diff options
Diffstat (limited to 'academic')
391 files changed, 5193 insertions, 1810 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/FreeFem/README b/academic/FreeFem/README index 99703a0063..c9a6765f55 100644 --- a/academic/FreeFem/README +++ b/academic/FreeFem/README @@ -1,12 +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 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. +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/Gridcoin-Research/Gridcoin-Research.SlackBuild b/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild index 6010e6a9ab..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 2018-2019 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 @@ -23,9 +23,10 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=Gridcoin-Research -VERSION=${VERSION:-4.0.6.0} +VERSION=${VERSION:-5.3.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +NUMJOBS=${NUMJOBS:-1} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -92,12 +93,12 @@ CXXFLAGS="$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 \ @@ -119,7 +120,7 @@ cp -a $TMP/$PRGNAM-$VERSION/share/pixmaps/* $PKG/usr/share/pixmaps mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/doc 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 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 47125005f4..a3675fa047 100644 --- a/academic/Gridcoin-Research/Gridcoin-Research.info +++ b/academic/Gridcoin-Research/Gridcoin-Research.info @@ -1,8 +1,8 @@ PRGNAM="Gridcoin-Research" -VERSION="4.0.6.0" +VERSION="5.3.1.0" HOMEPAGE="https://gridcoin.us/" -DOWNLOAD="https://github.com/gridcoin-community/Gridcoin-Research/archive/4.0.6.0/Gridcoin-Research-4.0.6.0.tar.gz" -MD5SUM="6c924899a3a75f0c072fb3e0a8d64b4f" +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/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=$HOME/.boinc_data/ +#boincdatadir=/var/lib/boinc-client/ + +## macOS +#boincdatadir=/Library/Application Support/BOINC Data/ ############################################################################# ######################## Optional Network settings ########################## ############################################################################# -## Maximum number of inbound+outbound connections.Default 125 -maxconnections=125 -## Maximum number of outbound connections.Default 8 -maxoutboundconnections=8 +## Maximum number of inbound+outbound connections. Default 125 +#maxconnections=125 +## Maximum number of outbound connections. Default 8 +#maxoutboundconnections=8 ## Manually Set-up Ports #upnp=false #externalip=<Your IP Address> -#port=32748
\ No newline at end of file + +############################################################################# +############################## Other Entries ################################ +############################################################################# + +## See detailed Other Entries description section below. + +#debug=true +#debug=<category> + +#enablestakesplit=1 +#stakingefficiency=<percentage between 75 and 98, defaults to 90> +#minstakesplitvalue=<value in GRC, minimum and defaults to 800> + +#enablesidestaking=1 +#sidestake=<address>,<allocation percentage> diff --git a/academic/HMMER/HMMER.SlackBuild b/academic/HMMER/HMMER.SlackBuild index 6fc40670d6..e0e4f5bfcf 100644 --- a/academic/HMMER/HMMER.SlackBuild +++ b/academic/HMMER/HMMER.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for HMMER -# Copyright 2016-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=HMMER -VERSION=${VERSION:-3.3} +VERSION=${VERSION:-3.3.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/HMMER/HMMER.info b/academic/HMMER/HMMER.info index f7a4d2d81d..80f7a1ebe5 100644 --- a/academic/HMMER/HMMER.info +++ b/academic/HMMER/HMMER.info @@ -1,8 +1,8 @@ PRGNAM="HMMER" -VERSION="3.3" +VERSION="3.3.1" HOMEPAGE="http://hmmer.org/" -DOWNLOAD="http://eddylab.org/software/hmmer/hmmer-3.3.tar.gz" -MD5SUM="507849e98a5a44b22f2c4a1cf192b36b" +DOWNLOAD="http://eddylab.org/software/hmmer/hmmer-3.3.1.tar.gz" +MD5SUM="07da6661a17bd4ddbaded4a0dc9c5b6d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="python3" diff --git a/academic/IGV/IGV.SlackBuild b/academic/IGV/IGV.SlackBuild new file mode 100644 index 0000000000..746d394ea4 --- /dev/null +++ b/academic/IGV/IGV.SlackBuild @@ -0,0 +1,84 @@ +#!/bin/sh + +# Slackware build script for IGV + +# Copyright 2020 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=IGV +VERSION=${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 afeb3068c8..fd9e8128f0 100644 --- a/academic/ITK/ITK.SlackBuild +++ b/academic/ITK/ITK.SlackBuild @@ -2,7 +2,7 @@ # SlackBuild script for ITK -# Copyright 2018-2019 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:-4.13.2} +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 . \ @@ -75,51 +75,28 @@ find -L . \ sed -i "s/lib\b/lib${LIBDIRSUFFIX}/" CMakeLists.txt sed -i "s|/opj_config.h|& \$\{CMAKE_CURRENT_BINARY_DIR\}/openjpeg_mangle.h|" \ Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeLists.txt -patch -p1 <<'endpatch' -diff --git a/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h b/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h -index 4865361421e..220b9cd49a8 100644 ---- a/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h -+++ b/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h -@@ -97,6 +97,17 @@ - # else - # define VCL_GCC_80 - # endif -+# elif (__GNUC__==9) -+# define VCL_GCC_9 -+# if (__GNUC_MINOR__ > 2 ) -+# define VCL_GCC_93 -+# elif (__GNUC_MINOR__ > 1 ) -+# define VCL_GCC_92 -+# elif (__GNUC_MINOR__ > 0 ) -+# define VCL_GCC_91 -+# else -+# define VCL_GCC_90 -+# endif - # else - # error "Dunno about this gcc" - # endif -endpatch mkdir -p build cd build + export "PATH=/opt/cmake-202x/bin:$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 d72260cfa6..9479aaaac9 100644 --- a/academic/ITK/ITK.info +++ b/academic/ITK/ITK.info @@ -1,10 +1,10 @@ PRGNAM="ITK" -VERSION="4.13.2" +VERSION="5.1.2" HOMEPAGE="https://itk.org" -DOWNLOAD="https://github.com/InsightSoftwareConsortium/ITK/releases/download/v4.13.2/InsightToolkit-4.13.2.tar.xz" -MD5SUM="d140ddabe22428e86bc5053e0d268872" +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/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/README b/academic/MetaPhlAn2/README index 15d1bc4265..55665c56e1 100644 --- a/academic/MetaPhlAn2/README +++ b/academic/MetaPhlAn2/README @@ -12,7 +12,7 @@ archaeal and ~500 eukaryotic), allowing: * unambiguous taxonomic assignments; * accurate estimation of organismal relative abundance; -* species-level resolution for bacteria, archaea, eukaryotes and viruses; +* 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 diff --git a/academic/Mnemosyne/README b/academic/Mnemosyne/README index 6149871479..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 using LaTeX) +Optional Dependency: texlive (for entering mathematical equations in +cards using LaTeX) diff --git a/academic/OpenFOAM/OpenFOAM.SlackBuild b/academic/OpenFOAM/OpenFOAM.SlackBuild index 94b7b00d56..14db243780 100644 --- a/academic/OpenFOAM/OpenFOAM.SlackBuild +++ b/academic/OpenFOAM/OpenFOAM.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for OpenFOAM -# Copyright 2017, 2018, 2019 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:-7} +VERSION=${VERSION:-8} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/OpenFOAM/OpenFOAM.info b/academic/OpenFOAM/OpenFOAM.info index 4ca7458532..df75c6f7c1 100644 --- a/academic/OpenFOAM/OpenFOAM.info +++ b/academic/OpenFOAM/OpenFOAM.info @@ -1,10 +1,10 @@ PRGNAM="OpenFOAM" -VERSION="7" +VERSION="8" HOMEPAGE="https://openfoam.org/" -DOWNLOAD="https://github.com/OpenFOAM/OpenFOAM-7/archive/version-7/OpenFOAM-7-version-7.tar.gz \ - https://github.com/OpenFOAM/ThirdParty-7/archive/version-7/ThirdParty-7-version-7.tar.gz" -MD5SUM="638b38ae0e80cbb1201abec3f5c88641 \ - 2a4fe46807730e70ce0b81d4a4dd4fc8" +DOWNLOAD="https://github.com/OpenFOAM/OpenFOAM-8/archive/version-8/OpenFOAM-8-version-8.tar.gz \ + https://github.com/OpenFOAM/ThirdParty-8/archive/version-8/ThirdParty-8-version-8.tar.gz" +MD5SUM="261dc0d01c4417b737487a60ab4784aa \ + a1beb9f9ce9ca547cd458ec6c1472bcd" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi CGAL" diff --git a/academic/OpenFOAM/OpenFOAM.sh b/academic/OpenFOAM/OpenFOAM.sh index e6164c0869..a4e69f6d1e 100644 --- a/academic/OpenFOAM/OpenFOAM.sh +++ b/academic/OpenFOAM/OpenFOAM.sh @@ -1 +1 @@ -. /opt/OpenFOAM/OpenFOAM-7/etc/bashrc +. /opt/OpenFOAM/OpenFOAM-8/etc/bashrc diff --git a/academic/OpenFOAM/README b/academic/OpenFOAM/README index fd23aef9b7..d91ec421c8 100644 --- a/academic/OpenFOAM/README +++ b/academic/OpenFOAM/README @@ -9,4 +9,5 @@ multi-core processors and multi-processor computers. Optional dependency: graphviz (for documentation with graphs) -You can build with multiple jobs by setting the MAKEFLAGS environment variable. +You can build with multiple jobs by setting the MAKEFLAGS environment +variable. diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild index bddb063c00..893454e123 100644 --- a/academic/PhyML/PhyML.SlackBuild +++ b/academic/PhyML/PhyML.SlackBuild @@ -25,7 +25,7 @@ # Thanks to Niels Horn for some handy modifications and corrections. PRGNAM=PhyML -VERSION=${VERSION:-3.3.20190909} +VERSION=${VERSION:-3.3.20200621} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -89,7 +89,9 @@ find -L . \ # Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$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 @@ -108,7 +110,7 @@ make install DESTDIR=$PKG # Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$SLKCFLAGS" CXXFLAGS="$SLKCFLAGS" make +CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG # This is Phyrex @@ -126,7 +128,7 @@ make install DESTDIR=$PKG # Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$SLKCFLAGS" CXXFLAGS="$SLKCFLAGS" make +CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG # This is PhyTime @@ -144,7 +146,7 @@ make install DESTDIR=$PKG # Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$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 \ diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info index f44eaca3de..ec04310e99 100644 --- a/academic/PhyML/PhyML.info +++ b/academic/PhyML/PhyML.info @@ -1,8 +1,8 @@ PRGNAM="PhyML" -VERSION="3.3.20190909" +VERSION="3.3.20200621" HOMEPAGE="https://github.com/stephaneguindon/phyml/" -DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20190909/phyml-3.3.20190909.tar.gz" -MD5SUM="35698ff61c1db57b238f5b2d2cc784b3" +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 6fb687f83a..3f31ad4a38 100644 --- a/academic/R/R.SlackBuild +++ b/academic/R/R.SlackBuild @@ -2,9 +2,8 @@ # SlackBuild script for R -# Copyright 2019 Andrew Payne, Boston, MA <phalange@komputermatrix.com> -# 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 @@ -25,7 +24,7 @@ # <http://www.gnu.org/licenses/>. PRGNAM=R -VERSION=${VERSION:-3.6.2} +VERSION=${VERSION:-4.0.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/R/R.info b/academic/R/R.info index 9ce4d10cd4..04109237e7 100644 --- a/academic/R/R.info +++ b/academic/R/R.info @@ -1,10 +1,10 @@ PRGNAM="R" -VERSION="3.6.2" +VERSION="4.0.0" HOMEPAGE="http://www.r-project.org/" -DOWNLOAD="https://cran.r-project.org/src/base/R-3/R-3.6.2.tar.gz" -MD5SUM="90d23d138cee26d275da14b58296e521" +DOWNLOAD="https://cran.r-project.org/src/base/R-4/R-4.0.0.tar.gz" +MD5SUM="48c487c68112cb3191f3015c6277a50b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="pcre2" MAINTAINER="Andrew Payne" EMAIL="phalange@komputermatrix.com" diff --git a/academic/RepeatMasker/RepeatMasker.SlackBuild b/academic/RepeatMasker/RepeatMasker.SlackBuild index b94763c2a8..2975550e19 100644 --- a/academic/RepeatMasker/RepeatMasker.SlackBuild +++ b/academic/RepeatMasker/RepeatMasker.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=RepeatMasker -VERSION=${VERSION:-4.1.0} +VERSION=${VERSION:-4.1.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/RepeatMasker/RepeatMasker.info b/academic/RepeatMasker/RepeatMasker.info index 62eacca432..322653dd70 100644 --- a/academic/RepeatMasker/RepeatMasker.info +++ b/academic/RepeatMasker/RepeatMasker.info @@ -1,8 +1,8 @@ PRGNAM="RepeatMasker" -VERSION="4.1.0" +VERSION="4.1.1" HOMEPAGE="http://www.repeatmasker.org/" -DOWNLOAD="http://www.repeatmasker.org/RepeatMasker-4.1.0.tar.gz" -MD5SUM="936894df2b8291f42afce22a5793b4bf" +DOWNLOAD="http://www.repeatmasker.org/RepeatMasker-4.1.1.tar.gz" +MD5SUM="6df7b188757b5ef2d2575320eb0b014e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="perl-Text-Soundex trfind HMMER ncbi-rmblastn" diff --git a/academic/STAR/STAR.SlackBuild b/academic/STAR/STAR.SlackBuild index 0e9417d8bf..d785f46923 100644 --- a/academic/STAR/STAR.SlackBuild +++ b/academic/STAR/STAR.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for STAR -# Copyright 2018-2019 Rob van Nues +# Copyright 2018-2021 Rob van Nues <sborg63@disroot.org> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=STAR -VERSION=${VERSION:-2.7.3a} +VERSION=${VERSION:-2.7.8a} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/STAR/STAR.info b/academic/STAR/STAR.info index 2257366358..68740e69a3 100644 --- a/academic/STAR/STAR.info +++ b/academic/STAR/STAR.info @@ -1,10 +1,10 @@ PRGNAM="STAR" -VERSION="2.7.3a" +VERSION="2.7.8a" HOMEPAGE="https://github.com/alexdobin/STAR" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.7.3a/STAR-2.7.3a.tar.gz" -MD5SUM_x86_64="6642ef8b8404d923fefe7c72348f12f4" +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/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/ViennaRNA/README b/academic/ViennaRNA/README index 6ad531d628..a82c7160b2 100644 --- a/academic/ViennaRNA/README +++ b/academic/ViennaRNA/README @@ -7,8 +7,9 @@ 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: +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/) @@ -22,29 +23,31 @@ Amongst other things, the ViennRNA implementations allow you to: - 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 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 +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`) +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. +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). +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: diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild index ff63062efc..8bc20e2a45 100644 --- a/academic/ViennaRNA/ViennaRNA.SlackBuild +++ b/academic/ViennaRNA/ViennaRNA.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=ViennaRNA -VERSION=${VERSION:-2.4.14} +VERSION=${VERSION:-2.4.17} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/ViennaRNA/ViennaRNA.info b/academic/ViennaRNA/ViennaRNA.info index 06e2675530..162b17f93a 100644 --- a/academic/ViennaRNA/ViennaRNA.info +++ b/academic/ViennaRNA/ViennaRNA.info @@ -1,10 +1,10 @@ PRGNAM="ViennaRNA" -VERSION="2.4.14" +VERSION="2.4.17" HOMEPAGE="https://www.tbi.univie.ac.at/RNA" -DOWNLOAD="https://github.com/ViennaRNA/ViennaRNA/releases/download/v2.4.14/ViennaRNA-2.4.14.tar.gz" -MD5SUM="b9c64be709d3dfef72cc27e615845a04" +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 gri" +REQUIRES="python3" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" 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/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 index a6f078794e..7954d1e751 100644 --- a/academic/abella/README +++ b/academic/abella/README @@ -1,16 +1,19 @@ 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. +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 +* 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 +* 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 @@ -23,8 +26,8 @@ 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. +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/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/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 796d4d8885..57645d2d25 100644 --- a/academic/amd/amd.SlackBuild +++ b/academic/amd/amd.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for AMD -# Copyright 2013-2020 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:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/amd/amd.info b/academic/amd/amd.info index 5a6b836b8c..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="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +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/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/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 $PKG/install diff --git a/academic/aris/aris.info b/academic/aris/aris.info index 8362eaa9bb..484ce06315 100644 --- a/academic/aris/aris.info +++ b/academic/aris/aris.info @@ -1,8 +1,8 @@ PRGNAM="aris" -VERSION="2.1.1" -HOMEPAGE="http://www.gnu.org/software/aris/" -DOWNLOAD="http://ftp.gnu.org/gnu/aris/aris-2.1.1.tar.bz2" -MD5SUM="ef1b8f3be8edac44305e36493068f745" +VERSION="2.2" +HOMEPAGE="https://www.gnu.org/software/aris/" +DOWNLOAD="https://ftp.gnu.org/gnu/aris/aris-2.2.tar.bz2" +MD5SUM="523e2c40f17e6e857b533c22a26ff4e1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/aris/help_path.diff b/academic/aris/help_path.diff new file mode 100644 index 0000000000..0d2853fcbe --- /dev/null +++ b/academic/aris/help_path.diff @@ -0,0 +1,11 @@ +--- a/aris.c 2021-02-10 17:51:33.532759576 +0400 ++++ b/aris.c 2021-02-10 17:52:15.210759108 +0400 +@@ -845,7 +845,7 @@ + if (the_app->working_dir) + { + parent = g_file_get_parent (parent); +- sprintf (the_app->help_file, "file://%s/doc/aris/index.html", g_file_get_path (parent)); ++ sprintf (the_app->help_file, "file:///usr/doc/aris-2.2/html/index.html", g_file_get_path (parent)); + } + + int ret; diff --git a/academic/aris/html_doc.patch b/academic/aris/html_doc.patch deleted file mode 100644 index 1b359b73d6..0000000000 --- a/academic/aris/html_doc.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- aris-2.0/configure 2012-09-25 05:06:22.000000000 -0300 -+++ aris-2.0b/configure 2013-03-23 18:34:59.483719378 -0300 -@@ -4610,3 +4610,1 @@ --cat >>confdefs.h <<_ACEOF --#define HELP_FILE "file://`pwd`/doc/aris/index.html" --_ACEOF -+echo "#define HELP_FILE \"file://"$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 aef002668d..51b0b0b55b 100644 --- a/academic/bcftools/README +++ b/academic/bcftools/README @@ -4,6 +4,6 @@ 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. -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. +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 526b44d687..9576a89c84 100644 --- a/academic/bcftools/bcftools.SlackBuild +++ b/academic/bcftools/bcftools.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for samtools -# Copyright 2017-2020 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: @@ -22,10 +22,10 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=bcftools -VERSION=${VERSION:-1.10.2} +PRGNAM=bcftools +VERSION=${VERSION:-1.12} BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} +TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in diff --git a/academic/bcftools/bcftools.info b/academic/bcftools/bcftools.info index b8201d734d..ad211ee207 100644 --- a/academic/bcftools/bcftools.info +++ b/academic/bcftools/bcftools.info @@ -1,8 +1,8 @@ PRGNAM="bcftools" -VERSION="1.10.2" +VERSION="1.12" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2" -MD5SUM="081ebb6138f5fdf394cb6a074effadb3" +DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.12/bcftools-1.12.tar.bz2" +MD5SUM="d3622cb3e52039055fd91ad65ea5131e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="htslib" diff --git a/academic/bedtools/bedtools.SlackBuild b/academic/bedtools/bedtools.SlackBuild index ee87fbbbe4..c29f69d3e2 100644 --- a/academic/bedtools/bedtools.SlackBuild +++ b/academic/bedtools/bedtools.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for bedtools -# Copyright 2014-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2014-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,7 +24,7 @@ PRGNAM=bedtools DIRNAM=bedtools2 -VERSION=${VERSION:-2.28.0} +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 8ebd0862f4..79634be6cb 100644 --- a/academic/bedtools/bedtools.info +++ b/academic/bedtools/bedtools.info @@ -1,8 +1,8 @@ PRGNAM="bedtools" -VERSION="2.28.0" +VERSION="2.29.2" HOMEPAGE="http://bedtools.readthedocs.org/" -DOWNLOAD="https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz" -MD5SUM="611d55ab9f03a7ee0fa6639af7299acf" +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 b6137880cc..7a44c6d012 100644 --- a/academic/bibletime/README +++ b/academic/bibletime/README @@ -1,6 +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 1.8.1 or higher, and qt5.9 or higher. -Homepage: http://bibletime.info/ +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 9af701fef1..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 2018/9 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:-3.0_beta2} -BUILD=${BUILD:-1} +VERSION=${VERSION:-3.0} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -68,21 +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 verson of cmake on slack14.2 -#these patches can be removed once cmake gets to 3.10 or higher -sed -i "s/VERSION 3.10/VERSION 3.5/g" CMakeLists.txt -sed -i "s/^CHECK_IPO_SUPPORTED(RESULT HAVE_IPO)/SET(HAVE_IPO FALSE)/g" CMakeLists.txt -sed -i "s/^INCLUDE(CheckIPO/#INCLUDE(CheckIPO/g" CMakeLists.txt -sed -i "/TARGET_COMPILE_FEATURES/s/.*/SET(CMAKE_CXX_STANDARD 11)/" 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:$PATH" cmake \ -Wno-dev \ -DCMAKE_BUILD_TYPE=Release \ @@ -90,7 +85,7 @@ cd build -DCMAKE_SKIP_RPATH:BOOL=ON \ -DCMAKE_C_FLAGS="$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 06b7202b16..43b5b02595 100644 --- a/academic/bibletime/bibletime.info +++ b/academic/bibletime/bibletime.info @@ -1,10 +1,10 @@ PRGNAM="bibletime" -VERSION="3.0_beta2" +VERSION="3.0" HOMEPAGE="http://www.bibletime.info/" -DOWNLOAD="https://github.com/bibletime/bibletime/releases/download/v3.0_beta2/bibletime-3.0_beta2.tar.xz" -MD5SUM="1874d442546791b5611343fbcf2aed73" +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/boinc/README b/academic/boinc/README index 5c3f695a28..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. - -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. +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. Building diff --git a/academic/boinc/boinc.SlackBuild b/academic/boinc/boinc.SlackBuild index 7e94c5251c..a35a0cce0f 100644 --- a/academic/boinc/boinc.SlackBuild +++ b/academic/boinc/boinc.SlackBuild @@ -25,10 +25,11 @@ # TODO: add rc.boinc. PRGNAM=boinc -VERSION=${VERSION:-7.16.4} +VERSION=${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 $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ diff --git a/academic/boinc/boinc.info b/academic/boinc/boinc.info index 8a3e9be145..9d7dbd0162 100644 --- a/academic/boinc/boinc.info +++ b/academic/boinc/boinc.info @@ -1,10 +1,10 @@ PRGNAM="boinc" -VERSION="7.16.4" +VERSION="7.16.16" HOMEPAGE="https://boinc.berkeley.edu/" -DOWNLOAD="https://github.com/BOINC/boinc/archive/client_release/7.16/7.16.4/boinc-client_release-7.16-7.16.4.tar.gz" -MD5SUM="33aa0de75425d7c0b8acca0301df18b1" +DOWNLOAD="https://github.com/BOINC/boinc/archive/client_release/7.16/7.16.16/boinc-client_release-7.16-7.16.16.tar.gz" +MD5SUM="debf658ed8748c1c434c12f8a8a932a1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="libwebp wxGTK3" +REQUIRES="wxGTK3" MAINTAINER="Edward W. Koenig" EMAIL="kingbeowulf@gmail.com" diff --git a/academic/bowtie2/bowtie2.SlackBuild b/academic/bowtie2/bowtie2.SlackBuild index 370b409bc0..fa8d2dfa04 100644 --- a/academic/bowtie2/bowtie2.SlackBuild +++ b/academic/bowtie2/bowtie2.SlackBuild @@ -25,7 +25,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=bowtie2 -VERSION=${VERSION:-2.4.1} +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 @@ -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 8c3fb45d87..c57cd185f3 100644 --- a/academic/bowtie2/bowtie2.info +++ b/academic/bowtie2/bowtie2.info @@ -1,8 +1,8 @@ PRGNAM="bowtie2" -VERSION="2.4.1" +VERSION="2.4.2" HOMEPAGE="https://github.com/BenLangmead/bowtie2/releases" -DOWNLOAD="https://github.com/BenLangmead/bowtie2/archive/v2.4.1/bowtie2-2.4.1.tar.gz" -MD5SUM="5938482fab363c6356f9662cce38f99c" +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 python3" 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 39ef98cc23..619dcb650c 100644 --- a/academic/btf/btf.SlackBuild +++ b/academic/btf/btf.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for BTF -# Copyright 2013-2020 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=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/btf/btf.info b/academic/btf/btf.info index 0b80a8d5cc..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="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +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/cadabra2/README b/academic/cadabra2/README index 5e8287722a..0533ffcdd3 100644 --- a/academic/cadabra2/README +++ b/academic/cadabra2/README @@ -28,5 +28,6 @@ command-line and a graphical interface are available. * Programmable using Python. -Mathematica (not on SBo) is an optional dependency, it will be -autodetected at build time. +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 53b6152b13..f6a618c3ff 100644 --- a/academic/cadabra2/cadabra2.SlackBuild +++ b/academic/cadabra2/cadabra2.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cadabra2 -# Copyright 2017-2019, 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=${VERSION:-2.2.8} +VERSION=${VERSION:-2.3.6.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +MMA=${MMA:-OFF} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -91,10 +92,14 @@ find ./ -type f -name '*.py' -exec \ mkdir -p build cd build + export "PATH=/opt/cmake-202x/bin:$PATH" cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ + -DSQLITE3_INCLUDE_DIR=/usr/include \ + -DENABLE_SYSTEM_JSONCPP=ON \ + -DENABLE_MATHEMATICA=${MMA^^} \ -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG @@ -108,7 +113,8 @@ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a 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 eba8bf8144..164ad63867 100644 --- a/academic/cadabra2/cadabra2.info +++ b/academic/cadabra2/cadabra2.info @@ -1,10 +1,10 @@ PRGNAM="cadabra2" -VERSION="2.2.8" +VERSION="2.3.6.3" HOMEPAGE="https://cadabra.science" -DOWNLOAD="https://downloads.sourceforge.net/slackbuildsdirectlinks/cadabra2/cadabra2-2.2.8.tar.gz" -MD5SUM="a4c91eca89e75a079038e9dae3c5d00e" +DOWNLOAD="https://downloads.sourceforge.net/slackbuildsdirectlinks/cadabra2/cadabra2-2.3.6.3.tar.gz" +MD5SUM="9e792260d2b6dea2bb7c5d8a0a627662" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="python3-matplotlib python3-gmpy2 python3-sympy" +REQUIRES="python3-matplotlib python3-gmpy2 python3-sympy jsoncpp cmake-202x" MAINTAINER="Alexander Verbovetsky" EMAIL="alik@ejik.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 15bf62a012..b7253a1aba 100644 --- a/academic/camd/camd.SlackBuild +++ b/academic/camd/camd.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CAMD -# Copyright 2013-2020 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=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/camd/camd.info b/academic/camd/camd.info index fc2cbaa211..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="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +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/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 a7cadea464..3a18cc1daa 100644 --- a/academic/cblas/cblas.SlackBuild +++ b/academic/cblas/cblas.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CBLAS -# Copyright 2016-2020 Kyle Guinn <elyk03@gmail.com> +# 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=${VERSION:-3.9.0} +VERSION=${VERSION:-3.9.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/cblas/cblas.info b/academic/cblas/cblas.info index 6c54824791..7821e1a648 100644 --- a/academic/cblas/cblas.info +++ b/academic/cblas/cblas.info @@ -1,8 +1,8 @@ PRGNAM="cblas" -VERSION="3.9.0" -HOMEPAGE="http://www.netlib.org/blas/" -DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.9.0/lapack-3.9.0.tar.gz" -MD5SUM="0b251e2a8d5f949f99b50dd5e2200ee2" +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 b1bdfaec1e..378acc8769 100644 --- a/academic/cblas/patches/cmake-piecewise.diff +++ b/academic/cblas/patches/cmake-piecewise.diff @@ -5,25 +5,25 @@ 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 -@@ -41,54 +39,8 @@ +@@ -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 @@ -34,7 +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 ${CBLASLIB}-targets.cmake) - - # Choose one of the cblas targets to use as a guard - # for cblas-config.cmake to load targets from the build tree. @@ -42,27 +42,27 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt -endif() - -configure_file(${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}-${LAPACK_VERSION} -# COMPONENT Development -# ) diff --git a/CBLAS/cmake/cblas-config-build.cmake.in b/CBLAS/cmake/cblas-config-build.cmake.in @@ -76,14 +76,14 @@ deleted file mode 100644 - -# Load lapack targets from the build tree, including lapacke targets. -if(NOT TARGET lapacke) -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() - -# Report cblas header search locations from build tree. -set(CBLAS_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report cblas libraries. --set(CBLAS_LIBRARIES cblas) +-set(CBLAS_LIBRARIES @CBLASLIB@) diff --git a/CBLAS/cmake/cblas-config-install.cmake.in b/CBLAS/cmake/cblas-config-install.cmake.in deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-install.cmake.in @@ -96,19 +96,19 @@ deleted file mode 100644 -get_filename_component(_CBLAS_PREFIX "${_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) @@ -128,16 +128,16 @@ 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 @@ -146,7 +146,7 @@ deleted file mode 100644 -# Load lapack targets from the build tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_build_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - @@ -168,7 +168,7 @@ deleted file mode 100644 -# Load lapack targets from the install tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_install_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("${_LAPACK_SELF_DIR}/lapack-targets.cmake") +- include("${_LAPACK_SELF_DIR}/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - @@ -184,11 +184,11 @@ deleted file mode 100644 diff --git a/CMakeLists.txt b/CMakeLists.txt --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -112,11 +112,8 @@ +@@ -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} @@ -196,7 +196,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Development LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT RuntimeLibraries RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT RuntimeLibraries -@@ -155,21 +152,6 @@ +@@ -204,21 +201,6 @@ include(CheckLAPACKCompilerFlags) CheckLAPACKCompilerFlags() @@ -204,7 +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) @@ -218,7 +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}") -@@ -193,8 +175,9 @@ +@@ -242,8 +224,9 @@ endif() # -------------------------------------------------- @@ -229,7 +229,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided BLAS libraries if(BLAS_LIBRARIES) -@@ -205,113 +188,108 @@ +@@ -254,113 +237,108 @@ if(BLAS_FOUND) message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRARIES}.") else() @@ -250,7 +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}" @@ -326,14 +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 ${TIME_FUNC}) + CHECK_TIME_FUNCTION(NONE TIME_FUNC) + CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) + CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) @@ -363,9 +363,9 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + add_subdirectory(TESTING) + endif() + -+ configure_file(${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 + ) @@ -393,8 +393,8 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt add_subdirectory(LAPACKE) endif() -@@ -338,109 +316,12 @@ - _display_cpp_implementation_msg("LAPACK") +@@ -414,111 +392,16 @@ + ExternalProject_Add_StepDependencies(lapackpp build blaspp ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) endif() -# -------------------------------------------------- @@ -430,23 +430,23 @@ 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 - ) - @@ -457,12 +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.") @@ -471,7 +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 ${LAPACKLIB}-targets.cmake) - - # Choose one of the lapack or lapacke targets to use as a guard - # for lapack-config.cmake to load targets from the build tree. @@ -480,36 +480,37 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt +if(NEED_LAPACK AND NOT LAPACK_FOUND) + message(FATAL_ERROR "--> No LAPACK library found. Specify LAPACK_LIBRARIES or enable USE_OPTIMIZED_LAPACK or BUILD_LAPACK.") endif() -- + -configure_file(${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}-${LAPACK_VERSION} - COMPONENT Development - ) -- -\ No newline at end of file + if (LAPACK++) + install( + DIRECTORY "${LAPACK_BINARY_DIR}/lib/" diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt --- a/LAPACKE/CMakeLists.txt +++ b/LAPACKE/CMakeLists.txt @@ -517,7 +518,7 @@ 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) @@ -526,38 +527,38 @@ diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt VERSION ${LAPACK_VERSION} SOVERSION ${LAPACK_MAJOR_VERSION} ) --target_include_directories(lapacke PUBLIC +-target_include_directories(${LAPACKELIB} PUBLIC - $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> - $<INSTALL_INTERFACE:include> -) -if(WIN32 AND NOT UNIX) -- target_compile_definitions(lapacke PUBLIC HAVE_LAPACK_CONFIG_H LAPACK_COMPLEX_STRUCTURE) +- target_compile_definitions(${LAPACKELIB} PUBLIC HAVE_LAPACK_CONFIG_H LAPACK_COMPLEX_STRUCTURE) - message(STATUS "Windows BUILD") -endif() if(LAPACKE_WITH_TMG) - target_link_libraries(lapacke PRIVATE tmglib) + 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 @@ -570,8 +571,8 @@ deleted file mode 100644 -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 @@ -581,7 +582,7 @@ deleted file mode 100644 -set(LAPACKE_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke ${LAPACK_LIBRARIES}) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) diff --git a/LAPACKE/cmake/lapacke-config-install.cmake.in b/LAPACKE/cmake/lapacke-config-install.cmake.in deleted file mode 100644 --- a/LAPACKE/cmake/lapacke-config-install.cmake.in @@ -594,12 +595,12 @@ deleted file mode 100644 -get_filename_component(_LAPACKE_PREFIX "${_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 @@ -609,7 +610,7 @@ deleted file mode 100644 -set(LAPACKE_INCLUDE_DIRS ${_LAPACKE_PREFIX}/include) - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke ${LAPACK_LIBRARIES}) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) - -unset(_LAPACKE_PREFIX) -unset(_LAPACKE_SELF_DIR) diff --git a/academic/ccolamd/ccolamd.SlackBuild b/academic/ccolamd/ccolamd.SlackBuild index cec5eb80f1..7a76de236b 100644 --- a/academic/ccolamd/ccolamd.SlackBuild +++ b/academic/ccolamd/ccolamd.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CCOLAMD -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=ccolamd SRCNAM=SuiteSparse SUBDIR=CCOLAMD VERSION=${VERSION:-2.9.6} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/ccolamd/ccolamd.info b/academic/ccolamd/ccolamd.info index e32e2118a3..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="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +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/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 aae466f098..5ac8ce8cf7 100644 --- a/academic/cholmod/cholmod.SlackBuild +++ b/academic/cholmod/cholmod.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CHOLMOD -# Copyright 2013-2020 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=cholmod SRCNAM=SuiteSparse SUBDIR=CHOLMOD -VERSION=${VERSION:-3.0.13} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-2} +VERSION=${VERSION:-3.0.14} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/cholmod/cholmod.info b/academic/cholmod/cholmod.info index 9b41a522e8..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="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +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 6cdb2b7b6a..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],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[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/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 ab7e39cb5a..3d2ceacd5a 100644 --- a/academic/colamd/colamd.SlackBuild +++ b/academic/colamd/colamd.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for COLAMD -# Copyright 2013-2020 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:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/colamd/colamd.info b/academic/colamd/colamd.info index f558ba3958..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="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +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/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 d446a59979..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:-4.27.217} +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 $PRGNAM build script..." - exit 1 -fi - # This is a repackage of a binary distribution # CFLAGS are not required diff --git a/academic/copasi/copasi.info b/academic/copasi/copasi.info index 6e5b69b94a..93b7729f70 100644 --- a/academic/copasi/copasi.info +++ b/academic/copasi/copasi.info @@ -1,10 +1,10 @@ PRGNAM="copasi" -VERSION="4.27.217" -HOMEPAGE="http://www.copasi.org" -DOWNLOAD="https://github.com/copasi/COPASI/releases/download/Build-217/COPASI-4.27.217-Linux-32bit.tar.gz" -MD5SUM="a218e91000bba6ca3071feddd95fd0d2" -DOWNLOAD_x86_64="https://github.com/copasi/COPASI/releases/download/Build-217/COPASI-4.27.217-Linux-64bit.tar.gz" -MD5SUM_x86_64="f9fd439a6b6a9f60bb2b54c666235aec" +VERSION="4.28.226" +HOMEPAGE="http://copasi.org" +DOWNLOAD="https://github.com/copasi/COPASI/releases/download/Build-226/COPASI-4.28.226-Linux-32bit.tar.gz" +MD5SUM="3fd18c60296def1158295b4b39a41085" +DOWNLOAD_x86_64="https://github.com/copasi/COPASI/releases/download/Build-226/COPASI-4.28.226-Linux-64bit.tar.gz" +MD5SUM_x86_64="9709892e02b9ec7e9ccb0d9ec7e8b08b" REQUIRES="" MAINTAINER="Pedro Mendes" EMAIL="pedro@gepasi.org" diff --git a/academic/cryptominisat/cryptominisat.SlackBuild b/academic/cryptominisat/cryptominisat.SlackBuild index 8a59f1367e..f8f0deea19 100644 --- a/academic/cryptominisat/cryptominisat.SlackBuild +++ b/academic/cryptominisat/cryptominisat.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=cryptominisat -VERSION=${VERSION:-5.6.8} +VERSION=${VERSION:-5.7.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/cryptominisat/cryptominisat.info b/academic/cryptominisat/cryptominisat.info index 4ceb3bef16..ecbc9f24ff 100644 --- a/academic/cryptominisat/cryptominisat.info +++ b/academic/cryptominisat/cryptominisat.info @@ -1,8 +1,8 @@ PRGNAM="cryptominisat" -VERSION="5.6.8" +VERSION="5.7.1" HOMEPAGE="https://www.msoos.org/cryptominisat5/" -DOWNLOAD="https://github.com/msoos/cryptominisat/archive/5.6.8/cryptominisat-5.6.8.tar.gz" -MD5SUM="ca1bf853e568c19968daa5464ab86843" +DOWNLOAD="https://github.com/msoos/cryptominisat/archive/5.7.1/cryptominisat-5.7.1.tar.gz" +MD5SUM="e4ff835bbfe1995cc5e62a6e464dfd98" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/csparse/README b/academic/csparse/README index 7119c1bf65..2726898d3c 100644 --- a/academic/csparse/README +++ b/academic/csparse/README @@ -1,5 +1,5 @@ -CSparse is a small yet feature-rich sparse matrix package. Its purpose is -to demonstrate a wide range of sparse matrix algorithms in as concise a -code as possible. +CSparse is a small yet feature-rich sparse matrix package. Its +purpose is to demonstrate a wide range of sparse matrix algorithms in +as concise a code as possible. This package is part of SuiteSparse. diff --git a/academic/csparse/csparse.SlackBuild b/academic/csparse/csparse.SlackBuild index 3f008bbe0b..4aa1aa9612 100644 --- a/academic/csparse/csparse.SlackBuild +++ b/academic/csparse/csparse.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CSparse -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=csparse SRCNAM=SuiteSparse SUBDIR=CSparse VERSION=${VERSION:-3.2.0} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-4} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-5} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/csparse/csparse.info b/academic/csparse/csparse.info index 4435e41189..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="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +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/cvc4/README b/academic/cvc4/README index 830c7394fb..ed00fa62b8 100644 --- a/academic/cvc4/README +++ b/academic/cvc4/README @@ -4,4 +4,8 @@ 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 as well as libraries. +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 index ce4b43bebf..d3a964cf03 100644 --- a/academic/cvc4/cvc4.SlackBuild +++ b/academic/cvc4/cvc4.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cvc4 -# Copyright 2019 Nick Smallbone, Gothenburg, Sweden +# Copyright 2019-2020 Nick Smallbone, Gothenburg, Sweden # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,8 +22,12 @@ # 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=${VERSION:-1.7} +VERSION=${VERSION:-1.8} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} SRCNAM=CVC4 @@ -70,22 +74,29 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -sed -i "s/DESTINATION lib/DESTINATION lib${LIBDIRSUFFIX}/" src/CMakeLists.txt src/parser/CMakeLists.txt -chmod +x $CWD/run-antlr +sed -i "s/LIBRARY_INSTALL_DIR lib/&${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="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Production \ - -DENABLE_OPTIMIZED=ON \ -DANTLR_INCLUDE_DIR=/usr/include/antlr3 \ - -DANTLR_BINARY="$CWD/run-antlr" \ + -DANTLR_BINARY="$TMP/$SRCNAM-$VERSION/run-antlr" \ + -DUSE_READLINE=OFF \ + -DBUILD_BINDINGS_PYTHON=OFF \ + -DBUILD_SWIG_BINDINGS_PYTHON=ON \ + -DBUILD_SWIG_BINDINGS_JAVA=OFF \ . make -make doc -make install/strip DESTDIR=$PKG +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 $PKG/usr/man -type f -exec gzip -9 {} \; diff --git a/academic/cvc4/cvc4.info b/academic/cvc4/cvc4.info index 9058f04efd..4fc4ede8c6 100644 --- a/academic/cvc4/cvc4.info +++ b/academic/cvc4/cvc4.info @@ -1,12 +1,12 @@ PRGNAM="cvc4" -VERSION="1.7" +VERSION="1.8" HOMEPAGE="https://cvc4.cs.stanford.edu/" -DOWNLOAD="https://github.com/CVC4/CVC4/archive/1.7/CVC4-1.7.tar.gz \ +DOWNLOAD="https://github.com/CVC4/CVC4/archive/1.8/CVC4-1.8.tar.gz \ https://www.antlr3.org/download/antlr-3.4-complete.jar" -MD5SUM="eadb05f5092c4310f3bbe52745f9b7b9 \ +MD5SUM="9f7657e21fec3c4042225b0b8f513c34 \ 1b91dea1c7d480b3223f7c8a9aa0e172" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk libantlr3c" +REQUIRES="jdk libantlr3c python-toml" MAINTAINER="Nick Smallbone" EMAIL="nick@smallbone.se" diff --git a/academic/cxsparse/cxsparse.SlackBuild b/academic/cxsparse/cxsparse.SlackBuild index 4695454e67..50237f46a6 100644 --- a/academic/cxsparse/cxsparse.SlackBuild +++ b/academic/cxsparse/cxsparse.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for CXSparse -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=cxsparse SRCNAM=SuiteSparse SUBDIR=CXSparse VERSION=${VERSION:-3.2.0} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-4} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-5} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/cxsparse/cxsparse.info b/academic/cxsparse/cxsparse.info index eb05c702a6..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="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +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/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/freechartgeany/freechartgeany.SlackBuild b/academic/datamash/datamash.SlackBuild index 13ac323d36..4661750499 100644 --- a/academic/freechartgeany/freechartgeany.SlackBuild +++ b/academic/datamash/datamash.SlackBuild @@ -1,8 +1,8 @@ #!/bin/sh -# Slackware build script for freechartgeany +# Slackware build script for datamash -# Copyright 2012-2016 Larry Hajali <larryhaja[at]gmail[dot]com> +# Copyright 2020 Petar Petrov slackalaxy@gmail.com # 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=freechartgeany -VERSION=${VERSION:-2.0.3} +PRGNAM=datamash +VERSION=${VERSION:-1.7} 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" @@ -69,30 +69,39 @@ 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 +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 install INSTALL_ROOT=$PKG +make check +make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# Install .desktop item and icons. -sed -i "/^Icon/s|=.*|=${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 +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 COPYING images/icons/Readme.rtf licenses/* $PKG/usr/doc/$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 -cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/datamash/datamash.info b/academic/datamash/datamash.info new file mode 100644 index 0000000000..ff23e91fa2 --- /dev/null +++ b/academic/datamash/datamash.info @@ -0,0 +1,10 @@ +PRGNAM="datamash" +VERSION="1.7" +HOMEPAGE="https://www.gnu.org/software/datamash/" +DOWNLOAD="https://ftp.gnu.org/gnu/datamash/datamash-1.7.tar.gz" +MD5SUM="e5474d3bfee13e7ab1c44ebaec497a0d" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/datamash/slack-desc b/academic/datamash/slack-desc new file mode 100644 index 0000000000..86ef966a72 --- /dev/null +++ b/academic/datamash/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +datamash: datamash (Basic numeric, textual and statistical operations) +datamash: +datamash: GNU Datamash is a command-line program which performs basic +datamash: numeric, textual and statistical operations on input textual +datamash: data files. +datamash: +datamash: https://www.gnu.org/software/datamash/ +datamash: +datamash: +datamash: +datamash: diff --git a/academic/diamond/diamond.SlackBuild b/academic/diamond/diamond.SlackBuild index 06d783043f..9a59218bbd 100644 --- a/academic/diamond/diamond.SlackBuild +++ b/academic/diamond/diamond.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=diamond -VERSION=${VERSION:-0.9.29} +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 e94f42b60b..e1160377d7 100644 --- a/academic/diamond/diamond.info +++ b/academic/diamond/diamond.info @@ -1,10 +1,10 @@ PRGNAM="diamond" -VERSION="0.9.29" +VERSION="0.9.36" HOMEPAGE="https://github.com/bbuchfink/diamond" -DOWNLOAD="UNSUPPORTED" -MD5SUM="" -DOWNLOAD_x86_64="https://github.com/bbuchfink/diamond/archive/v0.9.29/diamond-0.9.29.tar.gz" -MD5SUM_x86_64="c9a1cb0f2128e621695f7ee0a05c2af8" +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="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" 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 f6767b091d..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 2020 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:-8.1} +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 17023a3adf..475fe53290 100644 --- a/academic/ds9/ds9.info +++ b/academic/ds9/ds9.info @@ -1,8 +1,8 @@ PRGNAM="ds9" -VERSION="8.1" -HOMEPAGE="http://ds9.si.edu/site/Home.html" -DOWNLOAD="http://ds9.si.edu/archive/source/ds9.8.1.tar.gz" -MD5SUM="3dd24162553617565182d1016d24a6de" +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 index 373767752c..f116d5fc40 100644 --- a/academic/ed-v6/README +++ b/academic/ed-v6/README @@ -71,7 +71,7 @@ info page. This is the closest I can find to the original man page: -https://www.freebsd.org/cgi/man.cgi?query=ed&apropos=0&sektion=0&manpath=Unix%20Seventh%20Edition&arch=default&format=html +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 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/eprover.SlackBuild b/academic/eprover/eprover.SlackBuild index af3094b78b..5ab9c7485b 100644 --- a/academic/eprover/eprover.SlackBuild +++ b/academic/eprover/eprover.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for eprover -# Copyright 2019 Nick Smallbone, Gothenburg, Sweden +# Copyright 2019-2020 Nick Smallbone, Gothenburg, Sweden # 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=eprover -VERSION=${VERSION:-2.4} +VERSION=${VERSION:-2.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -90,7 +90,7 @@ 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 \ - README.md COPYING DOC/CONTRIBUTORS DOC/eprover.pdf DOC/NEWS \ + 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 diff --git a/academic/eprover/eprover.info b/academic/eprover/eprover.info index 542d9c982e..9371d82d3e 100644 --- a/academic/eprover/eprover.info +++ b/academic/eprover/eprover.info @@ -1,8 +1,8 @@ PRGNAM="eprover" -VERSION="2.4" +VERSION="2.5" HOMEPAGE="http://www.eprover.org" -DOWNLOAD="http://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_2.4/E.tgz" -MD5SUM="a303126a27deaedb0ce1bb884ab9ab97" +DOWNLOAD="http://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_2.5/E.tgz" +MD5SUM="f73852315dde1071acfa552b9532c7ab" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" 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/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/fet/fet.SlackBuild b/academic/fet/fet.SlackBuild index 91ec211628..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=${VERSION:-5.43.1} +VERSION=${VERSION:-5.49.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/fet/fet.info b/academic/fet/fet.info index 697155db4d..81c5073643 100644 --- a/academic/fet/fet.info +++ b/academic/fet/fet.info @@ -1,8 +1,8 @@ PRGNAM="fet" -VERSION="5.43.1" +VERSION="5.49.1" HOMEPAGE="https://www.lalescu.ro/liviu/fet/" -DOWNLOAD="https://www.lalescu.ro/liviu/fet/download/fet-5.43.1.tar.bz2" -MD5SUM="9d904384e36040378d77c42d425ff571" +DOWNLOAD="https://www.lalescu.ro/liviu/fet/download/fet-5.49.1.tar.bz2" +MD5SUM="063d3e4fa30c93820737fe8dbb28f55c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="qt5" 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/fiji.SlackBuild b/academic/fiji/fiji.SlackBuild index bad800afcd..68c84ec4a6 100644 --- a/academic/fiji/fiji.SlackBuild +++ b/academic/fiji/fiji.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=fiji -VERSION=${VERSION:-20191216_2110} +VERSION=${VERSION:-20200902_2101} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -31,7 +31,7 @@ DIRNAM=Fiji.app if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -42,12 +42,10 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -UPDATER=imagej-updater-0.10.3.jar - set -e # Stop if arch is not supported -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then +if [ "$ARCH" != "x86_64" ]; then printf "\n\n$ARCH is not supported... \n" exit 1 fi @@ -66,11 +64,7 @@ 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 $PRGNAM # We will put here two tools, so they are not run at startup. mkdir -p unused @@ -85,7 +79,7 @@ mv ../plugins/Scripts/Plugins/AutoRun/Check_Required_Update_Sites.js . # is your system, so if you want this functionality, then comment out # the line below. You can always "enable" it, by placing it in the jars # folder. -mv ../jars/$UPDATER . +mv ../jars/imagej-updater-* . cd .. diff --git a/academic/fiji/fiji.info b/academic/fiji/fiji.info index bab997b64e..20c501e557 100644 --- a/academic/fiji/fiji.info +++ b/academic/fiji/fiji.info @@ -1,10 +1,10 @@ PRGNAM="fiji" -VERSION="20191216_2110" +VERSION="20200902_2101" HOMEPAGE="https://fiji.sc/" -DOWNLOAD="https://downloads.imagej.net/fiji/archive/20191216-2110/fiji-nojre.tar.gz" -MD5SUM="692b2b0920d5d86bf5dfb6661444f19d" -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/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/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/gcompris-qt/doinst.sh b/academic/gcompris-qt/doinst.sh new file mode 100644 index 0000000000..3e5691a052 --- /dev/null +++ b/academic/gcompris-qt/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache 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]=ജികോംപàµà´°à´¿ +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]=Výuková 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 éducatif +GenericName[gl]=Xogo educativo +GenericName[it]=Gioco didattico +GenericName[ml]=വിദàµà´¯à´¾à´àµà´¯à´¾à´¸à´ªà´°à´®à´¾à´¯ കളി +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 educaÈ›ional +GenericName[sk]=Výuková hra +GenericName[sv]=Pedagogiskt spel +GenericName[uk]=ОÑÐ²Ñ–Ñ‚Ð½Ñ Ð³Ñ€Ð° +GenericName[x-test]=xxEducational Gamexx +GenericName[zh_CN]=æ•™è‚²æ¸¸æˆ +GenericName[zh_TW]=教育éŠæˆ² +Comment=Multi-Activity Educational game for children 2 to 10 +Comment[br]=C'hoari kelennadel gant oberezhioù a bep seurt evit ar vugale etre 2 ha 10 vloaz +Comment[ca]=Joc educatiu amb múltiples activitats per a infants de 2 a 10 anys +Comment[ca@valencia]=Joc educatiu amb múltiples activitats per a infants de 2 a 10 anys +Comment[de]=Lernspiel mit vielen Aktivitäten für Kinder von 2 bis 10 Jahren +Comment[el]=Εκπαιδευτικό παιχνίδι πολλαπλών δÏαστηÏιοτήτων 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 éducatif multi-activités pour les enfants de 2 à 10 ans +Comment[gl]=Xogo educativo con varias actividades para nenos entre 2 e 10 anos +Comment[hi]=२ से १० वरà¥à¤· के बचà¥à¤šà¥‹à¤‚ के लिठविà¤à¤¿à¤¨à¥à¤¨ कà¥à¤°à¤¿à¤¯à¤¾à¤à¤‚ वाला शेकà¥à¤·à¤£à¤¿à¤• खेल +Comment[id]=GCompris adalah kumpulan permainan kegiatan pendidikan untuk anak umur 2 sampai 10 tahun +Comment[it]=Gioco didattico multi-attività per bambini da 2 a 10 anni +Comment[ko]=2-10세 어린ì´ë¥¼ 위한 다양한 활ë™ì´ 있는 êµìœ¡ìš© 게임 +Comment[ml]=2 à´®àµà´¤àµ½ 10 വയസàµà´¸àµà´µà´°àµ†à´¯àµà´³àµà´³ à´•àµà´Ÿàµà´Ÿà´¿à´•àµ¾à´•àµà´•àµ വിവിധ à´ªàµà´°à´µàµ¼à´¤àµà´¤à´¨à´™àµà´™à´³à´¿à´²àµ‚ടെ പഠികàµà´•à´¾à´¨à´¾à´¯àµà´³àµà´³ കളി. +Comment[nl]=Educatief spel met meerdere activiteiten voor kinderen van 2 tot 10 +Comment[nn]=Leik-og-lærspel med mange aktivitetar – for barn frÃ¥ 2 til 10 Ã¥r +Comment[pl]=Gra edukacyjna z wieloma aktywnoÅ›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 educaÈ›ional cu activități multiple pentru copii între 2 È™i 10 ani +Comment[ru]=Обучающие игры Ð´Ð»Ñ Ð´ÐµÑ‚ÐµÐ¹ от 2 до 10 лет +Comment[sk]=Viac-aktivitová výuková hra pre deti od 2 do 10 rokov +Comment[sl]=Izobraževalna igra z veÄ dejavnostmi za otroke med drugim in desetim letom starosti +Comment[sv]=Pedagogiskt multiaktivitetsspel för barn frÃ¥n 2 till 10 Ã¥r +Comment[tr]=2-10 yaÅŸ arası çocuklar için Çoklu EtkileÅŸimli EÄŸitici oyun +Comment[uk]=Ðабір оÑвітніх ігор Ð´Ð»Ñ Ð´Ñ–Ñ‚ÐµÐ¹ від 2 до 10 років +Comment[x-test]=xxMulti-Activity Educational game for children 2 to 10xx +Comment[zh_CN]=为 2 到 10 å²å„¿ç«¥å‡†å¤‡çš„å¤šåŠŸèƒ½æ•™è‚²æ¸¸æˆ +Comment[zh_TW]=為 2-10 æ²å©åè¨è¨ˆçš„教育éŠæˆ² +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/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/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/README b/academic/getdp/README index dd3d1673d9..3dab37d132 100644 --- a/academic/getdp/README +++ b/academic/getdp/README @@ -1,3 +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. +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/getdp/slack-desc b/academic/getdp/slack-desc index 7e8b01e9fd..bed2d36f97 100644 --- a/academic/getdp/slack-desc +++ b/academic/getdp/slack-desc @@ -5,15 +5,15 @@ # exactly 11 lines for the formatting to be correct. It's also customary to # leave one space after the ':'. - |-----handy-ruler---------------------------------------------------------| + |-----handy-ruler------------------------------------------------------| getdp: getdp (Finite Element Solver) getdp: -getdp: GetDP a free finite element solver using mixed elements to discretize de -getdp: Rham-type complexes in one, two and three dimensions. The main feature of -getdp: GetDP is the closeness between the input data defining discrete problems -getdp: (written by the user in ASCII data files) and the symbolic mathematical -getdp: expressions of these problems. -getdp: -getdp: GetDP is distributed under the terms of the GNU General Public License. -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 index 4414b6009d..e2980522f6 100644 --- a/academic/gmsh/README +++ b/academic/gmsh/README @@ -1,7 +1,22 @@ -Gmsh (A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities) +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). +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. +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. +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/slack-desc b/academic/gmsh/slack-desc index f88f19320c..35305eed9d 100644 --- a/academic/gmsh/slack-desc +++ b/academic/gmsh/slack-desc @@ -5,15 +5,15 @@ # exactly 11 lines for the formatting to be correct. It's also customary to # leave one space after the ':'. - |-----handy-ruler---------------------------------------------------------| + |-----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, and is -gmsh: distributed under the terms of the GNU General Public License, Version 2 -gmsh: or later, with an exception to allow for easier linking with external -gmsh: libraries. +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/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/gri/gri.info b/academic/gri/gri.info index 4ca61c4974..6e4ee42dde 100644 --- a/academic/gri/gri.info +++ b/academic/gri/gri.info @@ -1,6 +1,6 @@ PRGNAM="gri" VERSION="2.12.23" -HOMEPAGE="https://gri.sourceforge.net/" +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="" 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/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 9537fb157d..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=${VERSION:-2.55} +VERSION=${VERSION:-2.58} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/gwyddion/gwyddion.info b/academic/gwyddion/gwyddion.info index ab4ec07b9d..13e0741611 100644 --- a/academic/gwyddion/gwyddion.info +++ b/academic/gwyddion/gwyddion.info @@ -1,8 +1,8 @@ PRGNAM="gwyddion" -VERSION="2.55" +VERSION="2.58" HOMEPAGE="http://gwyddion.net" -DOWNLOAD="http://downloads.sourceforge.net/gwyddion/gwyddion-2.55.tar.xz" -MD5SUM="91d7f7cdc2fb46ec639f87349425d3d2" +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/h5utils.info b/academic/h5utils/h5utils.info index aa2cd02582..a600f211b9 100644 --- a/academic/h5utils/h5utils.info +++ b/academic/h5utils/h5utils.info @@ -2,7 +2,7 @@ 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="f4d3eac775b6c2a18eac56138e659c37" +MD5SUM="b116cbb79ea22bbd1640cd8a1290f6f8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="hdf5" diff --git a/academic/io_lib/io_lib.SlackBuild b/academic/io_lib/io_lib.SlackBuild index 43a72cb84f..9a6f5a76d6 100644 --- a/academic/io_lib/io_lib.SlackBuild +++ b/academic/io_lib/io_lib.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=io_lib -VERSION=${VERSION:-1.14.11} +VERSION=${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 ba3fb88a0c..246c55cff8 100644 --- a/academic/io_lib/io_lib.info +++ b/academic/io_lib/io_lib.info @@ -1,8 +1,8 @@ PRGNAM="io_lib" -VERSION="1.14.11" +VERSION="1.14.13" HOMEPAGE="https://github.com/jkbonfield/io_lib" -DOWNLOAD="https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-11/io_lib-1.14.11.tar.gz" -MD5SUM="90fa0b6ad125e033a9b2c48b3fe4ac0a" +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/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/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 780ce2daf4..cff38308c6 100644 --- a/academic/klu/klu.SlackBuild +++ b/academic/klu/klu.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for KLU -# Copyright 2013-2020 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:-5.6.0} -BUILD=${BUILD:-3} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-4} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/klu/klu.info b/academic/klu/klu.info index 3865f63f7d..2a2faab22f 100644 --- a/academic/klu/klu.info +++ b/academic/klu/klu.info @@ -1,8 +1,8 @@ PRGNAM="klu" VERSION="1.3.9" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig amd colamd btf" diff --git a/academic/lalnview/README b/academic/lalnview/README index e91c30683f..364d8d0378 100644 --- a/academic/lalnview/README +++ b/academic/lalnview/README @@ -5,6 +5,13 @@ similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between segments. +A suitable alignment tool for protein sequences is SIM at ExPASy: +https://web.expasy.org/sim/ + +SIM finds a user-defined number of best non-intersecting alignments +between two protein sequences or within a sequence. Once the alignment +is computed, you can view it using LalnView. + For details and citation: Duret, L., Gasteiger, E. and Perriere, G. (1996) LalnView: a graphical viewer for pairwise sequence alignments. Comput. Applic. diff --git a/academic/lalnview/lalnview.SlackBuild b/academic/lalnview/lalnview.SlackBuild index cb92a3bcc3..3ba95c44d5 100644 --- a/academic/lalnview/lalnview.SlackBuild +++ b/academic/lalnview/lalnview.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for lalnview -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,12 +26,14 @@ PRGNAM=lalnview VERSION=${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 SantamarÃa (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 e0c9fe36d0..b7bac2704f 100644 --- a/academic/lapacke/lapacke.SlackBuild +++ b/academic/lapacke/lapacke.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for LAPACKE -# Copyright 2016-2020 Kyle Guinn <elyk03@gmail.com> +# 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:-3.9.0} +VERSION=${VERSION:-3.9.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -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 @@ -82,6 +86,7 @@ cd shared -DUSE_OPTIMIZED_LAPACK=ON \ -DBUILD_LAPACKE=ON \ -DBUILD_DEPRECATED=ON \ + $use_xblas \ -DBUILD_SHARED_LIBS=ON \ -DCMAKE_SKIP_RPATH=YES \ .. @@ -104,6 +109,7 @@ if [ "${STATIC:-no}" != "no" ]; then -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 80f3fc335b..aa77adac19 100644 --- a/academic/lapacke/lapacke.info +++ b/academic/lapacke/lapacke.info @@ -1,8 +1,8 @@ PRGNAM="lapacke" -VERSION="3.9.0" -HOMEPAGE="http://www.netlib.org/lapack/lapacke.html" -DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.9.0/lapack-3.9.0.tar.gz" -MD5SUM="0b251e2a8d5f949f99b50dd5e2200ee2" +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 b1bdfaec1e..378acc8769 100644 --- a/academic/lapacke/patches/cmake-piecewise.diff +++ b/academic/lapacke/patches/cmake-piecewise.diff @@ -5,25 +5,25 @@ 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 -@@ -41,54 +39,8 @@ +@@ -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 @@ -34,7 +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 ${CBLASLIB}-targets.cmake) - - # Choose one of the cblas targets to use as a guard - # for cblas-config.cmake to load targets from the build tree. @@ -42,27 +42,27 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt -endif() - -configure_file(${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}-${LAPACK_VERSION} -# COMPONENT Development -# ) diff --git a/CBLAS/cmake/cblas-config-build.cmake.in b/CBLAS/cmake/cblas-config-build.cmake.in @@ -76,14 +76,14 @@ deleted file mode 100644 - -# Load lapack targets from the build tree, including lapacke targets. -if(NOT TARGET lapacke) -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() - -# Report cblas header search locations from build tree. -set(CBLAS_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report cblas libraries. --set(CBLAS_LIBRARIES cblas) +-set(CBLAS_LIBRARIES @CBLASLIB@) diff --git a/CBLAS/cmake/cblas-config-install.cmake.in b/CBLAS/cmake/cblas-config-install.cmake.in deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-install.cmake.in @@ -96,19 +96,19 @@ deleted file mode 100644 -get_filename_component(_CBLAS_PREFIX "${_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) @@ -128,16 +128,16 @@ 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 @@ -146,7 +146,7 @@ deleted file mode 100644 -# Load lapack targets from the build tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_build_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - @@ -168,7 +168,7 @@ deleted file mode 100644 -# Load lapack targets from the install tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_install_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("${_LAPACK_SELF_DIR}/lapack-targets.cmake") +- include("${_LAPACK_SELF_DIR}/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - @@ -184,11 +184,11 @@ deleted file mode 100644 diff --git a/CMakeLists.txt b/CMakeLists.txt --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -112,11 +112,8 @@ +@@ -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} @@ -196,7 +196,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Development LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT RuntimeLibraries RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT RuntimeLibraries -@@ -155,21 +152,6 @@ +@@ -204,21 +201,6 @@ include(CheckLAPACKCompilerFlags) CheckLAPACKCompilerFlags() @@ -204,7 +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) @@ -218,7 +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}") -@@ -193,8 +175,9 @@ +@@ -242,8 +224,9 @@ endif() # -------------------------------------------------- @@ -229,7 +229,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided BLAS libraries if(BLAS_LIBRARIES) -@@ -205,113 +188,108 @@ +@@ -254,113 +237,108 @@ if(BLAS_FOUND) message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRARIES}.") else() @@ -250,7 +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}" @@ -326,14 +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 ${TIME_FUNC}) + CHECK_TIME_FUNCTION(NONE TIME_FUNC) + CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) + CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) @@ -363,9 +363,9 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + add_subdirectory(TESTING) + endif() + -+ configure_file(${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 + ) @@ -393,8 +393,8 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt add_subdirectory(LAPACKE) endif() -@@ -338,109 +316,12 @@ - _display_cpp_implementation_msg("LAPACK") +@@ -414,111 +392,16 @@ + ExternalProject_Add_StepDependencies(lapackpp build blaspp ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) endif() -# -------------------------------------------------- @@ -430,23 +430,23 @@ 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 - ) - @@ -457,12 +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.") @@ -471,7 +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 ${LAPACKLIB}-targets.cmake) - - # Choose one of the lapack or lapacke targets to use as a guard - # for lapack-config.cmake to load targets from the build tree. @@ -480,36 +480,37 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt +if(NEED_LAPACK AND NOT LAPACK_FOUND) + message(FATAL_ERROR "--> No LAPACK library found. Specify LAPACK_LIBRARIES or enable USE_OPTIMIZED_LAPACK or BUILD_LAPACK.") endif() -- + -configure_file(${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}-${LAPACK_VERSION} - COMPONENT Development - ) -- -\ No newline at end of file + if (LAPACK++) + install( + DIRECTORY "${LAPACK_BINARY_DIR}/lib/" diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt --- a/LAPACKE/CMakeLists.txt +++ b/LAPACKE/CMakeLists.txt @@ -517,7 +518,7 @@ 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) @@ -526,38 +527,38 @@ diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt VERSION ${LAPACK_VERSION} SOVERSION ${LAPACK_MAJOR_VERSION} ) --target_include_directories(lapacke PUBLIC +-target_include_directories(${LAPACKELIB} PUBLIC - $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> - $<INSTALL_INTERFACE:include> -) -if(WIN32 AND NOT UNIX) -- target_compile_definitions(lapacke PUBLIC HAVE_LAPACK_CONFIG_H LAPACK_COMPLEX_STRUCTURE) +- target_compile_definitions(${LAPACKELIB} PUBLIC HAVE_LAPACK_CONFIG_H LAPACK_COMPLEX_STRUCTURE) - message(STATUS "Windows BUILD") -endif() if(LAPACKE_WITH_TMG) - target_link_libraries(lapacke PRIVATE tmglib) + 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 @@ -570,8 +571,8 @@ deleted file mode 100644 -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 @@ -581,7 +582,7 @@ deleted file mode 100644 -set(LAPACKE_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke ${LAPACK_LIBRARIES}) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) diff --git a/LAPACKE/cmake/lapacke-config-install.cmake.in b/LAPACKE/cmake/lapacke-config-install.cmake.in deleted file mode 100644 --- a/LAPACKE/cmake/lapacke-config-install.cmake.in @@ -594,12 +595,12 @@ deleted file mode 100644 -get_filename_component(_LAPACKE_PREFIX "${_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 @@ -609,7 +610,7 @@ deleted file mode 100644 -set(LAPACKE_INCLUDE_DIRS ${_LAPACKE_PREFIX}/include) - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke ${LAPACK_LIBRARIES}) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) - -unset(_LAPACKE_PREFIX) -unset(_LAPACKE_SELF_DIR) diff --git a/academic/latex2html/latex2html.SlackBuild b/academic/latex2html/latex2html.SlackBuild index 31b157c4bb..5509805331 100644 --- a/academic/latex2html/latex2html.SlackBuild +++ b/academic/latex2html/latex2html.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=latex2html -VERSION=${VERSION:-2019.2} +VERSION=${VERSION:-2020} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -80,7 +80,9 @@ CXXFLAGS="$SLKCFLAGS" \ --with-perl=/usr/bin/perl \ --enable-eps \ --enable-gif \ - --enable-png \ + --enable-svg \ + --enable-pk \ + --enable-pipes \ --build=$ARCH-slackware-linux \ --host=$ARCH-slackware-linux diff --git a/academic/latex2html/latex2html.info b/academic/latex2html/latex2html.info index b732075636..199a5829f2 100644 --- a/academic/latex2html/latex2html.info +++ b/academic/latex2html/latex2html.info @@ -1,8 +1,8 @@ PRGNAM="latex2html" -VERSION="2019.2" +VERSION="2020" HOMEPAGE="http://www.latex2html.org" -DOWNLOAD="https://github.com/latex2html/latex2html/archive/v2019.2/latex2html-2019.2.tar.gz" -MD5SUM="e9ca34903ac23a6f51385f05fa63c6eb" +DOWNLOAD="https://github.com/latex2html/latex2html/archive/v2020/latex2html-2020.tar.gz" +MD5SUM="d5e2d765ed2bb4d52bd7331a6420f5be" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/latex2html/manual.pdf b/academic/latex2html/manual.pdf Binary files differindex 28a5159b38..699a2ce464 100644 --- a/academic/latex2html/manual.pdf +++ b/academic/latex2html/manual.pdf 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 b4652d420f..c0b4d98c5e 100644 --- a/academic/ldl/ldl.SlackBuild +++ b/academic/ldl/ldl.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for LDL -# Copyright 2013-2020 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:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/ldl/ldl.info b/academic/ldl/ldl.info index 5676d5bd4f..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="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +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/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 86ade486fc..9d906e36f5 100644 --- a/academic/libqalculate/libqalculate.SlackBuild +++ b/academic/libqalculate/libqalculate.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for libqalculate -# Copyright 2016-2019 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:-3.4.0} +VERSION=${VERSION:-3.10.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/libqalculate/libqalculate.info b/academic/libqalculate/libqalculate.info index 0ff5260bd8..a2ac9c6801 100644 --- a/academic/libqalculate/libqalculate.info +++ b/academic/libqalculate/libqalculate.info @@ -1,8 +1,8 @@ PRGNAM="libqalculate" -VERSION="3.4.0" -HOMEPAGE="http://qalculate.github.io/" -DOWNLOAD="https://github.com/Qalculate/libqalculate/releases/download/v3.4.0/libqalculate-3.4.0.tar.gz" -MD5SUM="71374cfffa41ccb7721543924dea3f8d" +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/mafft/mafft.SlackBuild b/academic/mafft/mafft.SlackBuild index 77bac2a01d..844be72f25 100644 --- a/academic/mafft/mafft.SlackBuild +++ b/academic/mafft/mafft.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=mafft -VERSION=${VERSION:-7.453} +VERSION=${VERSION:-7.471} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/mafft/mafft.info b/academic/mafft/mafft.info index 4fae8a0354..dcc03b7049 100644 --- a/academic/mafft/mafft.info +++ b/academic/mafft/mafft.info @@ -1,8 +1,8 @@ PRGNAM="mafft" -VERSION="7.453" +VERSION="7.471" HOMEPAGE="https://mafft.cbrc.jp/alignment/software/" -DOWNLOAD="https://mafft.cbrc.jp/alignment/software/mafft-7.453-with-extensions-src.tgz" -MD5SUM="749a7867831482a75b1a728928ec2a1a" +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 index 9baddd56dd..a0623df2cc 100644 --- a/academic/meep/README +++ b/academic/meep/README @@ -1,14 +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. +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 may wish to preinstall: harminv, mpb +You probably will also want to preinstall: harminv, openmpi You may wish to also install: h5utils -If the build script can find the ATLAS libraries, it will -adapt the configure options to use them rather than the -default lapack. +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 index 347fb3f9ae..114680d8ec 100644 --- a/academic/meep/meep.SlackBuild +++ b/academic/meep/meep.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=meep -VERSION=${VERSION:-1.12.0} +VERSION=${VERSION:-1.17.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -74,13 +74,27 @@ 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 {} \; -LOCALCONFIGS=" --without-python --with-mpi " +# 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${LIBDIRSUFFIX}/libatlas.a ] ; then - if [ -f /usr/lib${LIBIRSUFFIX}/libatlas.so ] ; then +if [ -f /usr/lib/libatlas.a ] ; then + if [ -f /usr/lib/libatlas.so ] ; then echo "NOTICE: libatlas was found, configure --with-blas=atlas" LOCALCONFIGS=${LOCALCONFIGS}" --with-blas=atlas" fi @@ -94,20 +108,14 @@ CPPFLAGS="$SLKCFLAGS" \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux \ - --disable-static \ $LOCALCONFIGS make make install DESTDIR=$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 @@ -115,11 +123,5 @@ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -###sbolint off -if [ -f $CWD/doinst.sh ] ; then - cat $CWD/doinst.sh > $PKG/install/doinst.sh -fi -###sbolint on - cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/meep/meep.info b/academic/meep/meep.info index 4c77d9c392..8faea2fd0f 100644 --- a/academic/meep/meep.info +++ b/academic/meep/meep.info @@ -1,10 +1,10 @@ PRGNAM="meep" -VERSION="1.12.0" +VERSION="1.17.1" HOMEPAGE="https://github.com/NanoComp/meep" -DOWNLOAD="https://github.com/NanoComp/meep/releases/download/v1.12.0/meep-1.12.0.tar.gz" -MD5SUM="ce2064167a540036f315b5b7b4b8253e" +DOWNLOAD="https://github.com/NanoComp/meep/releases/download/v1.17.1/meep-1.17.1.tar.gz" +MD5SUM="657ecf1fa5459c73fdddd749dd81ec04" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="lapack openmpi hdf5 libctl" +REQUIRES="lapack hdf5 libctl mpb" MAINTAINER="PaulKinsler" EMAIL="dr.paul@kinsler.org" diff --git a/academic/meep/slack-desc b/academic/meep/slack-desc index aa2462124c..8187e87c47 100644 --- a/academic/meep/slack-desc +++ b/academic/meep/slack-desc @@ -8,7 +8,7 @@ |-----handy-ruler------------------------------------------------------| meep: meep (electromagnetics simulation using FDTD) meep: -meep: Meep is a free and open-source software package for +meep: Meep is a free and open-source software package for meep: electromagnetics simulation via the finite-difference meep: time-domain (FDTD) method spanning a broad range of meep: applications. diff --git a/academic/megax/megax.SlackBuild b/academic/megax/megax.SlackBuild index 4710ababcc..e7ae3b4e24 100644 --- a/academic/megax/megax.SlackBuild +++ b/academic/megax/megax.SlackBuild @@ -25,7 +25,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=megax -VERSION=${VERSION:-10.1.6_1} +VERSION=${VERSION:-10.1.8_1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/megax/megax.info b/academic/megax/megax.info index 2f53c52fb5..cf1d99f562 100644 --- a/academic/megax/megax.info +++ b/academic/megax/megax.info @@ -1,10 +1,10 @@ PRGNAM="megax" -VERSION="10.1.6_1" +VERSION="10.1.8_1" HOMEPAGE="http://www.megasoftware.net/" -DOWNLOAD="https://www.megasoftware.net/releases/megax_10.1.6-1_i386.deb" -MD5SUM="04d125f5dc9fd43ee3550cc65c4c7fbd" -DOWNLOAD_x86_64="https://www.megasoftware.net/releases/megax_10.1.6-1_amd64.deb" -MD5SUM_x86_64="3f3d3f937443e6baca0b8530e075fab8" +DOWNLOAD="https://www.megasoftware.net/releases/megax_10.1.8-1_i386.deb" +MD5SUM="132278353e321cf8d6097aefb45dc582" +DOWNLOAD_x86_64="https://www.megasoftware.net/releases/megax_10.1.8-1_amd64.deb" +MD5SUM_x86_64="7083d62e933fd482aac50c98a13dd723" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/meme-suite/meme-suite.SlackBuild b/academic/meme-suite/meme-suite.SlackBuild index acc62dc3a5..558c35ebd6 100644 --- a/academic/meme-suite/meme-suite.SlackBuild +++ b/academic/meme-suite/meme-suite.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=meme-suite -VERSION=${VERSION:-5.1.0} +VERSION=${VERSION:-5.1.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/meme-suite/meme-suite.info b/academic/meme-suite/meme-suite.info index 4c8ad796e8..8c94b67b1f 100644 --- a/academic/meme-suite/meme-suite.info +++ b/academic/meme-suite/meme-suite.info @@ -1,8 +1,8 @@ PRGNAM="meme-suite" -VERSION="5.1.0" +VERSION="5.1.1" HOMEPAGE="http://meme-suite.org/" -DOWNLOAD="http://meme-suite.org/meme-software/5.1.0/meme-5.1.0.tar.gz" -MD5SUM="71e357be7bce1686f516858957de3921" +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" 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/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 9e69c5b702..2258892211 100644 --- a/academic/muscle/muscle.SlackBuild +++ b/academic/muscle/muscle.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for muscle -# Copyright 2011-2019 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 @@ -24,9 +24,11 @@ PRGNAM=muscle VERSION=${VERSION:-3.8.1551} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +MANUAL=muscle_userguide3.8.pdf + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -63,6 +65,7 @@ rm -rf ${PRGNAM}-${VERSION} mkdir -p ${PRGNAM}-${VERSION} cd ${PRGNAM}-${VERSION} tar xvf $CWD/${PRGNAM}_src_${VERSION}.tar.gz +tar xvf $CWD/stable.tar.gz chown -R root:root . find -L . \ @@ -78,12 +81,21 @@ CFLAGS="$SLKCFLAGS" \ make 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 $PKG/install diff --git a/academic/muscle/muscle.info b/academic/muscle/muscle.info index e7671cd1bc..e747bd6443 100644 --- a/academic/muscle/muscle.info +++ b/academic/muscle/muscle.info @@ -1,8 +1,12 @@ PRGNAM="muscle" VERSION="3.8.1551" HOMEPAGE="http://www.drive5.com/muscle/" -DOWNLOAD="http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz" -MD5SUM="1b7c9661f275a82d3cf708f923736bf8" +DOWNLOAD="http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz \ + http://www.drive5.com/muscle/stable.tar.gz \ + http://www.drive5.com/muscle/muscle_userguide3.8.pdf" +MD5SUM="1b7c9661f275a82d3cf708f923736bf8 \ + fceeab190ff13576bfd681a601e7859b \ + 58bb1b7989cf6f2c197dd46552759a40" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/muscle/slack-desc b/academic/muscle/slack-desc index 5e4e7da441..d3d95c0c28 100644 --- a/academic/muscle/slack-desc +++ b/academic/muscle/slack-desc @@ -13,7 +13,7 @@ muscle: or nucleotide sequences. A range of options is provided that give muscle: you the choice of optimizing accuracy, speed, or some compromise muscle: between the two. muscle: -muscle: Home: http://www.drive5.com/muscle/ -muscle: References: /usr/doc/muscle-3.8.31/References +muscle: http://www.drive5.com/muscle/ +muscle: http://www.drive5.com/muscle/stable.html muscle: muscle: diff --git a/academic/ncbi-blast+/ncbi-blast+.SlackBuild b/academic/ncbi-blast+/ncbi-blast+.SlackBuild index 8796217010..ded8e93c20 100644 --- a/academic/ncbi-blast+/ncbi-blast+.SlackBuild +++ b/academic/ncbi-blast+/ncbi-blast+.SlackBuild @@ -25,7 +25,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=ncbi-blast+ -VERSION=${VERSION:-2.10.0} +VERSION=${VERSION:-2.10.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/ncbi-blast+/ncbi-blast+.info b/academic/ncbi-blast+/ncbi-blast+.info index 4c2a4057d1..e41785d7da 100644 --- a/academic/ncbi-blast+/ncbi-blast+.info +++ b/academic/ncbi-blast+/ncbi-blast+.info @@ -1,10 +1,10 @@ PRGNAM="ncbi-blast+" -VERSION="2.10.0" +VERSION="2.10.1" HOMEPAGE="https://blast.ncbi.nlm.nih.gov/" -DOWNLOAD="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-src.tar.gz" -MD5SUM="0be82e26787579c5d14517af63502197" +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 index eebc302ed8..2b1492ef0e 100644 --- a/academic/nco/README +++ b/academic/nco/README @@ -1,9 +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). +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 index 3a20201103..74bd346139 100644 --- a/academic/nco/nco.SlackBuild +++ b/academic/nco/nco.SlackBuild @@ -24,7 +24,7 @@ PRGNAM=nco -VERSION=${VERSION:-4.9.2} +VERSION=${VERSION:-4.9.7} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -55,7 +55,7 @@ else LIBDIRSUFFIX="" fi -set -e # Exit on most errors +set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT @@ -83,7 +83,6 @@ CXXFLAGS="$SLKCFLAGS" \ --disable-static \ --build=$ARCH-slackware-linux -# Compile the application and install it into the $PKG directory make make install DESTDIR=$PKG @@ -93,18 +92,15 @@ 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 -# Compress info pages and remove the package's dir file rm -f $PKG/usr/info/dir gzip -9 $PKG/usr/info/*.info* -# Copy program documentation into the package 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 -# Copy the slack-desc (and a custom doinst.sh if necessary) into ./install mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/nco/nco.info b/academic/nco/nco.info index 3a4b113fb2..89cf7d6c3e 100644 --- a/academic/nco/nco.info +++ b/academic/nco/nco.info @@ -1,8 +1,8 @@ PRGNAM="nco" -VERSION="4.9.2" +VERSION="4.9.7" HOMEPAGE="http://nco.sf.net" -DOWNLOAD="https://github.com/nco/nco/archive/4.9.2/nco-4.9.2.tar.gz" -MD5SUM="366a949084d404b0380af7426ed94648" +DOWNLOAD="https://github.com/nco/nco/archive/4.9.7/nco-4.9.7.tar.gz" +MD5SUM="1ce73d3a65bcc7c9388665e57b05188f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="netcdf udunits antlr2" diff --git a/academic/nco/slack-desc b/academic/nco/slack-desc index 15c846b9c3..a65912dc40 100644 --- a/academic/nco/slack-desc +++ b/academic/nco/slack-desc @@ -9,7 +9,7 @@ nco: nco (netCDF Operators Software Stack) nco: nco: The NCO toolkit manipulates and analyzes data stored in netCDF- -nco: accessible formats, including DAP, HDF4, and HDF5. It exploits the +nco: accessible formats, including DAP, HDF4, and HDF5. It exploits the nco: geophysical expressivity of many CF (Climate & Forecast) metadata nco: conventions, the flexible description of physical dimensions nco: translated by UDUnits, the network transparency of OPeNDAP, the diff --git a/academic/ngspice/ngspice.SlackBuild b/academic/ngspice/ngspice.SlackBuild index 26525cf138..964f6d0aaf 100644 --- a/academic/ngspice/ngspice.SlackBuild +++ b/academic/ngspice/ngspice.SlackBuild @@ -7,8 +7,8 @@ # Set initial variables: PRGNAM=ngspice -VERSION=${VERSION:-31} -BUILD=${BUILD:-4} +VERSION=${VERSION:-34} +BUILD=${BUILD:-5} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -55,38 +55,48 @@ find -L . \ # Fix the lib path to the code modules if [ "$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 -./configure --prefix=/usr \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --with-readline=yes \ - --enable-xspice \ - --enable-cider \ - --enable-openmp \ - --with-ngshared +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-xspice \ - --enable-cider \ - --enable-shared \ - --disable-static \ - --enable-ndev \ - --enable-openmp \ - --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 @@ -94,17 +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${LIBDIRSUFFIX}/libngspice.so.0.0.0" -install -Dm755 src/.libs/libngspice.so.0.0.0 "$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" -mkdir -p $PKG/usr/share/icons/hicolor/48x48/apps -install -m644 $CWD/$PRGNAM.png $PKG/usr/share/icons/hicolor/48x48/apps/$PRGNAM.png +# 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/ + +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 cc47ace1ae..23f93fdba1 100644 --- a/academic/ngspice/ngspice.info +++ b/academic/ngspice/ngspice.info @@ -1,12 +1,12 @@ PRGNAM="ngspice" -VERSION="31" +VERSION="34" HOMEPAGE="http://ngspice.sourceforge.net/" -DOWNLOAD="https://sourceforge.net/projects/ngspice/files/ng-spice-rework/31/ngspice-31.tar.gz \ - https://sourceforge.net/projects/ngspice/files/ng-spice-rework/31/ngspice-31-manual.pdf" -MD5SUM="f50b4d8c6ecbf01acf121cd9edc3baab \ - cd746e20a1a23889acab51d918cc1f77" +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/octave/octave.SlackBuild b/academic/octave/octave.SlackBuild index fb2d909a46..11493d831c 100644 --- a/academic/octave/octave.SlackBuild +++ b/academic/octave/octave.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for octave -# Copyright 2012-2020 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=${VERSION:-5.2.0} +VERSION=${VERSION:-6.2.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/octave/octave.info b/academic/octave/octave.info index a4ea3e666a..d8b41a92ad 100644 --- a/academic/octave/octave.info +++ b/academic/octave/octave.info @@ -1,8 +1,8 @@ PRGNAM="octave" -VERSION="5.2.0" +VERSION="6.2.0" HOMEPAGE="https://www.gnu.org/software/octave/" -DOWNLOAD="https://ftp.gnu.org/gnu/octave/octave-5.2.0.tar.lz" -MD5SUM="3c621e85026d4a807f5639901a41ae71" +DOWNLOAD="https://ftpmirror.gnu.org/gnu/octave/octave-6.2.0.tar.lz" +MD5SUM="5de14d8561af9799e2ecf6bedfbdb346" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="%README% lapack" 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 09d2450383..536e7dd0d4 100644 --- a/academic/pari/pari.SlackBuild +++ b/academic/pari/pari.SlackBuild @@ -31,7 +31,7 @@ # Joachim Kruth -> update to version 2.11.2 PRGNAM=pari -VERSION=${VERSION:-2.11.2} +VERSION=${VERSION:-2.13.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -94,8 +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 4dab289fe4..1da54f9b76 100644 --- a/academic/pari/pari.info +++ b/academic/pari/pari.info @@ -1,8 +1,8 @@ PRGNAM="pari" -VERSION="2.11.2" +VERSION="2.13.1" HOMEPAGE="https://pari.math.u-bordeaux.fr/" -DOWNLOAD="https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-2.11.2.tar.gz" -MD5SUM="6afe748a472c33ae8787a5034d7742a9" +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/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 1583f3e62c..9eb56fc043 100644 --- a/academic/pyCRAC/README +++ b/academic/pyCRAC/README @@ -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-$VERSION/kinetic_crac_pipeline References @@ -26,10 +24,9 @@ Granneman S. If you want to run the test suite after installation, see README.tests. + Note on the Crac pipelines: -The CRAC_pipeline_PE.py and CRAC_pipeline_SE.py scripts now ONLY work -with pyCRAC version 1.3.3 and Flexbar version 3.4.0 and later(!) Use the -h flag to get a detailed help menu. The CRAC_pipeline_PE.py script needs to be run from the folder that @@ -44,4 +41,3 @@ The file containing the adapter sequences should be in the fasta format. The chromosome_lengths file should contain two tab-separated columns in which the first column has the chromosome name and the second the chromosome length. - diff --git a/academic/pyCRAC/README.tests b/academic/pyCRAC/README.tests index ee98d3fdaa..e1b634e6a3 100644 --- a/academic/pyCRAC/README.tests +++ b/academic/pyCRAC/README.tests @@ -1,7 +1,7 @@ To test the pyCRAC scripts after installing the package on Slackware: cp -R /usr/share/pyCRAC-$VERSION <path-to-your-work-directory>/ - cd <path-to-your-work-directory>/pyCRAC/tests + cd <path-to-your-work-directory>/pyCRAC-$VERSION/tests sh test.sh If all tests complete without an error, the package is working. diff --git a/academic/pyCRAC/pyCRAC.SlackBuild b/academic/pyCRAC/pyCRAC.SlackBuild index f94cec426b..6482133f42 100644 --- a/academic/pyCRAC/pyCRAC.SlackBuild +++ b/academic/pyCRAC/pyCRAC.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for pyCRAC -# Copyright 2017 Rob van Nues +# Copyright 2017-2021 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=pyCRAC -VERSION=${VERSION:-1.4.6} +VERSION=${VERSION:-1.5.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -36,9 +36,9 @@ PYTHON2=false PYTHON3=true -PIPENAM=kinetic_crac_pipeline -PIPEVER=${PIPEVER:-ffe91cc6bf7a} -PIPETAG=sgrann +PIPENAM=crac_pipelines +PIPEVER=master +#PIPETAG=sgrann if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -73,20 +73,21 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -rm -rf $PIPETAG-$PIPENAM-$PIPEVER +#rm -rf $PIPETAG-$PIPENAM-$PIPEVER +rm -rf $PIPENAM-$PIPEVER tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION mkdir $PRGNAM/$PIPENAM -if [[ -f $CWD/$PIPETAG-$PIPENAM-$PIPEVER.tar.gz ]]; then - tar xvf $CWD/$PIPETAG-$PIPENAM-$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 -elif [[ -f $CWD/$PIPEVER.tar.gz ]]; then - tar xvf $CWD/$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 +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 -rm setup.py +mv setup.py setup.py.ORIG cp $CWD/setup_slack.py setup.py rm tests/test.sh cp $CWD/test_slack.sh tests/test.sh @@ -108,14 +109,12 @@ 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 \ README.md \ + setup.py.ORIG \ + The_pyCRAC_Manual.pdf \ $CWD/README.tests $CWD/setup_slack.py \ $CWD/README \ $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/pyCRAC/pyCRAC.info b/academic/pyCRAC/pyCRAC.info index 8048dd69ec..0b293a216a 100644 --- a/academic/pyCRAC/pyCRAC.info +++ b/academic/pyCRAC/pyCRAC.info @@ -1,10 +1,10 @@ PRGNAM="pyCRAC" -VERSION="1.4.6" +VERSION="1.5.0" HOMEPAGE="http://sandergranneman.bio.ed.ac.uk/pycrac-software" -DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.4.6.tar.gz \ - https://bitbucket.org/sgrann/kinetic_crac_pipeline/get/ffe91cc6bf7a.tar.gz" -MD5SUM="ddbfbd08a5d8a178082056ef3efc99a8 \ - 8c19a15c439941cc5ae17e083f52143a" +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="python3 flexbar novocraft numpy3 pysam scipy3 pandas ruffus" diff --git a/academic/pyCRAC/setup_slack.py b/academic/pyCRAC/setup_slack.py index 421d43bebe..f76cd3868d 100644 --- a/academic/pyCRAC/setup_slack.py +++ b/academic/pyCRAC/setup_slack.py @@ -1,9 +1,9 @@ #!/usr/bin/python __author__ = "Sander Granneman" -__copyright__ = "Copyright 2019" -__version__ = "1.4.6" -__credits__ = ["Sander Granneman","Hywell Dunn Davies"] +__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" @@ -55,9 +55,8 @@ 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/crac_pipelines/CRAC_pipeline_PE.py', + 'pyCRAC/crac_pipelines/CRAC_pipeline_SE.py', ], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Environment :: Console', @@ -92,6 +91,3 @@ setup(name='pyCRAC', 'tests/genes.list']) ] ) - - - diff --git a/academic/pysam/pysam.SlackBuild b/academic/pysam/pysam.SlackBuild index 1145e63733..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 @@ -24,8 +24,8 @@ PRGNAM=pysam -VERSION=${VERSION:-0.15.4} -BUILD=${BUILD:-2} +VERSION=${VERSION:-0.16.0.1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} #set which python version to install it for @@ -75,8 +75,8 @@ 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 {} \; -###When pysam gets linked to htslib-1.10 this can be done again: -##use system htslib instead: +### pysam linked to htslib-1.10; SBo-htslib is at 1.11: +##use system htslib: #export HTSLIB_LIBRARY_DIR=/usr/lib$LIBDIRSUFFIX #export HTSLIB_INCLUDE_DIR=/usr/include diff --git a/academic/pysam/pysam.info b/academic/pysam/pysam.info index 8e87762f0f..724abb43a7 100644 --- a/academic/pysam/pysam.info +++ b/academic/pysam/pysam.info @@ -1,8 +1,8 @@ PRGNAM="pysam" -VERSION="0.15.4" +VERSION="0.16.0.1" HOMEPAGE="https://github.com/pysam-developers/pysam" -DOWNLOAD="https://pypi.python.org/packages/source/p/pysam/pysam-0.15.4.tar.gz" -MD5SUM="fed157466d6e267e32593119c05247b2" +DOWNLOAD="https://pypi.python.org/packages/source/p/pysam/pysam-0.16.0.1.tar.gz" +MD5SUM="5b4b73431f2511727f4fef43a67b392e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="python3-Cython" diff --git a/academic/qalculate-gtk/qalculate-gtk.SlackBuild b/academic/qalculate-gtk/qalculate-gtk.SlackBuild index 569baa8084..62576920e9 100644 --- a/academic/qalculate-gtk/qalculate-gtk.SlackBuild +++ b/academic/qalculate-gtk/qalculate-gtk.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for qalculate-gtk -# Copyright 2016-2019 Larry Hajali <larryhaja[at]gmail[dot]com> +# Copyright 2016-2020 Larry Hajali <larryhaja[at]gmail[dot]com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=qalculate-gtk -VERSION=${VERSION:-3.4.0} +VERSION=${VERSION:-3.10.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/qalculate-gtk/qalculate-gtk.info b/academic/qalculate-gtk/qalculate-gtk.info index e3b8170127..4884e43fbc 100644 --- a/academic/qalculate-gtk/qalculate-gtk.info +++ b/academic/qalculate-gtk/qalculate-gtk.info @@ -1,8 +1,8 @@ PRGNAM="qalculate-gtk" -VERSION="3.4.0" -HOMEPAGE="http://qalculate.github.io/" -DOWNLOAD="https://github.com/Qalculate/qalculate-gtk/releases/download/v3.4.0/qalculate-gtk-3.4.0.tar.gz" -MD5SUM="58a8670ce4f3e692acbd2f27d104f82e" +VERSION="3.10.0" +HOMEPAGE="https://qalculate.github.io/" +DOWNLOAD="https://github.com/Qalculate/qalculate-gtk/releases/download/v3.10.0/qalculate-gtk-3.10.0.tar.gz" +MD5SUM="5880b40c4a5beb9da290b28a54eb4f46" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="libqalculate" diff --git a/academic/rbio/rbio.SlackBuild b/academic/rbio/rbio.SlackBuild index 54bfe33088..e83a5cbc38 100644 --- a/academic/rbio/rbio.SlackBuild +++ b/academic/rbio/rbio.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for RBio -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=rbio SRCNAM=SuiteSparse SUBDIR=RBio VERSION=${VERSION:-2.2.6} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/rbio/rbio.info b/academic/rbio/rbio.info index a2a2652e08..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="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +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 83786cf637..a843ef1d3a 100644 --- a/academic/reduce-algebra/reduce-algebra.SlackBuild +++ b/academic/reduce-algebra/reduce-algebra.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=reduce-algebra -VERSION=${VERSION:-20200301svn5286} +VERSION=${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 a5f168bf25..46f79d0bcb 100644 --- a/academic/reduce-algebra/reduce-algebra.info +++ b/academic/reduce-algebra/reduce-algebra.info @@ -1,10 +1,10 @@ PRGNAM="reduce-algebra" -VERSION="20200301svn5286" +VERSION="20201007svn5424" HOMEPAGE="https://reduce-algebra.sourceforge.io" -DOWNLOAD="https://downloads.sourceforge.net/reduce-algebra/snapshot_2020-03-01/Reduce-svn5286-src.tar.gz \ - https://downloads.sourceforge.net/reduce-algebra/snapshot_2020-03-01/linux64/reduce-common_5286_all.tgz" -MD5SUM="28fa5a23835e5ec1474844e18bf29855 \ - 6a3b2b2e3243ff0894bef9f336597164" +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/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 ab5e912702..6772d6b5d3 100644 --- a/academic/sage/README +++ b/academic/sage/README @@ -14,11 +14,17 @@ 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 -This package does not include the doc files. Those can be found at doc.sagemath.org. +source /etc/profile.d/sage.ch -NOTE: -If you have ATOM processors, you need to run this command prior building: -export OPENBLAS_CONFIGURE="TARGET=ATOM" +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/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 7049bb6d27..6cb41edaa4 100644 --- a/academic/sage/sage.SlackBuild +++ b/academic/sage/sage.SlackBuild @@ -3,6 +3,8 @@ # Slackware build script for sage # Written by Jack Maddox <jack@auburn.edu> # 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=${VERSION:-9.0} +VERSION=${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 +76,10 @@ 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 < $CWD/sage-build-root.patch - -# Thanks to Philip Lacroix <slackph@posteo.de> -rm build/pkgs/python2/patches/sys_path_security-issue_16202.patch - -# The docs do not build correctly, so instead of make, do: +# The docs do not build correctly, so instead of make, do the following: +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}" \ + ./configure \ + --enable-build-as-root make build # test all examples in the documentation (over 93,000 line of input) @@ -114,6 +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 c88eea8153..141f25c9ef 100644 --- a/academic/sage/sage.info +++ b/academic/sage/sage.info @@ -1,8 +1,8 @@ PRGNAM="sage" -VERSION="9.0" +VERSION="9.1" HOMEPAGE="http://www.sagemath.org" -DOWNLOAD="http://mirrors.mit.edu/sage/src/sage-9.0.tar.gz" -MD5SUM="b864b8c19d376193e70eb2c8084bbd50" +DOWNLOAD="http://mirrors.mit.edu/sage/src/sage-9.1.tar.gz" +MD5SUM="35e0ecbc6cc2ae4e1a68479598e70b7a" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/samtools/README b/academic/samtools/README index 857bfbeaa7..d8e2540720 100644 --- a/academic/samtools/README +++ b/academic/samtools/README @@ -1,16 +1,16 @@ -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). +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. Note that the sam.h of htslib differs from sam.h coming -with samtools. +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. -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. +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/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild index 4a7efb30d8..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 2017-2020 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: @@ -22,8 +22,8 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=samtools -VERSION=${VERSION:-1.10} +PRGNAM=samtools +VERSION=${VERSION:-1.12} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -117,7 +117,7 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ AUTHORS LICENSE README INSTALL NEWS examples \ $PKG/usr/doc/$PRGNAM-$VERSION -cp $CWD/README.references $PKG/usr/doc/$PRGNAM-$VERSION +cp $CWD/README $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/samtools/samtools.info b/academic/samtools/samtools.info index 05fe9a33a0..91b54352ff 100644 --- a/academic/samtools/samtools.info +++ b/academic/samtools/samtools.info @@ -1,8 +1,8 @@ PRGNAM="samtools" -VERSION="1.10" +VERSION="1.12" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2" -MD5SUM="506b0b9b2628e1f3bbedd77855b4c709" +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/scilab/README b/academic/scilab/README index 300aaf1edf..66d62a3753 100644 --- a/academic/scilab/README +++ b/academic/scilab/README @@ -11,3 +11,6 @@ to run the updated profile scripts. If you have issues on upgrading/reinstalling or changing desktop environments, try delete/rename $HOME/.Scilab to resolve. + +Openjdk8 or jdk are optional. Scilab will use the system-wide installed +java if found. Otherwise, scilab will use its own internal jre. diff --git a/academic/scilab/scilab.SlackBuild b/academic/scilab/scilab.SlackBuild index dba3c52491..56e6904a67 100644 --- a/academic/scilab/scilab.SlackBuild +++ b/academic/scilab/scilab.SlackBuild @@ -24,7 +24,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=scilab -VERSION=${VERSION:-6.0.2} +VERSION=${VERSION:-6.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -70,13 +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 -# Fix an issue reported here: -#https://www.linuxquestions.org/questions/slackware-14/how-recover-from-damage-from-slackpkg-%27upgrade%27-scilab-4175656261/page3.html#post6009411 -# Slackware's versions should be plenty new enough. -mv $PKG/opt/$PRGNAM/lib/thirdparty/redist $PKG/opt/$PRGNAM/lib/thirdparty/NONWORKING_redist +# 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 2e04b16077..16c72a868c 100644 --- a/academic/scilab/scilab.info +++ b/academic/scilab/scilab.info @@ -1,10 +1,10 @@ PRGNAM="scilab" -VERSION="6.0.2" +VERSION="6.1.0" HOMEPAGE="http://www.scilab.org" -DOWNLOAD="http://www.scilab.org/download/6.0.2/scilab-6.0.2.bin.linux-i686.tar.gz" -MD5SUM="ace129667674a7292511a242fe6b921d" -DOWNLOAD_x86_64="http://www.scilab.org/download/6.0.2/scilab-6.0.2.bin.linux-x86_64.tar.gz" -MD5SUM_x86_64="667cb0789c365beab5c2b0a675ffe98d" -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 730af33108..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 scipy with the scipy3 SlackBuild. + 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/seaview/seaview.SlackBuild b/academic/seaview/seaview.SlackBuild index 522170872c..876be6afbc 100644 --- a/academic/seaview/seaview.SlackBuild +++ b/academic/seaview/seaview.SlackBuild @@ -26,7 +26,7 @@ # Thanks to developer Dr. Manolo Gouy for all his help. PRGNAM=seaview -VERSION=${VERSION:-5.0} +VERSION=${VERSION:-5.0.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/seaview/seaview.info b/academic/seaview/seaview.info index fc329f3fd3..8a1ff60d21 100644 --- a/academic/seaview/seaview.info +++ b/academic/seaview/seaview.info @@ -1,8 +1,8 @@ PRGNAM="seaview" -VERSION="5.0" +VERSION="5.0.4" HOMEPAGE="http://doua.prabi.fr/software/seaview/" -DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_5.0.tar.gz" -MD5SUM="d9f1a97672efb3fd24850cf542326915" +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 treerecs" 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/seqkit/slack-desc b/academic/seqkit/slack-desc new file mode 100644 index 0000000000..5cbf1904cb --- /dev/null +++ b/academic/seqkit/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------------------------------------------------------| +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/spades.SlackBuild b/academic/spades/spades.SlackBuild index 9111d7444e..c15747f33b 100644 --- a/academic/spades/spades.SlackBuild +++ b/academic/spades/spades.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=spades -VERSION=${VERSION:-3.14.0} +VERSION=${VERSION:-3.14.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/spades/spades.info b/academic/spades/spades.info index 34c460730b..33a015e53e 100644 --- a/academic/spades/spades.info +++ b/academic/spades/spades.info @@ -1,10 +1,10 @@ PRGNAM="spades" -VERSION="3.14.0" +VERSION="3.14.1" HOMEPAGE="http://cab.spbu.ru/software/spades/" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="http://cab.spbu.ru/files/release3.14.0/SPAdes-3.14.0.tar.gz" -MD5SUM_x86_64="e809eeb822fd103461a27eed39b6e709" +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 ffd9eb9657..8fff318251 100644 --- a/academic/spqr/patches/autoconfiscate.diff +++ b/academic/spqr/patches/autoconfiscate.diff @@ -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 576fb608ee..0ce28905bc 100644 --- a/academic/spqr/spqr.SlackBuild +++ b/academic/spqr/spqr.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for SPQR -# Copyright 2013-2020 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:-5.6.0} -BUILD=${BUILD:-2} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/spqr/spqr.info b/academic/spqr/spqr.info index 2bab1e6903..daa36cb95e 100644 --- a/academic/spqr/spqr.info +++ b/academic/spqr/spqr.info @@ -1,8 +1,8 @@ PRGNAM="spqr" VERSION="2.0.9" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="blas lapack suitesparseconfig cholmod tbb" diff --git a/academic/stellarium/README b/academic/stellarium/README index c4a3136eca..09942222a2 100644 --- a/academic/stellarium/README +++ b/academic/stellarium/README @@ -5,5 +5,5 @@ projectors. Just set your coordinates and go. For reasonable performance, you will want to have some kind of 3D acceleration. -gpsd is an optional dependency for enabling location detection through a GPS -device. +gpsd is an optional dependency for enabling location detection through +a GPS device. diff --git a/academic/stellarium/stellarium.SlackBuild b/academic/stellarium/stellarium.SlackBuild index 4c7e1ff99e..99d4bb2406 100644 --- a/academic/stellarium/stellarium.SlackBuild +++ b/academic/stellarium/stellarium.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=stellarium -VERSION=${VERSION:-0.18.1} +VERSION=${VERSION:-0.20.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/stellarium/stellarium.info b/academic/stellarium/stellarium.info index 35dd774260..ba33b79199 100644 --- a/academic/stellarium/stellarium.info +++ b/academic/stellarium/stellarium.info @@ -1,8 +1,8 @@ PRGNAM="stellarium" -VERSION="0.18.1" +VERSION="0.20.4" HOMEPAGE="http://www.stellarium.org" -DOWNLOAD="https://github.com/Stellarium/stellarium/releases/download/v0.18.1/stellarium-0.18.1.tar.gz" -MD5SUM="1eb0098db83f0543b44877a8e72acbb6" +DOWNLOAD="https://github.com/Stellarium/stellarium/releases/download/v0.20.4/stellarium-0.20.4.tar.gz" +MD5SUM="d02659c2e01582a4608a97b4aa0baf61" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="qt5" diff --git a/academic/suitesparse/README b/academic/suitesparse/README index 7eb56aa16e..a0a5eb5679 100644 --- a/academic/suitesparse/README +++ b/academic/suitesparse/README @@ -26,3 +26,7 @@ by default. SlackBuilds.org also has all the parts of this suite as individual builds - DO NOT try and install the individual parts and the suite; pick one or the other. + +For Slackware 14.2, suitesparse's version is being held at 5.7.2. +Later versions (5.8.n) are not compatible with 14.2 supplied version +of mpfr (3.1.4). diff --git a/academic/suitesparse/suitesparse.SlackBuild b/academic/suitesparse/suitesparse.SlackBuild index 938a5758fd..ea5d9248da 100644 --- a/academic/suitesparse/suitesparse.SlackBuild +++ b/academic/suitesparse/suitesparse.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for suitesparse -# Copyright 2017-2019 Christoph Willing, Brisbane Australia +# Copyright 2017-2021 Christoph Willing, Brisbane Australia # All rights reserved. # Thanks to Pablo Santamaria for previous versions # @@ -25,7 +25,7 @@ PRGNAM=suitesparse SRCNAM=SuiteSparse -VERSION=${VERSION:-5.4.0} +VERSION=${VERSION:-5.7.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -63,7 +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 \ @@ -93,7 +93,7 @@ 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 CONTRIBUTOR-LICENSE.txt README.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 9e33539498..d8b009880b 100644 --- a/academic/suitesparse/suitesparse.info +++ b/academic/suitesparse/suitesparse.info @@ -1,8 +1,8 @@ PRGNAM="suitesparse" -VERSION="5.4.0" +VERSION="5.7.2" 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/v5.7.2/SuiteSparse-5.7.2.tar.gz" +MD5SUM="7dc408bd99f825ef75fca0dda708f95d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="lapack OpenBLAS chrpath" 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 a6a40926ee..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],[5.6.0],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[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 f228f534cc..1845c790c9 100644 --- a/academic/suitesparseconfig/suitesparseconfig.SlackBuild +++ b/academic/suitesparseconfig/suitesparseconfig.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for SuiteSparse_config -# Copyright 2013-2020 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:-5.6.0} -SRCVER=${SRCVER:-5.6.0} +VERSION=${VERSION:-5.8.1} +SRCVER=${SRCVER:-5.8.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/suitesparseconfig/suitesparseconfig.info b/academic/suitesparseconfig/suitesparseconfig.info index 34bb7ee90f..17cea1c0bf 100644 --- a/academic/suitesparseconfig/suitesparseconfig.info +++ b/academic/suitesparseconfig/suitesparseconfig.info @@ -1,8 +1,8 @@ PRGNAM="suitesparseconfig" -VERSION="5.6.0" +VERSION="5.8.1" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/sundials/sundials.SlackBuild b/academic/sundials/sundials.SlackBuild index 67f7922291..149f9bd771 100644 --- a/academic/sundials/sundials.SlackBuild +++ b/academic/sundials/sundials.SlackBuild @@ -25,7 +25,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=sundials -VERSION=${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/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.${PKGTYPE:-tgz} diff --git a/academic/tiemu/tiemu.info b/academic/tiemu/tiemu.info new file mode 100644 index 0000000000..d665780f3f --- /dev/null +++ b/academic/tiemu/tiemu.info @@ -0,0 +1,10 @@ +PRGNAM="tiemu" +VERSION="3.03" +HOMEPAGE="http://lpg.ticalc.org/prj_tiemu/" +DOWNLOAD="http://download.sourceforge.net/project/gtktiemu/tiemu-linux/TIEmu%203.03/tiemu-3.03-nogdb.tar.gz" +MD5SUM="2736440d717a0ee97cdb35189814fc93" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="libticalcs2" +MAINTAINER="shelldweller" +EMAIL="shelldweller@beauxbead.com" diff --git a/academic/treerecs/README b/academic/treerecs/README index cd3794ca26..e338496bfb 100644 --- a/academic/treerecs/README +++ b/academic/treerecs/README @@ -28,3 +28,10 @@ Bio++ use. 2) genetreeEditor: a small program which provides editing of gene names using species names and format conversion (Newick, Nhx or PhyloXML) . + +For more information, see preprint at bioRxiv: +Treerecs: an integrated phylogenetic tool, from sequences to reconciliations +Nicolas Comte, Benoit Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, +Vincent Daubin, Simon Penel, Celine Scornavacca, Manolo Gouy, Alexandros +Stamatakis, Eric Tannier, View ORCID ProfileDavid P. Parsons +https://www.biorxiv.org/content/10.1101/782946v1 diff --git a/academic/treerecs/treerecs.SlackBuild b/academic/treerecs/treerecs.SlackBuild index 4bff8e9c09..ca63edaedc 100644 --- a/academic/treerecs/treerecs.SlackBuild +++ b/academic/treerecs/treerecs.SlackBuild @@ -22,17 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# Thanks to David Parsons for clarifications about the scipt and suggestions! + PRGNAM=treerecs -VERSION=${VERSION:-1.1_gitd1c1bfaf} +VERSION=${VERSION:-1.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -COMMIT=d1c1bfaf3e6f072436661c80346dee9ae54b3310 - -# Depending on whether you clicked or used wget to download, the tarball -# name is different. Bleh... -WGETNAME=archive -CLICKNAME=Treerecs-master +SRCNAM=Treerecs if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -66,15 +63,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $CLICKNAME-$COMMIT - -if [ -e $CWD/$WGETNAME.tar.gz ]; then - tar xvf $CWD/$WGETNAME.tar.gz -else - tar xvf $CWD/$CLICKNAME-$COMMIT.tar.gz -fi - -cd $CLICKNAME-$COMMIT +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 \ @@ -87,12 +78,12 @@ cd build cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_BUILD_TYPE=MinSizeRel .. + -DCMAKE_BUILD_TYPE=Release .. make cd .. # This is the program executable. Using "make install DESTDIR=$PKG" -# works, but is simply puts the treerecs in /usr/local/bin and that's it +# works, but it simply puts treerecs in /usr/local/bin and that's it install -D -m755 build/bin/$PRGNAM $PKG/usr/bin/$PRGNAM # Include the extra binaries @@ -115,6 +106,7 @@ 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.${PKGTYPE:-tgz} diff --git a/academic/treerecs/treerecs.info b/academic/treerecs/treerecs.info index 12feb2eed3..f6a81aa05b 100644 --- a/academic/treerecs/treerecs.info +++ b/academic/treerecs/treerecs.info @@ -1,8 +1,8 @@ PRGNAM="treerecs" -VERSION="1.1_gitd1c1bfaf" +VERSION="1.2" HOMEPAGE="https://project.inria.fr/treerecs/" -DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/repository/archive.tar.gz" -MD5SUM="1a378daca947481f08071b51950e021e" +DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/-/archive/v1.2/Treerecs-v1.2.tar.gz" +MD5SUM="a85d2dc0047278bfb0017c2b69824b56" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/trfind/trfind.SlackBuild b/academic/trfind/trfind.SlackBuild index 76783294e3..22702f68c8 100644 --- a/academic/trfind/trfind.SlackBuild +++ b/academic/trfind/trfind.SlackBuild @@ -23,16 +23,15 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=trfind -VERSION=${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 > $PKG/install/slack-desc diff --git a/academic/trfind/trfind.info b/academic/trfind/trfind.info index 2dfb07986d..adaf4da150 100644 --- a/academic/trfind/trfind.info +++ b/academic/trfind/trfind.info @@ -1,10 +1,10 @@ PRGNAM="trfind" -VERSION="4.09" +VERSION="4.09.1" HOMEPAGE="https://tandem.bu.edu/trf/trf.html" -DOWNLOAD="http://tandem.bu.edu/trf/downloads/trf409.linux32" -MD5SUM="285478f16f417d6e9c9700f556373e43" -DOWNLOAD_x86_64="http://tandem.bu.edu/trf/downloads/trf409.linux64" -MD5SUM_x86_64="0c594fe666e0332db1df9d160d7fabc8" +DOWNLOAD="https://github.com/Benson-Genomics-Lab/TRF/archive/v4.09.1/TRF-4.09.1.tar.gz" +MD5SUM="8569300f69776b65e22ad12caa682ab8" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/trimmomatic/trimmomatic.SlackBuild b/academic/trimmomatic/trimmomatic.SlackBuild index 1ed26bf60e..0d97cfc60f 100644 --- a/academic/trimmomatic/trimmomatic.SlackBuild +++ b/academic/trimmomatic/trimmomatic.SlackBuild @@ -24,7 +24,7 @@ PRGNAM=trimmomatic ZIPNAM=Trimmomatic -VERSION=${VERSION:-0.38} +VERSION=${VERSION:-0.39} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} 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 a75fc649e8..de420023f9 100644 --- a/academic/ugene/README +++ b/academic/ugene/README @@ -52,7 +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) -- MetaPhlAn2 (Metagenomic Phylogenetic Analysis) +- 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 c9c8a749b1..45a5a5885a 100644 --- a/academic/ugene/ugene.SlackBuild +++ b/academic/ugene/ugene.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=ugene -VERSION=${VERSION:-33.0} +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 6bacb212b0..e253011b26 100644 --- a/academic/ugene/ugene.info +++ b/academic/ugene/ugene.info @@ -1,8 +1,8 @@ PRGNAM="ugene" -VERSION="33" +VERSION="35.0" HOMEPAGE="http://ugene.net/" -DOWNLOAD="https://github.com/ugeneunipro/ugene/archive/33.0/ugene-33.0.tar.gz" -MD5SUM="d4314b2294d0bd48c26deba7101250e3" +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 b902c15281..de66ade417 100644 --- a/academic/umfpack/patches/autoconfiscate.diff +++ b/academic/umfpack/patches/autoconfiscate.diff @@ -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 c87f06711a..046a2501b6 100644 --- a/academic/umfpack/umfpack.SlackBuild +++ b/academic/umfpack/umfpack.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for UMFPACK -# Copyright 2013-2020 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=umfpack SRCNAM=SuiteSparse SUBDIR=UMFPACK VERSION=${VERSION:-5.7.9} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-1} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then diff --git a/academic/umfpack/umfpack.info b/academic/umfpack/umfpack.info index 283dfdc4cb..9b8e8496a8 100644 --- a/academic/umfpack/umfpack.info +++ b/academic/umfpack/umfpack.info @@ -1,8 +1,8 @@ PRGNAM="umfpack" VERSION="5.7.9" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="blas suitesparseconfig amd cholmod" diff --git a/academic/units/units.SlackBuild b/academic/units/units.SlackBuild index 3897551a24..188212ddbd 100644 --- a/academic/units/units.SlackBuild +++ b/academic/units/units.SlackBuild @@ -25,7 +25,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=units -VERSION=${VERSION:-2.19} +VERSION=${VERSION:-2.20} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/units/units.info b/academic/units/units.info index 679d03f203..72cad5e9c9 100644 --- a/academic/units/units.info +++ b/academic/units/units.info @@ -1,8 +1,8 @@ PRGNAM="units" -VERSION="2.19" +VERSION="2.20" HOMEPAGE="https://www.gnu.org/software/units/" -DOWNLOAD="https://ftpmirror.gnu.org/units/units-2.19.tar.gz" -MD5SUM="f38468b31a55baa926b449dfdaacc8aa" +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/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 7f72b64c93..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 3.2 at -https://veusz.github.io/releasenotes/3.2.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 41c21ffc1d..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 2016-2020, 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:-3.2} +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 > $PKG/usr/man/man1/veusz.1.gz diff --git a/academic/veusz/veusz.info b/academic/veusz/veusz.info index 9bc08e238a..eac4b5be7a 100644 --- a/academic/veusz/veusz.info +++ b/academic/veusz/veusz.info @@ -1,10 +1,10 @@ PRGNAM="veusz" -VERSION="3.2" +VERSION="3.3.1" HOMEPAGE="https://veusz.github.io/" -DOWNLOAD="https://github.com/veusz/veusz/releases/download/veusz-3.2/veusz-3.2.tar.gz" -MD5SUM="94e361a011001dda060e3a3b3c32c4f1" +DOWNLOAD="https://github.com/veusz/veusz/releases/download/veusz-3.3.1/veusz-3.3.1.tar.gz" +MD5SUM="1c7d42d6f87ea3b98fafc8dc52dbbc58" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="numpy PyQt5" +REQUIRES="numpy3 python3-PyQt5" MAINTAINER="Fellype do Nascimento" -EMAIL="fellype(at)gmail(dot)com" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/wehi-weasel/wehi-weasel b/academic/wehi-weasel/wehi-weasel index 994a389f76..f086e18ce9 100644 --- a/academic/wehi-weasel/wehi-weasel +++ b/academic/wehi-weasel/wehi-weasel @@ -3,4 +3,4 @@ # This starts the program jar file. The -Xmx1024m value indicates the # amount of RAM allocated to the program. You may wish to change this. -java -jar -Xmx1024m /usr/share/java/wehi-weasel/Weasel.jar +java -jar -Xmx2048m /opt/wehi-weasel/Weasel.jar diff --git a/academic/wehi-weasel/wehi-weasel.SlackBuild b/academic/wehi-weasel/wehi-weasel.SlackBuild index 5a8de5b25c..2eae95610b 100644 --- a/academic/wehi-weasel/wehi-weasel.SlackBuild +++ b/academic/wehi-weasel/wehi-weasel.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=wehi-weasel -VERSION=${VERSION:-3.6.11.8} +VERSION=${VERSION:-3.7.1.18} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -36,7 +36,7 @@ OUTPUT=${OUTPUT:-/tmp} SRCNAM=wsl JARNAM=Weasel -SRCVER=36118 +SRCVER=37118 SRCDIST=unix LICENSE=WeaselLicence.doc @@ -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 fd10edf09c..11c1529672 100644 --- a/academic/wehi-weasel/wehi-weasel.info +++ b/academic/wehi-weasel/wehi-weasel.info @@ -1,8 +1,8 @@ PRGNAM="wehi-weasel" -VERSION="3.6.11.8" +VERSION="3.7.1.18" HOMEPAGE="http://www.frankbattye.com.au/Weasel/" DOWNLOAD="http://www.frankbattye.com.au/Weasel/WeaselDownload.html" -MD5SUM="d13a157935311839de4a8b582389f809" +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/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/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/zotero/zotero.SlackBuild b/academic/zotero/zotero.SlackBuild index 5daa350027..8ad1d6a014 100644 --- a/academic/zotero/zotero.SlackBuild +++ b/academic/zotero/zotero.SlackBuild @@ -25,7 +25,7 @@ PRGNAM=zotero SRCNAM=Zotero -VERSION=${VERSION:-5.0.81} +VERSION=${VERSION:-5.0.85} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/zotero/zotero.info b/academic/zotero/zotero.info index b0d3909001..564a6702dd 100644 --- a/academic/zotero/zotero.info +++ b/academic/zotero/zotero.info @@ -1,10 +1,10 @@ PRGNAM="zotero" -VERSION="5.0.81" +VERSION="5.0.85" HOMEPAGE="https://www.zotero.org/" -DOWNLOAD="https://download.zotero.org/client/release/5.0.81/Zotero-5.0.81_linux-i686.tar.bz2" -MD5SUM="dac7c4c7ebae94d4b47dc3b05b0d8235" -DOWNLOAD_x86_64="https://download.zotero.org/client/release/5.0.81/Zotero-5.0.81_linux-x86_64.tar.bz2" -MD5SUM_x86_64="e39871c269ed89320f8503fc0091d765" +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" |
