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* biology/hyphy: Update to version 2.3.14.16Joseph Mingrone2018-10-203-5/+11
| | | | | | | | | | | | | | | | | | | This pulls in fixes after the 2.3.14 release. Upstream changes for version 2.3.14: https://github.com/veg/hyphy/releases/tag/2.3.14 Subsequent fixes: https://github.com/veg/hyphy/commit/1ecac31 https://github.com/veg/hyphy/commit/bec6833 https://github.com/veg/hyphy/commit/9847438 https://github.com/veg/hyphy/commit/02dcedd https://github.com/veg/hyphy/commit/8f44d3c https://github.com/veg/hyphy/commit/5297c30 https://github.com/veg/hyphy/commit/3d88d3e Notes: svn path=/head/; revision=482495
* biology/py-loompy: Update 2.0.14 -> 2.0.15Yuri Victorovich2018-10-192-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=482408
* New port: biology/py-gffutils: Work with GFF and GTF files in a flexible ↵Yuri Victorovich2018-10-194-0/+36
| | | | | | | database framework Notes: svn path=/head/; revision=482400
* New port: biology/py-pyfaidx: Efficient pythonic random access to fasta ↵Yuri Victorovich2018-10-194-0/+38
| | | | | | | subsequences Notes: svn path=/head/; revision=482399
* New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) ↵Yuri Victorovich2018-10-194-0/+32
| | | | | | | files Notes: svn path=/head/; revision=482398
* biology/ngs-sdk: Update 2.9.2 -> 2.9.3Yuri Victorovich2018-10-183-5/+5
| | | | Notes: svn path=/head/; revision=482381
* biology/py-orange3-single-cell: Update 0.8.1 -> 0.8.2Yuri Victorovich2018-10-172-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=482277
* biology/iqtree: Update to version 1.6.7.1Joseph Mingrone2018-10-162-4/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7.1 Notes: svn path=/head/; revision=482228
* biology/py-orange3-single-cell: Update 0.8.0 -> 0.8.1Yuri Victorovich2018-10-142-6/+11
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=482023
* biology/py-orange3-bioinformatics: Update 3.2.0 -> 3.2.2Yuri Victorovich2018-10-142-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=482019
* Deprecate most glib12 consumersAntoine Brodin2018-10-121-0/+3
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=481888
* Update devel/tbb to version 2019.1 and bump dependent ports' revisionsGanael LAPLANCHE2018-10-111-1/+1
| | | | | | | Also, reintegrate HTML documentation that was removed in previous version. Notes: svn path=/head/; revision=481833
* Update to 1.73Sunpoet Po-Chuan Hsieh2018-10-102-6/+10
| | | | | | | Changes: https://metacpan.org/changes/distribution/Bio-ASN1-EntrezGene Notes: svn path=/head/; revision=481714
* New port: biology/ncbi-cxx-toolkit: NCBI C++ ToolkitYuri Victorovich2018-10-085-0/+70
| | | | Notes: svn path=/head/; revision=481520
* biology/ncbi-toolkit: Update 2012.06.20 -> 2017.01.06Yuri Victorovich2018-10-076-175/+87
| | | | | | | | | | | Port changes: * Take maintainership * Add to LIB_DEPENDS and USExx * Remove lists of executables and manpages, use file listing instead (*) * Update WWW Notes: svn path=/head/; revision=481472
* biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/Yuri Victorovich2018-10-0713-1004/+0
| | | | | | | | | | | | | Port changes: * Take maintainership * Implement the 'benchmarks' target, and stop installing benchmarks * Add USES=gmake * Update license * Change MASTER_SITES and WWW to https * Silence some commands Notes: svn path=/head/; revision=481406
* biology/py-biom-format: Update to version 2.1.7Joseph Mingrone2018-10-062-16/+14
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=481369
* Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, exceptDag-Erling Smørgrav2018-10-0615-30/+30
| | | | | | | | | | for where it resulted in a change in output from build-depends-list or run-depends-list. Approved by: portmgr (adamw) Notes: svn path=/head/; revision=481365
* Update devel/tbb to version 2019 and bump dependent port's revisionsGanael LAPLANCHE2018-10-041-0/+1
| | | | Notes: svn path=/head/; revision=481215
* - Update to 1-14-10Danilo Egea Gondolfo2018-09-284-8/+9
| | | | | | | - Move USES to make portlint happy Notes: svn path=/head/; revision=480878
* - Unbreak by adding missing pkg-plistWen Heping2018-09-282-2/+136
| | | | | | | | PR: 228758 Submitted by: mzaki@niid.go.jp(maintainer) Notes: svn path=/head/; revision=480837
* Allow building on powerpc64.Mark Linimon2018-09-271-1/+1
| | | | | | | | | PR: 231759 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=480834
* Update Objective-C LLVM version to 6.0.Brooks Davis2018-09-261-1/+1
| | | | | | | | | | | | Fixes aarch64 build. Reduces depends on obsolete LLVM 4.0. PR: 230116 Submitted by: mikael.urankar@gmail.com Approved by: theraven (prior version) Sponsored by: DARPA, AFRL Notes: svn path=/head/; revision=480741
* Change 4 ports from net/mpich2 to net/mpichYuri Victorovich2018-09-221-3/+5
| | | | | | | | | | mpich2 is the obsolete version 2.x, mpich is at the current version 3.x Ports: biology/phyml benchmarks/mdtest benchmarks/imb math/parmetis Notes: svn path=/head/; revision=480425
* - Update to 1.63Wen Heping2018-09-222-4/+4
| | | | Notes: svn path=/head/; revision=480370
* Fix build on gcc-based archs by updating USES.Mark Linimon2018-09-221-1/+1
| | | | | | | | | | | Tested on powerpc64 and amd64 (for no regression). While here, pet portlint. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=480340
* Update to 1.5.2Sunpoet Po-Chuan Hsieh2018-09-212-6/+7
| | | | | | | Changes: https://github.com/bioruby/bioruby/blob/bioruby-1.5/RELEASE_NOTES.rdoc Notes: svn path=/head/; revision=480295
* New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq dataYuri Victorovich2018-09-214-0/+44
| | | | Notes: svn path=/head/; revision=480236
* biology/py-cutadapt: Upgrade to 1.18Jason W. Bacon2018-09-203-50/+9
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D17099 Notes: svn path=/head/; revision=480173
* biology/ngs-sdk: Update 2.9.1 -> 2.9.2Yuri Victorovich2018-09-193-5/+5
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=480103
* Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-basedMark Linimon2018-09-181-1/+1
| | | | | | | | | | | | | archs such as powerpc64. Tested for no effect on amd64. While here, pet portlint. Approved by: portgmr (tier-2 blanket) Notes: svn path=/head/; revision=480003
* More precisely specify USES=compiler to fix build on gcc-basedMark Linimon2018-09-183-3/+3
| | | | | | | | | | | platforms such as powerpc64. Tested on powerpc64, amd64. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=479990
* biology/py-pysam: Update 0.15.0 -> 0.15.1Yuri Victorovich2018-09-172-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=479938
* Add DOCS options to ports that should have one.Mathieu Arnold2018-09-103-0/+6
| | | | | | | | | | | Also various fixes related to said option. PR: 230864 Submitted by: mat exp-runs by: antoine Notes: svn path=/head/; revision=479406
* biology/seaview: Fix build with Clang 6Tobias Kortkamp2018-09-083-0/+65
| | | | | | | | | | | | | | | seaview.cxx:3352:24: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal] strcat(suggested, "."PDF_OR_PS_EXT); ^ http://beefy12.nyi.freebsd.org/data/head-amd64-default/p479076_s338486/logs/errors/seaview-4.7,1.log PR: 230881 Submitted by: tobik Approved by: bofh (maintainer timeout, 2 weeks) Notes: svn path=/head/; revision=479235
* Update science/hdf5 to 1.10.2Sunpoet Po-Chuan Hsieh2018-09-051-1/+1
| | | | | | | | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://portal.hdfgroup.org/display/support/HDF5%201.10.2#releasenotes https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2-RELEASE.txt PR: 231009 Exp-run by: antoine Notes: svn path=/head/; revision=479046
* Update to 1.31.0Jason E. Hale2018-09-0217-181/+201
| | | | | | | | PR: 229463 Approved by: Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer) Notes: svn path=/head/; revision=478818
* biology/stacks: Enable OpenMP (oversight in previous commit)Jason W. Bacon2018-09-011-2/+2
| | | | | | | | | | Upgrade to latest release will follow, after testing Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D16973 Notes: svn path=/head/; revision=478697
* biology/iqtree: Update to version 1.6.7Joseph Mingrone2018-08-272-5/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7 Notes: svn path=/head/; revision=478170
* biology/py-bx-python: Update 0.8.1 -> 0.8.2Yuri Victorovich2018-08-262-5/+5
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=478115
* biology/unanimity: Upgrade to latest release, soften dep version requirementsJason W. Bacon2018-08-252-11/+10
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D16902 Notes: svn path=/head/; revision=478089
* biology/protomol: Fix doubled USES overwriting the old valueTobias Kortkamp2018-08-251-3/+2
| | | | | | | - Make sure shebangfix is actually used Notes: svn path=/head/; revision=477997
* biology/protomol: Fix build with Clang 6Tobias Kortkamp2018-08-251-0/+1
| | | | | | | | | | | | | | | Report.cpp:208:12: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const std::__1::ostream' (aka 'const basic_ostream<char>')) *myStream << a; ~~~~~~~~~ ^ ~ /usr/include/c++/v1/ostream:218:20: note: candidate function not viable: no known conversion from 'const std::__1::ostream' (aka 'const basic_ostream<char>') to 'const void *' for 1st argument; take the address of the argument with & basic_ostream& operator<<(const void* __p); ^ ... and so on ... http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/protomol-2.0.3_13.log Notes: svn path=/head/; revision=477996
* biology/primer3: Fix build with Clang 6Tobias Kortkamp2018-08-251-0/+24
| | | | | | | | | | | | | | thal.c:426:13: error: comparison between pointer and integer ('int' and 'const unsigned char *') if ('\0' == oligo_f) { ~~~~ ^ ~~~~~~~ thal.c:431:13: error: comparison between pointer and integer ('int' and 'const unsigned char *') if ('\0' == oligo_r) { ~~~~ ^ ~~~~~~~ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/primer3-2.3.6.log Notes: svn path=/head/; revision=477995
* biology/libsbml: Fix build with Clang 6Tobias Kortkamp2018-08-251-9/+2
| | | | | | | | | | | | | | | | In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:41: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLDocument.h:298: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLTransforms.h:48: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/FunctionDefinition.h:129: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBO.h:207: /usr/include/c++/v1/map:629:15: error: object of type 'std::__1::pair<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>' cannot be assigned because its copy assignment operator is implicitly deleted {__nc = __v.__cc; return *this;} ^ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/libsbml-5.17.0.log Notes: svn path=/head/; revision=477994
* biology/avida: Fix build with Clang 6Tobias Kortkamp2018-08-251-0/+1
| | | | | | | | | | | | | | | | | | | | | avida-core/source/main/cPopulation.cc:2916:20: error: no matching member function for call to 'push_back' track_founders.push_back(make_pair(organism->GetBioGroup("genotype")->GetID(), new_genome.AsString())); ~~~~~~~~~~~~~~~^~~~~~~~~ /usr/include/c++/v1/vector:688:36: note: candidate function not viable: no known conversion from 'pair<[...], typename __make_pair_return<cString>::type>' to 'const pair<[...], std::__1::basic_string<char>>' for 1st argument _LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x); ^ /usr/include/c++/v1/vector:691:36: note: candidate function not viable: no known conversion from 'pair<[...], typename __make_pair_return<cString>::type>' to 'pair<[...], std::__1::basic_string<char>>' for 1st argument _LIBCPP_INLINE_VISIBILITY void push_back(value_type&& __x); ^ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/avida-2.12.4.log libs/tcmalloc-1.4/src/sysinfo.cc:832:88: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal] "%08"PRIx64"-%08"PRIx64" %c%c%c%c %08"PRIx64" %02x:%02x %-11"PRId64" %s\n", ^ Notes: svn path=/head/; revision=477993
* biology/lamarc: Fix build with Clang 6Tobias Kortkamp2018-08-251-0/+2
| | | | | | | | | | | | | | src/tools/mathx.cpp:781:12: error: no matching function for call to 'make_pair' return std::make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/utility:639:1: note: candidate function not viable: no known conversion from 'DoubleVec1d' (aka 'vector<double>') to 'std::__1::vector<double, std::__1::allocator<double> > &&' for 1st argument make_pair(_T1&& __t1, _T2&& __t2) ^ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/lamarc-2.1.8_1,1.log Notes: svn path=/head/; revision=477992
* Mark as broken with clang6 after r473289.Mark Linimon2018-08-241-1/+9
| | | | Notes: svn path=/head/; revision=477936
* - Update to 1.72Wen Heping2018-08-242-5/+4
| | | | | | | | | PR: 230723 Submitted by: wen@(myself) Approved by: maintainer Notes: svn path=/head/; revision=477931
* Remove expired ports:Rene Ladan2018-08-166-104/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2018-08-16 net/traceroute: Upstream gone 2018-08-15 net/e169-stats: unknown license 2018-08-15 net/l4ip: unknown license 2018-08-15 net/dhcprelay: unknown license 2018-08-15 emulators/m2000: unknown license 2018-08-15 textproc/ant-xinclude-task: unknown license 2018-08-15 textproc/bomstrip: unknown license 2018-08-15 x11-fonts/ecofont: unknown license 2018-08-15 mail/roundcube-groupvice: unknown license 2018-08-15 security/pft: unknown license 2018-08-15 devel/kickassembler: unknown license 2018-08-15 devel/gdbmods: unknown license 2018-08-15 devel/as31: unknown license 2018-08-15 databases/dbf2mysql: unknown license 2018-08-15 misc/xpns: unknown license 2018-08-15 misc/amfm: unknown license 2018-08-15 games/smashbattle: unknown license 2018-08-15 games/syobon: unknown license 2018-08-15 games/optimax: unknown license 2018-08-15 games/xgospel: unknown license 2018-08-15 biology/blat: unknown license 2018-08-15 x11-clocks/swisswatch: unknown license 2018-08-15 palm/ppmtoTbmp: unknown license 2018-08-15 dns/ghtool: unknown license 2018-08-15 x11-themes/beastie: unknown license 2018-08-15 converters/uudx: unknown license 2018-08-15 sysutils/areca-cli: unknown license Notes: svn path=/head/; revision=477371
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