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2018-04-16Recursive bump for new fribidi dependency in pango.wiz4-8/+8
2018-03-12Recursive bumps for fontconfig and libzip dependency changes.wiz4-8/+8
2018-02-11plinkseq: use httpswiz1-3/+3
2018-01-17Belated PKGREVISION bump for devel/protobuf update.jperkin1-2/+2
Fixes at least joyent/pkgsrc#60.
2018-01-07Fix indentation in buildlink3.mk files.rillig1-2/+2
The actual fix as been done by "pkglint -F */*/buildlink3.mk", and was reviewed manually. There are some .include lines that still are indented with zero spaces although the surrounding .if is indented. This is existing practice.
2018-01-01Sort PLIST files.rillig3-6/+6
Unsorted entries in PLIST files have generated a pkglint warning for at least 12 years. Somewhat more recently, pkglint has learned to sort PLIST files automatically. Since pkglint 5.4.23, the sorting is only done in obvious, simple cases. These have been applied by running: pkglint -Cnone,PLIST -Wnone,plist-sort -r -F
2018-01-01Replaced $(ROUND) with ${CURLY} variable references.rillig1-1/+1
This has been a pkglint warning for several years now, and pkglint can even fix it automatically. And it did for this commit. Only in lang/mercury, two passes of autofixing were necessary because there were nested variables.
2018-01-01Cleanup: replace curly braces with parentheses.rillig3-15/+15
2017-12-27Re-add patch to bring timeval definition and select prototype into scope.he3-2/+19
Bump PKGREVISION.
2017-12-24chemical-mime-data: comment out dead siteswiz1-4/+3
2017-12-17biology/bwa: Update to 0.7.17bacon4-34/+39
Numerous bug fixes, enhancements, and new command-line options ok wiz@
2017-10-03transfig: remove, replaced by print/fig2devwiz1-2/+2
2017-09-17p5-Bio-ASN1-EntrezGene: update to 1.72.wiz2-8/+10
1.72 2016-09-02 06:50:53-05:00 America/Chicago * Full release (no changes from 1.71 beyond version) 1.71 2016-09-01 22:57:25-05:00 America/Chicago (TRIAL RELEASE) * Minor bump for impending BioPerl 1.7 release. * #2 : 'Unescaped left brace in regex is deprecated' with newer versions of perl fixed [fjossandon]
2017-09-17bioperl: update to 1.007002.wiz2-7/+9
Add p5-Text-Diff as test dependency. 1.7.2 - "Entebbe" [Bugs] * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks] * #245 - Code coverage fixes [zmughal,cjfields] * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne] * #238 - Use a Travis cron job for network tests [zmughal,cjfields] * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne] * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne] * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields] * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields] * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne] * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne] * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields] * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp] [Code changes] * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
2017-09-04Comment out dead sites.wiz1-2/+2
2017-09-03Comment out dead MASTER_SITES/HOMEPAGEs.wiz1-3/+3
2017-08-01Comment out some dead HOMEPAGEs.wiz5-10/+10
2017-06-05Recursive revbump from lang/perl5 5.26.0ryoon1-2/+2
2017-05-10 Deleting p5-BioPerl. Duplicate with bioperl. Sorry.mef4-37/+1
2017-05-07Add following lines for make testmef1-1/+4
BUILD_DEPENDS+= p5-Test-Most-[0-9]*:../../devel/p5-Test-Most BUILD_DEPENDS+= p5-Text-Diff-[0-9]*:../../textproc/p5-Text-Diff
2017-05-07Added biology/p5-BioPerl version 1.007001mef1-1/+2
2017-05-07Import p5-BioPerl-1.007001 as biology/p5-BioPerl.mef3-0/+32
Easy first time access to BioPerl via functions.
2017-02-14Add missing include.joerg2-1/+14
2017-02-12Recursive revbump from fonts/harfbuzzryoon4-8/+8
2017-02-06Recursive bump for harfbuzz's new graphite2 dependency.wiz4-8/+8
2017-01-19Convert all occurrences (353 by my count) ofagc2-7/+7
MASTER_SITES= site1 \ site2 style continuation lines to be simple repeated MASTER_SITES+= site1 MASTER_SITES+= site2 lines. As previewed on tech-pkg. With thanks to rillig for fixing pkglint accordingly.
2017-01-01Add python-3.6 to incompatible versions.wiz1-2/+2
2016-12-17Fixed pkglint warnings.rillig3-10/+10
2016-11-10Give up maintainership.fhajny1-2/+2
2016-11-06Update to 1.007001wen3-11/+8
Upstream changes: 1.7.1 - "Election" [Bugs] * Minor release to incorporate fix for CPAN indexing, which prevented proper updates [cjfields] * Fix problem in managing Target attribute for gff3 [Jukes34] * Minor bug fixes related to NCBI HTTPS support [cjfields] 1.7.0 - "Disney" [New site] * We have migrated to Github Pages. This was actually planned, but the recent OBF server compromise forced our hand. Brian Osborne [bosborne] took this under his wing to move docs and has done a tremendous amount of work formatting the site and working out some of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul Cantalupo and Franscison Ossandon also helped. Kudos!! * Similarly, the official issue tracker is now Github Issues. This has been updated in the relevant documentation bits (we hope!) [Code changes] * Previously deprecated modules removed * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif * Bio::DB::SeqHound has been removed due to the service no longer being available * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security reasons due to the server no longer having a valid cert * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN * Bio::Coordinate, Bio::SearchIO::blastxml, Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be added on CPAN [New features] * Docker instances of tagged releases are available! [hlapp] * NCBI HTTPS support [mjohnson and others] * Bio::SearchIO::infernal - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo] * Bio::Search::HSP::ModelHSP - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH reports [pcantalupo] * Bio::Search::Result::INFERNALResult - Added new module to represent features of Infernal reports [pcantalupo] * Bio::DB::Taxonomy SQLite option [cjfields] * WrapperBase quoted option values [majensen] * Various documentation fixes and updates [bosborne] [Bug Fixes] * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields] * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne] * NeXML parser fixes [fjossandon] * Bug fix for Bio::DB::SeqFeature memory adapter [lstein] * RT 103272 : SeqFeature database deletion skipped features with a decimal - Joshua Fortriede (Xenbase) * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon] * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon] * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon] * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields] * Issue #84: EMBL format wrapping problem [nyamned] * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon] * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex or compiled C code (when Inline::C is installed) [rocky] * Fix various Bio::Tools::Analysis remote server config problems [cjfields] * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon] * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon] * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef to be consistent with "$hit->bits" behaviour [fjossandon] * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF aminoacids made "next_seq" confused and broke the parser [fjossandon] * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table Definition, so now "join(complement(C..D),complement(A..B))" is equivalent to "complement(join(A..B,C..D))" [fjossandon] * For the many many many fixes that weren't mentioned - blame the release guy!
2016-08-28Remove unnecessary PLIST_SUBST and FILES_SUBST that are now providedwiz1-3/+1
by the infrastructure. Mark a couple more packages as not ready for python-3.x.
2016-08-03Revbump after graphics/gd updateadam4-7/+8
2016-07-24Moved documentation to share/doc/$(PKGBASE). Bumped PKGREVISION.rillig3-83/+77
2016-07-24Moved documentation to share/doc/${PKGBASE}. Bumped PKGREVISION.rillig2-50/+49
2016-07-09Remove python33: adapt all packages that refer to it.wiz1-2/+2
2016-07-09Bump PKGREVISION for perl-5.24.0 for everything mentioning perl.wiz8-15/+16
2016-06-08Bump PKGREVISION for perl-5.24.wiz1-2/+2
2016-02-25Use OPSYSVARS.jperkin1-5/+2
2016-01-03If we have started forcing another Fortran compiler (like for MOPAC7asau1-2/+3
in biology/mopac), force it here too.
2015-12-29Whitespace.dholland1-2/+2
2015-12-26Fix build.dholland2-10/+7
1. Compile C code with the C compiler, not the fortran compiler. 2. Use f2c, not g95, as the fortran compiler. XXX This package builds only with f2c, not g95. XXX There does not appear to be any way to specify this other XXX than by abusively setting PKGSRC_FORTRAN. So do that for now.
2015-12-12Fix network libs on SunOSwiedi1-1/+3
2015-12-12Fix int types and network libs on SunOSwiedi3-2/+31
2015-12-05Extend PYTHON_VERSIONS_INCOMPATIBLE to 35adam1-2/+2
2015-11-07gets() considered harmful. What is this, 1985? Fixes the build on OpenBSD.dholland3-2/+139
2015-11-07Unconditionally uses <emmintrin.h>, so restrict to x86.dholland1-4/+4
2015-11-02Add SHA512 digests for distfiles for biology category.agc38-38/+78
Existing SHA1 digests verified, all found to be the same on the machine holding the existing distfiles (morden). Existing SHA1 digests retained for now as an audit trail.
2015-10-14Add bwa.leot1-1/+2
2015-10-14Import biology/bwa as bwa-0.7.9a.leot4-0/+40
Packaged in pkgsrc-wip by Jason Bacon. BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
2015-10-12Add cdhit.leot1-1/+2
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-23 20:01:36 +0000