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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.
2013-03-16+ mpqcasau1-1/+2
2013-03-16Import MPQC 2.3.1 as biology/mpqcasau8-0/+308
MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schroedinger equation. It runs on a wide range of architectures ranging from single many-core computers to massively parallel computers. Its design is object oriented, using the C++ programming language. Capabilities * Closed shell, unrestricted and general restricted open shell Hartree-Fock energies and gradients * Closed shell, unrestricted and general restricted open shell density functional theory energies and gradients * Second order open shell perturbation theory (OPT2[2]) and Z-averaged perturbation theory (ZAPT2) energies. * Second order closed shell Moller-Plesset perturbation theory energies and gradients. * Second order Moller-Plesset perturbation theory including an R12/F12 correlation factor. Energies of closed- and open-shell systems are supported. * Explicitly-correlated R12/F12 coupled-cluster methods via interface to Psi3 code and via native (experimental) implementation. * Explicitly-correlated multireference methods (MRCI, CASPT2) via interfaces to GAMESS and MOLCAS codes. * Robust internal coordinate geometry optimizer that efficiently optimizes molecules with many degrees of freedom. Nearly arbitrary internal coordinate constraints can be handled.
2013-02-16Recursive bump for png-1.6.wiz4-8/+8
2013-01-26Revbump after graphics/jpeg and textproc/icuadam1-2/+2
2013-01-19Add missing buildlink3s implied by openmotif but not lesstif.riastradh1-2/+4
2012-12-13Update to 2.1, from Wen Heping(myself) in PR 43395wen7-94/+13
Add LICENSE Remove unneeded MESSAGE file Upstream changes: Version 2.1 ---------------------------------------------------------------------- * Fixed bug 196 "clustalx: user feedback about use of secondary structure printed to console" - secondary structure is now used if specified in Alignment -> Alignment Parameters -> Secondary Structure Parameters UserParameters->getGui() should be used when ClustalW code needs to know if a function has been called from ClustalX * Fixed bug 204 "Nexus alignment format contain invalid line" - the amino acid alphabet line has been removed * Missing/corrupted file names in ClustalX status messages have been fixed * Fixed bug 175 "msf/pileup files cannot be read if sequences names are all numbers" - this happened if a line such as 528244 .......... .......... .......... .......... .......... was present in the first block of the file * Fixed bug 192 "Alignment in Phylip Format broken for big Alignments" * Fixed bug 198 "Warning about divergent sequences gets printed to console in ClustalX" * Fixed bug 151 "clustalx doesn't switch to profile alignment mode when profile12 is given on cmdline" ---------------------------------------------------------------------- Version 2.0.12 ---------------------------------------------------------------------- * Fixed bug 189 "Fixed filename used for iteration": Now Creating temporary file and added error check * Fixed bug 180 "Pairwise NJ tree: final bracket missing" * Fixed bug 178 "Seg-fault on 64bit when -quicktree -upgma for sequences with high identity": Using relative error now to avoid unsafe comparison which led to incorrect branching * Fixed Bug 176 "iteration doesn't iterate if -usetree is used as well" * Fixed bug 162 "percent identity file option in clustalW not working": Added -pim as command line option. See help * Fixed bug 155 "upgma trees cannot be read" * Fixed bug 147 "report duplicate sequences": "ClustalW/X now report offending sequences which are empty, duplicates etc * Fixed bug 134 "Exit when encountering unrecognized cmdline params": ClustalW now exits when encountering invalid values for command line arguments instead of just reverting to default values * Fixed bug 185 "clustal alignments differ between interactive and commandline mode" window-gap and ktuple initialisation now fixed and made the same between commandline and interactive mode * Fixed bug 184 "error messages are send to stdout" * Fixed bug when weights are 0, and nseq > INT_SCALE_FACTOR in UPGMA code (see RootedGuideTree.cpp) * General code cleanup - Introduced return values where control reached end of non-void function - Removed unused variables - Removed comparison between signed and unsigned integer expressions - Removed deprecated conversion from string constant to char* ---------------------------------------------------------------------- Version 2.0.11 ---------------------------------------------------------------------- * fixed file extension bug 166 in interactive mode * Fixed bug 169, memory violation for DNA/RNA k-tuple * Cut down distance calculation, symmetric matrix ---------------------------------------------------------------------- Version 2.0.10 ---------------------------------------------------------------------- * Fixed g++-4.3 compilation errors * Added new -quiet command line flag * Added new -stats=<file> command line flag * Fixed bug 142: command separator can now be mixed "/" and "-" on all platforms * Fixed bug 141: profile merging and saving failed * Fixed bug 139: saving of column quality scores * Updated help files (new flags, new colour parameter format) ---------------------------------------------------------------------- Version 2.0.9 ---------------------------------------------------------------------- * GUI now responding and giving feedback during alignment * automatic automake os detection * new OS_ define (set by clustalw/configure clustalx/clustalx.pro) * got rid of qt3 dependencies * removed QScrollArea bug workaround (fixed in Qt 4.3) * Fixed bug 135: Last sequence and last residue not displayed on MacOSX * Fixed bug 123: secondary structure profile alignment in clustalX on Mac * Fixed g++-4.3 build error (include climits.h) ---------------------------------------------------------------------- Version 2.0.8 ---------------------------------------------------------------------- * Implemented maxseqlen cmdline switch * Updated help-file * Fixed Bug 123: loading profile using gap penalties (ClustalX, Mac) * Fixed bug 133: providing profiles on command line fails (ClustalX) * Fixed bug 125: Angle bracket inside sequence * Fixed bug 129: Early exit on empty sequence * Fixed a couple of possible memory leaks ---------------------------------------------------------------------- Version 2.0.7 ---------------------------------------------------------------------- * Fixed bug 121: CRLF in sequence names (Pearson) are not trimmed * Fixed bug 122: convert option broken * Fixed reopened bug 114: profile alignment input didn't work with new getSeqRange routines * Fixed bug 119: build with g++ 4.3 ---------------------------------------------------------------------- Version 2.0.6 ---------------------------------------------------------------------- * Fixed bug 77: fasta input performance issue * Fixed bug 114: segfault while doing profile alignment with secondary structure mask * Removed unncessary id console output in EMBLFileParser.cpp * Fixed Bugs 108 and 109 and allowed mixed-case command line options ---------------------------------------------------------------------- Version 2.0.5 ---------------------------------------------------------------------- * Fixed bug 105: Disallowed combination of "Reset Gaps" and Iteration in GUI * Fixed bug 104 "reset all gaps doesn't work" * Changed command line separator for Mac to hyphen instead slash * Fixed full command line parsing for ClustalX after help flag ---------------------------------------------------------------------- Version 2.0.4 ---------------------------------------------------------------------- * Updated URLs in help files * Fixed bug 96: error message when loading alignment with identical sequence names * Made console output look more like 1.83 * Fixed bug 100: "Scores in clustalw2.0 don't match clustalw1.83" getMatrix was called with wrong scaling factor * Fixed bug 99: "stars in input not ignored" Asterisks were changed to gaps in alignment * New command line option: -fullhelp which dumps the built-in help file content. * Quickfix for bug 94 "quicktree seqfault" ---------------------------------------------------------------------- <= Version 2.0.3 ---------------------------------------------------------------------- * Added LICENSE file to distribution This file contains the information about commercial licensing of clustal as well as FAQ for licensing issues * Added README file to distribution This is the file that lists the files and directories on the Clustal FTP site. It also includes acknowledgements of people who have contributed binaries * Removed .pro Qt file from the distribution pro-file should be generated anew using qmake and modified according to build requirements, i.e. no need for version control. * Fixed bug where ClustalX2 was not processing command line args * Fixed Segfault on opening helpfile. Happened on Linux only with -O2 and when calling binary directly, not using the wrapper * Added debian packaging files * Added support for help command line flag GUI/xmenus version When requesting help file, graphical version of command line help is displayed (1.83 tried to open clustalw help) * Added complete automake (configure etc) system according to the following websites: - http://www.openismus.com/documents/linux/automake/automake.shtml - http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html * clustalw files source files have been moved to subdir * Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30. This fixes problem of large amount of space between sequence name and actual alignment in clustal output files * This solves bug #72 with long lines (5000+) in fasta files changed code to use strings rather than arrays. Needed to add delim parameter to getline in order to read files formatted for different OSs on different platforms. * Fixed Bug 79: "The count of amino acids in the ClustalX Postscript output not correct" Off-by-one issue * ClustalX and ClustalW version numbers are now the same and defined in ClustalW code (automake) * Fixed problem with compilation of ClustalX2 with gcc3 avoiding gcc3 error message: cannot declare member function QDir::currentPath' * Target now clustalw2 instead of clustalw * Fixed Bug 46 added in aminoacid code O for pyrrolysine * Fixed bug 89 changed clustalw2.0 to conform to 1.83 behaviour for width of sequence ID and alignment * Fixed bug 90 changed clustalw2.0 to conform to 1.83 behaviour leading spaces are stripped from FASTA identifiers. * Fixed bug 91 Clustalw2.0 now handles pseudo-FASTA/MoST format files. Strips out numbers and spaces.
2012-11-16Don't redefine local variables.joerg4-1/+72
2012-11-16Implicit int is not valid C++.joerg2-1/+15
2012-11-01+ plinkseqasau1-1/+2
2012-11-01Import PLINK/SEQ version 0.08 as biology/plinkseqasau4-0/+46
Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
2012-10-23Remove xextproto/buildlink3.mk in most cases where it occurs withwiz1-2/+1
libXext/buildlink3.mk, now that it is included there. Leave the places where its API version is set or variables from it are used directly (about 3 packages).
2012-10-21Add CONFLICTS between "azara" and "connect"cheusov1-2/+4
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-05 22:41:08 +0000