gz" +MD5SUM="826064cf75af268be8a482ade6e27501" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/parmetis/README b/academic/parmetis/README index 018f15ca02..ac2b847cf4 100644 --- a/academic/parmetis/README +++ b/academic/parmetis/README @@ -1,10 +1,10 @@ -ParMETIS (Parallel Graph Partitioning and Fill-reducing Matrix Ordering) +ParMETIS (Parallel Graph Partitioning and Fill-reducing Matrix +Ordering) -ParMETIS is an MPI-based parallel library that implements a variety -of algorithms for partitioning unstructured graphs, meshes, and for +ParMETIS is an MPI-based parallel library that implements a variety +of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. -Set precision type: -DP=yes (for 64-bit, default is 32-bit) +Set precision type: DP=yes (for 64-bit, default is 32-bit) The requirement is a MPI implementation, either mpich or openmpi. diff --git a/academic/pcalc/README b/academic/pcalc/README new file mode 100644 index 0000000000..f9812626c2 --- /dev/null +++ b/academic/pcalc/README @@ -0,0 +1,12 @@ +pcalc (command line util for doing hex/dec/oct/bin math quickly) + +pcalc is a programmer's calculator. It simplifies some operations +(especially working with multiple bases) that are hard work without +this or another programmer's calculator. Main features: + +o Full math parser, parentheses, add, sub, mult, div, exponential +o Automatic conversion between HEX DEC OCT BIN numbers +o Mixing different bases in one expression +o Definable variables +o Math constants (E PI ...) +o Built in math functions (sin/cos/sqrt ...) diff --git a/academic/pcalc/pcalc.SlackBuild b/academic/pcalc/pcalc.SlackBuild new file mode 100644 index 0000000000..e3df7b6d89 --- /dev/null +++ b/academic/pcalc/pcalc.SlackBuild @@ -0,0 +1,90 @@ +#!/bin/sh + +# Slackware build script for pcalc + +# Copyright 2019 Charles Daniels, United States +# 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. + +PRGNAM=pcalc +VERSION=${VERSION:-4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${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 {} \; + +make -j1 +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 + +# pcalc does not have manual/info pages + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS COPYING EXAMPLE README TODO \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/pcalc/pcalc.info b/academic/pcalc/pcalc.info new file mode 100644 index 0000000000..28018c76b5 --- /dev/null +++ b/academic/pcalc/pcalc.info @@ -0,0 +1,10 @@ +PRGNAM="pcalc" +VERSION="4" +HOMEPAGE="https://github.com/vapier/pcalc" +DOWNLOAD="https://github.com/vapier/pcalc/archive/v4/pcalc-4.tar.gz" +MD5SUM="b696aac622ec246e5dde13995c068292" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Charles Daniels" +EMAIL="charles@cdaniels.net" diff --git a/academic/sympy/slack-desc b/academic/pcalc/slack-desc index dafbe9279c..bfb7b16c1f 100644 --- a/academic/sympy/slack-desc +++ b/academic/pcalc/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -sympy: sympy (Python library for symbolic mathematics) -sympy: -sympy: SymPy aims to become a full-featured computer algebra system (CAS) -sympy: while keeping the code as simple as possible in order to be -sympy: comprehensible and easily extensible. SymPy is written entirely in -sympy: Python and does not require any external libraries. -sympy: -sympy: Homepage: http://code.google.com/p/sympy/ -sympy: -sympy: -sympy: +pcalc: pcalc (command line util for doing hex/dec/oct/bin math quickly) +pcalc: +pcalc: pcalc is a programmer's calculator. It simplifies some operations +pcalc: (especially working with multiple bases) that are hard work without +pcalc: this or another programmer's calculator, such as 0x1234 + 0x20. +pcalc: +pcalc: Homepage: https://github.com/vapier/pcalc +pcalc: +pcalc: +pcalc: +pcalc: diff --git a/academic/perlprimer/perlprimer.SlackBuild b/academic/perlprimer/perlprimer.SlackBuild index 686c973a34..105e42f9f0 100644 --- a/academic/perlprimer/perlprimer.SlackBuild +++ b/academic/perlprimer/perlprimer.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for perlprimer -# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2019 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,8 +23,8 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=perlprimer -VERSION=${VERSION:-1.2.3_f7d3bd0} -COMMIT=${COMMIT:-f7d3bd0b7f509d88cb0aded4fc08042bcff7f5dd} +VERSION=${VERSION:-1.2.4} +COMMIT=${COMMIT:-f415ea6d0170f2f62f10c678adac8fdc69a3298f} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -50,7 +50,7 @@ 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/perlprimer.pl +install -D -m755 $PRGNAM $PKG/usr/bin/${PRGNAM}.pl install -D -m644 gcg.603 $PKG/usr/share/$PRGNAM/gcg.603 mkdir -p $PKG/usr/share/{applications,pixmaps} diff --git a/academic/perlprimer/perlprimer.info b/academic/perlprimer/perlprimer.info index bb2859f430..b2589471c1 100644 --- a/academic/perlprimer/perlprimer.info +++ b/academic/perlprimer/perlprimer.info @@ -1,10 +1,10 @@ PRGNAM="perlprimer" -VERSION="1.2.3_f7d3bd0" +VERSION="1.2.4" HOMEPAGE="https://github.com/owenjm/perlprimer" -DOWNLOAD="https://github.com/owenjm/perlprimer/archive/f7d3bd0/perlprimer-f7d3bd0b7f509d88cb0aded4fc08042bcff7f5dd.tar.gz" -MD5SUM="c4fe53c120d3ed61514dacd355a93791" +DOWNLOAD="https://github.com/owenjm/perlprimer/archive/f415ea6/perlprimer-f415ea6d0170f2f62f10c678adac8fdc69a3298f.tar.gz" +MD5SUM="44b469575c960e2d1f496a98eb76d407" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="libwww-perl perl-tk" +REQUIRES="perl-tk perl-JSON perl-LWP-Protocol-https" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/pianobooster/README b/academic/pianobooster/README index bbc0a15b05..a191b9f461 100644 --- a/academic/pianobooster/README +++ b/academic/pianobooster/README @@ -1,7 +1,7 @@ pianobooster (educational music software) PianoBooster is a fun way of playing along with a musical accompaniment -and at the same time learning the basics of reading musical notation. The -difference between playing along to a CD or a standard midi file is -that PianoBooster listens and follows what you are playing on a midi -piano keyboard. +and at the same time learning the basics of reading musical +notation. The difference between playing along to a CD or a standard +midi file is that PianoBooster listens and follows what you are playing +on a midi piano keyboard. diff --git a/academic/pyCRAC/MANIFEST_slack.txt b/academic/pyCRAC/MANIFEST_slack.txt deleted file mode 100644 index 95a4931773..0000000000 --- a/academic/pyCRAC/MANIFEST_slack.txt +++ /dev/null @@ -1,69 +0,0 @@ -setup.py -MANIFEST.txt -LICENCE.txt -README.txt -pyCRAC/tests/test.novo -pyCRAC/tests/test.sh -pyCRAC/tests/test_coordinates.txt -pyCRAC/tests/test.gtf -pyCRAC/tests/test_f.fastq -pyCRAC/tests/test_f.fastq.gz -pyCRAC/tests/test_f_dm.fastq -pyCRAC/tests/test_r.fastq -pyCRAC/tests/test_r.fastq.gz -pyCRAC/tests/test_r_dm.fastq -pyCRAC/tests/indexes.txt -pyCRAC/tests/barcodes.txt -pyCRAC/tests/genes.lis -pyCRAC/Classes/NGSFormatWriters.py -pyCRAC/Classes/NGSFormatReaders.py -pyCRAC/Classes/PairedReads.py -pyCRAC/Classes/Pileups.py -pyCRAC/Classes/Aligner.py -pyCRAC/Classes/Motifs.py -pyCRAC/Classes/Barcodes.py -pyCRAC/Classes/Coverage.py -pyCRAC/Classes/Exceptions.py -pyCRAC/Classes/FDR.py -pyCRAC/Classes/Clustering -pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt -pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa -pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab -pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf -pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PE.py -pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PeakFinder.py -pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_SE.py -pyCRAC/kinetic_crac_pipeline/TrimNucs.py -pyCRAC/scripts/pybed2GTF.py -pyCRAC/scripts/pyGTF2bed.py -pyCRaC/scripts/pyGTF2bedGraph.py -pyCRAC/scripts/pyGTF2sgr.py -pyCRAC/scripts/pyNormalizeIntervalLengths.py -pyCRAC/scripts/pyFastqDuplicateRemover.py -pyCRAC/scripts/pyFastqJoiner.py -pyCRAC/scripts/pyFastqSplitter.py -pyCRAC/scripts/pyGetGeneNamesFromGTF.py -pyCRAC/scripts/pySelectMotifsFromGTF.py -pyCRAC/scripts/pyGetGTFSources.py -pyCRAC/scripts/pyFilterGTF.py -pyCRAC/scripts/pyFasta2tab.py -pyCRAC/scripts/pyAlignment2Tab.py -pyCRAC/scripts/pyExtractLinesFromGTF.py -pyCRAC/scripts/pyCheckGTFfile.py -pyCRAC/scripts/pyCalculateChromosomeLengths.py -pyCRAC/pyClusterReads.py -pyCRAC/pyCalculateFDRs.py -pyCRAC/pyCalculateMutationFrequencies.py -pyCRAC/pyBinCollector.py -pyCRAC/pyMotif.py -pyCRAC/pyPileup.py -pyCRAC/pyReadAligner.py -pyCRAC/pyReadCounters.py -pyCRAC/pyBarcodeFilter.py -pyCRAC/Parsers/Blast.py -pyCRAC/Parsers/GTF2.py -pyCRAC/Parsers/Novoalign.py -pyCRAC/Parsers/ParseAlignments.py -pyCRAC/Parsers/SAM.py -pyCRAC/Parsers/fasta2dict.py -pyCRAC/Parsers/tab2dict.py diff --git a/academic/pyCRAC/README b/academic/pyCRAC/README index a5be782d73..9eb56fc043 100644 --- a/academic/pyCRAC/README +++ b/academic/pyCRAC/README @@ -1,4 +1,4 @@ -The pyCRAC package is a collection of python2-scripts to analyse high +The pyCRAC package is a collection of python scripts to analyse high throughput data generated by RNA-sequencing, especially of molecules crosslinked by UV to an immunoprecipitated protein of interest (i.e. data generated by CLIP or CRAC protocols). @@ -8,8 +8,6 @@ and reports sense and anti-sense hits. Included is the pipeline used for the analysis of a group of CRAC data sets. -An R-function used for kinetic CRAC analysis can be found in -/usr/share/pyCRAC/kinetic_crac_pipeline References @@ -25,3 +23,21 @@ 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/README.tests b/academic/pyCRAC/README.tests index 15def4bfeb..e1b634e6a3 100644 --- a/academic/pyCRAC/README.tests +++ b/academic/pyCRAC/README.tests @@ -1,7 +1,9 @@ To test the pyCRAC scripts after installing the package on Slackware: - cp -R /usr/share/pyCRAC <path-to-your-work-directory>/ - cd <path-to-your-work-directory>/pyCRAC/tests + cp -R /usr/share/pyCRAC-$VERSION <path-to-your-work-directory>/ + cd <path-to-your-work-directory>/pyCRAC-$VERSION/tests sh test.sh If all tests complete without an error, the package is working. + +In case of any problems please email the SBo maintainer of pyCRAC diff --git a/academic/pyCRAC/pyCRAC.SlackBuild b/academic/pyCRAC/pyCRAC.SlackBuild index af4e827e0f..6482133f42 100644 --- a/academic/pyCRAC/pyCRAC.SlackBuild +++ b/academic/pyCRAC/pyCRAC.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for pyCRAC -# Copyright 2017 Rob van Nues +# Copyright 2017-2021 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,15 +23,22 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=pyCRAC -VERSION=${VERSION:-1.3.3} +VERSION=${VERSION:-1.5.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -SRCNAM=sgrann-pycrac -SRCVER=${SRCVER:-fafa1e7d1fae} +# pyCRAC works with python2 as well as python3; +# Note that python2 is being phased out; therefore python3 is set as default. +# This is the same for the python pyCrac dependencies -PIPENAM=kinetic_crac_pipeline -PIPEVER=${PIPEVER:-1bdb8c231d2d} +#set which python version to install it for +PYTHON2=false +PYTHON3=true + + +PIPENAM=crac_pipelines +PIPEVER=master +#PIPETAG=sgrann if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -65,20 +72,25 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM-$SRCVER -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz || tar xvf $CWD/$SRCVER.tar.gz -cd $SRCNAM-$SRCVER +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 -tar xvf $CWD/sgrann-$PIPENAM-$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 || \ - tar xvf $CWD/$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 -#replace setup.py -rm setup.py +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 cp $CWD/setup_slack.py setup.py -#replace Manifest -rm MANIFEST.txt -cp $CWD/MANIFEST_slack.txt MANIFEST.txt +rm tests/test.sh +cp $CWD/test_slack.sh tests/test.sh chown -R root:root . find -L . \ @@ -87,20 +99,23 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -python setup.py install --root=$PKG +if $PYTHON2; then + python setup.py install --root=$PKG +fi +if $PYTHON3; then + python3 setup.py install --root=$PKG +fi 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 -# The pipeline-R script -mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM -cp $PRGNAM/$PIPENAM/gaussianProcessAnalysis.R $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM - # the manual etc. mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - LICENCE.txt README.txt "The pyCRAC Manual.pdf" VERSION.txt \ - $CWD/README.tests $CWD/setup_slack.py $CWD/MANIFEST_slack.txt \ + README.md \ + setup.py.ORIG \ + The_pyCRAC_Manual.pdf \ + $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 diff --git a/academic/pyCRAC/pyCRAC.info b/academic/pyCRAC/pyCRAC.info index a2e57d33ba..0b293a216a 100644 --- a/academic/pyCRAC/pyCRAC.info +++ b/academic/pyCRAC/pyCRAC.info @@ -1,12 +1,12 @@ PRGNAM="pyCRAC" -VERSION="1.3.3" -HOMEPAGE="https://bitbucket.org/sgrann/" -DOWNLOAD="https://bitbucket.org/sgrann/pycrac/get/fafa1e7d1fae.tar.gz \ - https://bitbucket.org/sgrann/kinetic_crac_pipeline/get/1bdb8c231d2d.tar.gz" -MD5SUM="3e9ed2a34449176bb6680589c221c5df \ - e1dfcdb757af5f32d811c5458a68c15c" +VERSION="1.5.0" +HOMEPAGE="http://sandergranneman.bio.ed.ac.uk/pycrac-software" +DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.5.0.tar.gz \ + https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines/-/archive/master/crac_pipelines-master.tar.gz" +MD5SUM="73bfb92e8ae0f30fd73f21a77d265288 \ + 119c67d318a03ed29471e4caeb2690a4" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="flexbar novocraft numpy pysam scipy pandas ruffus" -MAINTAINER="rob van nues" +REQUIRES="python3 flexbar novocraft numpy3 pysam scipy3 pandas ruffus" +MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/pyCRAC/setup_slack.py b/academic/pyCRAC/setup_slack.py index 9f8adab605..f76cd3868d 100644 --- a/academic/pyCRAC/setup_slack.py +++ b/academic/pyCRAC/setup_slack.py @@ -1,11 +1,11 @@ #!/usr/bin/python -# not compatible with python 3 + __author__ = "Sander Granneman" -__copyright__ = "Copyright 2018" -__version__ = "1.3.3" -__credits__ = ["Sander Granneman","Hywell Dunn Davies"] -__maintainer__ = ["Rob van Nues, via SlackBuilds.org"] -__email__ = "sgrannem@staffmail.ed.ac.uk" +__copyright__ = "Copyright 2020" +__version__ = "1.5.0" +__credits__ = ["Sander Granneman","Grzegorz Kudla","Hywell Dunn Davies"] +__maintainer__ = ["Sander Granneman","Rob van Nues via SlackBuilds.org"] +__email__ = ["sgrannem@staffmail.ed.ac.uk", "sborg63@disroot.org"] __status__ = "Production" import sys @@ -13,18 +13,12 @@ import os import platform import setuptools from setuptools import setup +from setuptools.command import easy_install DEFAULT_PATH = "/usr/share/" -if sys.version[0:3] < '2.7' : raise ImportError('Python version 2.7 or above is required for pyCRAC') -if sys.version[0:3] >= '3.0': raise ImportError('pyCRAC is not compatible with Python 3.0 or higher') - sys.stdout.write("\nInstalling pyCRAC version %s...\n" % __version__) -path_files = open("pyCRAC/defaults.py","w") -#path_files.write("DEFAULT_PATH=\"%s\"\n" % DEFAULT_PATH) -path_files.write("GTF=\"%spyCRAC-%s/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf\"\nTAB=\"%spyCRAC-%s/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab\"\nCHROM=\"%spyCRAC-%s/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt\"\n" % (DEFAULT_PATH,__version__,DEFAULT_PATH,__version__,DEFAULT_PATH,__version__)) -path_files.close() setup(name='pyCRAC', version='%s' % __version__, @@ -33,7 +27,7 @@ setup(name='pyCRAC', author_email='sgrannem@staffmail.ed.ac.uk', url='http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html', packages=['pyCRAC','pyCRAC.Parsers','pyCRAC.Classes','pyCRAC.Methods'], - install_requires=['numpy >= 1.5.1', 'cython >=0.19', 'pysam >= 0.6'], + install_requires=['numpy >= 1.5.1', 'cython >=0.19', 'pysam >= 0.6','six >= 1.9.0'], scripts=[ 'pyCRAC/pyReadAligner.py', 'pyCRAC/pyMotif.py', @@ -61,20 +55,18 @@ setup(name='pyCRAC', 'pyCRAC/scripts/pyGTF2bedGraph.py', 'pyCRAC/scripts/pyFilterGTF.py', 'pyCRAC/scripts/pyNormalizeIntervalLengths.py', - 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PE.py', - 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PeakFinder.py', - 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_SE.py', - 'pyCRAC/kinetic_crac_pipeline/TrimNucs.py' + 'pyCRAC/crac_pipelines/CRAC_pipeline_PE.py', + 'pyCRAC/crac_pipelines/CRAC_pipeline_SE.py', ], classifiers=[ 'Development Status :: 5 - Production/Stable', - 'Environment :: Terminal', + 'Environment :: Console', 'Intended Audience :: Education', 'Intended Audience :: Developers', 'Intended Audience :: Science/Research', 'License :: Freeware', 'Operating System :: MacOS :: MacOS X', 'Operating System :: POSIX', - 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.6', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Topic :: Software Development :: Libraries :: Application Frameworks' ], @@ -99,6 +91,3 @@ setup(name='pyCRAC', 'tests/genes.list']) ] ) - - - diff --git a/academic/pyCRAC/test_slack.sh b/academic/pyCRAC/test_slack.sh new file mode 100644 index 0000000000..0606665d69 --- /dev/null +++ b/academic/pyCRAC/test_slack.sh @@ -0,0 +1,121 @@ +#!/usr/bin/env bash +echo +echo "##### testing all pyCRAC tools #####" +echo +echo "# pyBarcodeFilter.py..." +echo "...demultiplexing illumina indexes" +pyBarcodeFilter.py -f test_f.fastq -r test_r.fastq -b indexes.txt -i -m 1 +echo "...demultiplexing illumina indexes on compressed files" +pyBarcodeFilter.py -f test_f.fastq.gz -r test_r.fastq.gz -b indexes.txt -i -m 1 --file_type=fastq.gz +echo "...demultiplexing random barcodes in 5' adapter" +pyBarcodeFilter.py -f test_f_dm.fastq -r test_r_dm.fastq -b barcodes.txt -m 1 +echo "...demultiplexing random barcodes in 5' adapter on compressed data and compressing output files" +pyBarcodeFilter.py -f test_f_dm.fastq -r test_r_dm.fastq -b barcodes.txt -m 1 --gz +echo "# pyReadCounters..." +echo "...range 300 and deletions only" +pyReadCounters.py -f test.novo -m 10000 -r 300 --mutations=delsonly --discarded=pyReadCounters_discarded.txt --rpkm -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...same as above but counting hits for introns only" +pyReadCounters.py -f test.novo -m 10000 -r 300 --mutations=delsonly --discarded=pyReadCounters_discarded.txt --rpkm -a protein_coding --hittable -s intron -o test_intron -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...same as above but now counting hits in exons only" +pyReadCounters.py -f test.novo -m 10000 -r 300 --mutations=delsonly --discarded=pyReadCounters_discarded.txt --rpkm -a protein_coding --hittable -s exon -o test_exon -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "# pyClusterReads..." +pyClusterReads.py -f test_count_output_reads.gtf -r 300 --cic=5 --ch=5 --co=5 --mutsfreq=10 -o test_count_output_clusters.gtf -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...counting overlap between clusters and genomic features" +pyReadCounters.py -f test_count_output_clusters.gtf --file_type=gtf -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "# pyMotif..." +echo "...with range setting" +pyMotif.py -f test_count_output_clusters.gtf -r 300 -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "...with annotation = protein_coding" +pyMotif.py -f test_count_output_clusters.gtf -a protein_coding -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "# pyBinCollector..." +echo "...with annotation = protein_coding" +pyBinCollector.py -f test_count_output_clusters.gtf -a protein_coding -n 50 -o test_count_output_protein_coding_50.pileup -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...with all annotations" +pyBinCollector.py -f test_count_output_clusters.gtf -n 50 -o test_count_output_all_50.pileup -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...with --binoverlap flag" +pyBinCollector.py -f test_count_output_clusters.gtf -n 50 --binoverlap 1 5 -o test_count_output_selected_1_5.gtf -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...with --outputall flag" +pyBinCollector.py -f test_count_output_clusters.gtf -n 50 --outputall -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "# pyPileup..." +echo "...with genes list" +pyPileup.py -f test.novo -g genes.list --limit=1000 --discarded=pyPileup_discarded.txt -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "...with genes list and removal of duplicates" +pyPileup.py -f test.novo -g genes.list --limit=1000 --blocks -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "...with chromosome coordinates" +pyPileup.py -f test.novo --chr test_coordinates.txt --limit=1000 -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "...with chromosome coordinates and removal of duplicates" +pyPileup.py -f test.novo --chr test_coordinates.txt --limit=1000 --blocks -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "# pyReadAligner..." +echo "...with chromosome coordinates" +pyReadAligner.py -f test.novo --chr test_coordinates.txt --limit=1000 --discarded=pyReadAligner_discarded.txt -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "...with genes list and mutation filtering" +pyReadAligner.py -f test.novo -g genes.list --limit=500 --mutations=delsonly -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "# pyCalculateFDRs..." +pyCalculateFDRs.py -f test_count_output_reads.gtf -r 200 -o test_count_output_FDRs_005.gtf -v -m 0.05 --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "# pyCalculateMutationFrequencies..." +pyCalculateMutationFrequencies.py -i test_count_output_FDRs_005.gtf -r test_count_output_reads.gtf -o test_count_output_FDRs_005_with_muts.gtf --mutsfreq=20 -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo +echo "##### testing pyCRAC scripts #####" +echo +echo "# pyFastqJoiner.py..." +pyFastqJoiner.py -f test_f.fastq test_r.fastq -c "|" -o test_joined.fastq +echo "...with compressed data and output compression" +pyFastqJoiner.py -f test_f.fastq.gz test_r.fastq.gz --file_type=fastq.gz -c "|" --gz -o test_joined_compressed.fastq +echo "...with reverse-complementing the reverse read" +pyFastqJoiner.py -f test_f.fastq test_r.fastq --reversecomplement -c "|" -o test_reverse_joined.fastq +echo "# pyFastqDuplicateRemover.py..." +echo "...with single-end data" +pyFastqDuplicateRemover.py -f test_f.fastq -o test_f.fasta +echo "...with paired-end data" +pyFastqDuplicateRemover.py -f test_f.fastq -r test_r.fastq -o test +echo "# pyFastqSplitter.py..." +pyFastqSplitter.py -f test_joined.fastq -c "|" -o test_splitted +echo "...with compressed data" +pyFastqSplitter.py -f test_joined_compressed.fastq.gz --file_type=fastq.gz -c "|" -o test_compressed_splitted +echo "...with compressed data and compressing output" +pyFastqSplitter.py -f test_joined_compressed.fastq.gz --file_type=fastq.gz -c "|" -o test_compressed_splitted --gzip +echo "# pyCheckGTFfile.py..." +pyCheckGTFfile.py --gtf=test.gtf -o test_corrected.gtf +echo "# pyGetGTFSources.py..." +pyGetGTFSources.py --gtf=test.gtf -o test_gtf_sources.txt --count +echo "# pyGetGeneNamesFromGTF.py..." +pyGetGeneNamesFromGTF.py --gtf=test.gtf -a gene_name -o test_gtf_gene_names.txt --count +echo "# pyNormalizeIntervalLengths with various flags..." +pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --fixed 20 -o test_count_output_FDRs_fixed_20.gtf -v +pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --min 20 -o test_count_output_FDRs_min_20.gtf -v +pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --addboth 20 -o test_count_output_FDRs_addboth_20.gtf -v +pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --addleft 20 -o test_count_output_FDRs_addleft_20.gtf -v +pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --addright 20 -o test_count_output_FDRs_addright_20.gtf -v +echo "# pyAlignment2Tab.py..." +pyAlignment2Tab.py -f sense-reads_SNR17A_genomic_test.fasta -o sense-reads_SNR17A_genomic_test.tab +echo "# pyExtractLinesFromGTF.py..." +pyExtractLinesFromGTF.py --gtf=test.gtf -g genes.list -o test_snR17A.gtf -a gene_name +echo "# pyGTF2bed.py..." +pyGTF2bed.py --gtf=test_count_output_reads.gtf -o test.bed -n test_gtf -d test_gtf --color red +echo "# pyGTF2bedGraph.py..." +echo "...default settings" +pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out -t reads -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...normalized to hits per million" +pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out_norm --permillion -t reads -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...start positions" +pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out_norm_5end --permillion -t startpositions -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...end positions" +pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out_norm_3end --permillion -t endpositions -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "# pyGTF2sgr.py..." +echo "...default settings" +pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...normalized to hits per million" +pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out_norm --permillion -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...start positions" +pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out_norm_5end --permillion -t startpositions -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...end positions" +pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out_norm_3end --permillion -t endpositions -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "# pyFilterGTF.py..." +pyFilterGTF.py -f test_count_output_reads.gtf -o test_sense_filtered_reads.gtf -a protein_coding --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "# pybed2GTF.py..." +pybed2GTF.py --bed=test.bed -o test_bed2gtf.gtf --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "# pyFasta2tab.py..." +pyFasta2tab.py -f sense-reads_SNR17A_genomic_test.fasta -o sense-reads_SNR17A_genomic_test_f2a.tab +echo +echo "##### tests finished #####" +echo diff --git a/academic/pysam/pysam.SlackBuild b/academic/pysam/pysam.SlackBuild index c2ff916cc9..dcbc06e1a6 100644 --- a/academic/pysam/pysam.SlackBuild +++ b/academic/pysam/pysam.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for pysam -# Copyright 2017 Rob van Nues +# Copyright 2017-2020 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,10 +24,14 @@ PRGNAM=pysam -VERSION=${VERSION:-0.15.2} -BUILD=${BUILD:-1} +VERSION=${VERSION:-0.16.0.1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +#set which python version to install it for +PYTHON2=false +PYTHON3=true + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -64,13 +68,28 @@ 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 \ + \( -perm 777 -o -perm 775 -o -perm 751 -o -perm 750 -o -perm 711 -o -perm 555 \ -o -perm 511 \) -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=$PKG +### pysam linked to htslib-1.10; SBo-htslib is at 1.11: +##use system htslib: +#export HTSLIB_LIBRARY_DIR=/usr/lib$LIBDIRSUFFIX +#export HTSLIB_INCLUDE_DIR=/usr/include + +#the source does not allow 'read' to 'other', which could cause a problem on reloading a Jupyter-notebook +chmod 644 pysam.egg-info/* + + +if $PYTHON2; then + python setup.py install --root=$PKG +fi +if $PYTHON3; then + python3 setup.py install --root=$PKG +fi 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 @@ -81,6 +100,7 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/pysam/pysam.info b/academic/pysam/pysam.info index 2951c27d95..724abb43a7 100644 --- a/academic/pysam/pysam.info +++ b/academic/pysam/pysam.info @@ -1,10 +1,10 @@ PRGNAM="pysam" -VERSION="0.15.2" +VERSION="0.16.0.1" HOMEPAGE="https://github.com/pysam-developers/pysam" -DOWNLOAD="https://github.com/pysam-developers/pysam/archive/v0.15.2/pysam-0.15.2.tar.gz" -MD5SUM="3000f77fd997d864fe551b3001fbac22" +DOWNLOAD="https://pypi.python.org/packages/source/p/pysam/pysam-0.16.0.1.tar.gz" +MD5SUM="5b4b73431f2511727f4fef43a67b392e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="python3-Cython" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/qalculate-gtk/qalculate-gtk.SlackBuild b/academic/qalculate-gtk/qalculate-gtk.SlackBuild index 130606256a..62576920e9 100644 --- a/academic/qalculate-gtk/qalculate-gtk.SlackBuild +++ b/academic/qalculate-gtk/qalculate-gtk.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for qalculate-gtk -# Copyright 2016-2018 Larry Hajali <larryhaja[at]gmail[dot]com> +# Copyright 2016-2020 Larry Hajali <larryhaja[at]gmail[dot]com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=qalculate-gtk -VERSION=${VERSION:-2.8.2} +VERSION=${VERSION:-3.10.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -74,6 +74,7 @@ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ --docdir=/usr/doc/$PRGNAM-$VERSION \ + --mandir=/usr/man \ --disable-silent-rules \ --build=$ARCH-slackware-linux @@ -83,6 +84,8 @@ make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +find $PKG/usr/man -type f -exec gzip -9 {} \; + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a 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/qalculate-gtk/qalculate-gtk.info b/academic/qalculate-gtk/qalculate-gtk.info index 66bcd14b3f..4884e43fbc 100644 --- a/academic/qalculate-gtk/qalculate-gtk.info +++ b/academic/qalculate-gtk/qalculate-gtk.info @@ -1,8 +1,8 @@ PRGNAM="qalculate-gtk" -VERSION="2.8.2" -HOMEPAGE="http://qalculate.github.io/" -DOWNLOAD="https://github.com/Qalculate/qalculate-gtk/releases/download/v2.8.2/qalculate-gtk-2.8.2.tar.gz" -MD5SUM="6ee7168a1a335fed584f688e7260145e" +VERSION="3.10.0" +HOMEPAGE="https://qalculate.github.io/" +DOWNLOAD="https://github.com/Qalculate/qalculate-gtk/releases/download/v3.10.0/qalculate-gtk-3.10.0.tar.gz" +MD5SUM="5880b40c4a5beb9da290b28a54eb4f46" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="libqalculate" diff --git a/academic/qtoctave/README b/academic/qtoctave/README deleted file mode 100644 index d5d912e4a4..0000000000 --- a/academic/qtoctave/README +++ /dev/null @@ -1,2 +0,0 @@ -QtOctave is a graphical user interface for gnu octave, which is an -open source program alternative to Matlab. diff --git a/academic/qtoctave/qtoctave-0.8.1-gcc4.4.patch b/academic/qtoctave/qtoctave-0.8.1-gcc4.4.patch deleted file mode 100644 index 4bc26f858c..0000000000 --- a/academic/qtoctave/qtoctave-0.8.1-gcc4.4.patch +++ /dev/null @@ -1,8 +0,0 @@ -diff -Naur qtoctave-0.8.1/qtoctave/src/search_dialog.cpp qtoctave-0.8.1.new/qtoctave/src/search_dialog.cpp ---- qtoctave-0.8.1/qtoctave/src/search_dialog.cpp 2008-09-21 05:00:30.000000000 -0400 -+++ qtoctave-0.8.1.new/qtoctave/src/search_dialog.cpp 2009-07-31 09:04:20.000000000 -0400 -@@ -1,3 +1,4 @@ -+#include <cstdio> - #include "search_dialog.h" - - SearchDialog::SearchDialog(QWidget *parent): QDialog(parent) diff --git a/academic/qtoctave/qtoctave.SlackBuild b/academic/qtoctave/qtoctave.SlackBuild deleted file mode 100644 index e7b7aad619..0000000000 --- a/academic/qtoctave/qtoctave.SlackBuild +++ /dev/null @@ -1,110 +0,0 @@ -#!/bin/sh - -# Slackware build script for QtOctave - -# Written by Mauro Giachero (mauro dot giachero at gmail dot com) -# Modified by Robby Workman <rworkman@slackbuilds.org> - -PRGNAM=qtoctave -VERSION=${VERSION:-0.8.1} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i486 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION/$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 \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -# Fix building with gcc4.4 -patch -p2 < $CWD/qtoctave-0.8.1-gcc4.4.patch - -cmake \ - -DCMAKE_C_FLAGS_RELEASE:STRING="$SLKCFLAGS" \ - -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SLKCFLAGS" \ - -DCMAKE_INSTALL_PREFIX:PATH=/usr \ - -DLIB_SUFFIX:STRING=${LIBDIRSUFFIX} . - -make - -# The install target doesn't have a DESTDIR or INSTALL_ROOT or equivalent, -# and setting the CMAKE_INSTALL_PREFIX to $PKG/usr results in a lot of -# '/tmp/SBo/package-qtoctave' strings embedded in the qtoctave binary. -# This *could* have security implications (for example, if that binary first -# looks in the temp directory for things). It's low risk, and would require -# someone on the system to have knowledge of how the package was built, so -# I'm being a bit "chicken little" here, but correct is always better, so I'm -# going to do this the hard way... --rworkman -# -# Be sure to check the src/cmake_install.cmake file in version updates to -# make sure we don't miss something -mkdir -p $PKG/usr/share/qtoctave $PKG/usr/bin \ - $PKG/usr/share/applications $PKG/usr/share/icons/hicolor/64x64/apps -cp -a src/config_files/config.rc src/images src/lang src/menus \ - src/config_files/octave.xml src/octave_doc src/qtoctave_doc \ - src/scripts $PKG/usr/share/qtoctave -# QtOctave better fits in "Science & Math" (with Octave) than -# under "Edutainment" subcategories -# cp -a src/config_files/qtoctave.desktop $PKG/usr/share/applications/ -cat src/config_files/qtoctave.desktop |sed "s/Education/Development/g" \ - >$PKG/usr/share/applications/qtoctave.desktop -ln -s /usr/share/qtoctave/images/qtoctave.png $PKG/usr/share/icons/hicolor/64x64/apps/ -cp -a src/qtoctave $PKG/usr/bin -find $PKG/usr/share -type f -exec chmod 0644 {} \; -find $PKG/usr/share -type d -exec chmod 0755 {} \; - -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 leeme.txt news.txt LICENSE_GPL.txt readme.txt \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -( cd $PKG/usr/doc/$PRGNAM-$VERSION - ln -s /usr/share/$PRGNAM/qtoctave-doc . - ln -s /usr/share/$PRGNAM/octave-doc . -) - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh - -cd $PKG -/sbin/makepkg -l y -c n -p $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/qtoctave/qtoctave.info b/academic/qtoctave/qtoctave.info deleted file mode 100644 index 8f30815f8b..0000000000 --- a/academic/qtoctave/qtoctave.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="qtoctave" -VERSION="0.8.1" -HOMEPAGE="https://qtoctave.wordpress.com/" -DOWNLOAD="http://ponce.cc/slackware/sources/repo/qtoctave-0.8.1.tar.gz" -MD5SUM="b4e237b578f9c2624bb0fab2cb7ea691" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="octave" -MAINTAINER="Mauro Giachero" -EMAIL="mauro dot giachero at gmail dot com" diff --git a/academic/qtoctave/slack-desc b/academic/qtoctave/slack-desc deleted file mode 100644 index a1279dfa41..0000000000 --- a/academic/qtoctave/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------------------------------------------------------| -qtoctave: qtoctave (a qt-based gui for Octave) -qtoctave: -qtoctave: QtOctave is a graphical user interface for gnu octave, which is an -qtoctave: open source program alternative to Matlab. With QtOctave you can do -qtoctave: perform computationally intensive mathematical tasks that would take -qtoctave: much longer to code in C or C++ or practically any other modern -qtoctave: computer language. It is especailly good at matrix and vector -qtoctave: operations. The graphical capabilities are very advanced. It is -qtoctave: used heavily in engineering, and is a tool well worth learning. -qtoctave: -qtoctave: diff --git a/academic/qucs/qucs.SlackBuild b/academic/qucs/qucs.SlackBuild index d3a5520dca..dd8b555edb 100644 --- a/academic/qucs/qucs.SlackBuild +++ b/academic/qucs/qucs.SlackBuild @@ -3,6 +3,8 @@ # Slackware build script for Qucs # Copyright 2011-2014 Fridrich von Stauffenberg <cancellor2@gmail.com> +# Copyright 2020 Fellype do Nascimento, Campinas - Brazil +# # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,13 +25,13 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=qucs -VERSION=${VERSION:-0.0.18} +VERSION=${VERSION:-0.0.19} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -40,18 +42,15 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + SPEC="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" + SPEC="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" + SPEC="-spec linux-g++-64" fi set -e @@ -69,25 +68,17 @@ 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 {} \; -find . -type f -exec sed -i "s,QTDIR,QT4DIR,g" {} \; - -# in x86_64, qucs-doc and examples requires newer automake -cd qucs-doc -autoreconf -vi -cd ../examples -autoreconf -vi -cd .. - CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ --mandir=/usr/man \ + --disable-doc \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --build=$ARCH-slackware-linux make -make install-strip DESTDIR=$PKG +make install DESTDIR=$PKG 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 @@ -97,7 +88,7 @@ cat $CWD/$PRGNAM.desktop > $PKG/usr/share/applications/$PRGNAM.desktop cat $CWD/$PRGNAM.png > $PKG/usr/share/pixmaps/$PRGNAM.png mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS COPYING ChangeLog INSTALL NEWS* PLATFORMS README RELEASE THANKS TODO \ +cp -a qucs/AUTHORS qucs/COPYING README.md qucs/README \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/qucs/qucs.info b/academic/qucs/qucs.info index 4906252ac0..fd2e34b3ab 100644 --- a/academic/qucs/qucs.info +++ b/academic/qucs/qucs.info @@ -1,10 +1,10 @@ PRGNAM="qucs" -VERSION="0.0.18" +VERSION="0.0.19" HOMEPAGE="http://qucs.sourceforge.net" -DOWNLOAD="http://downloads.sourceforge.net/qucs/qucs-0.0.18.tar.gz" -MD5SUM="4985d66565e8c29c9e6d7e7c98781e60" +DOWNLOAD="http://downloads.sourceforge.net/qucs/qucs-0.0.19.tar.gz" +MD5SUM="321b22b88099c6c8ac42ee8b7ab637a8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="orphaned - no maintainer" -EMAIL="nobody@nowhere.com" +REQUIRES="adms" +MAINTAINER="Fellype do Nascimento" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/rbio/patches/autoconfiscate.diff b/academic/rbio/patches/autoconfiscate.diff index ff01785dc3..bfc02f387c 100644 --- a/academic/rbio/patches/autoconfiscate.diff +++ b/academic/rbio/patches/autoconfiscate.diff @@ -222,7 +222,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([RBio],[2.2.6],[DrTimothyAldenDavis@gmail.com],[rbio],[http://www.suitesparse.com/]) ++AC_INIT([RBio],[2.2.6],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[rbio],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/RBio.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/rbio/rbio.SlackBuild b/academic/rbio/rbio.SlackBuild index aa4b90861a..e83a5cbc38 100644 --- a/academic/rbio/rbio.SlackBuild +++ b/academic/rbio/rbio.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for RBio -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=rbio SRCNAM=SuiteSparse SUBDIR=RBio VERSION=${VERSION:-2.2.6} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-5} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/rbio/rbio.info b/academic/rbio/rbio.info index 90292502aa..0e914776cd 100644 --- a/academic/rbio/rbio.info +++ b/academic/rbio/rbio.info @@ -1,8 +1,8 @@ PRGNAM="rbio" VERSION="2.2.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/reduce-algebra/README b/academic/reduce-algebra/README index 5b6e1afcff..863d14a3ad 100644 --- a/academic/reduce-algebra/README +++ b/academic/reduce-algebra/README @@ -4,8 +4,8 @@ interactively for simple calculations but also provides a flexible and expressive user programming language. The development of the REDUCE computer algebra system was started in the -1960s by Anthony C. Hearn. Since then, many scientists from all over the -world have contributed to its development. REDUCE has a long and +1960s by Anthony C. Hearn. Since then, many scientists from all over +the world have contributed to its development. REDUCE has a long and distinguished place in the history of computer algebra systems. Other systems that address some of the same issues but sometimes with rather different emphasis are Axiom, Derive, Macsyma (Maxima), Maple, diff --git a/academic/reduce-algebra/reduce-algebra.SlackBuild b/academic/reduce-algebra/reduce-algebra.SlackBuild index 42c09d6cc4..a843ef1d3a 100644 --- a/academic/reduce-algebra/reduce-algebra.SlackBuild +++ b/academic/reduce-algebra/reduce-algebra.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for reduce-algebra -# Copyright 2016-2018 Alexander Verbovetsky, Moscow, Russia +# Copyright 2016-2020 Alexander Verbovetsky, Moscow, Russia # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=reduce-algebra -VERSION=${VERSION:-20180920svn4765} +VERSION=${VERSION:-20201007svn5424} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/reduce-algebra/reduce-algebra.info b/academic/reduce-algebra/reduce-algebra.info index d58f706311..46f79d0bcb 100644 --- a/academic/reduce-algebra/reduce-algebra.info +++ b/academic/reduce-algebra/reduce-algebra.info @@ -1,10 +1,10 @@ PRGNAM="reduce-algebra" -VERSION="20180920svn4765" -HOMEPAGE="http://reduce-algebra.sourceforge.net" -DOWNLOAD="http://downloads.sourceforge.net/reduce-algebra/snapshot_2018-09-20/Reduce-svn4765-src.tar.gz \ - http://downloads.sourceforge.net/reduce-algebra/snapshot_2018-09-20/linux64/reduce-common_4765_all.tgz" -MD5SUM="64626e9bfeca12181656864a5040c76d \ - d26101055d64247d9411ce87e0352159" +VERSION="20201007svn5424" +HOMEPAGE="https://reduce-algebra.sourceforge.io" +DOWNLOAD="https://downloads.sourceforge.net/reduce-algebra/snapshot_2020-10-07/Reduce-svn5424-src.tar.gz \ + https://downloads.sourceforge.net/reduce-algebra/snapshot_2020-10-07/linux64/reduce-common_5424_all.tgz" +MD5SUM="46eb107df176f965a2bd011c95451382 \ + 325258e8a864bb1098940ed82e9d17b8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/reduce-algebra/slack-desc b/academic/reduce-algebra/slack-desc index 964bf26bf6..55a60620ce 100644 --- a/academic/reduce-algebra/slack-desc +++ b/academic/reduce-algebra/slack-desc @@ -16,4 +16,4 @@ reduce-algebra: Portable Standard Lisp (PSL) or Codemist Standard Lisp (CSL), bo reduce-algebra: which are included in the SourceForge distribution. By modern reduce-algebra: standards, REDUCE is a surprisingly small and compact application. reduce-algebra: -reduce-algebra: Homepage: http://reduce-algebra.sourceforge.net +reduce-algebra: Homepage: https://reduce-algebra.sourceforge.io diff --git a/academic/rpy2/README b/academic/rpy2/README new file mode 100644 index 0000000000..702373878f --- /dev/null +++ b/academic/rpy2/README @@ -0,0 +1,22 @@ +Python interface to the R language. + +rpy2 is running an embedded R, providing access to it +from Python using R's own C-API through either: + +1) a high-level interface making R functions and objects +just like Python functions and providing a seamless +conversion to numpy and pandas data structures + +2) a low-level interface closer to the C-API + +It is also providing features for when working with +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) + +home:https://rpy2.github.io/ +documentation:https://rpy2.github.io/doc/latest/html/index.html diff --git a/academic/rpy2/Rlibs.conf b/academic/rpy2/Rlibs.conf new file mode 100644 index 0000000000..cd1ea265b7 --- /dev/null +++ b/academic/rpy2/Rlibs.conf @@ -0,0 +1,2 @@ +##placed as rpy2 cannot load R without "export LD_LIBRARY_PATH=/usr/lib64/R/lib/" +/usr/lib64/R/lib
\ No newline at end of file diff --git a/academic/rpy2/doinst.sh b/academic/rpy2/doinst.sh new file mode 100644 index 0000000000..bf984ccfe4 --- /dev/null +++ b/academic/rpy2/doinst.sh @@ -0,0 +1,2 @@ +#load the path to the R libraries to enable linking +ldconfig diff --git a/academic/rpy2/rpy2.SlackBuild b/academic/rpy2/rpy2.SlackBuild new file mode 100644 index 0000000000..b31616bdbe --- /dev/null +++ b/academic/rpy2/rpy2.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/sh +# +# SlackBuild for rpy2 +# +# Copyright 2020-2021 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: +# +# 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. + +PRGNAM=rpy2 +VERSION=${VERSION:-3.4.3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 {} \; + +## make sure there is R +if ! [ -x "$(command -v R)" ]; then + echo 'Error: R is not installed.' >&2 + exit 1 +fi + +## make sure that R has been compiled with +## --enable-R-shlib +## --enable-BLAS-shlib +RHOMLIB=$(R RHOME)/lib +echo "R libs are in $RHOMLIB" + +if ! [ "$(readelf -h $RHOMLIB/libR*.so | grep DYN)" ]; then + echo "Error: R is not compiled with shared libraries." >&2 + exit 1 +fi + +## this removes an error message from setup.py +## https://github.com/rpy2/rpy2/issues/675 +export LD_LIBRARY_PATH="${RHOMLIB}:${LD_LIBRARY_PATH}" +echo "LD_LIBRARY_PATH set to ${LD_LIBRARY_PATH}" + +python3 setup.py build install --root=$PKG + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS gpl-2.0.txt NEWS README* $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +## to facilitate dynamic linking with R, +## libR.so and libRblas.so still need to be found +## https://github.com/rpy2/rpy2/issues/675 +mkdir -p $PKG/etc/ld.so.conf.d/ +cat $CWD/Rlibs.conf > $PKG/etc/ld.so.conf.d/Rlibs.conf + +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:-tgz} diff --git a/academic/rpy2/rpy2.info b/academic/rpy2/rpy2.info new file mode 100644 index 0000000000..4671f1a69b --- /dev/null +++ b/academic/rpy2/rpy2.info @@ -0,0 +1,10 @@ +PRGNAM="rpy2" +VERSION="3.4.3" +HOMEPAGE="https://rpy2.github.io/" +DOWNLOAD="https://pypi.python.org/packages/source/r/rpy2/rpy2-3.4.3.tar.gz" +MD5SUM="bf3572caed450c5f88c5295f3eda6137" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="R cffi Jinja2 python3-pytest tzlocal" +MAINTAINER="Rob van Nues" +EMAIL="sborg63@disroot.org" diff --git a/academic/rpy2/slack-desc b/academic/rpy2/slack-desc new file mode 100644 index 0000000000..4b6f260ede --- /dev/null +++ b/academic/rpy2/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------------------------------------------------------| +rpy2: rpy2 (R in Python) +rpy2: +rpy2: rpy2 is an interface to R running embedded in a Python process. +rpy2: The project is mature, stable, documented, and widely used +rpy2: +rpy2: It is also providing features for when working +rpy2: with jupyter notebooks or ipython. +rpy2: +rpy2: home:https://rpy2.github.io/ +rpy2: https://rpy2.github.io/doc/latest/html/index.html +rpy2: diff --git a/academic/sage/README b/academic/sage/README index c69694fb19..6772d6b5d3 100644 --- a/academic/sage/README +++ b/academic/sage/README @@ -11,10 +11,20 @@ of a full Slackware installation). Building sage requires >12GB of disk space, so you may need to redefine $TMP and/or $OUTPUT. +Note that the build will likely spit out many "zero length file" errors, +which can safely be ignored. -See README.BUILDOPTS for additional (important) information about -build options and such. +See README.BUILDOPTS for additional (important) information +about build options and such. Specifically, if you do not move the +installation directory via a specification of SAGEROOT, you may need +to do something like -NOTE: -If you have ATOM processors, you need to run this command prior building: -export OPENBLAS_CONFIGURE="TARGET=ATOM" +source /etc/profile.d/sage.ch + +so make sure the binary is in your path. + +This package does not include the doc files. Those can be found at +doc.sagemath.org. + +NOTE: If you have ATOM processors, you need to run this command prior +building: export OPENBLAS_CONFIGURE="TARGET=ATOM" diff --git a/academic/sage/doinst.sh b/academic/sage/doinst.sh index 272b54cdf2..afc6c7588b 100644 --- a/academic/sage/doinst.sh +++ b/academic/sage/doinst.sh @@ -4,7 +4,7 @@ if [ -x usr/share/texmf/bin/texhash ]; then fi # run sage at least once as root after moving it to a new location -echo "exit" | SAGEROOT/sage +#echo "exit" | SAGEROOT/sage if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 diff --git a/academic/sage/pynac.patch b/academic/sage/pynac.patch deleted file mode 100644 index c8a0cdc26b..0000000000 --- a/academic/sage/pynac.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- build/pkgs/pynac/spkg-install.orig 2014-08-11 20:52:14.220516400 +0700 -+++ build/pkgs/pynac/spkg-install 2014-08-11 20:52:27.906551659 +0700 -@@ -31,6 +31,7 @@ - - build_pynac() - { -+ chmod -R g-w ${PYNACDIR} - cd ${PYNACDIR} - PKG_CONFIG_PATH=${SAGE_LOCAL}/lib/pkgconfig; export PKG_CONFIG_PATH - ./configure --disable-static --prefix=${SAGE_LOCAL} --libdir="$SAGE_LOCAL/lib" diff --git a/academic/sage/sage-build-root.patch b/academic/sage/sage-build-root.patch deleted file mode 100644 index 0daaca9c33..0000000000 --- a/academic/sage/sage-build-root.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- sage-6.10/configure.old 2015-12-19 08:15:37.404497471 +0700 -+++ sage-6.10/configure 2015-12-19 08:15:55.691461292 +0700 -@@ -2965,21 +2965,6 @@ - - #--------------------------------------------------------- - --{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for root user" >&5 --$as_echo_n "checking for root user... " >&6; } -- --uid=`id -u` --if test "x$uid" == "x0"; then -- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 --$as_echo "yes" >&6; } -- as_fn_error $? "You cannot build Sage as root, switch to an unpriviledged user" "$LINENO" 5 --else -- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 --$as_echo "no" >&6; } -- --fi; -- -- - # Check whether we are on a supported platform - # Make sure we can run config.sub. - $SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 || diff --git a/academic/sage/sage.SlackBuild b/academic/sage/sage.SlackBuild index 8e6e47ae47..6cb41edaa4 100644 --- a/academic/sage/sage.SlackBuild +++ b/academic/sage/sage.SlackBuild @@ -2,7 +2,9 @@ # Slackware build script for sage # Written by Jack Maddox <jack@auburn.edu> -# Currently maintained by Willy Sudiarto Raharjo <willysr@slackbuilds.org> +# Currently maintained by Christopher L Duston <christopher.duston@protonmail.com> +# Last update June 2020. +# # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +25,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=sage -VERSION=${VERSION:-8.0} +VERSION=${VERSION:-9.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -35,8 +37,22 @@ if [ -z "$ARCH" ]; then esac fi +#### These lines are to ensure the build can happen on multilib systems. +if [ "$ARCH" = "i586" ]; then +LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then +LIBDIRSUFFIX="64" +else +LIBDIRSUFFIX="" +fi +#### + +# SAGE_ROOT/bin/sage points to the build directory, which can't be +# in the /tmp folder if we want it to remain after installation. +# So we'll put it in /var/tmp. Maybe just sticking it in /usr is better. + CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} +TMP=${TMP:-/var/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -60,16 +76,11 @@ find -L . \ mkdir -p $PKG/$SAGEROOT $PKG/usr/share/{applications,pixmaps} \ $PKG/usr/doc/$PRGNAM-$VERSION $PKG/etc/profile.d -# Added freeBSD patch to build as root, thanks to Heinz for pointing it -patch -p0 < $CWD/pynac.patch - -# Added more patch to build as root. -patch -p1 < $CWD/sage-build-root.patch - -# Thanks to Philip Lacroix <slackph@posteo.de> -rm build/pkgs/python2/patches/sys_path_security-issue_16202.patch - -make +# The docs do not build correctly, so instead of make, do the following: +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}" \ + ./configure \ + --enable-build-as-root +make build # test all examples in the documentation (over 93,000 line of input) [ "${TEST:-no}" = "yes" ] && make test @@ -113,6 +124,8 @@ fi sed "s%SAGEROOT%${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/ +# Put a line here which *actually* adds sage to the path + # install sagetex to a location that is accessible to the system TeX installation cp -a local/share/texmf $PKG/usr/share diff --git a/academic/sage/sage.info b/academic/sage/sage.info index 24c282defa..141f25c9ef 100644 --- a/academic/sage/sage.info +++ b/academic/sage/sage.info @@ -1,10 +1,10 @@ PRGNAM="sage" -VERSION="8.0" +VERSION="9.1" HOMEPAGE="http://www.sagemath.org" -DOWNLOAD="http://mirrors.mit.edu/sage/src/sage-8.0.tar.gz" -MD5SUM="93bdd128991e9144c4b137d3d6655065" +DOWNLOAD="http://mirrors.mit.edu/sage/src/sage-9.1.tar.gz" +MD5SUM="35e0ecbc6cc2ae4e1a68479598e70b7a" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="orphaned - no maintainer" -EMAIL="nobody@nowhere.com" +MAINTAINER="Christopher L Duston" +EMAIL="christopher.duston@protonmail.com" diff --git a/academic/samtools-legacy/samtools-legacy.SlackBuild b/academic/samtools-legacy/samtools-legacy.SlackBuild index cbe5e6de2f..2e89ec4ff7 100644 --- a/academic/samtools-legacy/samtools-legacy.SlackBuild +++ b/academic/samtools-legacy/samtools-legacy.SlackBuild @@ -25,13 +25,14 @@ # With help about the install paths from Arch Linux AUR: # https://aur.archlinux.org/packages/sa/samtools/PKGBUILD -SRCNAM=samtools -SUFFIX=legacy -PRGNAM=${SRCNAM}-${SUFFIX} +PRGNAM=samtools-legacy VERSION=${VERSION:-0.1.19} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +SRCNAM=samtools +SUFFIX=legacy + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; diff --git a/academic/samtools/README b/academic/samtools/README index ea600cbe26..d8e2540720 100644 --- a/academic/samtools/README +++ b/academic/samtools/README @@ -1,11 +1,16 @@ -Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed -in a single samtools-0.1.x package. -This old version remains available from SBo as samtools-legacy +SAM (Sequence Alignment/Map) format is a generic format for storing +large nucleotide sequence alignments. The original samtools package has +been split into three separate but tightly coordinated projects: htslib +(C library for handling high-throughput sequencing data), samtools (for +handling SAM, BAM, CRAM), and bcftools (for handling VCF and BCF). -Samtools is now distributed as an individual package. -Installation is set up so that the code uses an external HTSlib (also at SBo). -Although deprecated upstream, in the case that people need parts of samtools-legacy -(e.g header files or libbam) these can be installed from this package by modifying -the samtools.Slackbuild. +Samtools is now distributed as an individual package. Installation is +set up so that the code uses an external HTSlib (also at SBo). Although +deprecated upstream, in the case that people need parts of +samtools-legacy (e.g header files or libbam) these can be installed from +this package by modifying the samtools.Slackbuild. Note that the sam.h +of htslib differs from sam.h coming with samtools. -Note that the sam.h of htslib differs from sam.h coming with samtools. +Prior to the introduction of HTSlib, SAMtools and BCFtools were +distributed in a single samtools-0.1.x package. This old version remains +available from SBo as samtools-legacy. diff --git a/academic/samtools/README.references b/academic/samtools/README.references new file mode 100644 index 0000000000..1d021bdd96 --- /dev/null +++ b/academic/samtools/README.references @@ -0,0 +1,64 @@ +References: + +====================== +File formats + + +The introduction of the SAM/BAM format and the samtools command line tool: + +Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and 1000 Genome Project Data Processing Subgroup, The Sequence alignment/map (SAM) format and SAMtools, Bioinformatics (2009) 25(16) 2078-9 [19505943] + + +Extension of the SAM/BAM format to support de novo assemblies: + +Cock PJA, Bonfield JK, Chevreux B, Li H, SAM/BAM format v1.5 extensions for de novo assemblies, bioRxiv (2015) 020024 [doi:10.1101/020024] + + +The introduction of the CRAM format: + +Hsi-Yang Fritz M, Leinonen R, Cochrane G, and Birney E, Efficient storage of high throughput DNA sequencing data using reference-based compression, Genome Research (2011) 21(5) 734-740. +The introduction of the VCF format: + +Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group, The variant call format and VCFtools, Bioinformatics (2011) 27(15) 2156-8 + +====================== +Calling and analysis + + +The original mpileup calling algorithm plus mathematical notes (mpileup/bcftools call -c): + +Li H, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics (2011) 27(21) 2987-93. +Li H, Mathematical Notes on SAMtools Algorithms (2010) + + +Mathematical notes for the updated multiallelic calling model (mpileup/bcftools call -m): + +Danecek P, Schiffels S, and Durbin R, Multiallelic calling model in bcftools (-m) (2014) + + +Hidden Markov model for detecting runs of homozygosity (bcftools roh): + +Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C, and Durbin R, BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data, Bioinformatics (2016) 32(11) 1749-51 + + +Copy number variation/aneuploidy calling from microarray data (bcftools cnv/bcftools polysomy): + +Danecek P, McCarthy SA, HipSci Consortium, and Durbin R, A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data, PLoS One (2016) 11(5) e0155014 + + +Haplotype-aware calling of variant consequences (bcftools csq): + +Danecek P, McCarthy SA, BCFtools/csq: Haplotype-aware variant consequences, Bioinformatics (2017) 33(13) 2037-39 + +====================== +Other + + +Base alignment quality (BAQ) method improve SNP calling around INDELs: + +Li H, Improving SNP discovery by base alignment quality, Bioinformatics (2011) 27(8) 1157-8 + + +Segregation based QC metric originally implemented in SGA: + +Durbin R, Segregation based metric for variant call QC (2014) diff --git a/academic/samtools/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild index daa7e87daf..2a3a784382 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 2017-2018 Rob van Nues # All rights reserved. +# Copyright 2017-2021 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: @@ -23,12 +23,12 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=samtools -VERSION=${VERSION:-1.9} +VERSION=${VERSION:-1.12} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -# 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: @@ -96,6 +96,17 @@ CXXFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a misc/*.lua $PKG/usr/share/$PRGNAM-$VERSION + +# include samtools-API if set above +if [ "$SAMLIB" = "yes" ] ; then + mkdir -p $PKG/usr/include/bam + mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} + install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}" + install -m644 *.h "$PKG/usr/include/bam" +fi + 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 @@ -106,24 +117,11 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ AUTHORS LICENSE README INSTALL NEWS 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 -mkdir -p $PKG/usr/share/$PRGNAM-$VERSION - -cp -a \ - misc/*.lua \ - $PKG/usr/share/$PRGNAM-$VERSION - mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -# include samtools-API if set above -if [ "$SAMLIB" = "yes" ] ; then - mkdir -p $PKG/usr/include/bam - mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} - install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}" - install -m644 *.h "$PKG/usr/include/bam" -fi - cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/samtools/samtools.info b/academic/samtools/samtools.info index 1d724a44e4..91b54352ff 100644 --- a/academic/samtools/samtools.info +++ b/academic/samtools/samtools.info @@ -1,8 +1,8 @@ PRGNAM="samtools" -VERSION="1.9" +VERSION="1.12" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2" -MD5SUM="cca9a40d9b91b007af2ff905cb8b5924" +DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.12/samtools-1.12.tar.bz2" +MD5SUM="14540f346cc2f438cea21b2fa7e40fb5" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="htslib" diff --git a/academic/samtools/slack-desc b/academic/samtools/slack-desc index 8f1c434e47..e2e844e357 100644 --- a/academic/samtools/slack-desc +++ b/academic/samtools/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| samtools: samtools (Sequence Alignment/Map Tools) samtools: -samtools: SAM (Sequence Alignment/Map) format is a generic format for -samtools: storing large nucleotide sequence alignments. The original samtools -samtools: package has been split into three separate but tightly coordinated -samtools: projects: htslib (C-library for handling high-throughput sequencing -samtools: data); samtools (for handling SAM, BAM, CRAM) and bcftools (for -samtools: handling VCF, BCF). Both samtools and bcftools are set up to use -samtools: system-wide installed hstlib sources. -samtools: Home: http://www.htslib.org +samtools: SAM (Sequence Alignment/Map) format is a generic format for storing +samtools: large nucleotide sequence alignments. The original samtools package +samtools: has been split into three separate but tightly coordinated projects: +samtools: htslib (C-library for handling high-throughput sequencing data), +samtools: samtools (for handling SAM, BAM, CRAM), and bcftools (for handling +samtools: VCF and BCF). +samtools: +samtools: Homepage: http://www.htslib.org samtools: diff --git a/academic/scidavis/fix-gh-issue-90.patch b/academic/scidavis/fix-gh-issue-90.patch deleted file mode 100644 index 67ffca3062..0000000000 --- a/academic/scidavis/fix-gh-issue-90.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/libscidavis/src/ApplicationWindow.cpp b/libscidavis/src/ApplicationWindow.cpp -index 90d282a4..167debee 100644 ---- libscidavis/src/ApplicationWindow.cpp -+++ libscidavis/src/ApplicationWindow.cpp -@@ -12521,8 +12521,11 @@ void ApplicationWindow::saveFolderAsProject(Folder *f) - - void ApplicationWindow::showFolderPopupMenu(const QPoint &p, bool fromFolders) - { -- if (fromFolders) -- showFolderPopupMenuImpl(folders->itemAt(p), fromFolders)->exec(folders->mapToGlobal(p)); -+ if (fromFolders) { -+ QMenu* cm = showFolderPopupMenuImpl(folders->itemAt(p), fromFolders); -+ if (cm) -+ cm->exec(folders->mapToGlobal(p)); -+ } - else - showFolderPopupMenuImpl(lv->itemAt(p), fromFolders)->exec(lv->mapToGlobal(p)); - } diff --git a/academic/scidavis/fix_issue_with_scipy_vesions.patch b/academic/scidavis/fix_issue_with_scipy_vesions.patch deleted file mode 100644 index 653ce97f9e..0000000000 --- a/academic/scidavis/fix_issue_with_scipy_vesions.patch +++ /dev/null @@ -1,184 +0,0 @@ ---- ../../scidavis-1.23/scidavis/scidavisrc.py 2018-06-04 03:22:50.000000000 -0300 -+++ /home/fellype/github/scidavis/scidavis/scidavisrc.py 2018-06-05 15:12:17.000000000 -0300 -@@ -50,6 +50,84 @@ - # Import standard math functions and constants into global namespace. - import_to_global("math", None, True) - -+# make Qt API available (it gets imported in any case by the scidavis module) -+global QtGui -+from PyQt4 import QtGui -+ -+global QtCore -+from PyQt4 import QtCore -+ -+global Qt -+from PyQt4.QtCore import Qt -+ -+# import SciDAVis' classes to the global namespace (particularly useful for fits) -+for name in dir(__main__.scidavis): -+ setattr(__main__, name, getattr(__main__.scidavis, name)) -+ -+# import selected methods of ApplicationWindow into the global namespace -+appImports = ( -+ "table", "newTable", -+ "matrix", "newMatrix", -+ "graph", "newGraph", -+ "note", "newNote", -+ "plot", "plotContour", "plotColorMap", "plotGrayScale", -+ "activeFolder", "rootFolder", "saveFolder", -+ "renameWindow", "clone", -+ "importImage" -+ ) -+for name in appImports: -+ setattr(__main__,name,getattr(__main__.scidavis.app,name)) -+ -+# make Y columns indexable (using lookup in corresponding X column) -+def __column_getitem(self, index): -+ if self.plotDesignation() != "Y": -+ return None -+ x = self.x() -+ for row in range(self.rowCount()): -+ if x.columnMode() == "Numeric": -+ xval = x.valueAt(row) -+ elif x.columnMode() == "Text": -+ xval = x.textAt(row) -+ else: -+ xval = x.dateTimeAt(row) -+ if xval == index: -+ if self.columnMode() == "Numeric": -+ return self.valueAt(row) -+ elif self.columnMode() == "Text": -+ return self.textAt(row) -+ else: -+ return self.dateTimeAt(row) -+__main__.scidavis.Column.__getitem__ = __column_getitem -+ -+def __column_setitem(self, index, value): -+ if self.plotDesignation() != "Y": -+ return None -+ x = self.x() -+ for row in range(x.rowCount()): -+ if x.columnMode() == "Numeric": -+ xval = x.valueAt(row) -+ elif x.columnMode() == "Text": -+ xval = x.textAt(row) -+ else: -+ xval = x.dateTimeAt(row) -+ if xval == index: -+ if self.columnMode() == "Numeric": -+ return self.setValueAt(row, value) -+ elif self.columnMode() == "Text": -+ return self.setTextAt(row, value) -+ else: -+ return self.setDateTimeAt(row, value) -+__main__.scidavis.Column.__setitem__ = __column_setitem -+ -+# import utility module -+import sys -+sys.path.append(".") -+try: -+ import_to_global("scidavisUtil") -+ print("scidavisUtil successfully imported") -+except(ImportError): -+ print("failed to import scidavisUtil") -+ - # Import selected parts of scipy.special (if available) into global namespace. - # See www.scipy.org for information on SciPy and how to get it. - have_scipy = False -@@ -76,7 +154,11 @@ - # Derivatives of Bessel Functions - "jvp", "yvp", "kvp", "ivp", "h1vp", "h2vp", - # Spherical Bessel Functions -- "sph_jn", "sph_yn", "sph_jnyn", "sph_in", "sph_kn", "sph_inkn", -+ ## if scipy version is < 1.0.0 -+ #"sph_jn", "sph_yn", "sph_jnyn", "sph_in", "sph_kn", "sph_inkn", -+ ## else -+ #"spherical_jn", "spherical_yn", "spherical_in", "spherical_kn", -+ ### removing SBFs for a while, until someone finds a way for these two options to coexist - # Ricatti-Bessel Functions - "riccati_jn", "riccati_yn", - # Struve Functions -@@ -246,83 +328,3 @@ - import_to_global("pygsl.sf", special_functions_doublets, True) - print("Loaded %d special functions from pygsl.sf." % (len(special_functions) + len(special_functions_doublets))) - except(ImportError): pass -- -- --# make Qt API available (it gets imported in any case by the scidavis module) --global QtGui --from PyQt4 import QtGui -- --global QtCore --from PyQt4 import QtCore -- --global Qt --from PyQt4.QtCore import Qt -- --# import SciDAVis' classes to the global namespace (particularly useful for fits) --for name in dir(__main__.scidavis): -- setattr(__main__, name, getattr(__main__.scidavis, name)) -- --# import selected methods of ApplicationWindow into the global namespace --appImports = ( -- "table", "newTable", -- "matrix", "newMatrix", -- "graph", "newGraph", -- "note", "newNote", -- "plot", "plotContour", "plotColorMap", "plotGrayScale", -- "activeFolder", "rootFolder", "saveFolder", -- "renameWindow", "clone", -- "importImage" -- ) --for name in appImports: -- setattr(__main__,name,getattr(__main__.scidavis.app,name)) -- --# make Y columns indexable (using lookup in corresponding X column) --def __column_getitem(self, index): -- if self.plotDesignation() != "Y": -- return None -- x = self.x() -- for row in range(self.rowCount()): -- if x.columnMode() == "Numeric": -- xval = x.valueAt(row) -- elif x.columnMode() == "Text": -- xval = x.textAt(row) -- else: -- xval = x.dateTimeAt(row) -- if xval == index: -- if self.columnMode() == "Numeric": -- return self.valueAt(row) -- elif self.columnMode() == "Text": -- return self.textAt(row) -- else: -- return self.dateTimeAt(row) --__main__.scidavis.Column.__getitem__ = __column_getitem -- --def __column_setitem(self, index, value): -- if self.plotDesignation() != "Y": -- return None -- x = self.x() -- for row in range(x.rowCount()): -- if x.columnMode() == "Numeric": -- xval = x.valueAt(row) -- elif x.columnMode() == "Text": -- xval = x.textAt(row) -- else: -- xval = x.dateTimeAt(row) -- if xval == index: -- if self.columnMode() == "Numeric": -- return self.setValueAt(row, value) -- elif self.columnMode() == "Text": -- return self.setTextAt(row, value) -- else: -- return self.setDateTimeAt(row, value) --__main__.scidavis.Column.__setitem__ = __column_setitem -- --# import utility module --import sys --sys.path.append(".") --try: -- import_to_global("scidavisUtil") -- print("scidavisUtil successfully imported") --except(ImportError): -- print("failed to import scidavisUtil") -- diff --git a/academic/scidavis/scidavis.SlackBuild b/academic/scidavis/scidavis.SlackBuild index 53589845d0..a6d3f7b75a 100644 --- a/academic/scidavis/scidavis.SlackBuild +++ b/academic/scidavis/scidavis.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for SciDAVis # Based on the Slackware 14.2 SlackBuild # -# Copyright 2017-2018, Fellype do Nascimento, Campinas - Brazil +# Copyright 2017-2019, Fellype do Nascimento, Campinas - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,8 +24,8 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=scidavis -VERSION=${VERSION:-1.23} -BUILD=${BUILD:-2} +VERSION=${VERSION:-1.26} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -68,18 +68,6 @@ find -L . \ # Correct the manpage path sed -i -e 's#share/man#man#' scidavis/scidavis.pro -# Correction needed in order to find qwtplot3d in its default path -grep -rl "qwtplot3d/" libscidavis/src/ | xargs sed -i "s:<qwtplot3d/:<:" - -# Patch to fix issues when SciPy is installed. Without this there may be a -# problem when running python scripts due to differences between SciPy versions -# higher or lower than 1.0.0 -patch -p1 < $CWD/fix_issue_with_scipy_vesions.patch scidavis/scidavisrc.py - -# Patch to fix crash on right-click inside the project explorer outside the icon for folders area -# For more information see: https://github.com/highperformancecoder/scidavis/issues/90 -patch -p1 < $CWD/fix-gh-issue-90.patch libscidavis/src/ApplicationWindow.cpp - # Since version 1.23 it is possible to build/use SciDAVis with Python 3 - just use # PYTHON3=yes before execute scidavis.SlackBuild. Default is to use python 2 (PYTHON3=no). # *** It does not build using Python 3 in Slackware 14.2 or previous because PyQt was not built with diff --git a/academic/scidavis/scidavis.info b/academic/scidavis/scidavis.info index 2527497640..526fd3b7f9 100644 --- a/academic/scidavis/scidavis.info +++ b/academic/scidavis/scidavis.info @@ -1,8 +1,8 @@ PRGNAM="scidavis" -VERSION="1.23" +VERSION="1.26" HOMEPAGE="http://scidavis.sourceforge.net/" -DOWNLOAD="https://ufpr.dl.sourceforge.net/project/scidavis/SciDAVis/1.23/scidavis-1.23.tar.gz" -MD5SUM="e6459782ce41e63266a32be9bd4f8cb3" +DOWNLOAD="https://ufpr.dl.sourceforge.net/project/scidavis/SciDAVis/1.26/scidavis-1.26.tar.gz" +MD5SUM="a3e6158c9607dbbaab193941836259bf" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="muParser qwt5 qwtplot3d" diff --git a/academic/scilab/README b/academic/scilab/README index 61342510b8..66d62a3753 100644 --- a/academic/scilab/README +++ b/academic/scilab/README @@ -5,3 +5,12 @@ enhancement, fluid dynamics simulations, numerical optimization, and modeling and simulation of explicit and implicit dynamical systems. MATLAB code, which is similar in syntax, can be converted to Scilab. Scilab is one of several open source alternatives to MATLAB. + +After installing/upgrading, it is a good idea to logout/login again +to run the updated profile scripts. + +If you have issues on upgrading/reinstalling or changing desktop +environments, try delete/rename $HOME/.Scilab to resolve. + +Openjdk8 or jdk are optional. Scilab will use the system-wide installed +java if found. Otherwise, scilab will use its own internal jre. diff --git a/academic/scilab/scilab.SlackBuild b/academic/scilab/scilab.SlackBuild index bd22d264d9..56e6904a67 100644 --- a/academic/scilab/scilab.SlackBuild +++ b/academic/scilab/scilab.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for Scilab # Copyright 2011-2015 Fridrich von Stauffenberg <cancellor2@gmail.com> -# Copyright 2018 Edward W. Koenig ,kingbeowulf@gmail.com> +# Copyright 2018-2019 Edward W. Koenig ,kingbeowulf@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,7 +24,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=scilab -VERSION=${VERSION:-6.0.1} +VERSION=${VERSION:-6.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -70,8 +70,14 @@ mv $PKG/opt/$PRGNAM/lib/pkgconfig $PKG/usr/lib${LIBDIRSUFFIX} mv $PKG/opt/$PRGNAM/share/mime $PKG/usr/share mv $PKG/opt/$PRGNAM/share/icons $PKG/usr/share +# Remove conflicting libs (esp. for current) +rm -f $PKG/opt/$PRGNAM/lib/thirdparty/redist/libncurses.so +rm -f /$PKG/opt/$PRGNAM/lib/thirdparty/redist/libncurses.so.5 +rm -f $PKG/opt/$PRGNAM/lib/thirdparty/redist/libncurses.so.5.7 + # fix issues with .desktop files due to upstream bugs -rm -rf $PKG/opt/$PRGNAM/share/applications +rm -rf $PKG/opt/$PRGNAM/share/applications +mkdir -p $PKG/usr/share/applications cp -a $CWD/*.desktop $PKG/usr/share/applications mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/scilab/scilab.info b/academic/scilab/scilab.info index 35dc5123cb..16c72a868c 100644 --- a/academic/scilab/scilab.info +++ b/academic/scilab/scilab.info @@ -1,10 +1,10 @@ PRGNAM="scilab" -VERSION="6.0.1" +VERSION="6.1.0" HOMEPAGE="http://www.scilab.org" -DOWNLOAD="http://www.scilab.org/download/6.0.1/scilab-6.0.1.bin.linux-i686.tar.gz" -MD5SUM="84c395da3049619396dfa1b151f70566" -DOWNLOAD_x86_64="http://www.scilab.org/download/6.0.1/scilab-6.0.1.bin.linux-x86_64.tar.gz" -MD5SUM_x86_64="f1b36ab08b77dfe62e7d60e2f3a06d51" -REQUIRES="jdk" +DOWNLOAD="http://www.scilab.org/download/6.1.0/scilab-6.1.0.bin.linux-i686.tar.gz" +MD5SUM="dd249770ff4e4c8ef7c7395b1efb713b" +DOWNLOAD_x86_64="http://www.scilab.org/download/6.1.0/scilab-6.1.0.bin.linux-x86_64.tar.gz" +MD5SUM_x86_64="e52f9a66d5a015bd03be86b77fd0d7a0" +REQUIRES="" MAINTAINER="Edward W. Koenig" EMAIL="kingbeowulf@gmail.com" diff --git a/academic/scipy/README b/academic/scipy/README index e03678305e..81198ddbe7 100644 --- a/academic/scipy/README +++ b/academic/scipy/README @@ -1,24 +1,26 @@ SciPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering. -The SciPy library is built to work with NumPy arrays, and provides many -user-friendly and efficient numerical routines such as routines for -numerical integration and optimization. Together, they run on all popular -operating systems, are quick to install, and are free of charge. NumPy -and SciPy are easy to use, but powerful enough to be depended upon by -some of the world's leading scientists and engineers. +The SciPy library is built to work with NumPy arrays, and provides +many user-friendly and efficient numerical routines such as routines +for numerical integration and optimization. Together, they run on +all popular operating systems, are quick to install, and are free of +charge. NumPy and SciPy are easy to use, but powerful enough to be +depended upon by some of the world's leading scientists and engineers. -matplotlib and ipython are nice to have in connection with scipy, but scipy -does not depend on them. +matplotlib and ipython are nice to have in connection with scipy, but +scipy does not depend on them. -Since ver. 0.14.0 scipy uses SuperLU instead of UMFPACK for solving unsymmetric -sparse linear systems. If you want to use UMFPACK you must install it in advance -of numpy and build numpy accordingly (see the README to numpy's SlackBuild). -Moreover, after installing scipy, you have to install scikit-umfpack, which -presently is not available on SlackBuilds.org. +Since ver. 0.14.0 scipy uses SuperLU instead of UMFPACK for solving +unsymmetric sparse linear systems. If you want to use UMFPACK you +must install it in advance of numpy and build numpy accordingly (see +the README to numpy's SlackBuild). Moreover, after installing scipy, +you have to install scikit-umfpack, which presently is not available on +SlackBuilds.org. If you need to build scipy for debugging, set DEBUG=y. NOTE: If you use this SlackBuild scipy will run with the python 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 scipy3. + 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. diff --git a/academic/scipy/scipy.SlackBuild b/academic/scipy/scipy.SlackBuild index d317dd0478..043194c101 100644 --- a/academic/scipy/scipy.SlackBuild +++ b/academic/scipy/scipy.SlackBuild @@ -30,7 +30,7 @@ PRGNAM=scipy VERSION=${VERSION:-1.1.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -63,12 +63,10 @@ find -L . \ -exec chmod 644 {} \; DEBUG=${DEBUG:-no} -case "$DEBUG" in - [yY]|[yY][eE][sS]) DEBUG="y" ;; - *) DEBUG="" ;; -esac +DEBUG=$(echo "$DEBUG"|cut -b 1|tr a-z A-Z) -if [ ! "$DEBUG" ]; then +if [ "$DEBUG" = "N" ] +then python setup.py install --root $PKG find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/scipy3/README b/academic/scipy3/README index 195c073545..5a72b73476 100644 --- a/academic/scipy3/README +++ b/academic/scipy3/README @@ -21,4 +21,5 @@ If you need to build scipy for debugging, set DEBUG=y. NOTE: If you use this SlackBuild scipy will run with the python 3 version installed on your system. If you'd like to use python 2.7.xx as - provided by Slackware Linux then you have to install scipy. + provided by Slackware Linux then you have to install it with the scipy + SlackBuild. diff --git a/academic/scipy3/scipy3.SlackBuild b/academic/scipy3/scipy3.SlackBuild index 8c0af2f33c..22cbb37f31 100644 --- a/academic/scipy3/scipy3.SlackBuild +++ b/academic/scipy3/scipy3.SlackBuild @@ -2,7 +2,7 @@ # Build script for the Python SciPy package to be used with python 3 -# Copyright 2016 Serban Udrea <s.udrea@gsi.de> +# Copyright 2016-2019 Serban Udrea <s.udrea@gsi.de> # All rights reserved. # # Redistribution and use of this script, with or without modification, @@ -25,12 +25,12 @@ # Written by Eugene Suter <easuter@gmail.com> # Updated to 0.7.2 by JoĂŁo Felipe Santos <joao.eel@gmail.com> -# Updated up to 0.18.0 by Serban Udrea <S.Udrea@gsi.de> +# Updated up to 1.1.0 by Serban Udrea <S.Udrea@gsi.de> # Added support for building with debugging symbols (S. Udrea) PRGNAM="scipy3" SRCNAM="scipy" -VERSION=${VERSION:-0.18.0} +VERSION=${VERSION:-1.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -53,7 +53,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf "$SRCNAM-$VERSION" -tar xvf $CWD/$SRCNAM-$VERSION.tar.xz +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz cd "$SRCNAM-$VERSION" chown -R root:root . @@ -64,12 +64,10 @@ find -L . \ -exec chmod 644 {} \; DEBUG=${DEBUG:-no} -case "$DEBUG" in - [yY]|[yY][eE][sS]) DEBUG="y" ;; - *) DEBUG="" ;; -esac +DEBUG=$(echo "$DEBUG"|cut -b 1|tr a-z A-Z) -if [ ! "$DEBUG" ]; then +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 diff --git a/academic/scipy3/scipy3.info b/academic/scipy3/scipy3.info index 70d7385422..afdc113a2e 100644 --- a/academic/scipy3/scipy3.info +++ b/academic/scipy3/scipy3.info @@ -1,8 +1,8 @@ PRGNAM="scipy3" -VERSION="0.18.0" +VERSION="1.1.0" HOMEPAGE="https://www.scipy.org/" -DOWNLOAD="https://github.com/scipy/scipy/releases/download/v0.18.0/scipy-0.18.0.tar.xz" -MD5SUM="59bceff108f58b0e72dfac6fb719476e" +DOWNLOAD="https://github.com/scipy/scipy/releases/download/v1.1.0/scipy-1.1.0.tar.gz" +MD5SUM="aa6bcc85276b6f25e17bcfc4dede8718" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="numpy3 lapack" diff --git a/academic/seaview/README b/academic/seaview/README index 70a537171c..e72249f563 100644 --- a/academic/seaview/README +++ b/academic/seaview/README @@ -1,28 +1,23 @@ SeaView is a multiplatform, graphical user interface for multiple -sequence alignment and molecular phylogeny. Important features are: +sequence alignment and molecular phylogeny. Features: -1) SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, - FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of - phylogenetic trees. - -2) SeaView drives programs muscle or Clustal Omega (clustalo) for - multiple sequence alignment, and also allows to use any external - alignment algorithm able to read and write FASTA-formatted files. - -3) Seaview drives the Gblocks program to select blocks of - evolutionarily conserved sites. - -4) SeaView computes phylogenetic trees by - a) parsimony, using PHYLIP's dnapars/protpars algorithm - b) distance, with NJ or BioNJ algorithms on a variety of - evolutionary distances, - c) maximum likelihood, driving program PhyML - -5) SeaView prints and draws phylogenetic trees on screen, SVG, PDF or - PostScript files. - -6) SeaView allows to download sequences from EMBL/GenBank/UniProt - using the Internet. +- Reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, + PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic + trees. +- Drives programs muscle or Clustal Omega for multiple sequence + alignment, and also allows to use any external alignment + algorithm able to read and write FASTA-formatted files. +- Drives the Gblocks program to select blocks of evolutionarily + conserved sites. +- Computes phylogenetic trees by parsimony, using PHYLIP's dnapars / + protpars algorithm, distance, with NJ or BioNJ algorithms on a variety + of evolutionary distances, maximum likelihood, driving program PhyML +- Can use the Transfer Bootstrap Expectation method to compute the + bootstrap support of PhyML and distance trees. +- Uses the Treerecs method to reconcile gene and species trees. +- Prints and draws phylogenetic trees on screen, SVG, PDF or PostScript + files. +- Allows to download sequences from EMBL / GenBank / UniProt. For details and citation: Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a diff --git a/academic/seaview/seaview.SlackBuild b/academic/seaview/seaview.SlackBuild index 2def34de14..876be6afbc 100644 --- a/academic/seaview/seaview.SlackBuild +++ b/academic/seaview/seaview.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for seaview -# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ # Thanks to developer Dr. Manolo Gouy for all his help. PRGNAM=seaview -VERSION=${VERSION:-4.7} +VERSION=${VERSION:-5.0.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -67,10 +67,10 @@ tar xvf $CWD/${PRGNAM}_${VERSION}.tar.gz 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 \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -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 our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile diff --git a/academic/seaview/seaview.info b/academic/seaview/seaview.info index 116ac4c44e..8a1ff60d21 100644 --- a/academic/seaview/seaview.info +++ b/academic/seaview/seaview.info @@ -1,10 +1,10 @@ PRGNAM="seaview" -VERSION="4.7" +VERSION="5.0.4" HOMEPAGE="http://doua.prabi.fr/software/seaview/" -DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.7.tar.gz" -MD5SUM="9c1ee28e7f870b76991de17b22d7dfcb" +DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_5.0.4.tar.gz" +MD5SUM="8b36176fb98a508e483285966ad7100c" 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/README b/academic/seqkit/README new file mode 100644 index 0000000000..d78d8069cd --- /dev/null +++ b/academic/seqkit/README @@ -0,0 +1,26 @@ +SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file +manipulation + +FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide +and protein sequences. Common manipulations of FASTA/Q file include +converting, searching, filtering, deduplication, splitting, shuffling, +and sampling. Existing tools only implement some of these manipulations, +and not particularly efficiently, and some are only available for +certain operating systems. Furthermore, the complicated installation +process of required packages and running environments can render these +programs less user friendly. + +This project describes a cross-platform ultrafast comprehensive toolkit +for FASTA/Q processing. SeqKit provides executable binary files for all +major operating systems, including Windows, Linux, and Mac OS X, and can +be directly used without any dependencies or pre-configurations. SeqKit +demonstrates competitive performance in execution time and memory usage +compared to similar tools. The efficiency and usability of SeqKit enable +researchers to rapidly accomplish common FASTA/Q file manipulations. + +Note: This just repackages the binaries provided from upstream. + +Please cite: +Wei Shen,Shuai Le,Yan Li ,Fuquan Hu. SeqKit: A Cross-Platform and +Ultrafast Toolkit for FASTA/Q File Manipulation. October 5, 2016 +https://doi.org/10.1371/journal.pone.0163962 diff --git a/academic/seqkit/seqkit.SlackBuild b/academic/seqkit/seqkit.SlackBuild new file mode 100644 index 0000000000..d0d7b7265d --- /dev/null +++ b/academic/seqkit/seqkit.SlackBuild @@ -0,0 +1,73 @@ +#!/bin/sh + +# Slackware build script for seqkit + +# Copyright 2020 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. + +PRGNAM=seqkit +VERSION=${VERSION:-0.13.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + ARCH=$( uname -m ) +fi + +case "$ARCH" in + i?86) ARCH=i386 + BINARCH="386" + ;; + x86_64) + BINARCH="amd64" + ;; + *) + printf "\n\n%s\n" "$ARCH is not supported." + exit 1 + ;; +esac + +CWD=$(pwd) +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 +tar xvf $CWD/${PRGNAM}_linux_${BINARCH}.tar.gz + +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 +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:-tgz} diff --git a/academic/seqkit/seqkit.info b/academic/seqkit/seqkit.info new file mode 100644 index 0000000000..791ed0fc60 --- /dev/null +++ b/academic/seqkit/seqkit.info @@ -0,0 +1,10 @@ +PRGNAM="seqkit" +VERSION="0.13.2" +HOMEPAGE="https://bioinf.shenwei.me/seqkit/" +DOWNLOAD="https://github.com/shenwei356/seqkit/releases/download/v0.13.2/seqkit_linux_386.tar.gz" +MD5SUM="9d5636a8f33651717775313798e1bd5d" +DOWNLOAD_x86_64="https://github.com/shenwei356/seqkit/releases/download/v0.13.2/seqkit_linux_amd64.tar.gz" +MD5SUM_x86_64="ec667c86988f968202f9413fb77ca91a" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/mpmath/slack-desc b/academic/seqkit/slack-desc index 4352c8d273..5cbf1904cb 100644 --- a/academic/mpmath/slack-desc +++ b/academic/seqkit/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -mpmath: mpmath (arithmetic library) -mpmath: -mpmath: Mpmath is a free (BSD licensed) Python library for real and complex -mpmath: floating-point arithmetic with arbitrary precision. It has been -mpmath: developed by Fredrik Johansson since 2007, with help from many -mpmath: contributors. -mpmath: -mpmath: http://mpmath.org/ -mpmath: -mpmath: -mpmath: +seqkit: seqkit (Ultrafast toolkit for FASTA/Q file manipulation) +seqkit: +seqkit: A cross-platform ultrafast comprehensive toolkit for FASTA/Q +seqkit: processing. +seqkit: +seqkit: https://bioinf.shenwei.me/seqkit/ +seqkit: https://github.com/shenwei356/seqkit +seqkit: https://doi.org/10.1371/journal.pone.0163962 +seqkit: +seqkit: +seqkit: diff --git a/academic/siril/README b/academic/siril/README index 3e9ef4ac5e..9d75056201 100644 --- a/academic/siril/README +++ b/academic/siril/README @@ -1,7 +1,7 @@ SIRIL is an astronomical image processing tool. -SIRIL is an image processing tool specially tailored for noise reduction and -improving the signal/noise ratio of an image from multiple captures as -required in astronomy. -SIRIL can align automatically or manually, stack and enhance pictures from -various file formats, even images sequences (movies and SER files). +SIRIL is an image processing tool specially tailored for noise +reduction and improving the signal/noise ratio of an image +from multiple captures as required in astronomy. SIRIL can align +automatically or manually, stack and enhance pictures from various file +formats, even images sequences (movies and SER files). diff --git a/academic/spades/slack-desc b/academic/spades/slack-desc index 42262d4899..bccb306223 100644 --- a/academic/spades/slack-desc +++ b/academic/spades/slack-desc @@ -11,7 +11,7 @@ spades: spades: SPAdes -- St. Petersburg genome assembler -- is intended for both spades: standard isolates and single-cell MDA bacteria assemblies. spades: -spades: Home: http://bioinf.spbau.ru/en/spades +spades: Homepage: http://bioinf.spbau.ru/en/spades spades: spades: spades: diff --git a/academic/spades/spades.SlackBuild b/academic/spades/spades.SlackBuild index 2d62682731..c15747f33b 100644 --- a/academic/spades/spades.SlackBuild +++ b/academic/spades/spades.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for spades -# Copyright 2015-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2015-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,11 +23,12 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=spades -SRCNAM=SPAdes -VERSION=${VERSION:-3.13.0} +VERSION=${VERSION:-3.14.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +SRCNAM=SPAdes + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; diff --git a/academic/spades/spades.info b/academic/spades/spades.info index 5b1b62004a..33a015e53e 100644 --- a/academic/spades/spades.info +++ b/academic/spades/spades.info @@ -1,10 +1,10 @@ PRGNAM="spades" -VERSION="3.13.0" +VERSION="3.14.1" HOMEPAGE="http://cab.spbu.ru/software/spades/" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="http://cab.spbu.ru/files/release3.13.0/SPAdes-3.13.0.tar.gz" -MD5SUM_x86_64="79ee72fe5bf066d8c8d25b42730bae5a" +DOWNLOAD_x86_64="http://cab.spbu.ru/files/release3.14.1/SPAdes-3.14.1.tar.gz" +MD5SUM_x86_64="239f76e0ffe0e06d26f0a24f8d38f278" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/spqr/patches/autoconfiscate.diff b/academic/spqr/patches/autoconfiscate.diff index 8bc53753dd..8fff318251 100644 --- a/academic/spqr/patches/autoconfiscate.diff +++ b/academic/spqr/patches/autoconfiscate.diff @@ -344,7 +344,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([SPQR],[2.0.9],[DrTimothyAldenDavis@gmail.com],[spqr],[http://www.suitesparse.com/]) ++AC_INIT([SPQR],[2.0.9],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[spqr],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/spqr_kernel.cpp]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) @@ -463,7 +463,7 @@ diff --git a/m4/ax_blas.m4 b/m4/ax_blas.m4 new file mode 100644 --- /dev/null +++ b/m4/ax_blas.m4 -@@ -0,0 +1,238 @@ +@@ -0,0 +1,241 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_blas.html +# =========================================================================== @@ -502,6 +502,7 @@ new file mode 100644 +# LICENSE +# +# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2019 Geoffrey M. Oxberry <goxberry@gmail.com> +# +# 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 @@ -529,7 +530,7 @@ new file mode 100644 +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + -+#serial 16 ++#serial 17 + +AU_ALIAS([ACX_BLAS], [AX_BLAS]) +AC_DEFUN([AX_BLAS], [ @@ -543,7 +544,9 @@ new file mode 100644 +case $with_blas in + yes | "") ;; + no) ax_blas_ok=disable ;; -+ -* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;; ++ -* | */* | *.a | *.so | *.so.* | *.dylib | *.dylib.* | *.o) ++ BLAS_LIBS="$with_blas" ++ ;; + *) BLAS_LIBS="-l$with_blas" ;; +esac + @@ -982,7 +985,7 @@ diff --git a/m4/ax_lapack.m4 b/m4/ax_lapack.m4 new file mode 100644 --- /dev/null +++ b/m4/ax_lapack.m4 -@@ -0,0 +1,131 @@ +@@ -0,0 +1,134 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_lapack.html +# =========================================================================== @@ -1022,6 +1025,7 @@ new file mode 100644 +# LICENSE +# +# Copyright (c) 2009 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2019 Geoffrey M. Oxberry <goxberry@gmail.com> +# +# 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 @@ -1049,7 +1053,7 @@ new file mode 100644 +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + -+#serial 9 ++#serial 10 + +AU_ALIAS([ACX_LAPACK], [AX_LAPACK]) +AC_DEFUN([AX_LAPACK], [ @@ -1061,7 +1065,9 @@ new file mode 100644 +case $with_lapack in + yes | "") ;; + no) ax_lapack_ok=disable ;; -+ -* | */* | *.a | *.so | *.so.* | *.o) LAPACK_LIBS="$with_lapack" ;; ++ -* | */* | *.a | *.so | *.so.* | *.dylib | *.dylib.* | *.o) ++ LAPACK_LIBS="$with_lapack" ++ ;; + *) LAPACK_LIBS="-l$with_lapack" ;; +esac + diff --git a/academic/spqr/spqr.SlackBuild b/academic/spqr/spqr.SlackBuild index 1bfa8d46d5..0ce28905bc 100644 --- a/academic/spqr/spqr.SlackBuild +++ b/academic/spqr/spqr.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for SPQR -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=spqr SRCNAM=SuiteSparse SUBDIR=SPQR VERSION=${VERSION:-2.0.9} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-1} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/spqr/spqr.info b/academic/spqr/spqr.info index 3f599628ad..daa36cb95e 100644 --- a/academic/spqr/spqr.info +++ b/academic/spqr/spqr.info @@ -1,8 +1,8 @@ PRGNAM="spqr" VERSION="2.0.9" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="blas lapack suitesparseconfig cholmod tbb" diff --git a/academic/stellarium/README b/academic/stellarium/README index c4a3136eca..09942222a2 100644 --- a/academic/stellarium/README +++ b/academic/stellarium/README @@ -5,5 +5,5 @@ projectors. Just set your coordinates and go. For reasonable performance, you will want to have some kind of 3D acceleration. -gpsd is an optional dependency for enabling location detection through a GPS -device. +gpsd is an optional dependency for enabling location detection through +a GPS device. diff --git a/academic/stellarium/stellarium.SlackBuild b/academic/stellarium/stellarium.SlackBuild index 4c7e1ff99e..99d4bb2406 100644 --- a/academic/stellarium/stellarium.SlackBuild +++ b/academic/stellarium/stellarium.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=stellarium -VERSION=${VERSION:-0.18.1} +VERSION=${VERSION:-0.20.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/stellarium/stellarium.info b/academic/stellarium/stellarium.info index 35dd774260..ba33b79199 100644 --- a/academic/stellarium/stellarium.info +++ b/academic/stellarium/stellarium.info @@ -1,8 +1,8 @@ PRGNAM="stellarium" -VERSION="0.18.1" +VERSION="0.20.4" HOMEPAGE="http://www.stellarium.org" -DOWNLOAD="https://github.com/Stellarium/stellarium/releases/download/v0.18.1/stellarium-0.18.1.tar.gz" -MD5SUM="1eb0098db83f0543b44877a8e72acbb6" +DOWNLOAD="https://github.com/Stellarium/stellarium/releases/download/v0.20.4/stellarium-0.20.4.tar.gz" +MD5SUM="d02659c2e01582a4608a97b4aa0baf61" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="qt5" diff --git a/academic/stringtie/stringtie.SlackBuild b/academic/stringtie/stringtie.SlackBuild index 51f471e71a..91f7fe98f8 100644 --- a/academic/stringtie/stringtie.SlackBuild +++ b/academic/stringtie/stringtie.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for stringtie -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2019 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=stringtie -VERSION=${VERSION:-1.3.5} +VERSION=${VERSION:-1.3.6} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -83,7 +83,6 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -# Copy the slack-desc (and a custom doinst.sh if necessary) into ./install mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/stringtie/stringtie.info b/academic/stringtie/stringtie.info index 6ab44c841a..0bda7b8dc4 100644 --- a/academic/stringtie/stringtie.info +++ b/academic/stringtie/stringtie.info @@ -1,8 +1,8 @@ PRGNAM="stringtie" -VERSION="1.3.5" +VERSION="1.3.6" HOMEPAGE="http://ccb.jhu.edu/software/stringtie/" -DOWNLOAD="https://github.com/gpertea/stringtie/archive/v1.3.5/stringtie-1.3.5.tar.gz" -MD5SUM="64e5a271dd1b4408728c5f16ce1222ff" +DOWNLOAD="https://github.com/gpertea/stringtie/archive/v1.3.6/stringtie-1.3.6.tar.gz" +MD5SUM="ac94323cb300e90b02bc82bc27e50a2f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/suitesparse/README b/academic/suitesparse/README index d4f385acca..a0a5eb5679 100644 --- a/academic/suitesparse/README +++ b/academic/suitesparse/README @@ -2,37 +2,31 @@ suitesparse is a collection of libraries for computations involving sparse matrices. The package includes the following libraries: AMD: approximate minimum degree ordering. -BTF: permutation to block triangular form (beta). CAMD: constrained approximate minimum degree ordering. COLAMD: column approximate minimum degree ordering. CCOLAMD: constrained column approximate minimum degree ordering. CHOLMOD: sparse Cholesky factorization. CXSparse: CSparse extended: complex matrix, int and long int support. -KLU: sparse LU factorization, primarily for circuit simulation. +KLU & BTF: sparse LU factorization, primarily for circuit simulation. LDL: a simple LDL^t factorization. SQPR: a multithread, multifrontal, rank-revealing sparse QR factorization method. UMFPACK: sparse LU factorization. -SuiteSparse_config: configuration file for all the above packages. RBio: read/write files in Rutherford/Boeing format. +GraphBLAS: graph algorithms in the language of linear algebra +Mongoose: graph partitioning +ssget: MATLAB and Java interface to the SuiteSparse Matrix Collection Suitesparse is an optional dependency for the octave package. -NOTES: - -* CHOLMOD is now compiled to use the METIS library. It was not -used previously because the licensing terms of earlier METIS -versions excluded it from Octave in some circumstances. Recent -versions of METIS now use the Apache License Version 2.0 and -should cause no problems. However if it is still desired to -build CHOLMOD without METIS, set the USEMETIS environment -variable to "no" when running the SlackBuild e.g. - USEMETIS=no sh suitesparse.SlackBuild - -* CXSparse is a superset of CSparse, and the two share common header +CXSparse is a superset of CSparse, and the two share common header names, so it does not make sense to build both. CXSparse is built by default. -* SlackBuilds.org also has all the parts of this suite as individual +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. + +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). diff --git a/academic/suitesparse/slack-desc b/academic/suitesparse/slack-desc index bdb991235e..657aa8db4a 100644 --- a/academic/suitesparse/slack-desc +++ b/academic/suitesparse/slack-desc @@ -11,7 +11,7 @@ suitesparse: suitesparse: suitesparse is a collection of libraries for computations involving suitesparse: sparse matrices. The package includes the following libraries: suitesparse: AMD, BTF, CAMD, COLAMD, CCOLAMD, CHOLMOD, CXSparse, KLU, LDL, -suitesparse: SQPR, UMFPACK. +suitesparse: SQPR, UMFPACK, GraphBLAS, Mongoose. suitesparse: suitesparse: suitesparse: diff --git a/academic/suitesparse/suitesparse.SlackBuild b/academic/suitesparse/suitesparse.SlackBuild index 27775d04d1..ea5d9248da 100644 --- a/academic/suitesparse/suitesparse.SlackBuild +++ b/academic/suitesparse/suitesparse.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for suitesparse -# Copyright 2017,2018 Christoph Willing, Brisbane Australia +# Copyright 2017-2021 Christoph Willing, Brisbane Australia # All rights reserved. # Thanks to Pablo Santamaria for previous versions # @@ -25,7 +25,7 @@ PRGNAM=suitesparse SRCNAM=SuiteSparse -VERSION=${VERSION:-5.3.0} +VERSION=${VERSION:-5.7.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -33,7 +33,6 @@ if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; arm*) ARCH=arm ;; - # Unless $ARCH is already set, use uname -m for all other archs: *) ARCH=$( uname -m ) ;; esac fi @@ -57,8 +56,6 @@ else LIBDIRSUFFIX="" fi -metis="" ; [ "${USEMETIS:-yes}" != "yes" ] && metis="CHOLMOD_CONFIG=-DNPARTITION" - set -e rm -rf $PKG @@ -66,7 +63,7 @@ mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $SRCNAM tar xvf $CWD/$SRCNAM-$VERSION.tar.gz -cd $SRCNAM +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -78,17 +75,25 @@ mkdir -p $PKG/usr/include/suitesparse mkdir -p $PKG/usr/lib$LIBDIRSUFFIX mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +make make install \ - MY_METIS_INC=/usr/include/metis MY_METIS_LIB=/usr/lib$LIBDIRSUFFIX/libmetis.so BLAS=-lblas \ - $metis \ - INSTALL_INCLUDE=$PKG/usr/include/suitesparse INSTALL_LIB=$PKG/usr/lib$LIBDIRSUFFIX \ - INSTALL_DOC=$PKG/usr/doc/$PRGNAM-$VERSION -chrpath --replace /usr/lib$LIBDIRSUFFIX $PKG/usr/lib$LIBDIRSUFFIX/* + INSTALL_INCLUDE=$PKG/usr/include/suitesparse \ + INSTALL_LIB=$PKG/usr/lib$LIBDIRSUFFIX \ + INSTALL_DOC=$PKG/usr/doc/$PRGNAM-$VERSION + +# Check that each library already has an rpath before attempting to modify it +# (libmetis.so does not, causing `chrpath --replace` to fail) +for l in $PKG/usr/lib${LIBDIRSUFFIX}/* +do + if chrpath -l $l ; then + chrpath --replace /usr/lib$LIBDIRSUFFIX $l + fi +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 -cp -a LICENSE.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE.txt CONTRIBUTOR-LICENSE.txt README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/suitesparse/suitesparse.info b/academic/suitesparse/suitesparse.info index 17769f9f56..d8b009880b 100644 --- a/academic/suitesparse/suitesparse.info +++ b/academic/suitesparse/suitesparse.info @@ -1,10 +1,10 @@ PRGNAM="suitesparse" -VERSION="5.3.0" +VERSION="5.7.2" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.3.0.tar.gz" -MD5SUM="d638a4369f3df0ca9e64b019af658a38" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.7.2/SuiteSparse-5.7.2.tar.gz" +MD5SUM="7dc408bd99f825ef75fca0dda708f95d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="lapack metis chrpath" +REQUIRES="lapack OpenBLAS chrpath" MAINTAINER="Christoph Willing" EMAIL="chris.willing@linux.com" diff --git a/academic/suitesparseconfig/README b/academic/suitesparseconfig/README index 1832b9d60e..88061d2d50 100644 --- a/academic/suitesparseconfig/README +++ b/academic/suitesparseconfig/README @@ -1,5 +1,6 @@ -SuiteSparse_config is a common configuration library for the SuiteSparse -family of sparse matrix packages, including SuiteSparseQR, AMD, CAMD, COLAMD, -CCOLAMD, CHOLMOD, KLU, BTF, LDL, CXSparse, RBio, and UMFPACK. +SuiteSparse_config is a common configuration library for the +SuiteSparse family of sparse matrix packages, including SuiteSparseQR, +AMD, CAMD, COLAMD, CCOLAMD, CHOLMOD, KLU, BTF, LDL, CXSparse, RBio, +and UMFPACK. This library was formerly named UFconfig. diff --git a/academic/suitesparseconfig/patches/autoconfiscate.diff b/academic/suitesparseconfig/patches/autoconfiscate.diff index a714b47d12..80b550a08a 100644 --- a/academic/suitesparseconfig/patches/autoconfiscate.diff +++ b/academic/suitesparseconfig/patches/autoconfiscate.diff @@ -34,7 +34,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([SuiteSparse_config],[5.4.0],[DrTimothyAldenDavis@gmail.com],[suitesparseconfig],[http://www.suitesparse.com/]) ++AC_INIT([SuiteSparse_config],[5.8.1],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[suitesparseconfig],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([SuiteSparse_config.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/suitesparseconfig/suitesparseconfig.SlackBuild b/academic/suitesparseconfig/suitesparseconfig.SlackBuild index 45f03a6dfb..1845c790c9 100644 --- a/academic/suitesparseconfig/suitesparseconfig.SlackBuild +++ b/academic/suitesparseconfig/suitesparseconfig.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for SuiteSparse_config -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,8 +25,8 @@ PRGNAM=suitesparseconfig SRCNAM=SuiteSparse SUBDIR=SuiteSparse_config -VERSION=${VERSION:-5.4.0} -SRCVER=${SRCVER:-5.4.0} +VERSION=${VERSION:-5.8.1} +SRCVER=${SRCVER:-5.8.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/suitesparseconfig/suitesparseconfig.info b/academic/suitesparseconfig/suitesparseconfig.info index 1d3135dcee..17cea1c0bf 100644 --- a/academic/suitesparseconfig/suitesparseconfig.info +++ b/academic/suitesparseconfig/suitesparseconfig.info @@ -1,8 +1,8 @@ PRGNAM="suitesparseconfig" -VERSION="5.4.0" +VERSION="5.8.1" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/sundials/sundials.SlackBuild b/academic/sundials/sundials.SlackBuild index 67f7922291..149f9bd771 100644 --- a/academic/sundials/sundials.SlackBuild +++ b/academic/sundials/sundials.SlackBuild @@ -25,7 +25,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=sundials -VERSION=${VERSION:-3.1.1} +VERSION=${VERSION:-5.6.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -82,6 +82,8 @@ sed -i \ src/*/CMakeLists.txt \ src/*/*/CMakeLists.txt +export PATH=/opt/cmake-202x/bin:$PATH + mkdir -p build cd build cmake \ diff --git a/academic/sundials/sundials.info b/academic/sundials/sundials.info index 609a18e7f3..561c6831af 100644 --- a/academic/sundials/sundials.info +++ b/academic/sundials/sundials.info @@ -1,10 +1,10 @@ PRGNAM="sundials" -VERSION="3.1.1" +VERSION="5.6.1" HOMEPAGE="https://computation.llnl.gov/projects/sundials" -DOWNLOAD="https://computation.llnl.gov/projects/sundials/download/sundials-3.1.1.tar.gz" -MD5SUM="e63f4de0be5be97f750b30b0fa11ef34" +DOWNLOAD="https://github.com/LLNL/sundials/releases/download/v5.6.1/sundials-5.6.1.tar.gz" +MD5SUM="a945bf3fa606fb6676ec025723688f15" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="cmake-202x" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/sword-data-kjv/README b/academic/sword-data-kjv/README index d4dc4c01ad..1ecea1c77b 100644 --- a/academic/sword-data-kjv/README +++ b/academic/sword-data-kjv/README @@ -10,12 +10,13 @@ Go to www.crosswire.org/sword/modules/ to find more texts, dictionaries, commentaries and other related stuff which can be used by the sword engine. -wget has problems using the urls directly at www.crosswire.org/sword/modules -allthough a browser such as firefox works fine. See the .info file for an -example of url location when using wget. +wget has problems using the urls directly at +www.crosswire.org/sword/modules allthough a browser such as firefox +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. +most sword based bible programs, such as bibletime or xiphos +(gnomesword) have a facility to download more content using their gui. Please Note: you need at least sword 1.7.0 or higher to read this data. It has been tested with sword 1.7.0 1.7.5a1 and 1.8.1 diff --git a/academic/sword-data-kjv/sword-data-kjv.SlackBuild b/academic/sword-data-kjv/sword-data-kjv.SlackBuild index 4b41aacc36..add1aa9c09 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 2015/6/8 Tim Dickson, email: tim at googlemail.com +# Copyright 2015-2021 Tim Dickson, email: tim at googlemail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=sword-data-kjv -VERSION=${VERSION:-1.8.1} +VERSION=${VERSION:-1.8.1_1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/sword-data-kjv/sword-data-kjv.info b/academic/sword-data-kjv/sword-data-kjv.info index d58f037e03..0bbedb43ef 100644 --- a/academic/sword-data-kjv/sword-data-kjv.info +++ b/academic/sword-data-kjv/sword-data-kjv.info @@ -1,10 +1,10 @@ PRGNAM="sword-data-kjv" -VERSION="1.8.1" +VERSION="1.8.1_1" 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="43b84512562a6b2406b34abf46fca4fa \ +MD5SUM="7488aadfd5b72c96b4601a0135c5786a \ 2acde501e6a33e84feeeaa62f8e53d89 \ 3cbbc69d7410efc9d1d7f6f6b30e3415" DOWNLOAD_x86_64="" diff --git a/academic/sword/README b/academic/sword/README index 2de1d80d89..a9972f2fae 100644 --- a/academic/sword/README +++ b/academic/sword/README @@ -1,13 +1,19 @@ -The SWORD Project is an effort to create an ever expanding software package -for research and study of God and His Word. The SWORD Bible Framework allows -easy manipulation of Bible texts, commentaries, lexicons, dictionaries, etc. -Many frontends are build using this framework. An installed module set may -be shared between any frontend using the framework. +The SWORD Project is an effort to create an ever expanding software +package for research and study of God and His Word. The SWORD Bible +Framework allows easy manipulation of Bible texts, commentaries, +lexicons,dictionaries, etc. +Many frontends are build using this framework. An installed module set +may be shared between any frontend using the framework. This engine/library needs data to operate on to be usefull. -A sword-data-kjv package is available on sbo to provide a basic bible with -strongs and Greek and Hebrew dictionaries for use with this library. Many -more bibles, commentries etc. can be found on the crosswire.org website. +A sword-data-kjv package is available on sbo to provide a basic bible +with strongs and Greek and Hebrew dictionaries for use with this +library. Many more bibles, commentries etc. can be found on the +crosswire.org website. + modules can be downloaded in raw format (zip) and extracted into the /usr/share/sword directory. + +You will also need a frontend, such as xiphos or bibletime (both on sbo) +to view the bible data. diff --git a/academic/sword/sword.SlackBuild b/academic/sword/sword.SlackBuild index ffdff4fc6a..9f12ed43b1 100644 --- a/academic/sword/sword.SlackBuild +++ b/academic/sword/sword.SlackBuild @@ -5,7 +5,7 @@ # Copyright 2008-2011 Heinz Wiesinger, Amsterdam, The Netherlands # All rights reserved. # -# changes updating to v1.7.5a1 and v1.8.1 Copyright 2015-2018 Tim Dickson, Scotland +# changes updating to v1.7.5a1 and v1.8.1 Copyright 2015-2020 Tim Dickson, Scotland # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -26,7 +26,7 @@ PRGNAM=sword VERSION=${VERSION:-1.8.1} -BUILD=${BUILD:-2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -64,6 +64,9 @@ cd $TMP rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION +#patch to fix pre-chapter text, required for xiphos. when sword tag>1.8.1 +#remove this patch as it will be included. +patch -p0 -i $CWD/$PRGNAM.diff chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ diff --git a/academic/sword/sword.diff b/academic/sword/sword.diff new file mode 100644 index 0000000000..ac57df456c --- /dev/null +++ b/academic/sword/sword.diff @@ -0,0 +1,75 @@ +Index: src/mgr/stringmgr.cpp +=================================================================== +--- src/mgr/stringmgr.cpp (revision 3718) ++++ src/mgr/stringmgr.cpp (revision 3721) +@@ -20,6 +20,7 @@ + * + */ + ++#include <ctype.h> + #include <stringmgr.h> + #include <swlog.h> + #include <localemgr.h> +Index: src/modules/filters/osisxhtml.cpp +=================================================================== +--- src/modules/filters/osisxhtml.cpp (revision 3718) ++++ src/modules/filters/osisxhtml.cpp (revision 3721) +@@ -849,7 +849,11 @@ + else if (tag.isEndTag()) { + outText("</div>", buf, u); + } +- else if (!(type == "colophon")) outText(tag, buf, u); ++ else if (!(type == "colophon")) { ++ if (tag.getAttribute("sID")) tag.setEmpty(false); ++ if (tag.getAttribute("eID")) tag.setEndTag(true); ++ outText(tag, buf, u); ++ } + + } + else if (!strcmp(tag.getName(), "span")) { +Index: src/utilfuns/utilxml.cpp +=================================================================== +--- src/utilfuns/utilxml.cpp (revision 3718) ++++ src/utilfuns/utilxml.cpp (revision 3721) +@@ -291,13 +291,16 @@ + tag.append('/'); + + tag.append(getName()); +- for (StringPairMap::iterator it = attributes.begin(); it != attributes.end(); it++) { +- //tag.appendFormatted(" %s=\"%s\"", it->first.c_str(), it->second.c_str()); +- tag.append(' '); +- tag.append(it->first.c_str()); +- tag.append((strchr(it->second.c_str(), '\"')) ? "=\'" : "=\""); +- tag.append(it->second.c_str()); +- tag.append((strchr(it->second.c_str(), '\"'))? '\'' : '\"'); ++ ++ if (!isEndTag()) { ++ for (StringPairMap::iterator it = attributes.begin(); it != attributes.end(); it++) { ++ //tag.appendFormatted(" %s=\"%s\"", it->first.c_str(), it->second.c_str()); ++ tag.append(' '); ++ tag.append(it->first.c_str()); ++ tag.append((strchr(it->second.c_str(), '\"')) ? "=\'" : "=\""); ++ tag.append(it->second.c_str()); ++ tag.append((strchr(it->second.c_str(), '\"'))? '\'' : '\"'); ++ } + } + + if (isEmpty()) +Index: include/utilxml.h +=================================================================== +--- include/utilxml.h (revision 3718) ++++ include/utilxml.h (revision 3721) +@@ -75,6 +75,13 @@ + * otherwise, we return if we're a simple XML end </tag>. + */ + bool isEndTag(const char *eID = 0) const; ++ inline void setEndTag(bool value) { ++ if (!parsed) ++ parse(); ++ endTag = value; ++ if (value) ++ empty = false; ++ } + + const StringList getAttributeNames() const; + int getAttributePartCount(const char *attribName, char partSplit = '|') const; diff --git a/academic/sympy/README b/academic/sympy/README deleted file mode 100644 index 26abdb06e1..0000000000 --- a/academic/sympy/README +++ /dev/null @@ -1,10 +0,0 @@ -SymPy is a Python library for symbolic mathematics. It aims to become -a full-featured computer algebra system (CAS) while keeping the -code as simple as possible in order to be comprehensible and easily -extensible. SymPy is written entirely in Python and does not require -any external libraries. - -Optional dependencies are pyglet (needed only for plotting) and ipython. - -Please read the release notes at https://github.com/sympy/sympy/wiki/_pages -for any backward compatibility issues. diff --git a/academic/sympy/sympy.SlackBuild b/academic/sympy/sympy.SlackBuild deleted file mode 100644 index 3f9688eb60..0000000000 --- a/academic/sympy/sympy.SlackBuild +++ /dev/null @@ -1,57 +0,0 @@ -#!/bin/sh - -# Slackware build script for sympy - -# Written by Grissiom <chaos.proton@gmail.com> -# Updated for 0.6.7 by JoĂŁo Felipe Santos <joao.eel@gmail.com> -# Updated up to 0.7.5 by Serban Udrea <S.Udrea@gsi.de> - -PRGNAM=sympy -VERSION=${VERSION:-0.7.6} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i486 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -CWD=$(pwd) -TMP=${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 {} \; - -python setup.py install --root=$PKG - -mv $PKG/usr/share/man $PKG/usr/man -rmdir $PKG/usr/share -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 LICENSE PKG-INFO 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.${PKGTYPE:-tgz} diff --git a/academic/sympy/sympy.info b/academic/sympy/sympy.info deleted file mode 100644 index d6bd2fcfd0..0000000000 --- a/academic/sympy/sympy.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="sympy" -VERSION="0.7.6" -HOMEPAGE="http://sympy.org" -DOWNLOAD="https://github.com/sympy/sympy/releases/download/sympy-0.7.6/sympy-0.7.6.tar.gz" -MD5SUM="3d04753974306d8a13830008e17babca" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Serban Udrea" -EMAIL="S.Udrea@gsi.de" diff --git a/academic/t_coffee/slack-desc b/academic/t_coffee/slack-desc index 89fef07053..5fca2e78ef 100644 --- a/academic/t_coffee/slack-desc +++ b/academic/t_coffee/slack-desc @@ -13,7 +13,7 @@ t_coffee: T-Coffee to align sequences or to combine the output of your t_coffee: favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) t_coffee: into one unique alignment (M-Coffee). t_coffee: -t_coffee: Home: http://www.tcoffee.org/ -t_coffee: References: /usr/doc/t_coffee-11.00.8cbe486/References +t_coffee: Homepage: http://www.tcoffee.org/ +t_coffee: t_coffee: t_coffee: diff --git a/academic/t_coffee/t_coffee.SlackBuild b/academic/t_coffee/t_coffee.SlackBuild index 7329c61e2f..e54497f7a9 100644 --- a/academic/t_coffee/t_coffee.SlackBuild +++ b/academic/t_coffee/t_coffee.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for t_coffee -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,15 +23,16 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=t_coffee -VERSION=${VERSION:-11.00.8cbe486} +VERSION=${VERSION:-13.41.0_git28bdc39} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -SRCNAM=T-COFFEE_distribution_Version +TARNAM=tcoffee +COMMIT=28bdc39911d10d8597db8513f9515fb2ed7a9158 if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -42,8 +43,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -61,9 +62,9 @@ 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} +rm -rf ${TARNAM}-${COMMIT} +tar xvf $CWD/${TARNAM}-${COMMIT}.tar.gz +cd ${TARNAM}-${COMMIT} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -71,24 +72,18 @@ 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 t_coffee_source +# Use our CFLAGS +sed -i "/^CFLAGS/s/=/+=/" t_coffee/src/makefile -CFLAGS="$SLKCFLAGS" \ -CC="gcc" \ -FCC="gfortran" \ -make -i all - -install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM -install -D -m755 TMalign $PKG/usr/bin/TMalign - -cd - +CFLAGS="$SLKCFLAGS" make t_coffee -C t_coffee/src +install -D -m755 t_coffee/src/$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 \ - install license.txt \ + HOW_BUILD_WORKS.md README.md docs/*.rst \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References diff --git a/academic/t_coffee/t_coffee.info b/academic/t_coffee/t_coffee.info index 129a6c258d..ec75e49f23 100644 --- a/academic/t_coffee/t_coffee.info +++ b/academic/t_coffee/t_coffee.info @@ -1,8 +1,8 @@ PRGNAM="t_coffee" -VERSION="11.00.8cbe486" +VERSION="13.41.0_git28bdc39" HOMEPAGE="http://www.tcoffee.org/" -DOWNLOAD="http://www.tcoffee.org/Packages/Stable/Version_11.00.8cbe486/T-COFFEE_distribution_Version_11.00.8cbe486.tar.gz" -MD5SUM="bd91485c06eda4f2ffcb61542d3ce302" +DOWNLOAD="https://github.com/cbcrg/tcoffee/archive/28bdc39/tcoffee-28bdc39911d10d8597db8513f9515fb2ed7a9158.tar.gz" +MD5SUM="3392d55a2817575ce90c1c3e94e08c0b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/tabix-legacy/tabix-legacy.SlackBuild b/academic/tabix-legacy/tabix-legacy.SlackBuild index 5ca182d611..d20dc5ade9 100644 --- a/academic/tabix-legacy/tabix-legacy.SlackBuild +++ b/academic/tabix-legacy/tabix-legacy.SlackBuild @@ -22,13 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -SRCNAM=tabix -SUFFIX=legacy -PRGNAM=${SRCNAM}-${SUFFIX} +PRGNAM=tabix-legacy VERSION=${VERSION:-0.2.6} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +SRCNAM=tabix +SUFFIX=legacy + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; diff --git a/academic/tabix/README b/academic/tabix/README deleted file mode 100644 index 143a5d5684..0000000000 --- a/academic/tabix/README +++ /dev/null @@ -1,8 +0,0 @@ -Tabix indexes a TAB-delimited genome position file in.tab.bgz and -creates an index file in.tab.bgz.tbi when region is absent from the -command-line. The input data file must be position sorted and -compressed by bgzip which has a gzip like interface. After indexing, -tabix is able to quickly retrieve data lines overlapping regions -specified in the format "chr:beginPos-endPos". Fast data retrieval -also works over network if URI is given as a file name and in this -case the index file will be downloaded if it is not present locally. diff --git a/academic/tabix/slack-desc b/academic/tabix/slack-desc deleted file mode 100644 index 5a387152f0..0000000000 --- a/academic/tabix/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------------------------------------------------------| -tabix: tabix (Generic indexer for TAB-delimited genome position files) -tabix: -tabix: Tabix indexes a TAB-delimited genome position file in.tab.bgz -tabix: and creates an index file in.tab.bgz.tbi when region is absent -tabix: from the command-line. The input data file must be position -tabix: sorted and compressed by bgzip which has a gzip like interface. -tabix: Tabix is able to quickly retrieve data lines overlapping regions -tabix: specified in the format "chr:beginPos-endPos". -tabix: -tabix: Home: http://samtools.sourceforge.net/tabix.shtml -tabix: diff --git a/academic/tabix/tabix.info b/academic/tabix/tabix.info deleted file mode 100644 index bac2016304..0000000000 --- a/academic/tabix/tabix.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="tabix" -VERSION="0.2.6" -HOMEPAGE="http://samtools.sourceforge.net/tabix.shtml" -DOWNLOAD="http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2" -MD5SUM="36a61ceac2f5bed36018434282bbcc5d" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Petar Petrov" -EMAIL="slackalaxy@gmail.com" diff --git a/academic/tiemu/README b/academic/tiemu/README new file mode 100644 index 0000000000..83497217ab --- /dev/null +++ b/academic/tiemu/README @@ -0,0 +1,7 @@ +TiEmu is a multi-platform emulator for TI89 / TI89 Titanium / TI92 / +TI92+ / V200PLT hand-helds. + +TiEmu does not emulate TI82, 83, ... hand-helds but TiLem does. + +TiEmu requires a ROM for your calculator. A GPL'd ROM called PedroM +is included. diff --git a/academic/freechartgeany/doinst.sh b/academic/tiemu/doinst.sh index 65c7e2eeb9..65c7e2eeb9 100644 --- a/academic/freechartgeany/doinst.sh +++ b/academic/tiemu/doinst.sh diff --git a/academic/tiemu/patches/01-build-fix.patch b/academic/tiemu/patches/01-build-fix.patch new file mode 100644 index 0000000000..7660b69430 --- /dev/null +++ b/academic/tiemu/patches/01-build-fix.patch @@ -0,0 +1,487 @@ +# This patch is based on the Ubuntu patch for TiEmu 3.02, see +# http://packages.ubuntu.com/de/oneiric/tiemu + + +diff -purN tiemu-3.03.orig/src/gui/calc/calc.c tiemu-3.03/src/gui/calc/calc.c +--- tiemu-3.03.orig/src/gui/calc/calc.c 2007-12-16 16:29:16.000000000 +0100 ++++ tiemu-3.03/src/gui/calc/calc.c 2011-11-04 23:11:40.000000000 +0100 +@@ -313,7 +313,7 @@ on_drawingarea1_expose_event ( + { + gdk_draw_pixmap( + widget->window, +- widget->style->fg_gc[GTK_WIDGET_STATE (widget)], ++ widget->style->fg_gc[gtk_widget_get_state (widget)], + pixmap, + event->area.x, event->area.y, + event->area.x, event->area.y, +@@ -586,7 +586,7 @@ int hid_init(void) + + // Install LCD refresh: 100 FPS (10 ms) + tid = g_timeout_add((params.lcd_rate == -1) ? 50 : params.lcd_rate, +- (GtkFunction)hid_refresh, NULL); ++ (GSourceFunc)hid_refresh, NULL); + + explicit_destroy = 0; + gtk_widget_show(main_wnd); // show wnd here +@@ -640,7 +640,7 @@ void hid_lcd_rate_set(void) + g_source_remove(tid); + + tid = g_timeout_add((params.lcd_rate == -1) ? 50 : params.lcd_rate, +- (GtkFunction)hid_refresh, NULL); ++ (GSourceFunc)hid_refresh, NULL); + } + + int hid_switch_with_skin(void) +diff -purN tiemu-3.03.orig/src/gui/calc/popup.c tiemu-3.03/src/gui/calc/popup.c +--- tiemu-3.03.orig/src/gui/calc/popup.c 2009-05-08 22:43:47.000000000 +0200 ++++ tiemu-3.03/src/gui/calc/popup.c 2011-11-04 22:45:28.000000000 +0100 +@@ -26,7 +26,9 @@ + # include <config.h> + #endif + ++#undef GTK_DISABLE_DEPRECATED + #include <gtk/gtk.h> ++#define GTK_DISABLE_DEPRECATED + #include <glade/glade.h> + #include <stdlib.h> + #include <string.h> +diff -purN tiemu-3.03.orig/src/gui/calc/screen.c tiemu-3.03/src/gui/calc/screen.c +--- tiemu-3.03.orig/src/gui/calc/screen.c 2006-11-06 18:18:51.000000000 +0100 ++++ tiemu-3.03/src/gui/calc/screen.c 2011-11-04 23:12:09.000000000 +0100 +@@ -187,7 +187,7 @@ void redraw_skin(void) + skin_infos.image = gdk_pixbuf_scale_simple(skin_infos.raw, wr.wr.w, wr.wr.h, GDK_INTERP_NEAREST); + + // and draw image into pixmap (next, into window on expose event) +- gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[GTK_WIDGET_STATE(main_wnd)], ++ gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[gtk_widget_get_state(main_wnd)], + skin_infos.image, 0, 0, 0, 0, -1, -1, GDK_RGB_DITHER_NONE, 0, 0); + gdk_window_invalidate_rect(main_wnd->window, &wr.gr, FALSE); + } +@@ -204,7 +204,7 @@ void redraw_lcd(void) + gdk_pixbuf_scale_simple(skin_infos.raw, sr.w, sr.h, GDK_INTERP_NEAREST); + + // and draw +- gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[GTK_WIDGET_STATE(main_wnd)], ++ gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[gtk_widget_get_state(main_wnd)], + skin_infos.image, ls.x, ls.y, lr.x, lr.y, lr.w, lr.h, GDK_RGB_DITHER_NONE, 0, 0); + gtk_widget_queue_draw_area(area, lr.x, lr.y, lr.w, lr.h); + } +@@ -324,7 +324,7 @@ int hid_update_lcd(void) + skin_infos.image = gdk_pixbuf_scale_simple(lcd, lr.w, lr.h, GDK_INTERP_NEAREST); + + // and draw image into pixmap (next, into window on expose event) +- gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[GTK_WIDGET_STATE(main_wnd)], ++ gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[gtk_widget_get_state(main_wnd)], + skin_infos.image, src.x, src.y, lr.x, lr.y, src.w, src.h, + GDK_RGB_DITHER_NONE, 0, 0); + gtk_widget_queue_draw_area(area, lr.x, lr.y, src.w, src.h); +@@ -332,7 +332,7 @@ int hid_update_lcd(void) + else + { + // and draw image into pixmap (next, into window on expose event) +- gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[GTK_WIDGET_STATE(main_wnd)], ++ gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[gtk_widget_get_state(main_wnd)], + lcd_mem, src.x, src.y, lr.x, lr.y, src.w, src.h, + GDK_RGB_DITHER_NONE, 0, 0); + gtk_widget_queue_draw_area(area, lr.x, lr.y, src.w, src.h); +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_all.c tiemu-3.03/src/gui/debugger/dbg_all.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_all.c 2009-05-08 12:56:40.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_all.c 2011-11-04 22:46:29.000000000 +0100 +@@ -90,21 +90,21 @@ void gtk_debugger_refresh(void) + { + WND_TMR_START(); + +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.regs)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.regs)) + dbgregs_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.mem)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.mem)) + dbgmem_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.bkpts)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.bkpts)) + dbgbkpts_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.pclog)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.pclog)) + dbgpclog_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.code)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.code)) + dbgcode_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.stack)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.stack)) + dbgstack_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.heap)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.heap)) + dbgheap_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.iop)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.iop)) + dbgiop_refresh_window(); + + WND_TMR_STOP("Debugger Refresh Time"); +@@ -163,7 +163,7 @@ int gtk_debugger_enter(int context) + gtk_debugger_refresh(); + + // enable the debugger if GDB disabled it +- if (!options3.dbg_dock && !GTK_WIDGET_SENSITIVE(dbgw.regs)) ++ if (!options3.dbg_dock && !gtk_widget_get_sensitive(dbgw.regs)) + gtk_debugger_enable(); + + // handle automatic debugging requests +@@ -180,7 +180,7 @@ int gtk_debugger_enter(int context) + + ti68k_bkpt_get_pgmentry_offset(id, &handle, &offset); + ti68k_bkpt_del_pgmentry(handle); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.bkpts)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.bkpts)) + dbgbkpts_refresh_window(); + + delete_command(NULL, 0); +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_bkpts.c tiemu-3.03/src/gui/debugger/dbg_bkpts.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_bkpts.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_bkpts.c 2011-11-04 22:46:29.000000000 +0100 +@@ -388,7 +388,7 @@ GtkWidget* dbgbkpts_display_window(void) + gtk_window_iconify(GTK_WINDOW(wnd)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.bkpts) && !options3.bkpts.closed) ++ if(!gtk_widget_get_visible(dbgw.bkpts) && !options3.bkpts.closed) + gtk_widget_show(wnd); + + return wnd; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_code.c tiemu-3.03/src/gui/debugger/dbg_code.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_code.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_code.c 2011-11-04 22:46:29.000000000 +0100 +@@ -1117,7 +1117,7 @@ void gdbcallback_refresh_debugger(void) + + int dbgcode_quit_enabled(void) + { +- return GTK_WIDGET_SENSITIVE(mi.m8); ++ return gtk_widget_get_sensitive(mi.m8); + } + + static int close_debugger_wrapper(gpointer data) +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_dock.c tiemu-3.03/src/gui/debugger/dbg_dock.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_dock.c 2008-05-26 18:48:30.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_dock.c 2011-11-04 23:05:02.000000000 +0100 +@@ -151,22 +151,22 @@ void dbgdock_set_sensitivity(int state) +
+ void dbgdock_show_all(int all)
+ {
+- if(!GTK_WIDGET_VISIBLE(dbgw.dock) && all)
++ if(!gtk_widget_get_visible(dbgw.dock) && all)
+ gtk_widget_show(dbgw.dock);
+
+- if(GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(gtk_widget_get_visible(dbgw.iop))
+ gtk_window_iconify(GTK_WINDOW(dbgw.iop));
+- if(GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(gtk_widget_get_visible(dbgw.pclog))
+ gtk_window_iconify(GTK_WINDOW(dbgw.pclog));
+ }
+
+ void dbgdock_hide_all(int all)
+ {
+- if(GTK_WIDGET_VISIBLE(dbgw.dock) && all)
++ if(gtk_widget_get_visible(dbgw.dock) && all)
+ gtk_widget_hide(dbgw.dock);
+
+- if(GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(gtk_widget_get_visible(dbgw.pclog))
+ gtk_widget_hide(dbgw.pclog);
+- if(GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(gtk_widget_get_visible(dbgw.iop))
+ gtk_widget_hide(dbgw.iop);
+ }
+diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_heap.c tiemu-3.03/src/gui/debugger/dbg_heap.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_heap.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_heap.c 2011-11-04 22:46:29.000000000 +0100 +@@ -171,7 +171,7 @@ GtkWidget* dbgheap_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.heap)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.heap) && !options3.heap.closed) ++ if(!gtk_widget_get_visible(dbgw.heap) && !options3.heap.closed) + gtk_widget_show(dbgw.heap); + + return dbgw.heap; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_iop.c tiemu-3.03/src/gui/debugger/dbg_iop.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_iop.c 2009-05-02 21:46:04.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_iop.c 2011-11-04 22:46:29.000000000 +0100 +@@ -455,7 +455,7 @@ GtkWidget* dbgiop_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.iop)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.iop) && !options3.iop.closed) ++ if(!gtk_widget_get_visible(dbgw.iop) && !options3.iop.closed) + gtk_widget_show(dbgw.iop); + + return dbgw.iop; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_mem.c tiemu-3.03/src/gui/debugger/dbg_mem.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_mem.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_mem.c 2011-11-04 22:46:29.000000000 +0100 +@@ -435,7 +435,7 @@ GtkWidget* dbgmem_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.mem)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.mem) && !options3.mem.closed) ++ if(!gtk_widget_get_visible(dbgw.mem) && !options3.mem.closed) + gtk_widget_show(dbgw.mem); + + return dbgw.mem; +@@ -605,7 +605,7 @@ dbgmem_button6_clicked + + GLADE_CB void + on_notebook1_switch_page (GtkNotebook *notebook, +- GtkNotebookPage *page, ++ gpointer *page, + guint page_num, + gpointer user_data) + { +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_pclog.c tiemu-3.03/src/gui/debugger/dbg_pclog.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_pclog.c 2009-05-02 21:46:04.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_pclog.c 2011-11-04 22:46:29.000000000 +0100 +@@ -163,7 +163,7 @@ GtkWidget* dbgpclog_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.pclog)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.pclog) && !options3.pclog.closed) ++ if(!gtk_widget_get_visible(dbgw.pclog) && !options3.pclog.closed) + gtk_widget_show(dbgw.pclog); + + return dbgw.pclog; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_regs.c tiemu-3.03/src/gui/debugger/dbg_regs.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_regs.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_regs.c 2011-11-04 22:46:29.000000000 +0100 +@@ -302,7 +302,7 @@ GtkWidget* dbgregs_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.regs)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.regs) && !options3.regs.closed) ++ if(!gtk_widget_get_visible(dbgw.regs) && !options3.regs.closed) + gtk_widget_show(dbgw.regs); + + return dbgw.regs; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_romcall.c tiemu-3.03/src/gui/debugger/dbg_romcall.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_romcall.c 2007-07-05 13:36:10.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_romcall.c 2011-11-04 22:46:29.000000000 +0100 +@@ -29,7 +29,9 @@ + # include <config.h> + #endif + +-#include <gtk/gtk.h> ++#undef GTK_DISABLE_DEPRECATED ++ #include <gtk/gtk.h> ++#define GTK_DISABLE_DEPRECATED + #include <glade/glade.h> + #include <string.h> + +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_stack.c tiemu-3.03/src/gui/debugger/dbg_stack.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_stack.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_stack.c 2011-11-04 22:46:29.000000000 +0100 +@@ -197,7 +197,7 @@ GtkWidget* dbgstack_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.stack)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.stack) && !options3.stack.closed) ++ if(!gtk_widget_get_visible(dbgw.stack) && !options3.stack.closed) + gtk_widget_show(dbgw.stack); + + return dbgw.stack; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_wnds.c tiemu-3.03/src/gui/debugger/dbg_wnds.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_wnds.c 2009-05-07 09:18:02.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_wnds.c 2011-11-04 23:07:54.000000000 +0100 +@@ -74,21 +74,21 @@ void dbgwnds_minimize_all(int all) + if(options3.dbg_dock)
+ return;
+
+- if(GTK_WIDGET_VISIBLE(dbgw.regs))
++ if(gtk_widget_get_visible(dbgw.regs))
+ gtk_window_iconify(GTK_WINDOW(dbgw.regs));
+- if(GTK_WIDGET_VISIBLE(dbgw.bkpts))
++ if(gtk_widget_get_visible(dbgw.bkpts))
+ gtk_window_iconify(GTK_WINDOW(dbgw.bkpts));
+- if(GTK_WIDGET_VISIBLE(dbgw.mem))
++ if(gtk_widget_get_visible(dbgw.mem))
+ gtk_window_iconify(GTK_WINDOW(dbgw.mem));
+- if(GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(gtk_widget_get_visible(dbgw.pclog))
+ gtk_window_iconify(GTK_WINDOW(dbgw.pclog));
+- if(GTK_WIDGET_VISIBLE(dbgw.code) & all)
++ if(gtk_widget_get_visible(dbgw.code) & all)
+ gtk_window_iconify(GTK_WINDOW(dbgw.code));
+- if(GTK_WIDGET_VISIBLE(dbgw.stack))
++ if(gtk_widget_get_visible(dbgw.stack))
+ gtk_window_iconify(GTK_WINDOW(dbgw.stack));
+- if(GTK_WIDGET_VISIBLE(dbgw.heap))
++ if(gtk_widget_get_visible(dbgw.heap))
+ gtk_window_iconify(GTK_WINDOW(dbgw.heap));
+- if(GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(gtk_widget_get_visible(dbgw.iop))
+ gtk_window_iconify(GTK_WINDOW(dbgw.iop));
+ }
+
+@@ -98,21 +98,21 @@ void dbgwnds_unminimize_all(int all) + if(options3.dbg_dock)
+ return;
+
+- if(GTK_WIDGET_VISIBLE(dbgw.regs))
++ if(gtk_widget_get_visible(dbgw.regs))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.regs));
+- if(GTK_WIDGET_VISIBLE(dbgw.bkpts))
++ if(gtk_widget_get_visible(dbgw.bkpts))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.bkpts));
+- if(GTK_WIDGET_VISIBLE(dbgw.mem))
++ if(gtk_widget_get_visible(dbgw.mem))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.mem));
+- if(GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(gtk_widget_get_visible(dbgw.pclog))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.pclog));
+- if(GTK_WIDGET_VISIBLE(dbgw.code) & all)
++ if(gtk_widget_get_visible(dbgw.code) & all)
+ gtk_window_deiconify(GTK_WINDOW(dbgw.code));
+- if(GTK_WIDGET_VISIBLE(dbgw.stack))
++ if(gtk_widget_get_visible(dbgw.stack))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.stack));
+- if(GTK_WIDGET_VISIBLE(dbgw.heap))
++ if(gtk_widget_get_visible(dbgw.heap))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.heap));
+- if(GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(gtk_widget_get_visible(dbgw.iop))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.iop));
+ }
+
+@@ -122,21 +122,21 @@ void dbgwnds_show_all(int all) + if(options3.dbg_dock)
+ return;
+
+- if(!GTK_WIDGET_VISIBLE(dbgw.regs))
++ if(!gtk_widget_get_visible(dbgw.regs))
+ gtk_widget_show(dbgw.regs);
+- if(!GTK_WIDGET_VISIBLE(dbgw.bkpts))
++ if(!gtk_widget_get_visible(dbgw.bkpts))
+ gtk_widget_show(dbgw.bkpts);
+- if(!GTK_WIDGET_VISIBLE(dbgw.mem))
++ if(!gtk_widget_get_visible(dbgw.mem))
+ gtk_widget_show(dbgw.mem);
+- if(!GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(!gtk_widget_get_visible(dbgw.pclog))
+ gtk_widget_show(dbgw.pclog);
+- if(!GTK_WIDGET_VISIBLE(dbgw.code) && all)
++ if(!gtk_widget_get_visible(dbgw.code) && all)
+ gtk_widget_show(dbgw.code);
+- if(!GTK_WIDGET_VISIBLE(dbgw.stack))
++ if(!gtk_widget_get_visible(dbgw.stack))
+ gtk_widget_show(dbgw.stack);
+- if(!GTK_WIDGET_VISIBLE(dbgw.heap))
++ if(!gtk_widget_get_visible(dbgw.heap))
+ gtk_widget_show(dbgw.heap);
+- if(!GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(!gtk_widget_get_visible(dbgw.iop))
+ gtk_widget_show(dbgw.iop);
+ }
+
+@@ -146,21 +146,21 @@ void dbgwnds_hide_all(int all) + if(options3.dbg_dock)
+ return;
+
+- if(GTK_WIDGET_VISIBLE(dbgw.regs))
++ if(gtk_widget_get_visible(dbgw.regs))
+ gtk_widget_hide(dbgw.regs);
+- if(GTK_WIDGET_VISIBLE(dbgw.bkpts))
++ if(gtk_widget_get_visible(dbgw.bkpts))
+ gtk_widget_hide(dbgw.bkpts);
+- if(GTK_WIDGET_VISIBLE(dbgw.mem))
++ if(gtk_widget_get_visible(dbgw.mem))
+ gtk_widget_hide(dbgw.mem);
+- if(GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(gtk_widget_get_visible(dbgw.pclog))
+ gtk_widget_hide(dbgw.pclog);
+- if(GTK_WIDGET_VISIBLE(dbgw.code) && all)
++ if(gtk_widget_get_visible(dbgw.code) && all)
+ gtk_widget_hide(dbgw.code);
+- if(GTK_WIDGET_VISIBLE(dbgw.stack))
++ if(gtk_widget_get_visible(dbgw.stack))
+ gtk_widget_hide(dbgw.stack);
+- if(GTK_WIDGET_VISIBLE(dbgw.heap))
++ if(gtk_widget_get_visible(dbgw.heap))
+ gtk_widget_hide(dbgw.heap);
+- if(GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(gtk_widget_get_visible(dbgw.iop))
+ gtk_widget_hide(dbgw.iop);
+ }
+
+@@ -338,7 +338,7 @@ void update_submenu(GtkWidget *widget, g + if(!options3.dbg_dock)
+ {
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_registers1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.regs));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.regs));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_registers1_activate, NULL);
+ }
+ else
+@@ -350,7 +350,7 @@ void update_submenu(GtkWidget *widget, g + if(!options3.dbg_dock)
+ {
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_breakpoints1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.bkpts));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.bkpts));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_breakpoints1_activate, NULL);
+ }
+ else
+@@ -362,7 +362,7 @@ void update_submenu(GtkWidget *widget, g + if(!options3.dbg_dock)
+ {
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_memory1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.mem));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.mem));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_memory1_activate, NULL);
+ }
+ else
+@@ -372,7 +372,7 @@ void update_submenu(GtkWidget *widget, g + elt = g_list_nth(list, 3);
+ item = GTK_CHECK_MENU_ITEM(elt->data);
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_pc_log1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.pclog));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.pclog));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_pc_log1_activate, NULL);
+
+ // stack
+@@ -381,7 +381,7 @@ void update_submenu(GtkWidget *widget, g + if(!options3.dbg_dock)
+ {
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_stack_frame1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.stack));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.stack));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_stack_frame1_activate, NULL);
+ }
+ else
+@@ -393,7 +393,7 @@ void update_submenu(GtkWidget *widget, g + if(!options3.dbg_dock)
+ {
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_heap_frame1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.heap));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.heap));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_heap_frame1_activate, NULL);
+ }
+ else
+@@ -403,7 +403,7 @@ void update_submenu(GtkWidget *widget, g + elt = g_list_nth(list, 6);
+ item = GTK_CHECK_MENU_ITEM(elt->data);
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_ioports_frame1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.iop));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.iop));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_ioports_frame1_activate, NULL);
+
+ // dock/multi mode
+diff -purN tiemu-3.03.orig/src/gui/filesel.c tiemu-3.03/src/gui/filesel.c +--- tiemu-3.03.orig/src/gui/filesel.c 2007-12-16 16:54:33.000000000 +0100 ++++ tiemu-3.03/src/gui/filesel.c 2011-11-04 22:45:28.000000000 +0100 +@@ -41,7 +41,9 @@ + + #include <stdio.h> + #include <stdlib.h> ++#undef GTK_DISABLE_DEPRECATED + #include <gtk/gtk.h> ++#define GTK_DISABLE_DEPRECATED + #include <string.h> + + #ifdef __WIN32__ diff --git a/academic/tiemu/patches/sysdeps.patch b/academic/tiemu/patches/sysdeps.patch new file mode 100644 index 0000000000..8a4addb76e --- /dev/null +++ b/academic/tiemu/patches/sysdeps.patch @@ -0,0 +1,15 @@ +--- sysdeps.h.orig 2018-10-18 19:48:03.258705538 -0700 ++++ tiemu-3.03/src/core/uae/sysdeps.h 2018-10-18 19:48:34.178704986 -0700 +@@ -137,12 +137,6 @@ + #define ENUMDECL typedef enum + #define ENUMNAME(name) name + +-/* While we're here, make abort more useful. */ +-#define abort() \ +- do { \ +- fprintf (stderr, "UAE: Internal error; file %s, line %d\n", __FILE__, __LINE__); \ +- (abort) (); \ +-} while (0) + #else + #define ENUMDECL enum + #define ENUMNAME(name) ; typedef int name diff --git a/academic/tiemu/slack-desc b/academic/tiemu/slack-desc new file mode 100644 index 0000000000..36e348bc0a --- /dev/null +++ b/academic/tiemu/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------------------------------------------------------| +tiemu: tiemu (TI-89/92/V200 emulator for linux) +tiemu: +tiemu: TiEmu emulates Texas Instruments calculators TI-89/92/92+/V200PLT +tiemu: (no GDB). +tiemu: +tiemu: Homepage: http://lpg.ticalc.org/prj_tiemu/ +tiemu: +tiemu: +tiemu: +tiemu: +tiemu: diff --git a/academic/tiemu/tiemu.SlackBuild b/academic/tiemu/tiemu.SlackBuild new file mode 100644 index 0000000000..19e4cbaca5 --- /dev/null +++ b/academic/tiemu/tiemu.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/sh + +# Slackbuild for tiemu + +# Written by shelldweller <shelldweller@beauxbead.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. + +PRGNAM=tiemu +VERSION=${VERSION:-3.03} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${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-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 {} \; + +# A few necessary patches +# https://aur.archlinux.org/packages/tiemu/#comment-667308 +patch -p1 < $CWD/patches/01-build-fix.patch +patch -p1 < $CWD/patches/sysdeps.patch + +OPT_CFLAGS="" \ +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --build=$ARCH-slackware-linux \ + --without-kde \ + --disable-gdb + +make + +DESTDIR=$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 {} \; + +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.${PKGTYPE:-tgz} diff --git a/academic/tiemu/tiemu.info b/academic/tiemu/tiemu.info new file mode 100644 index 0000000000..d665780f3f --- /dev/null +++ b/academic/tiemu/tiemu.info @@ -0,0 +1,10 @@ +PRGNAM="tiemu" +VERSION="3.03" +HOMEPAGE="http://lpg.ticalc.org/prj_tiemu/" +DOWNLOAD="http://download.sourceforge.net/project/gtktiemu/tiemu-linux/TIEmu%203.03/tiemu-3.03-nogdb.tar.gz" +MD5SUM="2736440d717a0ee97cdb35189814fc93" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="libticalcs2" +MAINTAINER="shelldweller" +EMAIL="shelldweller@beauxbead.com" diff --git a/academic/tophat/slack-desc b/academic/tophat/slack-desc index 72180b86b6..22fb29099f 100644 --- a/academic/tophat/slack-desc +++ b/academic/tophat/slack-desc @@ -14,6 +14,6 @@ tophat: high-throughput short read aligner Bowtie, and then analyzes the tophat: mapping results to identify splice junctions between exons. tophat: tophat: Home: http://tophat.cbcb.umd.edu/ -tophat: References: /usr/doc/tophat-2.1.1/References +tophat: https://github.com/infphilo/tophat/ tophat: tophat: diff --git a/academic/tophat/tophat.SlackBuild b/academic/tophat/tophat.SlackBuild index e579ff1e9a..f32fb590f5 100644 --- a/academic/tophat/tophat.SlackBuild +++ b/academic/tophat/tophat.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for tophat -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2019 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,13 +23,13 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=tophat -VERSION=${VERSION:-2.1.1} +VERSION=${VERSION:-2.1.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -40,8 +40,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -69,6 +69,8 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +./autogen.sh + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ diff --git a/academic/tophat/tophat.info b/academic/tophat/tophat.info index 32ecba312c..f2fc213b90 100644 --- a/academic/tophat/tophat.info +++ b/academic/tophat/tophat.info @@ -1,8 +1,8 @@ PRGNAM="tophat" -VERSION="2.1.1" +VERSION="2.1.2" HOMEPAGE="http://ccb.jhu.edu/software/tophat/" -DOWNLOAD="http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz" -MD5SUM="4b2391de46457ba6b2b7268a9da593e4" +DOWNLOAD="https://github.com/infphilo/tophat/archive/v2.1.2/tophat-2.1.2.tar.gz" +MD5SUM="db844fd7f53c519e716cd6222e6195b2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/treebest-ensembl/README b/academic/treebest-ensembl/README new file mode 100644 index 0000000000..b6639d304d --- /dev/null +++ b/academic/treebest-ensembl/README @@ -0,0 +1,29 @@ +TreeBeST: Tree Building guided by Species Tree +(Ensembl Compara modifications) + +TreeBeST, which stands for (gene) Tree Building guided by Species Tree, +is a versatile program that builds, manipulates and displays +phylogenetic trees. It is particularly designed for building gene trees +with a known species tree and is highly efficient and accurate. + +TreeBeST is previously known as NJTREE. It has been largely used in the +TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting +group. + +This is the Ensembl Compara modifications version. The main new features +are: + +1) -s option in treebest sdi, to allow a user-defined species tree. + T node-tag in the NHX output: a bit-field listing the input trees +2) that support the node. +3) -I option in treebest nj, to carry on the T tags from the input tree +4) -Z option in treebest best, to redefine the PhyML variable MIN_DIFF_LK +5) -X option in treebest best, to give a higher weight to the likelihood + that comes from the reconciliation with the species tree (default 1) +6) -I option in treebest best, to start from the input tree instead of + building one +7) Species-intersection scores are now also reported as floating-point + values under the DCS node-tag. The value is between 0 and 1, and + displayed with 4 decimals. + +The script builds both the command line and GUI versions of treebest. diff --git a/academic/treebest-ensembl/doinst.sh b/academic/treebest-ensembl/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/treebest-ensembl/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/treebest-ensembl/slack-desc b/academic/treebest-ensembl/slack-desc new file mode 100644 index 0000000000..88564708b1 --- /dev/null +++ b/academic/treebest-ensembl/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------------------------------------------------------| +treebest-ensembl: treebest-ensembl (Tree Building guidEd by Species Tree) +treebest-ensembl: +treebest-ensembl: TreeBeST, which stands for (gene) Tree Building guided by Species +treebest-ensembl: Tree, is a versatile program that builds, manipulates and displays +treebest-ensembl: phylogenetic trees. It is particularly designed for building gene +treebest-ensembl: trees with a known species tree and is highly efficient and accurate. +treebest-ensembl: +treebest-ensembl: This is TreeBeST with Ensembl Compara modifications. +treebest-ensembl: +treebest-ensembl: http://treesoft.sourceforge.net/ +treebest-ensembl: https://github.com/Ensembl/treebest diff --git a/academic/treebest-ensembl/treebest-ensembl.SlackBuild b/academic/treebest-ensembl/treebest-ensembl.SlackBuild new file mode 100644 index 0000000000..b3a8844539 --- /dev/null +++ b/academic/treebest-ensembl/treebest-ensembl.SlackBuild @@ -0,0 +1,112 @@ +#!/bin/sh + +# Slackware build script for treebest + +# Copyright 2020 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. + +PRGNAM=treebest-ensembl +VERSION=${VERSION:-1.9.2_git347fa82} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=treebest +COMMIT=347fa82a0ce1c169849053fdc9ff7d19d221f290 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${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 $SRCNAM-$COMMIT +tar xvf $CWD/$SRCNAM-$COMMIT.tar.gz +cd $SRCNAM-$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 {} \; + +# Use our CFLAGS +sed -i "/^CFLAGS/s/=/+=/" Makefile + +# Make the CLI treebest and the FLTK GUI +CFLAGS="$SLKCFLAGS" \ +make + +CFLAGS="$SLKCFLAGS" \ +make fltreebest + +install -D -m755 treebest $PKG/usr/bin/treebest +install -D -m755 fltreebest $PKG/usr/bin/fltreebest +install -D -m755 make_ng86 $PKG/usr/bin/make_ng86 + +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 + +# Pack some exmples and scripts +mkdir -p $PKG/usr/share/$PRGNAM +cp -a examples scripts $PKG/usr/share/$PRGNAM + +# Use our icon +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/$SRCNAM.desktop $PKG/usr/share/applications +cp $CWD/$SRCNAM.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + ACKNOWLEDGEMENTS AUTHORS ChangeLog COPYING FUTURES INSTALL NEWS README.md treebest.texi \ + $PKG/usr/doc/$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:-tgz} diff --git a/academic/treebest-ensembl/treebest-ensembl.info b/academic/treebest-ensembl/treebest-ensembl.info new file mode 100644 index 0000000000..8e97295a93 --- /dev/null +++ b/academic/treebest-ensembl/treebest-ensembl.info @@ -0,0 +1,10 @@ +PRGNAM="treebest-ensembl" +VERSION="1.9.2_git347fa82" +HOMEPAGE="https://github.com/Ensembl/treebest/" +DOWNLOAD="https://github.com/Ensembl/treebest/archive/347fa82/treebest-347fa82a0ce1c169849053fdc9ff7d19d221f290.tar.gz" +MD5SUM="619622cadea6da5d9c74defa761cfdda" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="fltk" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/treebest-ensembl/treebest.desktop b/academic/treebest-ensembl/treebest.desktop new file mode 100644 index 0000000000..cff35dd7b0 --- /dev/null +++ b/academic/treebest-ensembl/treebest.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Categories=Education; +Comment=Tree Building guidEd by Species Tree +Exec=fltreebest +Icon=treebest +Name=FLTreeBeST +StartupNotify=false +Type=Application diff --git a/academic/treebest-ensembl/treebest.png b/academic/treebest-ensembl/treebest.png Binary files differnew file mode 100644 index 0000000000..e9b30dc447 --- /dev/null +++ b/academic/treebest-ensembl/treebest.png diff --git a/academic/treerecs/README b/academic/treerecs/README new file mode 100644 index 0000000000..e338496bfb --- /dev/null +++ b/academic/treerecs/README @@ -0,0 +1,37 @@ +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..ca63edaedc --- /dev/null +++ b/academic/treerecs/treerecs.SlackBuild @@ -0,0 +1,112 @@ +#!/bin/sh + +# Slackware build script for treerecs + +# Copyright 2020 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! + +PRGNAM=treerecs +VERSION=${VERSION:-1.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=Treerecs + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 {} \; + +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:-tgz} 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/README b/academic/treeviewx/README index 9e1dcb3422..218f85f4cf 100644 --- a/academic/treeviewx/README +++ b/academic/treeviewx/README @@ -15,7 +15,8 @@ Some of its features include: Note! This program is different from Michael Eisen's TreeView for matrix- -like display of expression data. +like display of expression data. Also, we build the sources distributed +by Debian. For details and citation: Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic diff --git a/academic/treeviewx/cstring.patch b/academic/treeviewx/cstring.patch deleted file mode 100644 index cae987703f..0000000000 --- a/academic/treeviewx/cstring.patch +++ /dev/null @@ -1,71 +0,0 @@ ---- tv-0.5.1/ncl-2.0/src/charactersblock.cpp.orig 2017-08-13 08:38:11.451581249 +0700 -+++ tv-0.5.1/ncl-2.0/src/charactersblock.cpp 2017-08-13 08:38:25.267599533 +0700 -@@ -8,6 +8,7 @@ - #include "discretematrix.h" - #include "assumptionsblock.h" - #include "charactersblock.h" -+#include <cstring> - - using namespace std; - ---- tv-0.5.1/ncl-2.0/src/nexus.cpp.orig 2017-08-13 08:40:07.443734383 +0700 -+++ tv-0.5.1/ncl-2.0/src/nexus.cpp 2017-08-13 08:40:17.625747774 +0700 -@@ -2,6 +2,7 @@ - #include "xnexus.h" - #include "nexustoken.h" - #include "nexus.h" -+#include <cstring> - - #define NCL_NAME_AND_VERSION "NCL version 2.01" - #define NCL_COPYRIGHT "Copyright (c) 2000 by Paul O. Lewis" ---- tv-0.5.1/ncl-2.0/src/nexustoken.cpp.orig 2017-08-13 08:41:41.569857692 +0700 -+++ tv-0.5.1/ncl-2.0/src/nexustoken.cpp 2017-08-13 08:41:52.463871895 +0700 -@@ -1,6 +1,7 @@ - #include "nexusdefs.h" - #include "xnexus.h" - #include "nexustoken.h" -+#include <cstring> - - using namespace std; - ---- tv-0.5.1/ncl-2.0/src/nxsstring.cpp.orig 2017-08-13 08:42:36.847929712 +0700 -+++ tv-0.5.1/ncl-2.0/src/nxsstring.cpp 2017-08-13 08:42:48.870945321 +0700 -@@ -20,6 +20,7 @@ - #include <stdio.h> - #include <assert.h> - #include <math.h> -+#include <cstring> - #include "nxsstring.h" - - nxsstring& nxsstring::operator+=( const double d ) ---- tv-0.5.1/TreeLib/Parse.cpp.orig 2017-08-13 08:43:50.188024809 +0700 -+++ tv-0.5.1/TreeLib/Parse.cpp 2017-08-13 08:44:00.407038015 +0700 -@@ -23,6 +23,7 @@ - - #include <ctype.h> - #include "Parse.h" -+#include <cstring> - - // Return the next token in the string - tokentype Parser::NextToken () ---- tv-0.5.1/TreeLib/TreeLib.cpp.orig 2017-08-13 08:45:24.898146879 +0700 -+++ tv-0.5.1/TreeLib/TreeLib.cpp 2017-08-13 08:45:33.518157938 +0700 -@@ -23,6 +23,7 @@ - - #include "TreeLib.h" - #include "Parse.h" -+#include <cstdlib> - - #include <vector> - ---- tv-0.5.1/TreeLib/treereader.cpp.orig 2017-08-13 08:47:09.041280171 +0700 -+++ tv-0.5.1/TreeLib/treereader.cpp 2017-08-13 08:51:04.192577614 +0700 -@@ -22,6 +22,8 @@ - // $Id: treereader.cpp,v 1.5 2003/09/10 12:58:16 rdmp1c Exp $ - - #include "treereader.h" -+#include <cstring> -+#include <stdlib.h> - - #if __MWERKS__ - #include <string.h> diff --git a/academic/treeviewx/slack-desc b/academic/treeviewx/slack-desc index 3d1a87af6b..7130ac2dc0 100644 --- a/academic/treeviewx/slack-desc +++ b/academic/treeviewx/slack-desc @@ -11,7 +11,7 @@ treeviewx: treeviewx: TreeView X provides a simple way to view the contents of a NEXUS, treeviewx: PHYLIP, Hennig86, Clustal, or other format tree file. treeviewx: -treeviewx: Home: http://code.google.com/p/treeviewx/ +treeviewx: treeviewx: treeviewx: treeviewx: diff --git a/academic/treeviewx/treeviewx.1 b/academic/treeviewx/treeviewx.1 new file mode 100644 index 0000000000..e286165f47 --- /dev/null +++ b/academic/treeviewx/treeviewx.1 @@ -0,0 +1,65 @@ +'\" t +.\" Title: TREEVIEW X +.\" Author: [see the "AUTHOR" section] +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/23/2011 +.\" Manual: User Manuals +.\" Source: TreeView X 0.5 +.\" Language: English +.\" +.TH "TREEVIEW X" "1" "06/23/2011" "TreeView X 0.5" "User Manuals" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +TreeView_X \- displays and prints phylogenetic trees +.SH "SYNOPSIS" +.HP \w'\fBtv\fR\ 'u +\fBtv\fR [\fIfilename\fR] +.SH "DESCRIPTION" +.PP +\fBtv\fR +is the program that starts the TreeView X GUI\&. +.PP +TreeView X is an open source and multi\-platform program to display phylogenetic trees\&. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE\-PUZZLE, and other programs)\&. It allows one to order the branches of the trees, and to export the trees in SVG format\&. +.PP +If started from the command line with +filename +as an argument, TreeView X will open the tree stored in +filename\&. +.SH "SEE ALSO" +.PP +At present there is is no documentation for TreeView X\&. In the meantime please see the online documentation for TreeView (remember that TreeView X has only a subset of the features of TreeView)\&. http://taxonomy\&.zoology\&.gla\&.ac\&.uk/rod/treeview/treeview_manual\&.html +.SH "REFERENCE" +.PP +Page, R\&. D\&. M\&. 1996\&. TREEVIEW: An application to display phylogenetic trees on personal computers\&. Computer Applications in the Biosciences 12: 357\-358\&. +.SH "AUTHOR" +.PP +TreeView X +was written by Rod Page (r\&.page@bio\&.gla\&.ac\&.uk) URL: http://darwin\&.zoology\&.gla\&.ac\&.uk/~rpage/treeviewx\&. +.PP +This manual page was written by Charles Plessy (plessy@debian\&.org) for the +Debian(TM) +system (but may be used by others)\&. +.PP +Permission is granted to copy, distribute and/or modify TreeView\ \&X and this document under the terms of the +GNU +General Public License, Version 2 or any later version published by the Free Software Foundation\&. +.PP +On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common\-licenses/GPL\-2\&. diff --git a/academic/treeviewx/treeviewx.SlackBuild b/academic/treeviewx/treeviewx.SlackBuild index f229fe052f..5929e48f2d 100644 --- a/academic/treeviewx/treeviewx.SlackBuild +++ b/academic/treeviewx/treeviewx.SlackBuild @@ -5,7 +5,7 @@ # Renamed to from "treeview" to "treeviewx" in 2018 to avoid confusion # with Michael Eisen's TreeView for matrix-like display of expression data. -# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -27,7 +27,9 @@ PRGNAM=treeviewx SRCNAM=tv -VERSION=${VERSION:-0.5.1} +SRCVER=0.5 +VERSION=${VERSION:-0.5.1_20100723} +SRCDATE=20100823 BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -63,9 +65,9 @@ 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 +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/${PRGNAM}_${SRCVER}.1+${SRCDATE}.orig.tar.gz +cd $SRCNAM-$SRCVER chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -78,8 +80,6 @@ find -L . \ # Then, of course comment the next line. sed "s:USE_SVG=1:USE_SVG=0:" -i configure -patch -p1 < $CWD/cstring.patch - CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS -fpermissive" \ ./configure \ @@ -93,9 +93,20 @@ CXXFLAGS="$SLKCFLAGS -fpermissive" \ make make install DESTDIR=$PKG +# Let's rename the executable +cd $PKG/usr/bin +mv $SRCNAM $PRGNAM +cd - + +# Thanks Debian for the man page +install -D -m644 $CWD/$PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.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/share/{applications,pixmaps} cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps diff --git a/academic/treeviewx/treeviewx.desktop b/academic/treeviewx/treeviewx.desktop index ab8e3727c3..2ef02ac0d0 100644 --- a/academic/treeviewx/treeviewx.desktop +++ b/academic/treeviewx/treeviewx.desktop @@ -1,6 +1,6 @@ [Desktop Entry] Categories=Education; -Exec=tv +Exec=treeviewx Icon=treeviewx Name=TreeView X StartupNotify=false diff --git a/academic/treeviewx/treeviewx.info b/academic/treeviewx/treeviewx.info index 09997ad2b9..8de22d44fb 100644 --- a/academic/treeviewx/treeviewx.info +++ b/academic/treeviewx/treeviewx.info @@ -1,8 +1,8 @@ PRGNAM="treeviewx" -VERSION="0.5.1" -HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/" -DOWNLOAD="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz" -MD5SUM="07e1ed8873c5f19ded7294668233bae1" +VERSION="0.5.1_20100723" +HOMEPAGE="https://github.com/rdmpage" +DOWNLOAD="http://deb.debian.org/debian/pool/main/t/treeviewx/treeviewx_0.5.1+20100823.orig.tar.gz" +MD5SUM="8059a306b723e6fb4d3befcf302b2920" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="wxPython" diff --git a/academic/trfind/trfind.SlackBuild b/academic/trfind/trfind.SlackBuild index 76783294e3..22702f68c8 100644 --- a/academic/trfind/trfind.SlackBuild +++ b/academic/trfind/trfind.SlackBuild @@ -23,16 +23,15 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=trfind -VERSION=${VERSION:-4.09} -BUILD=${BUILD:-2} +VERSION=${VERSION:-4.09.1} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -SRCNAM=trf -BINVER=409 +SRCNAM=TRF if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -43,30 +42,64 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -set -e - -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - -# Determine binary architecture -if [ "$ARCH" = "x86_64" ]; then - BINARCH="linux64" +if [ "$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 - BINARCH="linux32" + 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="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +make + +# "make install" works, but it is simpler this way +install -D -m755 src/trf $PKG/usr/bin/trf + +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 -D -m755 $CWD/${SRCNAM}${BINVER}.${BINARCH} $PKG/usr/bin/$SRCNAM +# Include FASTA examples, but let's compress the file first +mkdir -p $PKG/usr/share/$PRGNAM +gzip test_seqs.fasta +cp test_seqs.fasta.gz $PKG/usr/share/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README.md COPYING INSTALL history.txt \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References -cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/trfind/trfind.info b/academic/trfind/trfind.info index 2dfb07986d..adaf4da150 100644 --- a/academic/trfind/trfind.info +++ b/academic/trfind/trfind.info @@ -1,10 +1,10 @@ PRGNAM="trfind" -VERSION="4.09" +VERSION="4.09.1" HOMEPAGE="https://tandem.bu.edu/trf/trf.html" -DOWNLOAD="http://tandem.bu.edu/trf/downloads/trf409.linux32" -MD5SUM="285478f16f417d6e9c9700f556373e43" -DOWNLOAD_x86_64="http://tandem.bu.edu/trf/downloads/trf409.linux64" -MD5SUM_x86_64="0c594fe666e0332db1df9d160d7fabc8" +DOWNLOAD="https://github.com/Benson-Genomics-Lab/TRF/archive/v4.09.1/TRF-4.09.1.tar.gz" +MD5SUM="8569300f69776b65e22ad12caa682ab8" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/trimmomatic/trimmomatic.SlackBuild b/academic/trimmomatic/trimmomatic.SlackBuild index c419e77b89..0d97cfc60f 100644 --- a/academic/trimmomatic/trimmomatic.SlackBuild +++ b/academic/trimmomatic/trimmomatic.SlackBuild @@ -24,16 +24,16 @@ PRGNAM=trimmomatic ZIPNAM=Trimmomatic -VERSION=${VERSION:-0.38} +VERSION=${VERSION:-0.39} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} ARCH=noarch CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} # For consistency's sake, use this +TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} # Drop the package in /tmp +OUTPUT=${OUTPUT:-/tmp} set -e diff --git a/academic/trimmomatic/trimmomatic.info b/academic/trimmomatic/trimmomatic.info index b16aab676e..6c32699d20 100644 --- a/academic/trimmomatic/trimmomatic.info +++ b/academic/trimmomatic/trimmomatic.info @@ -1,8 +1,8 @@ PRGNAM="trimmomatic" -VERSION="0.38" +VERSION="0.39" HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic" -DOWNLOAD="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip" -MD5SUM="4b3df3caf7fe803ca54c79db1a99c464" +DOWNLOAD="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip" +MD5SUM="271ed9dca91132eee0c960e0ae487bcd" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="jdk" diff --git a/academic/tuxmath/README b/academic/tuxmath/README index 6f0d31eb6c..c41e37853f 100644 --- a/academic/tuxmath/README +++ b/academic/tuxmath/README @@ -1,4 +1,4 @@ -"Tux, of Math Command" (aka. tuxmath) is a math drill game starring Tux, -the Linux Penguin. Lessons are included from simple number typing through -addition, subtraction, multiplication, and division of positive and -negative numbers. It is intended for kids ~4-10. +"Tux, of Math Command" (aka. tuxmath) is a math drill game starring +Tux, the Linux Penguin. Lessons are included from simple number typing +through addition, subtraction, multiplication, and division of positive +and negative numbers. It is intended for kids ~4-10. diff --git a/academic/ugene/README b/academic/ugene/README index 515ecec210..de420023f9 100644 --- a/academic/ugene/README +++ b/academic/ugene/README @@ -35,7 +35,7 @@ program. All of them are available at SlackBuilds.org: - bedGraphToBigWig (Convert bedGraph to bigWig file) - bedtools (A powerful toolset for genome arithmetic) - bowtie (A short read aligner of DNA sequences) -- bowtie2-legacy (A tool for aligning sequencing reads) +- 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) @@ -52,6 +52,7 @@ program. All of them are available at SlackBuilds.org: - fastqc (A quality control tool for high throughput sequence data) - 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) - ncbi-blast+ (BLAST+ Command Line Applications) - PhyML (Phylogenetic estimation using Maximum Likelihood) diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild index c93a523b65..45a5a5885a 100644 --- a/academic/ugene/ugene.SlackBuild +++ b/academic/ugene/ugene.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for ugene -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=ugene -VERSION=${VERSION:-1.31.1} +VERSION=${VERSION:-35.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -79,7 +79,8 @@ sed -i "s:/share/man:/man:g" src/ugene_globals.pri qmake-qt5 $QMAKECONFIG -r \ QMAKE_CFLAGS="$SLKCFLAGS" \ -QMAKE_CXXFLAGS="$SLKCFLAGS" +QMAKE_CXXFLAGS="$SLKCFLAGS" \ +UGENE_EXCLUDE_LIST_ENABLED=1 make make install INSTALL_ROOT=$PKG diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info index 7f2ad37c91..e253011b26 100644 --- a/academic/ugene/ugene.info +++ b/academic/ugene/ugene.info @@ -1,8 +1,8 @@ PRGNAM="ugene" -VERSION="1.31.1" +VERSION="35.0" HOMEPAGE="http://ugene.net/" -DOWNLOAD="https://github.com/ugeneunipro/ugene/archive/1.31.1/ugene-1.31.1.tar.gz" -MD5SUM="ec32889089b7b9f6c6a9668aa56c198e" +DOWNLOAD="https://github.com/ugeneunipro/ugene/archive/35.0/ugene-35.0.tar.gz" +MD5SUM="c1cb1ee73140d09568706f1fc1b798dd" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="qt5-webkit" diff --git a/academic/umfpack/patches/autoconfiscate.diff b/academic/umfpack/patches/autoconfiscate.diff index 43f3515299..de66ade417 100644 --- a/academic/umfpack/patches/autoconfiscate.diff +++ b/academic/umfpack/patches/autoconfiscate.diff @@ -749,7 +749,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([UMFPACK],[5.7.8],[DrTimothyAldenDavis@gmail.com],[umfpack],[http://www.suitesparse.com/]) ++AC_INIT([UMFPACK],[5.7.9],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[umfpack],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Source/umfpack_solve.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) @@ -866,7 +866,7 @@ diff --git a/m4/ax_blas.m4 b/m4/ax_blas.m4 new file mode 100644 --- /dev/null +++ b/m4/ax_blas.m4 -@@ -0,0 +1,238 @@ +@@ -0,0 +1,241 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_blas.html +# =========================================================================== @@ -905,6 +905,7 @@ new file mode 100644 +# LICENSE +# +# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2019 Geoffrey M. Oxberry <goxberry@gmail.com> +# +# 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 @@ -932,7 +933,7 @@ new file mode 100644 +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + -+#serial 16 ++#serial 17 + +AU_ALIAS([ACX_BLAS], [AX_BLAS]) +AC_DEFUN([AX_BLAS], [ @@ -946,7 +947,9 @@ new file mode 100644 +case $with_blas in + yes | "") ;; + no) ax_blas_ok=disable ;; -+ -* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;; ++ -* | */* | *.a | *.so | *.so.* | *.dylib | *.dylib.* | *.o) ++ BLAS_LIBS="$with_blas" ++ ;; + *) BLAS_LIBS="-l$with_blas" ;; +esac + diff --git a/academic/umfpack/umfpack.SlackBuild b/academic/umfpack/umfpack.SlackBuild index 82a4eb2bb3..046a2501b6 100644 --- a/academic/umfpack/umfpack.SlackBuild +++ b/academic/umfpack/umfpack.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for UMFPACK -# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,9 +25,9 @@ PRGNAM=umfpack SRCNAM=SuiteSparse SUBDIR=UMFPACK -VERSION=${VERSION:-5.7.8} -SRCVER=${SRCVER:-5.4.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-5.7.9} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -70,9 +70,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM/$SUBDIR -cd $SRCNAM/$SUBDIR +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz $SRCNAM-$SRCVER/$SUBDIR +cd $SRCNAM-$SRCVER/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . diff --git a/academic/umfpack/umfpack.info b/academic/umfpack/umfpack.info index 7db842bf5e..9b8e8496a8 100644 --- a/academic/umfpack/umfpack.info +++ b/academic/umfpack/umfpack.info @@ -1,8 +1,8 @@ PRGNAM="umfpack" -VERSION="5.7.8" +VERSION="5.7.9" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="blas suitesparseconfig amd cholmod" diff --git a/academic/units/units.SlackBuild b/academic/units/units.SlackBuild index c1fb0bd111..188212ddbd 100644 --- a/academic/units/units.SlackBuild +++ b/academic/units/units.SlackBuild @@ -25,7 +25,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=units -VERSION=${VERSION:-2.18} +VERSION=${VERSION:-2.20} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/units/units.info b/academic/units/units.info index aeddc6debd..72cad5e9c9 100644 --- a/academic/units/units.info +++ b/academic/units/units.info @@ -1,8 +1,8 @@ PRGNAM="units" -VERSION="2.18" +VERSION="2.20" HOMEPAGE="https://www.gnu.org/software/units/" -DOWNLOAD="https://ftpmirror.gnu.org/units/units-2.18.tar.gz" -MD5SUM="402395abfc0cc3bba6a76ee4c118bc72" +DOWNLOAD="https://ftpmirror.gnu.org/units/units-2.20.tar.gz" +MD5SUM="28e2ba6fd2dbf056b7559e03c31577d5" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="Unidecode" diff --git a/academic/vCAPS_coevolution/README b/academic/vCAPS_coevolution/README new file mode 100644 index 0000000000..51350cd21e --- /dev/null +++ b/academic/vCAPS_coevolution/README @@ -0,0 +1,29 @@ +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. + +In addition, a test which assesses whether two proteins are interacting +is implemented. + +NOTE: +This applies an _unofficial_ patch by Petrov et al 2020, to enable more +verbose output of the program, including CAPS generated phylogenetic +trees and p-values of the pairwise results. The produced executable is +called "vCAPS" and can be installed along "caps" from CAPS_coevolution. +Building CAPS from source requires the Bio++ 1.9 suite. + +CITING: +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/caps_verbose.patch b/academic/vCAPS_coevolution/caps_verbose.patch new file mode 100644 index 0000000000..7f64d80f34 --- /dev/null +++ b/academic/vCAPS_coevolution/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/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..bdd3b3e794 --- /dev/null +++ b/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/sh + +# Slackware build script for vCAPS_coevolution + +# Copyright 2020 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. + +PRGNAM=vCAPS_coevolution +VERSION=${VERSION:-2.0_1UN} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=caps +SRCVER=2.0 +BINNAM=vCAPS + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# This is needed for vCAPS to find its libraries at runtime. Thanks Urachlay! +LIBDIRPATH="-Wl,-rpath,/usr/lib${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++ -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 unofficial patch +patch -p1 -i $CWD/caps_verbose.patch + +make all + +# Install the binary produced from our patched source, as "vCAPS" +install -D -m755 $BINNAM $PKG/usr/bin/$BINNAM + +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:-tgz} diff --git a/academic/vCAPS_coevolution/vCAPS_coevolution.info b/academic/vCAPS_coevolution/vCAPS_coevolution.info new file mode 100644 index 0000000000..84ebd91d4c --- /dev/null +++ b/academic/vCAPS_coevolution/vCAPS_coevolution.info @@ -0,0 +1,10 @@ +PRGNAM="vCAPS_coevolution" +VERSION="2.0_1UN" +HOMEPAGE="http://bioinf.gen.tcd.ie/~faresm/software/software.html" +DOWNLOAD="http://bioinf.gen.tcd.ie/~faresm/software/files/caps2_src.zip" +MD5SUM="0914007c32ed22a9cb8a47b55cd18a39" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp1.9-phyl" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/verilator/README b/academic/verilator/README new file mode 100644 index 0000000000..84c46a7177 --- /dev/null +++ b/academic/verilator/README @@ -0,0 +1,9 @@ +Installing gperftools may improve compilation performance, but is not +required. + +GTKWave is recommended for use at run-time, but not required. + +Verilator supports integration with SystemC. However I don't need this +for my use case so I ahve not enabled it. If someone else wants to do +the legwork of porting it, I will gladly make the changes to this port +to support it. -- Charles diff --git a/academic/verilator/slack-desc b/academic/verilator/slack-desc new file mode 100644 index 0000000000..1bb74ecb6d --- /dev/null +++ b/academic/verilator/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------------------------------------------------------| +verilator: verilator (the fastest free Verilog HDL simulator) +verilator: +verilator: Verilator is invoked with parameters similar to GCC or Synopsys’s VCS. +verilator: It "Verilates" the specified synthesizable Verilog or SystemVerilog +verilator: code by reading it, performing lint checks, and optionally inserting +verilator: assertion checks and coverage-analysis points. It outputs single- or +verilator: multi-threaded .cpp and .h files, the "Verilated" code. +verilator: +verilator: homepage: https://www.veripool.org/wiki/verilator +verilator: +verilator: diff --git a/academic/tabix/tabix.SlackBuild b/academic/verilator/verilator.SlackBuild index 017733aaa0..3b410de54d 100644 --- a/academic/tabix/tabix.SlackBuild +++ b/academic/verilator/verilator.SlackBuild @@ -1,8 +1,8 @@ #!/bin/sh -# Slackware build script for tabix +# Slackware build script for verilator -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2020 Charles Daniels, United States # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,14 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=tabix -VERSION=${VERSION:-0.2.6} +PRGNAM=verilator +VERSION=${VERSION:-4.030} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -40,8 +40,8 @@ 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" @@ -60,29 +60,28 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 +tar xvf $CWD/$PRGNAM-$VERSION.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 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ -make - -# Install executables -install -D -m755 tabix $PKG/usr/bin/tabix -install -D -m755 bgzip $PKG/usr/bin/bgzip +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux -# Place manpage -install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1 - -# Include examples -mkdir -p $PKG/usr/share/$PRGNAM -cp -a example.gtf.gz example.gtf.gz.tbi $PKG/usr/share/$PRGNAM +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 @@ -92,7 +91,7 @@ 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 \ - ChangeLog NEWS \ + LICENSE Changes Artistic README.adoc verilator.txt verilator.pdf \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/verilator/verilator.info b/academic/verilator/verilator.info new file mode 100644 index 0000000000..b67785a98d --- /dev/null +++ b/academic/verilator/verilator.info @@ -0,0 +1,10 @@ +PRGNAM="verilator" +VERSION="4.030" +HOMEPAGE="https://www.veripool.org/wiki/verilator" +DOWNLOAD="https://www.veripool.org/ftp/verilator-4.030.tgz" +MD5SUM="f412f817a8eeb142f6d27684e5fd4809" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3" +MAINTAINER="Charles Daniels" +EMAIL="charles [at] cdaniels [dot] net" diff --git a/academic/verilog/README b/academic/verilog/README index c8ebda2ee7..9df78abc32 100644 --- a/academic/verilog/README +++ b/academic/verilog/README @@ -1,5 +1,6 @@ -Icarus Verilog is a Verilog simulation and synthesis tool. It operates as -a compiler, compiling source code written in Verilog (IEEE-1364) into some -target format. For batch simulation, the compiler can generate an intermediate -form called vvp assembly. This intermediate form is executed by the 'vvp' -command. For synthesis, the compiler generates netlists in the desired format. +Icarus Verilog is a Verilog simulation and synthesis tool. It operates +as a compiler, compiling source code written in Verilog (IEEE-1364) +into some target format. For batch simulation, the compiler can +generate an intermediate form called vvp assembly. This intermediate +form is executed by the 'vvp' command. For synthesis, the compiler +generates netlists in the desired format. diff --git a/academic/veusz/README b/academic/veusz/README index 6699d7305a..f8e783a6ac 100644 --- a/academic/veusz/README +++ b/academic/veusz/README @@ -10,7 +10,13 @@ SAMP interfaces to its plotting facilities. It also allows for manipulation and editing of datasets. Data can be captured from external sources such as Internet sockets or other programs. -See the complete release notes for Veusz 3.0.1 at -https://veusz.github.io/releasenotes/3.0.1.txt +See the complete release notes for Veusz 3.3.1 at +https://veusz.github.io/releasenotes/3.3.1.txt Sphinx is an optional dependency (used to rebuild the manual). + +**** +Note: +The veusz.SlackBuild script moved from Python2 to Python3 in version +3.3.1. Please, check the dependencies. +**** diff --git a/academic/veusz/veusz.SlackBuild b/academic/veusz/veusz.SlackBuild index 119648fd3d..b11846a622 100644 --- a/academic/veusz/veusz.SlackBuild +++ b/academic/veusz/veusz.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for veusz # Based on Slackware 14.2 SlackBuild and Andrea Sciucca's SlackBuild for veusz # -# Copyright 2016-2018, Fellype do Nascimento, Campinas - Brazil +# Copyright 2016-2020, Fellype do Nascimento, Guaratingueta - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=veusz -VERSION=${VERSION:-3.0.1} +VERSION=${VERSION:-3.3.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -70,16 +70,15 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; PYTHONVER=$(python -V 2>&1 | cut -f 2 -d' ' | cut -f 1-2 -d.) -export SIP_EXE=/usr/bin/python2-sip -export SIP_INCLUDE_DIR="/usr/include/python$PYTHONVER/python2-sip" +export SIP_EXE=/usr/bin/python3-sip -python setup.py install --root $PKG +python3 setup.py install --root $PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING INSTALL README VERSION $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS ChangeLog COPYING INSTALL README.md VERSION $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cp Documents/manual/pdf/veusz.pdf $PKG/usr/doc/$PRGNAM-$VERSION @@ -94,8 +93,11 @@ done install -m 644 -p -D veusz.svg $PKG/usr/share/icons/hicolor/scalable/apps/veusz.svg cd - -# Installing desktop menu file +# Install support files install -m 644 -p -D support/veusz.desktop $PKG/usr/share/applications/veusz.desktop +install -m 644 -p -D support/veusz.appdata.xml $PKG/usr/share/appdata/veusz.appdata.xml +install -m 644 -p -D support/veusz.xml $PKG/usr/share/mime/packages/veusz.xml + mkdir -p $PKG/usr/man/man1 gzip Documents/man-page/veusz.1 > $PKG/usr/man/man1/veusz.1.gz diff --git a/academic/veusz/veusz.info b/academic/veusz/veusz.info index 9817f9df2f..eac4b5be7a 100644 --- a/academic/veusz/veusz.info +++ b/academic/veusz/veusz.info @@ -1,10 +1,10 @@ PRGNAM="veusz" -VERSION="3.0.1" +VERSION="3.3.1" HOMEPAGE="https://veusz.github.io/" -DOWNLOAD="https://github.com/veusz/veusz/releases/download/veusz-3.0.1/veusz-3.0.1.tar.gz" -MD5SUM="1d02f63a245d4cb0e2f343c628216f50" +DOWNLOAD="https://github.com/veusz/veusz/releases/download/veusz-3.3.1/veusz-3.3.1.tar.gz" +MD5SUM="1c7d42d6f87ea3b98fafc8dc52dbbc58" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="numpy PyQt5" +REQUIRES="numpy3 python3-PyQt5" MAINTAINER="Fellype do Nascimento" -EMAIL="fellype(at)gmail(dot)com" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/wehi-weasel/wehi-weasel b/academic/wehi-weasel/wehi-weasel index 994a389f76..f086e18ce9 100644 --- a/academic/wehi-weasel/wehi-weasel +++ b/academic/wehi-weasel/wehi-weasel @@ -3,4 +3,4 @@ # This starts the program jar file. The -Xmx1024m value indicates the # amount of RAM allocated to the program. You may wish to change this. -java -jar -Xmx1024m /usr/share/java/wehi-weasel/Weasel.jar +java -jar -Xmx2048m /opt/wehi-weasel/Weasel.jar diff --git a/academic/wehi-weasel/wehi-weasel.SlackBuild b/academic/wehi-weasel/wehi-weasel.SlackBuild index f4c57aa018..2eae95610b 100644 --- a/academic/wehi-weasel/wehi-weasel.SlackBuild +++ b/academic/wehi-weasel/wehi-weasel.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for wehi-weasel -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=wehi-weasel -VERSION=${VERSION:-3.5.0.17} +VERSION=${VERSION:-3.7.1.18} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -36,9 +36,9 @@ OUTPUT=${OUTPUT:-/tmp} SRCNAM=wsl JARNAM=Weasel -SRCVER=35017 +SRCVER=37118 SRCDIST=unix -LICENSE=Weaselv3_5Licence.doc +LICENSE=WeaselLicence.doc set -e @@ -57,10 +57,10 @@ find -L . \ # Copy the jar file and the icons. I am not sure the icons are needed # by the program at runtime, but it will not hurt to have them there. -mkdir -p $PKG/usr/share/java/$PRGNAM +mkdir -p $PKG/opt/$PRGNAM cp -a \ $JARNAM.jar WeaselIcon16.gif WeaselIcon32.gif WeaselIcon.ico \ - $PKG/usr/share/java/$PRGNAM + $PKG/opt/$PRGNAM # You may wish to check this simple wrapper for the amount of RAM that # is allocated to the program. diff --git a/academic/wehi-weasel/wehi-weasel.info b/academic/wehi-weasel/wehi-weasel.info index 09d8c3f621..11c1529672 100644 --- a/academic/wehi-weasel/wehi-weasel.info +++ b/academic/wehi-weasel/wehi-weasel.info @@ -1,8 +1,8 @@ PRGNAM="wehi-weasel" -VERSION="3.5.0.17" +VERSION="3.7.1.18" HOMEPAGE="http://www.frankbattye.com.au/Weasel/" DOWNLOAD="http://www.frankbattye.com.au/Weasel/WeaselDownload.html" -MD5SUM="72eaa148c7de13cf2fe1af659e783c57" +MD5SUM="d9154f7e71dbd1a8311f8cbd03b44090" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="jdk" diff --git a/academic/wmcalc/README b/academic/wmcalc/README index 6b8bee5461..b898b6bfce 100644 --- a/academic/wmcalc/README +++ b/academic/wmcalc/README @@ -1,6 +1,6 @@ wmcalc (calculator dockapp for windowmaker) -wmcalc is a program designed to act as a simple four-function calculator. -It is different from other calculator programs, however in that it is -designed to take up very little desktop space. As such, it can be left -running on the desktop at all times. +wmcalc is a program designed to act as a simple four-function +calculator. It is different from other calculator programs, however +in that it is designed to take up very little desktop space. As such, +it can be left running on the desktop at all times. diff --git a/academic/wxMaxima/slack-desc b/academic/wxMaxima/slack-desc index 9ae6f3b3ff..5fe290b31d 100644 --- a/academic/wxMaxima/slack-desc +++ b/academic/wxMaxima/slack-desc @@ -11,7 +11,7 @@ wxMaxima: wxMaxima: wxMaxima is a cross platform GUI for the computer algebra system wxMaxima: Maxima based on wxWidgets. wxMaxima: -wxMaxima: Homepage: https://andrejv.github.io/wxmaxima/ +wxMaxima: Homepage: https://wxmaxima-developers.github.io/wxmaxima/ wxMaxima: wxMaxima: wxMaxima: diff --git a/academic/wxMaxima/wxMaxima.SlackBuild b/academic/wxMaxima/wxMaxima.SlackBuild index fb42b15df6..80b7aa18e0 100644 --- a/academic/wxMaxima/wxMaxima.SlackBuild +++ b/academic/wxMaxima/wxMaxima.SlackBuild @@ -22,15 +22,17 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# Mar 2021 - updated for v. 21.01, Judah Milgram, milgram at cgpp com + PRGNAM=wxMaxima SRCNAM=wxmaxima -VERSION=${VERSION:-16.04.2} +VERSION=${VERSION:-21.01.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -41,8 +43,8 @@ TMP=${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" @@ -60,9 +62,9 @@ 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 +rm -rf $SRCNAM-Version-$VERSION +tar xvf $CWD/Version-$VERSION.tar.gz +cd $SRCNAM-Version-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -70,44 +72,33 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Fix man directory. -sed -i '/^mandatadir/s|=.*|= \$(mandir)|' data/Makefile* -#Fix end-of-line encoding. -for i in art/*.txt; do - sed -e 's/\r//' $i > ${i}.new - touch -r $i ${i}.new - mv ${i}.new $i -done - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --disable-dependency-tracking \ - --disable-silent-rules \ - --enable-printing \ - --build=$ARCH-slackware-linux - -make -make allmo -make install DESTDIR=$PKG +BUILDDIR=build +mkdir -p $BUILDDIR + +export PATH="/opt/cmake-202x/bin:$PATH" +cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=$PKG/usr \ + -DCMAKE_BUILD_TYPE=Release \ + -G Ninja -S . -B $BUILDDIR +cmake --build $BUILDDIR +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 +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 -rm -f $PKG/usr/info/dir -gzip -9 $PKG/usr/info/*.info* - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING README.md art/*.txt $PKG/usr/doc/$PRGNAM-$VERSION -rm -f $PKG/usr/share/$PRGNAM/{COPYING,README} +mkdir $PKG/usr/doc +mv $PKG/usr/share/doc/$SRCNAM $PKG/usr/doc/$PRGNAM-$VERSION +rmdir $PKG/usr/share/doc cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/examples +cp -a examples/*.wxm $PKG/usr/doc/$PRGNAM-$VERSION/examples + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh diff --git a/academic/wxMaxima/wxMaxima.info b/academic/wxMaxima/wxMaxima.info index 2c1f2c97d3..a67cce8f49 100644 --- a/academic/wxMaxima/wxMaxima.info +++ b/academic/wxMaxima/wxMaxima.info @@ -1,10 +1,10 @@ PRGNAM="wxMaxima" -VERSION="16.04.2" -HOMEPAGE="https://andrejv.github.io/wxmaxima/" -DOWNLOAD="http://downloads.sourceforge.net/wxmaxima/wxmaxima-16.04.2.tar.gz" -MD5SUM="6d98324d70115615e7b4f7413b594dd5" +VERSION="21.01.0" +HOMEPAGE="https://wxmaxima-developers.github.io/wxmaxima/" +DOWNLOAD="https://github.com/wxMaxima-developers/wxmaxima/archive/Version-21.01.0.tar.gz" +MD5SUM="2c9b97c786806172aa6ed000784e995e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="maxima wxGTK3" +REQUIRES="maxima wxGTK3 cmake-202x ninja" MAINTAINER="Larry Hajali" EMAIL="larryhaja[at]gmail[dot]com" diff --git a/academic/xcircuit/xcircuit.info b/academic/xcircuit/xcircuit.info index 744304aa74..02b589bf38 100644 --- a/academic/xcircuit/xcircuit.info +++ b/academic/xcircuit/xcircuit.info @@ -6,5 +6,5 @@ MD5SUM="25e60837e5db6b4ff71615505493a481" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="B. Jogai" -EMAIL="jogaib <at> comcast {dot} net" +MAINTAINER="Glenn Becker" +EMAIL="glenn.becker@gmail.com" diff --git a/academic/xephem/README b/academic/xephem/README index ab546d369a..fb0bde75c4 100644 --- a/academic/xephem/README +++ b/academic/xephem/README @@ -1,6 +1,7 @@ xephem - Astronomy program -xephem is a scientific-grade interactive astronomical ephemeris software -package for UNIX-like* systems. +xephem is a scientific-grade interactive astronomical ephemeris +software package for UNIX-like* systems. -Note that this is not free software: read the license agreement carefully. +Note that this is not free software: read the license agreement +carefully. diff --git a/academic/xflr5/link_directly.patch b/academic/xflr5/link_directly.patch new file mode 100644 index 0000000000..722a238556 --- /dev/null +++ b/academic/xflr5/link_directly.patch @@ -0,0 +1,13 @@ +--- 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/xflr5.SlackBuild b/academic/xflr5/xflr5.SlackBuild index 1e20a40f35..48a6186c63 100644 --- a/academic/xflr5/xflr5.SlackBuild +++ b/academic/xflr5/xflr5.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for xflr5 -# Copyright 2018 Daniel Prosser, Lexington Park, MD, USA +# Copyright 2020 Daniel Prosser, Lexington Park, MD, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=xflr5 -VERSION=${VERSION:-6.42} +VERSION=${VERSION:-6.47} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -60,7 +60,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM -tar xvf $CWD/${PRGNAM}_${VERSION}_src.tar.gz +tar xvf $CWD/${PRGNAM}_v${VERSION}_src.tar.gz cd $PRGNAM chown -R root:root . find -L . \ @@ -70,11 +70,14 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Change default path for libraries installation -sed -i "s/target\.path = \/usr\/local\/lib/target\.path = \/usr\/lib${LIBDIRSUFFIX}/g" \ +sed -i "s/target\.path = \$\$PREFIX\/lib/target\.path = \$\$PREFIX\/lib${LIBDIRSUFFIX}/g" \ XFoil-lib/XFoil-lib.pro -sed -i "s/target\.path = \/usr\/local\/lib/target\.path = \/usr\/lib${LIBDIRSUFFIX}/g" \ +sed -i "s/target\.path = \$\$PREFIX\/lib/target\.path = \$\$PREFIX\/lib${LIBDIRSUFFIX}/g" \ xflr5-engine/xflr5-engine.pro +# Fix linking +patch -p0 < $CWD/link_directly.patch + qmake-qt5 \ PREFIX=/usr \ QMAKE_CFLAGS+="$SLKCFLAGS" \ diff --git a/academic/xflr5/xflr5.info b/academic/xflr5/xflr5.info index b9ad0e8653..8fff4322ae 100644 --- a/academic/xflr5/xflr5.info +++ b/academic/xflr5/xflr5.info @@ -1,8 +1,8 @@ PRGNAM="xflr5" -VERSION="6.42" +VERSION="6.47" HOMEPAGE="http://www.xflr5.com/xflr5.htm" -DOWNLOAD="https://phoenixnap.dl.sourceforge.net/project/xflr5/6.42/xflr5_6.42_src.tar.gz" -MD5SUM="ec1586f2257ef82921500c888686dcd9" +DOWNLOAD="https://ayera.dl.sourceforge.net/project/xflr5/6.47/xflr5_v6.47_src.tar.gz" +MD5SUM="272484cc3fe077af31bbe2ad7ef4205b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="qt5" diff --git a/academic/xfoil/README b/academic/xfoil/README index c9bb85dfea..6eb218961a 100644 --- a/academic/xfoil/README +++ b/academic/xfoil/README @@ -1,7 +1,8 @@ -XFOIL is an interactive program for the design and analysis of subsonic isolated -airfoils. It consists of a collection of menu-driven routines which perform -various useful functions, such as viscous (or inviscid) analysis of an existing -airfoil, airfoil design and redesign by interactive modification of surface -speed distributions or geometric parameters, blending of airfoils, writing and -reading of airfoil coordinates and polar save files, and plotting of geometry, -pressure distributions, and multiple polars. +XFOIL is an interactive program for the design and analysis of subsonic +isolated airfoils. It consists of a collection of menu-driven routines +which perform various useful functions, such as viscous (or inviscid) +analysis of an existing airfoil, airfoil design and redesign by +interactive modification of surface speed distributions or geometric +parameters, blending of airfoils, writing and reading of airfoil +coordinates and polar save files, and plotting of geometry, pressure +distributions, and multiple polars. diff --git a/academic/xiphos/README b/academic/xiphos/README index 1860dba832..166b55e9b6 100644 --- a/academic/xiphos/README +++ b/academic/xiphos/README @@ -2,27 +2,15 @@ xiphos (formerly gnomesword. A bible study application) Xiphos is a bible study program for GNOME. Xiphos is based on the Sword project by the CrossWire Bible Society. -computer reading of the text using festival has not been tested. -if it works let me know, and i'll remove these two lines from the readme. +computer reading of the text using festival has not been tested. if +it works let me know, and i'll remove these two lines from the readme. -if you pass the variable WK2=yes to the build script, the dependencies -change slightly. instead of webkitgtk3, webkit2gtk and gtkhtml (v4) are -required. +xiphos version 4.2.1 requires sword v1.8.1-3 or higher +and biblesync v2.0.1 or higher -note: End program differences between webkit and webkit2 versions. -webkit: - studypad is missing the image for the "bold" text button (but it works) - reported not to work with current -webkit2: - studypad has an "add emoticon" button, but the images included are not -found, so an empty imagebox is added in the text if you try to add an icon. - a few warnings shown on compile (but seems to work just fine). - try this one for current. if it works, let me know, and I might change - the default to WK2 :-). - -For both versions, there is an issue where if the previewer is in the sidebar, -text is offset to the left, so you can't see the first 2 characters of each -line. This can be fixed by making the sidebar a little bit wider. - -Note. xiphos version 4.1.0 requires sword v1.8 or higher -and biblesync v1.2 or higher +xiphos needs a version of cmake 3.11 or higher. A private version is +included in the slackbuild to enable xiphos to be built. If you want to +use a different cmake to that included here, pass CMVERSION with the +version you need (and make sure that the source tar.gz is available) +There are a few new dependencies as the documentation is now created by +the build process rather than shipped preprocessed in the source. diff --git a/academic/xiphos/xiphos.SlackBuild b/academic/xiphos/xiphos.SlackBuild index cd9533ba6f..f1f484b971 100644 --- a/academic/xiphos/xiphos.SlackBuild +++ b/academic/xiphos/xiphos.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for xiphos -# Copyright 2015-2018 Tim Dickson, email: dickson.tim@googlemail.com +# Copyright 2015-2020 Tim Dickson, email: dickson.tim@googlemail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,13 +23,10 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=xiphos -VERSION=${VERSION:-4.1.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-4.2.1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} -#if WK2 is yes use webkit2. this requires webkit2gtk and gtkhtml (v4) instead of webkitgtk3 -WK2=${WK2:-no} - if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -65,45 +62,51 @@ cd $TMP rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION + +#we will use a newer version of cmake (at least 3.11) + +#sane permissions for everything chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ -o -perm 511 \) -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 {} \; - -./waf distclean +# +#lets make newer cmake available to the xiphos build +OLDPATH=$PATH +export PATH=/opt/cmake-202x/bin:$PATH # patch navbar_versekey.gtkbuilder to work with gtk shipped with slackware 14.2 # patch won't be needed for slackware 15 sed -i "s/3.20/3.14/g" ui/navbar_versekey.gtkbuilder -if [ "x$WK2" = "xyes" ]; then - CFLAGS="$SLKCFLAGS" \ - CXXFLAGS="$SLKCFLAGS" \ - ./waf configure \ - --prefix=/usr \ - --enable-webkit2 \ - --gtk=3 - # --disable-dbus - # --gtk=2 doesn't work with webkitgtk as gtk2 is disabled -else - CFLAGS="$SLKCFLAGS" \ - CXXFLAGS="$SLKCFLAGS" \ - ./waf configure \ - --prefix=/usr \ - --enable-webkit-editor \ - --gtk=3 - # --disable-dbus - # --gtk=2 doesn't work with webkitgtk as gtk2 is disabled -fi - -./waf build -./waf install --destdir=$PKG - +mkdir -p build +cd build +export "PATH=/opt/cmake-202x/bin:$PATH" +cmake -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DCMAKE_INSTALL_MANDIR=man \ + -DHTMLHELP=ON \ + -DCMAKE_BUILD_TYPE=Release \ + -DDBUS=OFF -DSTRIP=ON -DPOSTINST=OFF -DGTKHTML=ON .. + +#cmake should have created make file so restore PATH +export PATH=$OLDPATH +make +make install DESTDIR=$PKG +cd .. + +#output should be stripped but we just make sure.. 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 +#compress man pages. +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 mv $PKG/usr/share/doc/$PRGNAM/* $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/xiphos/xiphos.info b/academic/xiphos/xiphos.info index d2cd894617..1fa129b3f2 100644 --- a/academic/xiphos/xiphos.info +++ b/academic/xiphos/xiphos.info @@ -1,10 +1,10 @@ PRGNAM="xiphos" -VERSION="4.1.0" +VERSION="4.2.1" HOMEPAGE="http://xiphos.org" -DOWNLOAD="https://github.com/crosswire/xiphos/releases/download/4.1.0/xiphos-4.1.0.tar.gz" -MD5SUM="f40c5b249c50a49af71de94420ee720d" +DOWNLOAD="https://github.com/crosswire/xiphos/releases/download/4.2.1/xiphos-4.2.1.tar.gz" +MD5SUM="77d8a99c063433bea3006954710b2fd5" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="sword webkitgtk3 biblesync rarian %README%" +REQUIRES="sword webkitgtk3 biblesync rarian gtkhtml libminizip appstream-glib yelp cmake-202x" MAINTAINER="Tim Dickson" EMAIL="dickson.tim@googlemail.com" diff --git a/academic/z3/README b/academic/z3/README new file mode 100644 index 0000000000..a1f132277a --- /dev/null +++ b/academic/z3/README @@ -0,0 +1,12 @@ +Z3 is an automated theorem prover and satisfiability modulo theories +(SMT) solver. Given a formula in first-order logic, it attempts to +either prove the formula or find a counterexample. Z3 supports +arithmetic, reasoning about arrays, and several other built-in +theories. Input problems are written in SMT-LIB format. + +This package includes the z3 program as well as the C++ and +Python APIs. By default the Python 2 version of the API is built; +if you also want the Python 3 version, run the SlackBuild with +PYTHON3=yes, like so: + + PYTHON3=yes ./z3.SlackBuild diff --git a/academic/z3/slack-desc b/academic/z3/slack-desc new file mode 100644 index 0000000000..e389de655a --- /dev/null +++ b/academic/z3/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------------------------------------------------------| +z3: z3 (a first-order theorem prover and SMT solver) +z3: +z3: Z3 is an automated theorem prover and satisfiability modulo theories +z3: (SMT) solver. Given a formula in first-order logic, it attempts to +z3: either prove the formula or find a counterexample. Z3 supports +z3: arithmetic, reasoning about arrays, and several other built-in +z3: theories. Input problems are written in SMT-LIB format. +z3: +z3: This package includes the z3 program as well as C++ and Python APIs. +z3: +z3: Homepage: https://github.com/Z3Prover/z3/wiki diff --git a/academic/z3/z3.SlackBuild b/academic/z3/z3.SlackBuild new file mode 100644 index 0000000000..741a7c6e4a --- /dev/null +++ b/academic/z3/z3.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/sh + +# Slackware build script for z3 + +# Copyright 2019 Nick Smallbone, Gothenburg, Sweden +# 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. + +PRGNAM=z3 +VERSION=${VERSION:-4.8.7} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${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 +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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +Z3_INSTALL_LIB_DIR=lib${LIBDIRSUFFIX} \ +./configure \ + --prefix=/usr \ + --python + +cd build +make +make install DESTDIR=$PKG +cd ../doc +python mk_api_doc.py +cd .. + +if [ z$PYTHON3 = zyes ]; then + # Copy the Python bindings to python3.X/site-packages. + PYTHON_VERSION=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') + PYLIB=$PKG/usr/lib${LIBDIRSUFFIX}/python${PYTHON_VERSION}/site-packages + mkdir -p $PYLIB + cp -a build/python/z3 $PYLIB/z3 + find $PYLIB/z3 -name '*.pyc' -delete +fi + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README.md RELEASE_NOTES LICENSE.txt \ + $PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/examples +cp -a \ + examples/c examples/c++ examples/maxsat examples/python examples/tptp \ + $PKG/usr/doc/$PRGNAM-$VERSION/examples +find $PKG/usr/doc/$PRGNAM-$VERSION/examples -name CMakeLists.txt -delete +cp -a \ + doc/api/html \ + $PKG/usr/doc/$PRGNAM-$VERSION/api +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.${PKGTYPE:-tgz} diff --git a/academic/z3/z3.info b/academic/z3/z3.info new file mode 100644 index 0000000000..71512a125f --- /dev/null +++ b/academic/z3/z3.info @@ -0,0 +1,10 @@ +PRGNAM="z3" +VERSION="4.8.7" +HOMEPAGE="https://github.com/Z3Prover/z3/wiki" +DOWNLOAD="https://github.com/Z3Prover/z3/archive/z3-4.8.7.tar.gz" +MD5SUM="18e7332ab136c1d8686ea719ed7107ed" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Nick Smallbone" +EMAIL="nick@smallbone.se" diff --git a/academic/zotero/slack-desc b/academic/zotero/slack-desc index 07b232a414..d051f78252 100644 --- a/academic/zotero/slack-desc +++ b/academic/zotero/slack-desc @@ -16,4 +16,4 @@ zotero: anything else. Zotero automatically indexes the full-text content zotero: of your library, enabling you to find exactly what you are looking zotero: for with just a few keystrokes. zotero: -zotero: Home: https://www.zotero.org/ +zotero: Homepage: https://www.zotero.org/ diff --git a/academic/zotero/zotero.SlackBuild b/academic/zotero/zotero.SlackBuild index 7bced4ed9b..8ad1d6a014 100644 --- a/academic/zotero/zotero.SlackBuild +++ b/academic/zotero/zotero.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for zotero -# Copyright 2018 Andrew Payne phalange@komputermatrix.com +# Copyright 2018-2020 Andrew Payne phalange@komputermatrix.com # Copyright 2014-2018 Petar Petrov slackalaxy@gmail.com # All rights reserved. # @@ -25,7 +25,7 @@ PRGNAM=zotero SRCNAM=Zotero -VERSION=${VERSION:-5.0.58} +VERSION=${VERSION:-5.0.85} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/zotero/zotero.info b/academic/zotero/zotero.info index b883696f17..564a6702dd 100644 --- a/academic/zotero/zotero.info +++ b/academic/zotero/zotero.info @@ -1,10 +1,10 @@ PRGNAM="zotero" -VERSION="5.0.58" +VERSION="5.0.85" HOMEPAGE="https://www.zotero.org/" -DOWNLOAD="https://download.zotero.org/client/release/5.0.58/Zotero-5.0.58_linux-i686.tar.bz2" -MD5SUM="460284aacf6958b0ec7bbf3a0af02547" -DOWNLOAD_x86_64="https://download.zotero.org/client/release/5.0.58/Zotero-5.0.58_linux-x86_64.tar.bz2" -MD5SUM_x86_64="eb3f3dcab8bbbcbd31f44da9e558a0e0" +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" REQUIRES="" MAINTAINER="Andrew Payne" EMAIL="phalange@komputermatrix.com" |
