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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
2015-10-12Import biology/cdhit as cdhit-4.6.4.leot4-0/+86
Packaged in pkgsrc-wip by Jason Bacon. CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
2015-07-27Skip portability checks for sample scripts.asau1-1/+5
2015-07-22+ gabeditasau1-1/+2
2015-07-22Import Gabedit 2.4.8 as biology/gabedit.asau5-0/+86
Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess and Q-Chem. It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations. Major features * Gabedit can create input file for GAMESS(US), GAUSSIAN, MOLCAS, MOLPRO , MPQC, OpenMopac, Orca, PCGamess and Q-Chem. * Gabedit can graphically display a variety of Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess, Q-Chem, (partially) ErgoSCF and (partially) ADF calculation results, including the following: + Molecular orbitals. + Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties. + Surfaces may be displayed in solid, translucent and wire mesh modes. they are can be colorcoded by a separate property. + Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes and the principal axes of the molecule. + Animation of the normal modes corresponding to vibrational frequencies. + Animation of the rotation of geometry, surfaces, contours, planes colorcoded, xyz and the principal axes of the molecule. + Animation of contours, Animation of planes colorcoded. * Gabedit can display UV-Vis, IR and Raman computed spectra. * Gabedit can generate a povray file for geometry (including hydrogen's bond),surfaces (including colorcoded surfaces), contours, planes colorcoded. * Gabedit can save picture in BMP, JPEG, PNG, PPM and PS format. * Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, planes colorcoded). * Simulated Annealing with Molecular Dynamics is implemented in Gabedit (using Amber 99 molecular mechanics parameters).
2015-07-12Comment out dependencies of the stylewiz1-5/+5
{perl>=5.16.6,p5-ExtUtils-ParseXS>=3.15}:../../devel/p5-ExtUtils-ParseXS since pkgsrc enforces the newest perl version anyway, so they should always pick perl, but sometimes (pkg_add) don't due to the design of the {,} syntax. No effective change for the above reason. Ok joerg
2015-06-27Pass -freal-loops if the compiler is clang or gcc. This does not fixdholland2-2/+7
the build, but it gets further now.
2015-06-12Recursive PKGREVISION bump for all packages mentioning 'perl',wiz7-13/+14
having a PKGNAME of p5-*, or depending such a package, for perl-5.22.0.
2015-04-25Recursive revbump following MesaLib update, categories a through f.tnn5-9/+10
2015-01-31Use INSTALL_PROGRAM for executables (instead of INSTALL_DATA).mef1-2/+2
2015-01-31Update 2.2.3 to 2.3.6mef3-13/+15
--------------------- ChangeLog unknown.
2014-12-20Update HOMEPAGE, was Host Unknown. But the link to download still gets 404.mef1-2/+2
2014-12-11Don't depend on implicit ${PREFIX}/lib.joerg1-2/+2
2014-11-24Adjust !TR1 support again.joerg2-12/+18
2014-11-21Wants pkg-config.joerg1-2/+2
2014-11-20Correction to PLIST when option wx-gui is enabled.mef1-2/+3
2014-11-20(upstream) update 2.3.0 to 2.3.2mef5-28/+46
(ChangeLog) 2012-08-20 Paolo Tosco <paolo.tosco@unito.it> * src/formats/mol2format.cpp: added a check for N.4 nitrogens (fixes PR#3557898) 2012-06-09 Paolo Tosco <paolo.tosco@unito.it> * src/kekulize.cpp: reverted the r4862 patch to kekulize.cpp; the incorrect aromaticity perception of oxonium salts concerned only the MOL2 format, so the fix was applied to mol2format.cpp instead * src/formats/mol2format.cpp: added a check to improve downstream aromaticity perception on charged molecules containing oxygen 2012-06-07 Paolo Tosco <paolo.tosco@unito.it> * include/openbabel/atom.h: added protos for CountFreeSulfurs() and IsThiocarboxylSulfur() functions which are equivalent to CountFreeOxygens() and IsCarboxylOxygen() and address (di)thiocarboxyl groups * src/atom.cpp: added the CountFreeSulfurs() and IsThiocarboxylSulfur() functions * src/forcefields/forcefieldmmff94.cpp: added some additional checks to make MMFF94 atom type assignment more robust * src/formats/mol2format.cpp: added some checks to improve downstream aromaticity perception on charged molecules containing nitrogen, oxygen and sulfur * src/kekulize.cpp: added a check to fix incorrect perception of aromatic oxonium and thionium cations (NEWS) Open Babel 2.3.1 (2011-10-14) This release represents a major bug-fix release and is a stable upgrade, strongly recommended for all users of Open Babel. Many bugs and enhancements have been added since the 2.3.0 release. Citation: Please consider citing this work if you publish work which used Open Babel: Noel M. O'Boyle , Michael Banck , Craig A. James , Chris Morley , Tim Vandermeersch and Geoffrey R. Hutchison. "Open Babel: An open chemical toolbox." Journal of Cheminformatics 2011, 3:33. http://dx.doi.org/10.1186/1758-2946-3-33
2014-10-09Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.wiz5-15/+5
2014-09-23Fix "call of overloaded 'abs(unsigned int)' is ambiguous".jperkin2-1/+26
2014-07-17Update to 1.6.924wen2-8/+10
Upstream changes: 1.6.924 [Significant changes] * Bug/feature issue tracking has moved to GitHub Issues: https://github.com/bioperl/bioperl-live/issues * DB_File has been demoted from "required" to "recommended", which should make easier for Windows users to install BioPerl if they don't need that module. [New features] * Bio::Search::HSP::GenericHSP - Bug #3370, added a "posterior_string" method to retrieve the posterior probability lines (PP) from HMMER3 reports [fjossandon] - Added a "consensus_string" method to retrieve the consensus structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon] * Bio::SearchIO::hmmer2 - The number of identical and conserved residues are now calculated directly from the homology line [fjossandon] - Now the Query Length and Hit Length are reported when the alignment runs until the end of the sequence/model ('.]' or '[]') [fjossandon] - Implemented the capture of the consensus structure lines [fjossandon] * Bio::SearchIO::hmmer3 - The number of identical and conserved residues are now calculated directly from the homology line [fjossandon] - Now the Hit Length is reported when the alignment runs until the end of the sequence/model ('.]' or '[]') [fjossandon] - Implemented the capture of the consensus structure lines [fjossandon] - Implemented the capture of the posterior probability lines [fjossandon] - Completed the development of NHMMER parsing, including alignments [fjossandon] * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder - Feature #2615, moved "_init_parse_params", "max_significance, "signif", "min_score", "min_bits, and "hit_filter" methods from 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'. This means that the Bio::SearchIO->new() parameters '-signif', '-score', '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats besides Blast, instead of being ignored. Added tests for all moved methods using HMMER outputs and run the full test suite and everything pass [fjossandon] * Bio::SeqIO::MultiFile - Autodetection of file format [fangly] * Bio::Tools::GuessSeqFormat: - Format detection from non-seekable filehandles such as STDIN [fangly] [Bug fixes] * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley] * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley] * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks] * Abstract: Fixed ActivePerl incapability of removing temporary files because of problems closing tied filehandles [fjossandon] * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing because ActivePerl were producing a ".index.pag" and ".index.dir" files instead of a single ".index" file (like Strawberry Perl). Now those temporary files are correctly considered and deleted. [fjossandon] * Test files: Added missing module requirements (DB_File and Data::Stag) to several tests files that were failing because those modules were not present. Now those test files are correctly skipped instead. [fjossandon] * Blast: Added support to changes in bl2seq from BLAST+ output, which now uses "Subject=" instead of ">" to start hit lines [yschensandiego] * Phylip: Return undef in "next_aln" at file end to avoid an infinite loop [yschensandiego] * HMMER3: When a hit description is too long, it is truncated in the Scores table. In those cases, the more complete description from the Annotation line (>>) will be used [fjossandon] * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN), since it is now used by HMMER3 format in alignments [fjossandon] * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit" to return undef if the query/hit length is unknown (like in some HMMER outputs), to avoid division by 0 crashes. Also "query_length" now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon] * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs, added support to multi-query reports, reduced code redundancy, and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon] * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon] * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon] * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne] * Fixed some Bio::Root::Utilities subroutines [fjossandon] * Double-quotes on paths are needed in some places [fjossandon] * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon] * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon] * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml with the latest changes made in their own repositories [fjossandon] * General synching of files with the master branch [fjossandon] * Fixed tests failing in Windows because of using Linux commands [fjossandon] * Closed many open filehandles that prevented temporary files deletion [fjossandon] * Fixed broken MeSH parser [fjossandon] * Fixed missing detection of format in SeqIO when given a -string [fangly]
2014-06-02DB_File was first released with perl 5obache1-2/+2
2014-06-02perl>=5.19.6 contains Module::Build>0.42obache1-5/+5
perl>=5.10.1 contains ExtUtils::Manifest>=1.52 perl>=5.8.1 contains Storable>=2.05
2014-05-29Bump for perl-5.20.0.wiz7-12/+14
Do it for all packages that * mention perl, or * have a directory name starting with p5-*, or * depend on a package starting with p5- like last time, for 5.18, where this didn't lead to complaints. Let me know if you have any this time.
2014-05-09Mark packages that are not ready for python-3.3 also not ready for 3.4,wiz1-2/+2
until proven otherwise.
2014-05-05Recursive revbump from x11/pixmanryoon3-5/+6
Fix PR pkg/48777
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