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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
2014-04-17__BSD_VISIBLE is needed on FreeBSD for PF_INET.asau2-5/+19
2014-04-07SunOS has rpc/xdr.h and builds xtcformat.so too.fhajny1-0/+2
2014-02-20Update biology/bioperl to 1.6.923.fhajny6-133/+153
Way too many changes (0.7.0 was released in 2001!). See changelog at: https://github.com/bioperl/bioperl-live/blob/master/Changes
2014-02-20Add p5-Bio-ASN1-EntrezGenefhajny1-1/+2
2014-02-20Import biology/p5-Bio-ASN1-EntrezGene.fhajny3-0/+25
Bio::ASN1::EntrezGene is a regular expression-based Perl Parser for NCBI Entrez Gene genome databases (http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene). It parses an ASN.1-formatted Entrez Gene record and returns a data structure that contains all data items from the gene record.
2014-02-17Add standard comment to not-ready-for-python line.wiz1-2/+2
2014-02-17Mark as not ready for python-3.x.wiz2-9/+11
While here, slightly clean up Makefile and fix conflict with itself by adding ${PYVERSSUFFIX} to pymol binary. Bump PKGREVISION.
2014-02-08fix build on SunOSwiedi7-2/+140
2014-01-18Convert to versioned_dependencies.mk for Pmw.wiz1-2/+4
2014-01-01Recursive PKGREVISION bump for libgcrypt-1.6.0 shlib major bump.wiz1-2/+2
2013-12-10Add socket libraries on SunOS. Patch from Sebastian Wiedenroth.jperkin1-1/+6
2013-11-29Fix extraction of rpath options from Fortran linker.joerg2-8/+40
2013-10-30Update to chemtool 1.6.14asau2-7/+6
Fixes and enhancements in chemtool 1.6.14 - Updated configure script to support ARM64. - Fixed potential crash during EPS output. - Fixed detection of openbabel 2.3.x
2013-10-10Recursive revbump from pango-1.36.0ryoon3-6/+6
2013-10-09Use CMake builtin variable for mandir.obache3-6/+5
2013-09-02Revbump after cairo updateadam3-6/+6
2013-07-21Update to 3.0wen4-79/+40
Add LICENSE Add more distfile mirrors Upstream changelog please visit: http://selab.janelia.org/software/hmmer3/3.0/RELEASE-NOTES
2013-07-03Revbump from devel/libexecinfo/builtin.mk.ryoon1-2/+2
2013-06-06Bump PKGREVISION for libXft changes for NetBSD native X support onwiz3-6/+6
NetBSD 6, requested by tron.
2013-06-04Try to fix the fallout caused by the fix for PR pkg/47882. Part 3:tron4-8/+8
Recursively bump package revisions again after the "freetype2" and "fontconfig" handling was fixed.
2013-06-03Bump freetype2 and fontconfig dependencies to current pkgsrc versions,wiz4-7/+8
to address issues with NetBSD-6(and earlier)'s fontconfig not being new enough for pango. While doing that, also bump freetype2 dependency to current pkgsrc version. Suggested by tron in PR 47882
2013-05-31Bump all packages for perl-5.18, thatwiz6-11/+12
a) refer 'perl' in their Makefile, or b) have a directory name of p5-*, or c) have any dependency on any p5-* package Like last time, where this caused no complaints.
2013-05-09Make the gross hack even more gross to ensure the destdir installationjoerg1-3/+3
works.
2013-05-09Fix missing include. Don't use libstdc++ implementation detail.joerg5-3/+44
Free correct variable. Bump revision.
2013-05-06When using C++11 or libc++, prefer <memory> and <unordered_map> withoutjoerg4-1/+74
the tr1 namespace.
2013-04-29Add a number of includes hidden by libstdc++'s name space pollution.joerg2-1/+14
2013-04-14Update to pymol 1.5.0.1:joerg3-9/+38
- bug fixes - improvements to performance and render quality
2013-04-08Revert pkglint-induced nonsense.asau1-22/+26
2013-04-07Edited DESCR in the case of:rodent1-26/+22
File too long (should be no more than 24 lines). Line too long (should be no more than 80 characters). Trailing empty lines. Trailing white-space. Trucated the long files as best as possible while preserving the most info contained in them.
2013-04-06Various MASTER_SITES-related fixes.rodent1-2/+2
2013-04-06".for variable names should not contain uppercase letters"rodent3-11/+11
2013-04-01Leave a note about Tk dependency so that the story doesn't repeat.asau1-1/+4
Skip interpreter check for tkmolrender.
2013-04-01Revert. It doesn't require Tk to be functional.asau1-2/+2
2013-04-01Mark as not MAKE_JOBS safe.sbd1-1/+2
2013-04-01Add PLIST.Linux with extra file.sbd2-2/+4
Bump PKGREVISION.
2013-04-01Use PKGMANDIRsbd3-5/+6
2013-04-01Uses wish at runtime.sbd1-2/+2
2013-04-01Skip the interpreter ckeck on the demo script.sbd1-1/+3
2013-04-01Use host_alias for file paths (as it doesn't contain '-gnu').sbd2-8/+29
2013-03-26Fix build against newer protocol buffers library.asau3-1/+80
Regenerate source from missing protocol description fetched from: https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/variant.proto https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/pp.proto Bump PKGREVISION.
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