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* - Update to 1.54wen2010-07-023-49/+146
| | | | | | | PR: ports/148274 Submitted by: Ju Pengfei <jupengfei@gmail.com> Approved by: maintainer Feature safe: yes
* - Update to 2.11wen2010-06-302-4/+4
| | | | Feature safe: yes
* - Update to 1.17wen2010-06-302-4/+4
| | | | Feature safe: yes
* - Update to 1.16wen2010-06-242-4/+4
| | | | Feature safe: yes
* - Update to 2.04wen2010-06-223-7/+6
| | | | | - Pass maintainership to perl@ Feature safe: yes
* BROKEN should not be quoted.erwin2010-06-131-1/+1
| | | | No functional change.
* - Update to 1.15wen2010-06-122-5/+4
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* Update to 1.10.tobez2010-06-112-7/+6
| | | | Changes: http://search.cpan.org/dist/Bio-MAGETAB/Changes
* - Update to 1.4.0pgollucci2010-06-083-75/+188
| | | | | - Sort pkg-plist - seperate NOPORTDOCS and NOPORTEXAMPLES
* LICENSE GPLv2dinoex2010-06-062-1/+3
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* LICENSE LGPL21dinoex2010-06-051-0/+2
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* - Update to 1.4.1wen2010-06-013-4/+25
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* Bounce PORTREVISION for gettext-related ports. Have fun, ya'll.ade2010-05-311-1/+1
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* - Update to 3.1.6sylvio2010-05-313-5/+5
| | | | | PR: ports/147194 Submitted by: Glen Barber <glen.j.barber@gmail.com> (maintainer)
* - drop USE_GNUSTEP_PREFIXdinoex2010-05-304-320/+318
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* - Update to 4.0.1wen2010-05-242-4/+4
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* - fix build for gnustep-base 1.21.0dinoex2010-05-241-2/+3
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* - Update to 1.12.2wen2010-05-213-6/+7
| | | | - Reset maintainer
* - Update to 2.09wen2010-05-182-4/+4
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* - Update to 2.0.8wen2010-05-143-5/+4
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* - Update to 2.0.7wen2010-05-102-5/+5
| | | | - Set maintainer to perl@
* - Update to 3.1.4sylvio2010-05-093-11/+18
| | | | | PR: ports/146411 Submitted by: Glen Barber <glen.j.barber@gmail.com> (maintainer)
* - Update to 1.00wen2010-05-082-5/+6
| | | | - Set maintainer to perl@
* - Removed BROKEN because file fetches and checksums correctlyglarkin2010-04-291-3/+2
| | | | | | | - Added another MASTER_SITES for redundancy PR: ports/144733 Submitted by: Fernan Aguero <fernan.aguero@gmail.com> (maintainer)
* - Update to 2.04wen2010-04-202-4/+5
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* - Update to 4.4awen2010-04-202-7/+7
| | | | - Update my mail address to FreeBSD
* - update to 0.81dinoex2010-04-143-10/+32
| | | | - fix build on amd64
* - Update to 6.2.0wen2010-04-076-75/+232
| | | | | Submitted by: Wen Heping(myself) Approved by: maintainer(via Email)
* - Update to 2.03wen2010-04-022-4/+4
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* Mark various ports as broken or ignore on powerpc.linimon2010-04-013-3/+21
| | | | While here, remove remnants of alpha.
* - Update to 2.02wen2010-03-303-5/+6
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* - Bump PORTREVISION to chase the update of math/gslwen2010-03-291-2/+2
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* - update to 1.4.1dinoex2010-03-2818-20/+22
| | | | | Reviewed by: exp8 run on pointyhat Supported by: miwi
* - Update to 3.1.3wen2010-03-242-5/+5
| | | | | | | - Pass maintainership to submitter PR: ports/144992 Submitted by: Glen Barber <glen.j.barber@gmail.com>
* - Chase x11-toolkits/fltk updategahr2010-03-242-5/+5
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* - Update to 3.22sylvio2010-03-222-4/+4
| | | | Approved by: itetcu (mentor)
* - Update to 0.3.9wen2010-03-192-4/+4
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* - Update to 2.01wen2010-03-102-4/+4
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* - Update to 0.21wen2010-03-093-47/+41
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* - Update to 0.18wen2010-03-033-35/+72
| | | | | | - Adopt Feature safe: yes
* p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XMLwen2010-03-015-0/+42
| | | | | | | | over HTTP primarily for biological-data). WWW: http://search.cpan.org/dist/Bio-Das-Lite/ Feature safe: yes
* - Update to 0.7wen2010-02-243-9/+8
| | | | Feature safe: yes
* - Reset more ports I don't use anymorepgollucci2010-02-111-1/+1
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* Update to 3.1.2edwin2010-02-102-4/+4
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* - Update to 2.00wen2010-02-103-5/+5
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* - update to jpeg-8dinoex2010-02-0518-18/+19
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* - Update to 0.99wen2010-02-032-5/+5
| | | | - Update my mail address to FreeBSD
* - Update to 3.1.1miwi2010-02-035-88/+40
| | | | | PR: 143437 Submitted by: Ports Fury
* - use $SUB_FILES to dynamically adjust pkg-messagepgollucci2010-01-311-2/+1
| | | | | | PR: ports/142408 Submitted by: Sevan Janiyan <venture37@geeklan.co.uk> Approved by: fernan@iib.unsam.edu.ar (maintainer)
* - Remove unneeded dependencies which is in perl-5.8.9 distkuriyama2010-01-294-11/+7
| | | | | | (part 19; last!). Approved by: portmgr (itetcu)
* - actually remove old patchpgollucci2010-01-171-31/+0
| | | | Reported by: QAT
* - Fix on amd64pgollucci2010-01-174-0/+60
| | | | | PR: ports/142472 Submitted by: Edmund Sumbar <esumbar@ualberta.ca>
* - Remove unneeded dependencies which is in perl-5.8.9 dist from portskuriyama2010-01-161-2/+2
| | | | | | | | maintained by (perl|ports|kuriyama)@FreeBSD.org. - Targets are: Test::Simple, Digest::MD5, Locale-Maketext, ExtUtils::MakeMaker, ExtUtils::ParseXS, File::Temp, Getopt::Long, Encode, Digest, Pod::Parser, File::Spec.
* - SUB_FILES += pkg-messagepgollucci2010-01-101-4/+1
| | | | | | PR: ports/142407 Submitted by: Sevan Janiyan <venture37@geeklan.co.uk> Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 1.03wen2010-01-092-5/+5
| | | | - Update my mail address to FreeBSD
* - SBU_FILES += pkg-messagepgollucci2010-01-084-56/+54
| | | | | PR: ports/142409 Submitted by: Sevan Janiyan <venture37@geeklan.co.uk>
* - Update to 1.995wen2010-01-072-4/+4
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* - Update to 1.53wen2010-01-063-99/+39
| | | | | | PR: ports/142221 Submitted by: Wen Heping (myself) Approved by: maintainer
* python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees)wen2009-12-295-0/+35
| | | | | | reader for python. WWW: http://simon.net.nz/articles/python-nexus
* - Fix fetch errorwen2009-12-271-2/+2
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* - Update to 0.3.7wen2009-12-242-4/+4
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* - Update to 7.1.11miwi2009-12-224-41/+49
| | | | | PR: 141812 Submitted by: Ports Fury
* - Update to 0.3.5wen2009-12-212-4/+4
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* For ports maintained by ports@FreeBSD.org, remove names and/ordougb2009-12-2111-22/+0
| | | | | | | | e-mail addresses from the pkg-descr file that could reasonably be mistaken for maintainer contact information in order to avoid confusion on the part of users looking for support. As a pleasant side effect this also avoids confusion and/or frustration for people who are no longer maintaining those ports.
* - Update to 1.1.4wen2009-12-182-11/+11
| | | | | Submitted by: Wen Heping (myself) Approved by: maintainer (via Email)
* - Update to 1.4wen2009-12-173-30/+126
| | | | - Update my mail address to FreeBSD
* - Update to 0.3.4wen2009-12-162-4/+4
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* - Turn over a bunch of p5- ports that change infrequently to perl@pgollucci2009-12-141-1/+1
| | | | so more people can look at them.
* - Update to 1.994wen2009-12-113-4/+6
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* - Update to 0.3.3wen2009-12-063-7/+7
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* - Update to 1.993wen2009-12-042-4/+4
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* - Update to 1.6.1wen2009-12-045-912/+939
| | | | Approved by: maintainer (via Email)
* Chase math/gsl update,makc2009-12-021-2/+2
| | | | bump PORTREVISION
* - Update to 2.0.12wen2009-11-292-6/+5
| | | | - Update my mail address to FreeBSD
* - Update my mail address to FreeBSDsylvio2009-11-281-1/+1
| | | | Approved by: miwi (mentor)
* - Mark MAKE_JOBS_UNSAFEpav2009-11-212-0/+2
| | | | Reported by: pointyhat
* - Update to 1.992wen2009-11-202-5/+5
| | | | - Update my mail address to FreeBSD
* - broken checksum mismatchmiwi2009-11-191-0/+2
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* - Mark MAKE_JOBS_UNSAFEpav2009-11-191-0/+1
| | | | Reported by: pointyhat
* pyfasta is a python module for fast, memory-efficient, pythonicwen2009-11-185-0/+52
| | | | | | access to fasta sequence files. WWW: http://bitbucket.org/brentp/biostuff/src/
* - Update to 21.1.1wen2009-11-184-29/+17
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* Velvet is a de novo genomic assembler specially designed for short readamdmi32009-11-077-0/+244
| | | | | | | | | | | | | | | sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) WWW: http://www.ebi.ac.uk/~zerbino/velvet/ PR: 140147 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
* - Annotate that 8.x no longer needs libmap hackpav2009-10-011-1/+1
| | | | Reported by: rene
* - Update to 4.0.0wen2009-09-234-13/+23
| | | | | | | | | - Update my mail address to FreeBSD PR: ports/137652 Submitted by: wenheping@gmail.com(myself) Approved by: miwi(mentor) Feature safe: yes
* Update to Crux 1.2.0.jasone2009-09-203-26/+29
| | | | Feature safe: yes
* UNBREAK: Probably was a temporary failure, checksums are ok now.garga2009-09-161-2/+0
| | | | Feature safe: yes
* -Update to 3.69miwi2009-09-162-14/+10
| | | | | | PR: 138813 Submitted by: Ports Fury Feature safe: yes
* Bump PORTREVISION for everything that sets USE_FORTRAN=yes which nowgerald2009-09-136-5/+6
| | | | | | implies lang/gcc44 up from lang/gcc43. Approved by: portmgr
* - Update to 1.14jadawin2009-09-082-4/+4
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* - Update to 138038miwi2009-09-054-444/+152
| | | | | | PR: 138038 Submitted by: Wen Heping <wenheping@gmail.com> Approved by: maintainer
* - Update to 0.982miwi2009-08-292-5/+5
| | | | | PR: 138264 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* Bio::SCF module allows you to read and update (in a restrictedmiwi2009-08-295-0/+46
| | | | | | | | | | | way) SCF chromatographic sequence files. It is an interface to Roger Staden's io-lib. See the installation directions for further instructions. WWW: http://search.cpan.org/dist/Bio-SCF/ PR: ports/138263 Submitted by: Wen Heping <wenheping at gmail.com>
* Io_lib is a library of file reading and writing code to provide amiwi2009-08-295-0/+107
| | | | | | | | | | | | general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. WWW: http://staden.sourceforge.net/ PR: ports/138254 Submitted by: Wen Heping <wenheping at gmail.com>
* - Update to 3.21.araujo2009-08-282-5/+5
| | | | | | | - Reset maintainer to submitter. PR: ports/138192 Submitted by: Sylvio Cesar <scjamorim@bsd.com.br>
* - Update to 1.12miwi2009-08-282-5/+4
| | | | | PR: 138230 Submitted by: Wen Heping <wenheping@gmail.com>
* Update to 35.4.9makc2009-08-232-4/+4
| | | | | PR: ports/137991 Submitted by: Fernan Aguero (maintainer)
* Bio::NEXUS package provides an object-oriented, Perl-basedmiwi2009-08-235-0/+91
| | | | | | | | | | | | | | | | | | | applications programming interface (API) to the NEXUS file format of Maddison, et al., 1997 (Syst. Biol. 46:590-621). NEXUS is a powerful and extensible format designed for use in evolutionary analysis, including the analysis of molecular sequence data as well as classical morphological and life-history data. NEXUS is the input or output format for software such as PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data). WWW: http://search.cpan.org/dist/Bio-NEXUS/ PR: ports/137983 Submitted by: Wen Heping <wenheping at gmail.com>
* - BROKEN checksum mismatchmiwi2009-08-221-0/+2
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* - Switch SourceForge ports to the new File Release System: categories ↵amdmi32009-08-225-8/+5
| | | | starting with B,C
* - Fix fetchmiwi2009-08-171-1/+1
| | | | | PR: 137840 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update MASTER_SITESmiwi2009-08-142-4/+2
| | | | | PR: 137750 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 4.3miwi2009-08-142-6/+6
| | | | | PR: 137625 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* Fix PKGORIGINerwin2009-08-081-1/+1
| | | | Submitted by: pointyhat
* - Relax check on bioperl version; people keep forgetting to update this checkpav2009-08-031-1/+1
| | | | | | when updating bioperl port Reported by: pointyhat
* - Unbreak fetchpav2009-08-031-1/+1
| | | | Submitted by: maintainer
* -Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.mezz2009-08-032-2/+2
| | | | | | | | | | | | | | | | | | -Update libtool and libltdl to 2.2.6a. -Remove devel/libtool15 and devel/libltdl15. -Fix ports build with libtool22/libltdl22. -Bump ports that depend on libltdl22 due to shared library version change. -Explain what to do update in the UPDATING. It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop and applications in the runtime. With help: marcus and kwm Pointyhat-exp: a few times by pav Tested by: pgollucci, "Romain Tartière" <romain@blogreen.org>, and a few MarcusCom CVS users. Also, I might have missed a few. Repocopy by: marcus Approved by: portmgr
* - bump all port that indirectly depends on libjpeg and have not yet been ↵dinoex2009-07-3114-7/+14
| | | | | | bumped or updated Requested by: edwin
* Utilize %%SITE_PERL%% and %%PERL_ARCH%% in pkg-plistspgollucci2009-07-311-3/+3
| | | | | | PR: ports/136771 Exp Run by: pav Approved by: portmgr (pav)
* - lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checkspgollucci2009-07-232-14/+1
| | | | | | PR: ports/135398 Tested by: 2 -exp runs by pav Approved by: portmgr (pav)
* PhyML is a software that estimates maximum likelihood phylogenies fromamdmi32009-07-216-0/+75
| | | | | | | | | | | | | | | | | | | | | | | alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the "comfort zone" for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. WWW: http://code.google.com/p/phyml/ PR: 136877 Submitted by: Ben Allen <ben@sysadminschronicles.com>
* - update to jpeg7dinoex2009-07-181-2/+2
| | | | Tested by: pav on pointyhat
* - Flip MAKE_JOBS_SAFE to MAKE_JOBS_UNSAFEpav2009-07-081-1/+1
| | | | Reported by: pointyhat
* - fix PORTSCOUTdinoex2009-07-061-1/+1
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* - Update to 1.97miwi2009-07-063-4/+14
| | | | | PR: 136310 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* - cleanup ADDITIONAL_LIB_DIRSdinoex2009-07-051-1/+1
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* p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. Thismiwi2009-07-015-0/+177
| | | | | | | | | | | | | is a beta release. All functions have now been implemented and most have test suites; the exceptions include the modules involved in export of MAGE-TAB documents, which are still a little experimental in nature. The API is mostly finalised (and fully documented), but some details may yet change where necessary to improve usability. WWW: http://search.cpan.org/dist/Bio-MAGETAB/ PR: ports/136021 Submitted by: Wen Heping <wenheping at gmail.com>
* PyCogent is a software library for genomic biology. It is a fully integratedmiwi2009-06-225-0/+887
| | | | | | | | | | | | | | and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data. WWW: http://pycogent.sourceforge.net/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com>
* Update to Crux 1.1.0.jasone2009-06-213-9/+7
| | | | Fix the ATLAS/LAPACK build option.
* - Update to 6.0.0amdmi32009-06-173-406/+438
| | | | | | | - Unbreak PR: 135376 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Change CONFIGURE_ENV --> USE_CSTD. [1]jasone2009-06-102-2/+6
| | | | | | | | | Add missing pkg-plist entry for Parsing.so. [2] Change RUN_DEPENDS --> LIB_DEPENDS for optional math/atlas dependency. Submitted by: [1] erwin Reported by: [2] QAT
* Convert most of remaining ports that depend on xorg-libraries toamdmi32009-06-092-2/+4
| | | | | | | | | | | | | modular xorg. - supply corresponding USE_XORG for all imake-using ports that need it - USE_IMAKE no longer implies USE_XLIB in absence of USE_XORG - retire USE_X_PREFIX which is not really used anywhere after the above change - a few minor nits like whitespace and SF macro Tested by: 2 tinderbox runs by pav Approved by: portmgr (pav)
* - Update to 35.4.7 [1]itetcu2009-06-094-8/+27
| | | | | | | - Obey PREFIX [2] Submitted by: maintainer [1] [2] Reported by: QATty [2]
* Add the biology/crux port.jasone2009-06-095-0/+131
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* - Update lang/python26 and make Python 2.6.2 to the default Python versionmiwi2009-06-092-4/+3
| | | | | Tested by: 3 pointyhat runs Thanks to: pav, gahr, lwhsu, mva, amdmi3
* - Update to 1.11jadawin2009-06-082-4/+4
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* 2009-05-31 biology/p5-bioperl-devel: no longer under developmentmiwi2009-06-0611-3118/+0
| | | | | | 2009-05-31 biology/p5-bioperl-run-devel: no longer under development 2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead 2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either
* - Update to 1.95miwi2009-06-032-4/+4
| | | | | PR: 135141 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* - fix build for custom LOCALBASE in UL subdirdinoex2009-06-021-1/+1
| | | | Reported by: QAT
* - fix build for custom LOCALBASEdinoex2009-06-011-0/+2
| | | | Reported by: QAT
* LibSBML is an open-source programming library to help you read, write,miwi2009-05-296-0/+343
| | | | | | | | | | | | | | | | manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications. LibSBML understands all Levels and Versions of SBML, as well as the SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in ISO C and C++ but can be used from all the languages listed in the right-hand box. WWW: http://www.sbml.org/ PR: ports/135022 Submitted by: Wen Heping <wenheping at gmail.com>
* - fix build with gnustep-make-2.2.0dinoex2009-05-211-2/+4
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* - Mark most of my ports MAKE_JOBS_SAFE=yespgollucci2009-05-162-0/+4
| | | | Tested by: several builds in P6 TB
* Fix LIB_DEPENDS on devel/readline: its sh lib version was bumped recently fromitetcu2009-05-121-1/+2
| | | | | | | 5 to 6. Forgotten by: araujo@ Reported by: QAT
* - Update to 1.94miwi2009-05-012-4/+4
| | | | Approved by: maintainer implicit
* - Update to 1.7miwi2009-05-014-281/+29
| | | | | | | - Pass maintainership to submitter PR: 134056 Submitted by: Wen Heping <wenheping@gmail.com>
* - Update to 1.93miwi2009-04-052-4/+4
| | | | | PR: 133342 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* Bio::Glite is an interface to G-language Genome Analysis Environmentmiwi2009-04-035-0/+52
| | | | | | | | | | | | | | | | | | | | | | | through its REST web service (http://www.g-language.org). This module allows almost everything G-language GAE can do, without installing all necessary tookits and modules. Advantage of this module over the standard installation of G-language GAE package is: 1. Easy installation from CPAN 2. Extremely light-weight (less than 1000 lines of code) 3. Does not require much CPU/RAM (all calculation is done on the cloud) Disadvantages includes: 1. Slower analysis speed 2. Internet connection is required 3. No other software interfaces such as the G-language Shell WWW: http://search.cpan.org/dist/Bio-Glite/ PR: ports/133273 Submitted by: Wen Heping <wenheping at gmail.com>
* - Update to 2009.03.01miwi2009-03-293-30/+93
| | | | | | PR: 133099 Submitted by: Fernan Aguero <fernan.aguero@gmail.com> Approved by: maintainer
* - Update to 1.91miwi2009-03-263-4/+5
| | | | | PR: 133065 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* bump PORTREVISION after cmake updatemakc2009-03-251-0/+1
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* - Mark BROKEN does not compilemiwi2009-03-241-0/+2
| | | | Submitted by: maintainer via private mail
* - Update to 1.6.1miwi2009-03-203-683/+216
| | | | | | PR: 132122 Submitted by: Wen Heping <wenheping@gmail.com> Approved by: maintainer
* - Mark DEPRECATED (no longer under development)miwi2009-03-202-0/+6
| | | | | PR: 132122 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
* Welcome to the new linux ports infrastructure which allows usingbsam2009-03-201-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | both current (fc4) and future linux (f8) distributions at one ports tree. The patch contains full changes to ports/Mk files and all ports involved. But only infrastructure is changed. The resulting packages are the same as before. Hence no need to bump PORTREVISIONs. The idea was taken from bsd.gnome.mk and others. More than 130 ports are switched to follow a new linux infrastructure introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new bsd.linux-apps.mk. Thanks for all who was involved and helped me with this work. And help from Alexander Leidinger was incredible. Other changes are coming. Stay tuned! PR: ports/132510 Submitted by: bsam (me) Exp-run by: portmgr (pav)
* - Update to 1.90miwi2009-03-203-6/+9
| | | | | PR: 132659 Submitted by: Wen heping <wenheping@gmail.com> (maintainer)
* - Update to 0.1.24miwi2009-03-143-485/+571
| | | | | | PR: 132527 Submitted by: Wen Heping <wenheping@gmail.com> Approved by: maintainer
* p5-Bio-Graphics is a simple GD-based renderer (diagram drawer)miwi2009-03-115-0/+222
| | | | | | | | | for DNA and protein sequences. WWW: http://search.cpan.org/dist/Bio-Graphics/ PR: ports/132088 Submitted by: Wen Heping <wenheping at gmail.com>
* Rename PERL_VER to PERL_VERSION.skv2009-03-081-2/+2
| | | | Pointed by: pav
* Remove variable PERL_VER from the ports tree at all - becauseskv2009-03-061-2/+2
| | | | it is obsolete since Perl 5.6.0.
* - Update to 4.2bmiwi2009-03-032-6/+6
| | | | | PR: 132249 Submitted by: Wen Heping <wenheping@gmail.com>
* - Update to 1.6.0garga2009-02-246-1082/+1559
| | | | | PR: ports/131989 Submitted by: maintainer
* - Add forgotten patchamdmi32009-02-241-0/+11
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* - Update to 35.4.4amdmi32009-02-243-25/+47
| | | | | PR: 132007 Submitted by: Fernan Aguero <fernan at iib dot unsam dot edu dot ar> (maintainer)
* - update PORTSCOUTdinoex2009-02-161-1/+1
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* - Update download locations, update WWWpgollucci2009-02-042-3/+2
| | | | Reported by: -fetch-original pointyhat run
* Reset dyeske@gmail.com at his request.linimon2009-02-034-8/+2
| | | | Hat: portmgr
* - Update download locations, update WWWpgollucci2009-02-012-2/+2
| | | | Reported by: -fetch-original pointyhat run
* - Update download locationpav2009-02-011-2/+2
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* - Update X.org ports to 7.4+ (few ports are more recent than the katamari).flz2009-01-244-5/+6
| | | | | | | | - Bump PORTREVISION for all ports depending on libglut since the shlib version number went from 4 to 3. - Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't installed anymore. - Couple of ports fixes (mostly missing xorg components added to USE_XORG).
* - add LICENSE:dinoex2009-01-172-0/+4
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* - Unbreak after p5-bioperl changed portrevisionpav2009-01-161-1/+1
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* - Update to 3.0.3miwi2009-01-156-57/+122
| | | | | PR: 130459 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* Fix plist with perl 5.8.9.tobez2009-01-141-1/+2
| | | | Approved by: portmgr (pav, implicit)
* - Chase math/gsl slib bumpmiwi2009-01-131-2/+2
| | | | Reported by: pavbot
* - Unbreak distinfo after portrevision bumppav2009-01-102-4/+3
| | | | Reported by: pointyhat
* Bump PORTREVISION due to change of USE_FORTRAN=yes to GCC 4.3.gerald2009-01-085-4/+5
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* - Remove conditional checks relevant only on FreeBSD 5.x and olderpav2009-01-066-31/+1
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* - Update to 4.2miwi2008-12-262-4/+4
| | | | | PR: 129895 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* Update to 1.92pgollucci2008-12-242-4/+4
| | | | | | Changes http://search.cpan.org/src/LDS/AcePerl-1.92/ChangeLog Approved by: gabor (mentor)
* - Mark as brokenwxs2008-12-171-0/+2
| | | | | PR: ports/129597 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
* - update to 1.10leeym2008-12-113-14/+21
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* Reset nemoliu due to maintainer-timeouts and no response to email.linimon2008-12-081-1/+1
| | | | Hat: portmgr
* - Roll back to 4.6 as 4.7 is the development version and is constantly beingwxs2008-11-115-110/+117
| | | | | | | | re-rolled. - Move post-patch target into files/patch-xwin.c to remove sed invocation. - Respect NOPORTDATA and DATADIR. - Bring files/patch-aa back (to preserve history) and retire patch-makefile. - Fixup files/patch-xwin.c so it applies cleanly to this version.
* Mark as broken since it has been re-rolled for the 4th(?) time.wxs2008-11-081-0/+2
|
* Distfile was re-rolled. The changes were to fix some bugs in the code.wxs2008-11-073-10/+13
| | | | While I'm here, make it respect NOPORTDOCS.
* Update to 4.7wxs2008-11-058-140/+309
| | | | | PR: ports/128476 Submitted by: fulvio ciriaco <oivulf@gmail.com>
* - Update to 2.8.1amdmi32008-10-234-150/+40
| | | | | PR: 128057 Submitted by: Christian Sturm <athaba at inode dot at>
* - Unbreakrafan2008-10-213-7/+42
| | | | | PR: ports/128193 Submitted by: Mauricio Herrera Cuadra <mauricio at arareko.net> (maintainer)
* - Update to 1.48miwi2008-10-113-19/+16
| | | | | | PR: 127776 Submitted by: Wen heping <wenheping@gmail.com> Approved by: maintainer
* - Update to 4.1miwi2008-09-303-8/+13
| | | | | | | - Pass maintainership to submitter PR: 127683 Submitted by: Wen heping <wenheping@gmail.com>
* - Respect PORTDOCS/PORTEXAMPLESgahr2008-09-092-188/+186
| | | | | Reported by: QA Tindie Approved by: portmgr
* Reset sf@slappy.org due to maintainer-timeouts and no response to email.linimon2008-09-031-1/+1
| | | | Hat: portmgr
* - Fix buildgahr2008-08-281-2/+2
| | | | Reported by: QA Tindie
* - Update to 3.68gahr2008-08-272-6/+5
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* Add -lf2c, this is the correct dependency. Bump portrevision.maho2008-08-232-0/+9
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* Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.rafan2008-08-214-5/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Specifically, newer autoconf (> 2.13) has different semantic of the configure target. In short, one should use --build=CONFIGURE_TARGET instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning and the old semantic may be removed in later autoconf releases. To workaround this issue, many ports hack the CONFIGURE_TARGET variable so that it contains the ``--build='' prefix. To solve this issue, under the fact that some ports still have configure script generated by the old autoconf, we use runtime detection in the do-configure target so that the proper argument can be used. Changes to Mk/*: - Add runtime detection magic in bsd.port.mk - Remove CONFIGURE_TARGET hack in various bsd.*.mk - USE_GNOME=gnometarget is now an no-op Changes to individual ports, other than removing the CONFIGURE_TARGET hack: = pkg-plist changed (due to the ugly CONFIGURE_TARGET prefix in * executables) - comms/gnuradio - science/abinit - science/elmer-fem - science/elmer-matc - science/elmer-meshgen2d - science/elmerfront - science/elmerpost = use x86_64 as ARCH - devel/g-wrap = other changes - print/magicfilter GNU_CONFIGURE -> HAS_CONFIGURE since it's not generated by autoconf Total # of ports modified: 1,027 Total # of ports affected: ~7,000 (set GNU_CONFIGURE to yes) PR: 126524 (obsoletes 52917) Submitted by: rafan Tested on: two pointyhat 7-amd64 exp runs (by pav) Approved by: portmgr (pav)
* Unbreak building for 8-x.bsam2008-08-162-4/+114
| | | | Submitted by: Steve Kargl <sgk at troutmask.apl.washington.edu> at ports@ ML
* - update PORTSCOUTdinoex2008-08-131-1/+3
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* - Update to 1.47miwi2008-08-123-53/+92
| | | | | | PR: 125912 Submitted by: Wen heping <wenheping@gmail.com> Approved by: maintainer timeout
* - Update to 2.1.3pgollucci2008-08-013-4/+5
| | | | Approved by: gabor (mentor)
* - Remove USE_GCC where it can be satisfied with base compiler on followingpav2008-07-252-2/+0
| | | | FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT
* - Remove duplicates from MAKE_ENV after inclusion of CC and CXX in default ↵pav2008-07-253-3/+5
| | | | MAKE_ENV
* - Delete biology/nab port after being marked DEPRECATED for three monthspav2008-07-2415-1093/+0
| | | | | PR: ports/125891 Submitted by: M. L. Dodson <mldodson@comcast.net> (maintainer)
* Update my ports to my freebsd addresspgollucci2008-07-232-2/+2
| | | | Approved by: araujo (mentor)
* - respect NOPORTEXAMPLES/NOPORTDOCS and fix plistitetcu2008-07-122-14/+15
| | | | | | - bump PORTREVISION Prompted by: QA Tindy run
* - Update to 2.1.2c.araujo2008-07-122-5/+5
| | | | | | | - Pass maintainership to submitter. PR: ports/125497 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com>
* - extened PORTSCOUTdinoex2008-07-091-1/+1
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* - Mark BROKEN: missing cpan dependency (interactive loop)pav2008-07-081-0/+2
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* - Bump portrevision after openbabel updatebeech2008-07-071-1/+1
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* - Update to 1.5.2.lippe2008-07-074-1355/+1063
| | | | | | | PR: ports/124648 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer) Reviewed by: lippe Approved by: gabor (mentor, implicit)
* - Update to 1.45beech2008-07-043-26/+79
| | | | | | PR: ports/125134 Submitted by: Wen heping <wenheping@gmail.com> Approved by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
* - extend PORTSCOUTdinoex2008-06-241-1/+1
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* - Fix plist files installation.lippe2008-06-211-1/+2
| | | | | | | - Bump PORTREVISION. Reported by: QA Tindy Approved by: gabor (mentor, implicit)
* SSAHA is a software tool for very fast matching and alignment of DNAlippe2008-06-2136-0/+1362
| | | | | | | | | | | | | sequences. It stands for Sequence Search and Alignment by Hashing Algorithm. It achieves its fast search speed by converting sequence information into a `hash table' data structure, which can then be searched very rapidly for matches. WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ PR: ports/124525 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: gabor (mentor, implicit)
* - Fix fetch, update WWWpav2008-06-192-2/+2
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* - Fix build dependsgahr2008-06-091-0/+3
| | | | | | - Bump port revision Reported by: pointyhat via pav
* Bump portrevision due to upgrade of devel/gettext.edwin2008-06-0613-11/+13
| | | | | | | | | | The affected ports are the ones with gettext as a run-dependency according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT in Makefile (29 of them). PR: ports/124340 Submitted by: edwin@ Approved by: portmgr (pav)
* - Update to 3.67gahr2008-06-042-12/+7
| | | | - Sanitize Makefile a little bit
* - cleanup FreeBSD 5.xdinoex2008-06-021-7/+1
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* - Update to 1.09miwi2008-05-312-4/+4
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* Teach the building cluster that these ports are not to be buildedwin2008-05-264-0/+12
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* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-249-0/+221
| | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-244-0/+22
| | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-242-0/+49
| | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-249-0/+1174
| | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* Update to 1.08mat2008-05-232-4/+4
|
* - Update MASTER_SITES and WWW: linemiwi2008-05-224-61/+46
| | | | | | | | - Support CC/CFLAGS properly - Strip binary PR: 123866 Submitted by: Ports Fury
* - Include some ports in perl5 category.araujo2008-05-191-1/+1
| | | | | | | PR: ports/123530 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com> Reworked by: araujo (myself) Approved by: flz (portmgr)
* - Update maintainer's email addresspav2008-05-183-3/+3
| | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
* - Try to fix fetchpav2008-05-181-0/+2
| | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
* Update to 1.23erwin2008-05-152-4/+4
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* NJplot is a tree drawing program able to draw any phylogenetic tree expressedpav2008-05-145-0/+145
| | | | | | | | | | | | | | | | | | | | | | in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. The package contains the following programs: njplot - draw phylogenetic trees and interactively modify them newicktops - non-interactive version rendering into a PostScript file newicktotxt - non-interactive version rendering into a text file unrooted - draw unrooted circular trees If you use NJplot in a published work, please cite the following reference: Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for biological sequence banks. Biochimie, 78, 364-369. WWW: http://pbil.univ-lyon1.fr/software/njplot.html PR: ports/118438 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* MUSCLE is multiple alignment software for protein and nucleotide sequences.pav2008-05-147-0/+232
| | | | | | | | | | | | | | | | | | | | | | | | | | | The name stands for multiple sequence comparison by log-expectation. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in the published tests. MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options. Citation: Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797. Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113. The NAR paper gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see the BMC paper. WWW: http://www.drive5.com/muscle/ PR: ports/118460 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* - add PORTSCOUTdinoex2008-05-041-0/+2
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* Update to version 34.okazaki2008-05-012-11/+5
| | | | | | | Remove BROKEN. PR: 123218 Submitted by: maintainer
* - update to 0.8.2dinoex2008-04-309-456/+205
| | | | | - take maintainership Approved by: maintainer
* - Update to 2.0.6miwi2008-04-292-5/+5
| | | | | | | - Pass maintainership to submitter PR: 123193 Submitted by: Wen heping <wenheping@gmail.com>
* Reset aaron's port maintainerships due to many maintainer-timeouts.linimon2008-04-291-1/+1
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* - Mark BROKEN on -CURRENT: error: 'linkat' redeclared as different kind of ↵pav2008-04-261-0/+4
| | | | | | symbol Reported by: pointyhat
* - Remove unneeded dependency from gtk12/gtk20 [1]miwi2008-04-2019-50/+43
| | | | | | | | | | | | | | | - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG - Remove X11BASE support in favor of LOCALBASE or PREFIX - Use USE_LDCONFIG instead of INSTALLS_SHLIB - Remove unneeded USE_GCC 3.4+ Thanks to all Helpers: Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr, ehaupt, nox, itetcu, flz, pav PR: 116263 Tested on: pointyhat Approved by: portmgr (pav)
* implement @dirrmtry macro for the pkg-plistedwin2008-04-191-1/+1
|
* - Update mastersite.jmelo2008-04-181-1/+2
| | | | | PR: ports/122130 Submitted by: Ganael Laplanche <ganael.laplanche@martymac.com>
* - Replace SF with second working master sitepav2008-04-181-1/+1
| | | | Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Take advantage of CPAN macro from bsd.sites.mk, change ↵araujo2008-04-176-10/+6
| | | | | | | | | ${MASTER_SITE_PERL_CPAN} to CPAN. PR: ports/122674 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com> Reworked by: araujo (myself) Approved by: portmgr (pav)
* - It seems that upstream removes their distfiles from sourceforge, so addrafan2008-04-171-1/+2
| | | | | | the download site pointed by their webpage as first choice. Noticed by: pointyhat via pav
* - Update to 5.0.0rafan2008-04-1317-6851/+707
| | | | | PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
* - Sort pkg-plist before updating to 5.0.0rafan2008-04-131-888/+888
| | | | | PR: ports/122437 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Change maintainers e-mail address.ehaupt2008-04-111-2/+2
| | | | Requested over: IRC
* - Update to 35.3.6clsung2008-04-102-5/+5
| | | | | PR: ports/122607 Submitted by: maintainer (Fernan Aguero)
* - Chase the gsl shared lib bump.jadawin2008-04-081-2/+2
| | | | Approved by: thierry (mentor)
* - Update maintainer's emailrafan2008-04-061-3/+5
| | | | | | | - Mark as deprecated PR: ports/122474 Submitted by: M. L. Dodson <mldodson at comcast.net> (maintainer with another email)
* MAPMAKER/EXP is a linkage analysis package designed to help construct primaryrafan2008-04-0628-0/+1101
| | | | | | | | | | | | | | | | | | linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP performs full multipoint linkage analysis (simultaneous estimation of all recombination fractions from the primary data) for dominant, recessive, and co- dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only successor to the original MAPMAKER program. MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map genes controlling polygenic quantitative traits in F2 intercrosses and BC1 backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL can be found in the technical report (included with MAPMAKER/QTL). WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ PR: ports/122452 Submitted by: Tassilo Philipp <tphilipp at potion-studios.com>
* - Update to 5.68rafan2008-04-053-10/+10
| | | | | | | - Remove gcc version restriction PR: ports/122435 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
* - Update to 1.1.3pav2008-04-053-185/+203
| | | | | | PR: ports/122374 Submitted by: Wen heping <wenheping@gmail.com> Patch revised: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Chase fasta3 updatepav2008-04-021-1/+1
| | | | Reported by: pointyhat
* - Update to 35.3.5rafan2008-03-303-53/+49
| | | | | | | | | | - Switch to .tar.gz distfile so that we don't define our do-extract - While I'm here, using substitution for version numbers in pkg-plist for easier upgrade PR: ports/121690 Submitted by: Wen heping <wenheping at gmail.com> Approved by: maintainer timeout (2 weeks)
* - Fix build with GCC 4.2gahr2008-03-292-5/+18
| | | | Approved by: miwi (mentor)
* - Add missing dependensmiwi2008-03-271-1/+3
| | | | | | - Bump PORTREVISION Submitted by: pointyhat via pav
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGmiwi2008-03-261-2/+1
| | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup)
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGmiwi2008-03-241-2/+2
| | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup)
generated by cgit (git 2.34.1) at 2024-11-18 08:33:14 +0800