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* all: Bump PORTREVISION after lang/go120 updateDmitri Goutnik2023-09-085-5/+5
| | | | Approved by: ports-secteam (blanket)
* all: Bump PORTREVISION after lang/go{119,120} updateDmitri Goutnik2023-08-045-3/+5
| | | | Approved by: ports-secteam (blanket)
* biology/vcflib: not for armv6/7Robert Clausecker2023-07-301-0/+3
| | | | | | | | | Requires OpenMP which is not supported on armv6/armv7. Approved by: portmgr (build fix blanket) MFH: 2023Q3 (cherry picked from commit 931dd7ad39c20013888e5427f78a0120cc2682e3)
* biology/hyphy: fix build on armv7Robert Clausecker2023-06-301-0/+12
| | | | | | | With OpenMP not present, the code had a duplicate function definition. Get rid of one of the two to enable a build on armv7. Approved by: portmgr (build fix blanket)
* all: remove explicit versions in USES=python for "3.x+"Rene Ladan2023-06-2740-41/+41
| | | | | | | | | | | | | | | | | | | The logic in USES=python will automatically convert this to 3.8+ by itself. Adjust two ports that only had Python 3.7 mentioned but build fine on Python 3.8 too. finance/quickfix: mark BROKEN with PYTHON libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++ -DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable -Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi -Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings -Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x -MT _quickfix_la-QuickfixPython.lo -MD -MP -MF .deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o .libs/_quickfix_la-QuickfixPython.o warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean '-Wno-uninitialized'? [-Wunknown-warning-option] QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found ^~~~~~~~~~ 1 warning and 1 error generated. Reviewed by: portmgr, vishwin, yuri Differential Revision: <https://reviews.freebsd.org/D40568>
* biology/ncbi-cxx-toolkit: Update 26.0.1 → 27.0.0Yuri Victorovich2023-06-274-16/+18
| | | | Reported by: portscout
* biology/ngs-sdk: Update 2.11.2 → 3.0.1Yuri Victorovich2023-06-262-5/+5
| | | | Reported by: portscout
* biology/py-ete3: Update 3.1.2 → 3.1.3Yuri Victorovich2023-06-262-5/+4
| | | | Reported by: portscout
* biology/py-resdk: Update 17.0.0 → 18.0.0Yuri Victorovich2023-06-262-5/+5
| | | | Reported by: portscout
* biology/py-pyrodigal: Update 2.1.0 → 2.2.0Yuri Victorovich2023-06-262-4/+6
| | | | Reported by: portscout
* biology/py-PySCeS: Update 1.0.3 → 1.1.0Yuri Victorovich2023-06-262-5/+4
| | | | Reported by: portscout
* biology/py-python-libsbml: Update 5.19.0 → 5.20.1Yuri Victorovich2023-06-263-5/+2598
| | | | Reported by: portscout
* biology/py-deeptools: Update to 3.5.2Jason W. Bacon2023-06-192-5/+4
| | | | | Numerous enhancements and bug fixes Changes: https://github.com/deeptools/deepTools/releases
* biology/jalview: Fix build by using gradle-7.6.1 instead of gradle-8.0.1Yuri Victorovich2023-06-181-2/+2
| | | | | | The gradle upgrade seems to have broken jalview. Reported by: fallout
* biology/py-pysam: Update 0.20.0 → 0.21.0Yuri Victorovich2023-06-162-6/+5
| | | | Reported by: portscout
* biology/chip-seq: Metaport for ChIP-Seq analysisJason W. Bacon2023-06-144-0/+31
| | | | | | | Metaport to install tools for typical ChIP-Seq analysis, including QC, adapter trimming, alignment, and differential analysis. Presently identical to biology/atac-seq, but may diverge in the future.
* biology/biolibc: Update to 0.2.4.3Jason W. Bacon2023-06-102-4/+5
| | | | Add extern "C" to support use from C++ apps
* biology/peak-classifier: Update to 0.1.4.8Jason W. Bacon2023-06-102-6/+5
| | | | | Updates for libxtend API Minor fixes
* biology/fasda: Update to 0.1.3Jason W. Bacon2023-06-102-4/+4
| | | | | | | Improvements to test scripts and results analysis scripts Updates for libxtend API changes Code clean up Changes: outpaddling/libxtend/releases
* biology/biolibc-tools: Update to 0.1.4.6Jason W. Bacon2023-06-102-5/+5
| | | | | Improvements to deromanize Updates for libxtend API changes
* biology/abyss: Fix build with llvm15Muhammad Moinur Rahman2023-06-071-1/+7
| | | | Approved by: portmgr (blanket)
* biology/ncbi-toolkit: Fix build with llvm15Muhammad Moinur Rahman2023-06-061-1/+7
| | | | Approved by: portmgr (blanket)
* biology/gatk: Update 4.3.0.0 → 4.4.0.0Yuri Victorovich2023-06-042-8/+10
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* biology/fastp: Update to 0.23.4Jason W. Bacon2023-05-312-7/+4
| | | | | | | Fix regression in FASTQ reader Changes: https://github.com/OpenGene/fastp/releases Reported by: portscout
* biology/ncbi-blast+: Tag only for 64-bit architecturesJason W. Bacon2023-05-291-0/+3
| | | | | No longer builds on i386 or ppc Nobody does bioinformatics on 32-bit processors anymore
* biology/hyphy: Update to 2.5.51hfJoseph Mingrone2023-05-292-4/+4
| | | | | | FEL test still fails. See https://github.com/veg/hyphy/issues/1585. Sponsored by: The FreeBSD Foundation
* biology/libsedml: Fix build with libsbml 5.20.0Po-Chuan Hsieh2023-05-271-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/libsedml/work/.build -- The CXX compiler identification is Clang 13.0.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so - found -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) CMake Error at /usr/local/share/cmake/Modules/Internal/CheckSourceCompiles.cmake:51 (message): check_source_compiles: C: needs to be enabled before use. Call Stack (most recent call first): /usr/local/share/cmake/Modules/CheckCSourceCompiles.cmake:76 (cmake_check_source_compiles) CMakeModules/FindLIBXML.cmake:115 (CHECK_C_SOURCE_COMPILES) /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) /usr/local/share/cmake/Modules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:338 (find_package) -- LIBXML_LIBXML_TEST = CMake Error at /usr/local/share/cmake/Modules/Internal/CheckSourceCompiles.cmake:51 (message): check_source_compiles: C: needs to be enabled before use. Call Stack (most recent call first): /usr/local/share/cmake/Modules/CheckCSourceCompiles.cmake:76 (cmake_check_source_compiles) CMakeModules/FindLIBXML.cmake:125 (CHECK_C_SOURCE_COMPILES) /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) /usr/local/share/cmake/Modules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:338 (find_package) -- LIBXML_LIBXML_TEST2 = CMake Error at CMakeModules/FindLIBXML.cmake:132 (message): Unable to compile a test executable against LIBXML LIBXML_INCLUDE_DIR = /usr/local/include/libxml2 LIBXML_LIBRARY = /usr/local/lib/libxml2.so Call Stack (most recent call first): /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) /usr/local/share/cmake/Modules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:338 (find_package) -- Configuring incomplete, errors occurred! *** Error code 1 Stop.
* biology/libcombine: Fix build with libsbml 5.20.0Po-Chuan Hsieh2023-05-271-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ===> Configuring for libcombine-0.2.20 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/libcombine/work/.build -- The CXX compiler identification is Clang 13.0.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so - found -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) CMake Error at /usr/local/share/cmake/Modules/Internal/CheckSourceCompiles.cmake:51 (message): check_source_compiles: C: needs to be enabled before use. Call Stack (most recent call first): /usr/local/share/cmake/Modules/CheckCSourceCompiles.cmake:76 (cmake_check_source_compiles) CMakeModules/FindLIBXML.cmake:115 (CHECK_C_SOURCE_COMPILES) /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) CMakeModules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:308 (find_package) -- LIBXML_LIBXML_TEST = CMake Error at /usr/local/share/cmake/Modules/Internal/CheckSourceCompiles.cmake:51 (message): check_source_compiles: C: needs to be enabled before use. Call Stack (most recent call first): /usr/local/share/cmake/Modules/CheckCSourceCompiles.cmake:76 (cmake_check_source_compiles) CMakeModules/FindLIBXML.cmake:125 (CHECK_C_SOURCE_COMPILES) /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) CMakeModules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:308 (find_package) -- LIBXML_LIBXML_TEST2 = CMake Error at CMakeModules/FindLIBXML.cmake:132 (message): Unable to compile a test executable against LIBXML LIBXML_INCLUDE_DIR = /usr/local/include/libxml2 LIBXML_LIBRARY = /usr/local/lib/libxml2.so Call Stack (most recent call first): /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) CMakeModules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:308 (find_package) -- Configuring incomplete, errors occurred! *** Error code 1 Stop.
* biology/libsbml: Update to 5.20.0Po-Chuan Hsieh2023-05-275-566/+199
| | | | | | | | - Update MASTER_SITES - Update WWW - Sort PLIST Changes: https://github.com/sbmlteam/libsbml/releases
* biology/ncbi-blast+: Update to 2.14.0Jason W. Bacon2023-05-274-123/+827
| | | | | | A few bug fixes, enhancements, and performance improvements Changes: https://www.ncbi.nlm.nih.gov/books/NBK131777/
* biology/py-pysam: unbundle biology/htslibRobert Clausecker2023-05-251-2/+6
| | | | | | | | | This fixes the build on armv7 by picking up our custom fixed libhts over the bundled unfixed version. The CFLAGS workaround is now no longer required either. Approved by: yuri (maintainer) Differential Revision: https://reviews.freebsd.org/D40251
* biology/seqtk: Update to 1.4Jason W. Bacon2023-05-232-4/+4
| | | | | | | Several new subcommands Faster FASTX parsing Reported by: portscout
* biology/py-macs2: Update to 2.2.8Jason W. Bacon2023-05-222-5/+4
| | | | | | Adds support for python 3.11 Reported by: portscout
* biology/kmcp: Update 0.9.1 → 0.9.2Yuri Victorovich2023-05-222-7/+6
| | | | Reported by: portscout
* biology/gff2ps: drop maintainershipVinícius Zavam2023-05-211-1/+1
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* biology/biosoup: Update 0.10.0-2 → 0.11.0Yuri Victorovich2023-05-192-6/+4
| | | | Reported by: portscout
* */*: llvm15 build fixesMuhammad Moinur Rahman2023-05-172-2/+2
| | | | | | | llvm15 was also merged into 13.2-STABLE effective from OSVERSION 1302505. Fix the ports that failed to build with llvm15. Approved by: portmgr (blanket)
* biology/wise: Unbreak on HEADMuhammad Moinur Rahman2023-05-141-6/+16
| | | | | - Add LICENSE BSD3CLAUSE GPLv2 - Pet portclippy
* biology/fastp: Update to 0.23.3Jason W. Bacon2023-05-142-5/+6
| | | | | | | | Fix hang on bad input and a few other bugs Changes: https://github.com/OpenGene/fastp/releases Reported by: portscout
* biology/biosig: Unbreak on HEADMuhammad Moinur Rahman2023-05-121-1/+7
| | | | Approved by: portmgr (blanket)
* biology/py-multiqc: Update to 1.14Jason W. Bacon2023-05-123-28/+15
| | | | | | Numerous new features, enhancements and bug fixes Changes: https://github.com/ewels/MultiQC/releases
* biology/phyml: fix build on non-x86Robert Clausecker2023-05-084-2/+100
| | | | | | | | - only initialise x86-only fields on x86. - make code compatible with platforms where char is unsigned Obtained from: https://github.com/stephaneguindon/phyml/commit/9c55b683c875fb9923e7cb2a1092596f72040882 MFH: 2023Q2
* www/py-cachecontrol: Fix portPo-Chuan Hsieh2023-05-071-1/+1
| | | | | | | | | | | - Use lowercase PORTNAME - Fix WWW - Fix LICENSE - Fix FILECACHE and REDIS options: add missing RUN_DEPENDS - Bump PORTREVISION for package change PR: 266640 Approved by: maintainer (timeout, 3+ months)
* biology/minimap2: Update to 2.25Jason W. Bacon2023-04-293-10/+4
| | | | | | | | New feature to output sequences in secondary alignments Several minor enhancements and fixes Changes: https://github.com/lh3/minimap2/releases Reported by: portscout
* biology/bedtools: Update to 2.31.0Jason W. Bacon2023-04-292-4/+4
| | | | | | | | New summary tool Numerous minor fixes and enhancements Changes: https://github.com/arq5x/bedtools2/releases Reported by: portscout
* */*: bump all direct Boost cunsumersDima Panov2023-04-274-4/+4
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* biology/py-resdk: Update 16.0.0 → 17.0.0Yuri Victorovich2023-04-272-5/+4
| | | | Reported by: portscout
* audio/opus: bump consumers after update to 1.4Christian Weisgerber2023-04-256-5/+6
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* *: Bump PORTREVISIONs for math/mpc update to 1.3.1Gerald Pfeifer2023-04-2353-28/+53
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* devel/grpc: Update to 1.54.0 (should be part of ↵Po-Chuan Hsieh2023-04-191-1/+1
| | | | | | | | 8f17596cf5a75f2dca4b4c9f65ba02a53e1b2cd9) - Bump PORTREVISION of dependent ports for shlib change Changes: https://github.com/grpc/grpc/releases
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