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* biology/molden: unbreak by chasing latest intransparent distfile update.Johannes M Dieterich2017-09-282-4/+4
| | | | | | | | | Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D12521 Notes: svn path=/head/; revision=450799
* devel/boost-*: update to 1.65.1Jan Beich2017-09-251-1/+1
| | | | | | | | | | | | Changes: http://www.boost.org/users/history/version_1_65_1.html PR: 218835 Approved by: maintainer timeout (1.65.1: 2 weeks; 1.65.0: 1 month) Tested by: jhibbits (on powerpc64, earlier version) Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D11582 Notes: svn path=/head/; revision=450560
* devel/boost-*: enable C++11 featuresJan Beich2017-09-251-1/+1
| | | | | | | | | | | PR: 218835 Obtained from: https://github.com/DragonFlyBSD/DeltaPorts/pull/690 Approved by: maintainer timeout (2 months) Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D11582 Notes: svn path=/head/; revision=450557
* biology/ssaha: unbreak with gcc7Jan Beich2017-09-241-0/+9
| | | | | | | | | | | | | In file included from Binary/..//Global/SSAHAMain.cpp:51:0: Binary/..//Global/SSAHAMain.cpp: In function 'void processQuery(QueryParameterStruct&)': Binary/..//Global/SSAHAMain.cpp:968:23: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] assert( pAligner!=false); ^ PR: 222542 Notes: svn path=/head/; revision=450500
* Remove USES=execinfo.Mathieu Arnold2017-09-222-2/+2
| | | | | | | | | | PR: 220271 Submitted by: mat (review), Yasuhiro KIMURA (PR) Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D11488 Notes: svn path=/head/; revision=450351
* Update tbb to 2018 and bump dependent ports' revisionsGanael LAPLANCHE2017-09-171-1/+1
| | | | Notes: svn path=/head/; revision=449986
* Update to 1.007002Sunpoet Po-Chuan Hsieh2017-09-153-23/+5
| | | | | | | Changes: http://search.cpan.org/dist/BioPerl-Run/Changes Notes: svn path=/head/; revision=449927
* Add p5-Bio-FeatureIO 1.6.905Sunpoet Po-Chuan Hsieh2017-09-155-0/+67
| | | | | | | | | | | | | | | | | | | | | | | | | Bio::FeatureIO is an iterator subsystem for genomic sequence features. Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg, Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::FeatureIO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (eg, GFF format, or BED format) and can either read or write feature objects (Bio::SeqFeature objects, or more correctly, Bio::FeatureHolderI implementing objects, of which Bio::SeqFeature is one such object). If you want to know what to do with a Bio::SeqFeatureI object, read Bio::SeqFeatureI. The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular FeatureIO object instance is configured for either input or output. A specific example of a stream object is the Bio::FeatureIO::gff object. WWW: http://search.cpan.org/dist/Bio-FeatureIO/ Notes: svn path=/head/; revision=449922
* Fix license information for portgs that use "the same license as Perl".Mathieu Arnold2017-09-1510-10/+10
| | | | | | | Sponsored by: Absolight Notes: svn path=/head/; revision=449893
* - Update to 1.007002Wen Heping2017-09-133-15/+4
| | | | | | | Changes: http://search.cpan.org/src/CJFIELDS/BioPerl-1.007002/Changes Notes: svn path=/head/; revision=449746
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2017-09-1015-15/+15
| | | | | | | | | | | | | | | | | (via Mk/bsd.default-versions.mk and lang/gcc) which has moved from GCC 5.4 to GCC 6.4 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang, c++14-lang, c++0x, c11, or gcc-c++11-lib. PR: 219275 Notes: svn path=/head/; revision=449591
* Update to 3.3.20170530Sunpoet Po-Chuan Hsieh2017-09-042-3/+5
| | | | | | | Changes: https://github.com/stephaneguindon/phyml/releases Notes: svn path=/head/; revision=449234
* Remove expired ports:Rene Ladan2017-08-235-87/+0
| | | | | | | | | | | | | | | | | | | | | 2017-08-23 games/plee-the-bear: Broken for more than 6 months 2017-08-23 x11-themes/kde-icons-umicons: Broken for more than 6 months 2017-08-23 lang/bigloo: Broken for more than 6 months 2017-08-23 audio/linux-neroaaccodec: Broken for more than 6 months 2017-08-23 x11-themes/kde-icons-dark-glass: Broken for more than 6 months 2017-08-23 misc/fortune-mod-ferengi_rules_of_acquisition: Broken for more than 6 months 2017-08-23 misc/fortune-mod-culmea-culmilor: Broken for more than 6 months 2017-08-23 misc/xyzcmd: Broken for more than 6 months 2017-08-23 russian/fortuneru: Broken for more than 6 months 2017-08-23 security/bdc: Broken for more than 6 months 2017-08-23 x11-themes/kde-icons-icosx: Broken for more than 6 months 2017-08-23 devel/insight: Broken for more than 6 months 2017-08-23 devel/gdb66: Broken for more than 6 months 2017-08-23 biology/biojava: Broken for more than 6 months 2017-08-23 games/xroach: Broken for more than 6 months Notes: svn path=/head/; revision=448603
* Update GNUstep core libraries.David Chisnall2017-08-211-1/+1
| | | | | | | | | | | | | Update the default Objective-C compiler. Fix various build failures in GNUstep ports from newer versions of the GNUstep core libraries and from changes to GNUstep Make. Update various ports that use GNUstep and bump the portrevision of the ones that haven't had a new release. Notes: svn path=/head/; revision=448472
* - update to 1.70Wen Heping2017-08-182-4/+4
| | | | | | | | | PR: 221443 Submitted by: wen@(myself) Approved by: maintainer Notes: svn path=/head/; revision=448228
* biology/diamond: Update to version 0.9.10Joseph Mingrone2017-08-152-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.10 Notes: svn path=/head/; revision=448009
* - Update to 1.53Wen Heping2017-07-232-4/+4
| | | | Notes: svn path=/head/; revision=446458
* Deprecate ports BROKEN for more than 6 monthsAntoine Brodin2017-07-221-0/+2
| | | | Notes: svn path=/head/; revision=446387
* biology/seaview: Update version 4.6.1=>4.6.2Muhammad Moinur Rahman2017-07-212-4/+4
| | | | Notes: svn path=/head/; revision=446346
* Chase next distfile update. Upstream contacted whether we would be allowed ↵Johannes M Dieterich2017-07-132-4/+4
| | | | | | | | | | | to host a distfile copy. Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D11586 Notes: svn path=/head/; revision=445717
* biology/molden: Unbreak by chasing their latest opaque update to the ↵Johannes M Dieterich2017-07-122-7/+5
| | | | | | | | | | | distribution. Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D11338 Notes: svn path=/head/; revision=445570
* Update math/gsl to 2.4Tobias C. Berner2017-07-031-1/+1
| | | | | | | | Exp-Run by: antoine PR: 220408 Notes: svn path=/head/; revision=444988
* biology/diamond: Update to version 0.9.9Joseph Mingrone2017-07-032-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.9 Notes: svn path=/head/; revision=444981
* Update devel/readline to 7.0 patch 3Sunpoet Po-Chuan Hsieh2017-06-271-1/+1
| | | | | | | | | | | | | | - Bump PORTREVISION for shlib change Changes: https://cnswww.cns.cwru.edu/php/chet/readline/CHANGES https://lists.gnu.org/archive/html/bug-bash/2016-09/msg00107.html https://lists.gnu.org/archive/html/bug-readline/2017-01/msg00002.html Differential Revision: https://reviews.freebsd.org/D11172 PR: 219947 Exp-run by: antoine Notes: svn path=/head/; revision=444463
* Begin deorbit burn of ia64. We have not attempted to build packages forMark Linimon2017-06-251-1/+1
| | | | | | | | | | | it for many years. While here, alphabetize ARCHs, pet portlint, and modernize usages. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=444251
* Mark BROKEN.Mathieu Arnold2017-06-221-0/+2
| | | | | | | | | | | => Attempting to fetch ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz fetch: ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz: size mismatch: expected 5339411, actual 5339467 => Couldn't fetch it - please try to retrieve this Sponsored by: Absolight Notes: svn path=/head/; revision=444104
* biology/diamond: Update to version 0.9.8Joseph Mingrone2017-06-162-4/+4
| | | | Notes: svn path=/head/; revision=443706
* - Update WWWDmitry Marakasov2017-06-102-8/+7
| | | | | | | | - Add LICENSE - Simplify installation Notes: svn path=/head/; revision=443073
* - Update to 0.11.2.2Wen Heping2017-06-102-4/+4
| | | | | | | | PR: 219892 Submitted by: yuri@rawbw.com(maintainer) Notes: svn path=/head/; revision=443056
* Previous commit unbroke the port.Mark Linimon2017-06-031-2/+0
| | | | | | | Reported by: xmj Notes: svn path=/head/; revision=442480
* biology/diamond: Update to version 0.9.4Joseph Mingrone2017-06-032-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.4 Notes: svn path=/head/; revision=442478
* Remove outdated PERL_LEVEL checkSunpoet Po-Chuan Hsieh2017-06-011-8/+2
| | | | Notes: svn path=/head/; revision=442335
* Remove outdated PERL_LEVEL checkSunpoet Po-Chuan Hsieh2017-06-011-8/+2
| | | | Notes: svn path=/head/; revision=442334
* Update WWWSunpoet Po-Chuan Hsieh2017-05-301-1/+1
| | | | Notes: svn path=/head/; revision=442081
* biology/diamond: Update to version 0.9.3Joseph Mingrone2017-05-292-4/+4
| | | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases Approved by: swills (mentor, implicit) Notes: svn path=/head/; revision=441991
* Mark some ports failing on armv6, for errors classified as "clang".Mark Linimon2017-05-271-0/+2
| | | | | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=441847
* Mark some ports failing on armv6, for errors classified as "???".Mark Linimon2017-05-262-3/+6
| | | | | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=441814
* biology/molden: Chase recent upstream change of molden distfile.Johannes M Dieterich2017-05-242-4/+4
| | | | | | | | | Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D10864 Notes: svn path=/head/; revision=441560
* - Update to 0.11.2.1Jochen Neumeister2017-05-232-5/+5
| | | | | | | | | | PR: 219396 Submitted by: Yuri Victorovich (Maintainer) <yuri@rawbw.com> Approved by: rene (mentor) Differential Revision: https://reviews.freebsd.org/D10856 Notes: svn path=/head/; revision=441555
* biology/diamond: Update to version 0.9.1Joseph Mingrone2017-05-232-6/+6
| | | | | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases - License has changed to AGPLv3 Approved by: swills (mentor, implicit) Notes: svn path=/head/; revision=441513
* Revision bump of all ports with USE_GL after consolidation of mesa-libsMatthew Rezny2017-05-233-3/+3
| | | | | | | | Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D10845 Notes: svn path=/head/; revision=441503
* It is possible that r441426 will fix the build problem on armv6. GiveMark Linimon2017-05-211-1/+0
| | | | | | | | | it a try. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=441431
* Mark some ports failing on power64. In cases where the error messageMark Linimon2017-05-211-0/+2
| | | | | | | | | | | | was a stub, provide a real one. While here, pet portlint. Approved by: portmgr (tier-2 blanket) Reported by: swills Notes: svn path=/head/; revision=441429
* Mark BROKEN: checksum and size mismatchAntoine Brodin2017-05-191-0/+2
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=441258
* - Update to 5.15.0Wen Heping2017-05-183-3/+14
| | | | Notes: svn path=/head/; revision=441126
* Mark some ports failing on power64. In cases where the error messageMark Linimon2017-05-135-3/+6
| | | | | | | | | | | was a stub, provide a real one. While here, pet portlint. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=440746
* - Update to 0.11.1Martin Wilke2017-05-072-4/+4
| | | | | | | | PR: 219122 Submitted by: maintainer Notes: svn path=/head/; revision=440347
* - Update to 1.5.1Martin Wilke2017-05-072-6/+4
| | | | Notes: svn path=/head/; revision=440343
* bx-python is a python library and associated set of scripts to allow for rapidMartin Wilke2017-05-064-0/+47
| | | | | | | | | | | | | | | | | | | | | | | | | implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats). Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems). Data structures for working with intervals on sequences: * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation WWW: https://github.com/bxlab/bx-python PR: 218757 Submitted by: Yuri Victorovich <yuri@rawbw.com> Notes: svn path=/head/; revision=440232
* pysam is a lightweight wrapper of the htslib C-API and provides facilities toMartin Wilke2017-05-065-0/+47
| | | | | | | | | | | | | | | | | | read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing. This module provides a low-level wrapper around the htslib C-API as using cython and a high-level API for convenient access to the data within standard genomic file formats. WWW: https://pypi.python.org/pypi/pysam PR: 218745 Submitted by: Yuri Victorovich <yuri@rawbw.com> Notes: svn path=/head/; revision=440231
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