Commit graph

404 commits

Author SHA1 Message Date
mef
cc535ed362 Use INSTALL_PROGRAM for executables (instead of INSTALL_DATA). 2015-01-31 06:21:39 +00:00
mef
fc96e80a63 Update 2.2.3 to 2.3.6
---------------------
ChangeLog unknown.
2015-01-31 06:18:42 +00:00
mef
5d1643bcbd Update HOMEPAGE, was Host Unknown. But the link to download still gets 404. 2014-12-20 12:02:28 +00:00
joerg
7e52fa03d6 Don't depend on implicit ${PREFIX}/lib. 2014-12-11 22:06:08 +00:00
joerg
67ad55aa8d Adjust !TR1 support again. 2014-11-24 00:47:48 +00:00
joerg
a18826148d Wants pkg-config. 2014-11-21 22:14:52 +00:00
mef
081f03f18c Correction to PLIST when option wx-gui is enabled. 2014-11-20 09:10:32 +00:00
mef
ea926497d1 (upstream) update 2.3.0 to 2.3.2
(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
2014-11-20 09:05:56 +00:00
wiz
cda18437be Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles. 2014-10-09 14:05:50 +00:00
jperkin
4ef19a60c0 Fix "call of overloaded 'abs(unsigned int)' is ambiguous". 2014-09-23 14:33:40 +00:00
wen
964cd83308 Update to 1.6.924
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]
2014-07-17 12:12:26 +00:00
obache
3994080cf7 DB_File was first released with perl 5 2014-06-02 12:51:38 +00:00
obache
78940b3039 perl>=5.19.6 contains Module::Build>0.42
perl>=5.10.1 contains ExtUtils::Manifest>=1.52
perl>=5.8.1 contains Storable>=2.05
2014-06-02 10:06:06 +00:00
wiz
7eeb51b534 Bump for perl-5.20.0.
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.
2014-05-29 23:35:13 +00:00
wiz
c1b44346cd Mark packages that are not ready for python-3.3 also not ready for 3.4,
until proven otherwise.
2014-05-09 07:36:53 +00:00
ryoon
60806aa001 Recursive revbump from x11/pixman
Fix PR pkg/48777
2014-05-05 00:47:34 +00:00
asau
5aac8e7753 __BSD_VISIBLE is needed on FreeBSD for PF_INET. 2014-04-17 21:23:19 +00:00
fhajny
dc42978d41 SunOS has rpc/xdr.h and builds xtcformat.so too. 2014-04-07 09:36:53 +00:00
fhajny
354d10fbe0 Update biology/bioperl to 1.6.923.
Way too many changes (0.7.0 was released in 2001!).

See changelog at:

https://github.com/bioperl/bioperl-live/blob/master/Changes
2014-02-20 14:44:16 +00:00
fhajny
c00a54ff57 Add p5-Bio-ASN1-EntrezGene 2014-02-20 11:44:51 +00:00
fhajny
2535650865 Import biology/p5-Bio-ASN1-EntrezGene.
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.
2014-02-20 11:43:56 +00:00
wiz
74706f73eb Add standard comment to not-ready-for-python line. 2014-02-17 14:32:48 +00:00
wiz
d562647396 Mark as not ready for python-3.x.
While here, slightly clean up Makefile and fix conflict with itself
by adding ${PYVERSSUFFIX} to pymol binary.
Bump PKGREVISION.
2014-02-17 14:32:28 +00:00
wiedi
1f326d79ad fix build on SunOS 2014-02-08 12:27:14 +00:00
wiz
aece887324 Convert to versioned_dependencies.mk for Pmw. 2014-01-18 19:56:36 +00:00
wiz
e03c03b6dc Recursive PKGREVISION bump for libgcrypt-1.6.0 shlib major bump. 2014-01-01 11:52:02 +00:00
jperkin
d35e64c22e Add socket libraries on SunOS. Patch from Sebastian Wiedenroth. 2013-12-10 14:18:05 +00:00
joerg
9755c6395e Fix extraction of rpath options from Fortran linker. 2013-11-29 12:53:26 +00:00
asau
4fe2717ab4 Update to chemtool 1.6.14
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
2013-10-30 15:13:02 +00:00
ryoon
3fba1a52dd Recursive revbump from pango-1.36.0 2013-10-10 14:41:44 +00:00
obache
ec69670169 Use CMake builtin variable for mandir. 2013-10-09 11:39:28 +00:00
adam
d2cb6dec32 Revbump after cairo update 2013-09-02 19:50:38 +00:00
wen
cb96245235 Update to 3.0
Add LICENSE
Add more distfile mirrors

Upstream changelog please visit:
http://selab.janelia.org/software/hmmer3/3.0/RELEASE-NOTES
2013-07-21 15:58:51 +00:00
ryoon
7d9b0f4882 Revbump from devel/libexecinfo/builtin.mk. 2013-07-03 14:48:00 +00:00
wiz
e0b49a2fed Bump PKGREVISION for libXft changes for NetBSD native X support on
NetBSD 6, requested by tron.
2013-06-06 12:53:40 +00:00
tron
a36fb86593 Try to fix the fallout caused by the fix for PR pkg/47882. Part 3:
Recursively bump package revisions again after the "freetype2" and
"fontconfig" handling was fixed.
2013-06-04 22:15:37 +00:00
wiz
c83ffb8583 Bump freetype2 and fontconfig dependencies to current pkgsrc versions,
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
2013-06-03 10:04:30 +00:00
wiz
98c3768c3a Bump all packages for perl-5.18, that
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.
2013-05-31 12:39:35 +00:00
joerg
1093a6cafa Make the gross hack even more gross to ensure the destdir installation
works.
2013-05-09 20:03:51 +00:00
joerg
8dc03f3103 Fix missing include. Don't use libstdc++ implementation detail.
Free correct variable. Bump revision.
2013-05-09 13:45:44 +00:00
joerg
5bd162c3d9 When using C++11 or libc++, prefer <memory> and <unordered_map> without
the tr1 namespace.
2013-05-06 14:22:42 +00:00
joerg
3769fa0bfc Add a number of includes hidden by libstdc++'s name space pollution. 2013-04-29 21:31:09 +00:00
joerg
425c5336f2 Update to pymol 1.5.0.1:
- bug fixes
- improvements to performance and render quality
2013-04-14 19:48:56 +00:00
asau
6929b96ca2 Revert pkglint-induced nonsense. 2013-04-08 18:29:37 +00:00
rodent
6b46c62d2e Edited DESCR in the case of:
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.
2013-04-07 20:49:31 +00:00
rodent
76e83cbf5c Various MASTER_SITES-related fixes. 2013-04-06 14:09:32 +00:00
rodent
dea2f05b46 ".for variable names should not contain uppercase letters" 2013-04-06 13:24:18 +00:00
asau
8868637051 Leave a note about Tk dependency so that the story doesn't repeat.
Skip interpreter check for tkmolrender.
2013-04-01 22:23:17 +00:00
asau
a55733f5d4 Revert. It doesn't require Tk to be functional. 2013-04-01 18:39:05 +00:00
sbd
b3d75efb83 Mark as not MAKE_JOBS safe. 2013-04-01 08:56:43 +00:00