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* chase math/gsl lib versionijliao2007-06-291-2/+2
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* Bump to v0.16.aaron2007-06-203-6/+53
| | | | | PR: 111719 Submitted by: araujo@bsdmail.org
* - Fix the build with GCC 4.2danfe2007-06-192-7/+32
| | | | | | - Remove BROKEN tag Reported by: pointyhat (logs)
* - Fix typos.miwi2007-05-311-3/+3
| | | | Reported by: stas@
* - Update to 1.43miwi2007-05-304-92/+167
| | | | | | PR: 111817 Submitted by: "P.BandieraPaiva" <paiva@unifesp.br> Approved by: maintainer
* BROKEN: Unfetchablekris2007-05-271-0/+2
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* BROKEN with gcc 4.2kris2007-05-271-1/+7
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* - update for gnustep-make-2.0.0dinoex2007-05-252-71/+79
| | | | Approved by: gurkan (maintainer)
* - update for gnustep-make-2.0.0dinoex2007-05-251-1/+1
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* swap MASTER_SITES to improve fetchiness on pointyhat which is blocked from ↵edwin2007-05-251-4/+2
| | | | dasher.wustl.edu
* BROKEN: Unfetchablekris2007-05-251-0/+2
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* - Chase openbabel updatepav2007-05-251-2/+2
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* - Welcome X.org 7.2 \o/.flz2007-05-2035-20/+40
| | | | | - Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}. - Bump PORTREVISION for ports intalling files in ${X11BASE}.
* [patch] cleanup non-supported FreeBSD versionsedwin2007-05-021-7/+2
| | | | | | PR: ports/111728 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout
* [patch] cleanup non-supported FreeBSD versionsedwin2007-05-021-7/+1
| | | | | | PR: ports/111726 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout
* [patch] cleanup non-supported FreeBSD versionsedwin2007-05-021-6/+2
| | | | | | PR: ports/111725 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout
* [patch] cleanup non-supported FreeBSD versionsedwin2007-05-021-7/+1
| | | | | | PR: ports/111724 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout
* Use my @FreeBSD.org address.nemoliu2007-04-301-1/+1
| | | | Approved by: delphij (mentor)
* - Update to 4.5clsung2007-04-243-14/+13
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* - Unbreakmiwi2007-04-211-3/+3
| | | | | | | - Add backup MASTER_SITES PR: 111963 Submitted by: Jason Harris <jharris@widomaker.com>
* BROKEN: Unfetchablekris2007-04-201-0/+2
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* [patch] cleanup non-supported FreeBSD versionsedwin2007-04-173-41/+1
| | | | | | PR: ports/111727 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: Bob Zimmermann <rpz@cse.wustl.edu>
* Remove always-true condition due to OSVERSIONedwin2007-04-161-1/+1
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* - Remove unreachable OSVERSION code.edwin2007-04-161-13/+9
| | | | - Make portlint happier
* - Fix after objformat removalpav2007-03-291-0/+3
| | | | Reported by: pointyhat
* - Update to 1.5-beta2miwi2007-03-273-13/+14
| | | | | | | - Pass maintainership to submitter PR: 110621 Submitted by: Nemo Liu<nemoliu@gmail.com>
* - MASTER_SITE is back, remove BROKENgabor2007-03-171-2/+0
| | | | | PR: ports/109954 Submitted by: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
* Reset razi@genet.sickkids.on.ca due to maintainer-timeouts and no response tolinimon2007-03-141-1/+1
| | | | | | email. Hat: portmgr
* Reset dbader@eece.unm.edu due to maintainer-timeouts.linimon2007-03-111-1/+1
| | | | Hat: portmgr
* Reset dbader@eece.unm.edu due to maintainer-timeout. While here, fix fetch.linimon2007-03-111-2/+2
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* Reset chuynh@biolateral.com.au: address bounces.linimon2007-03-112-2/+2
| | | | Hat: portmgr
* - Update to 4.96miwi2007-03-093-10/+143
| | | | | PR: 110080 Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 34.26.2miwi2007-03-092-8/+6
| | | | | PR: 110079 Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
* - Release distfile was renamed.miwi2007-03-082-5/+5
| | | | | PR: 110078 Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
* BROKEN: Unfetchablekris2007-02-271-0/+2
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* - mark ignore on FreeBSD 5.xdinoex2007-02-191-1/+7
| | | | Approved by: maintainer
* Schedule these broken ports for removal on 2007-04-10 if they are stillkris2007-02-111-0/+2
| | | | broken at that time and no fix has been submitted.
* Update to 0.99rc6.maho2007-02-092-5/+5
| | | | | PR: 108940 Submitted by: CHAO Shin
* BROKEN: Does not buildkris2007-02-051-0/+2
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* Use libtool port instead of included version to avoid objformat a.out botchkris2007-02-011-0/+1
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* - add category gnustepdinoex2007-02-012-2/+2
| | | | | PR: 103931 Approved by: pav
* Build fix.maho2007-01-291-1/+2
| | | | Submitted by: kris via pointyhat and pav.
* Update to 3.66itetcu2007-01-282-4/+4
| | | | | PR: ports/108434 Submitted by: Marcelo Araujo
* Fix master sites, un-deprecate and update biology/recombine to 1.41.vd2007-01-254-86/+19
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* Remove expired leaf port:vd2007-01-256-78/+0
| | | | | | | | | 2007-01-07 biology/coalesce: distfile disappeared from homepage Actually the software is still available at: http://evolution.gs.washington.edu/lamarc/coalesce.html, but it is not supported by the authors. Last version is from 1995 and biology/fluctuate can be used instead.
* Get rid of biology/coalesce dependency, it is deprecated and will be removedvd2007-01-251-2/+2
| | | | shortly.
* Fix master site and un-deprecatevd2007-01-251-4/+1
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* - Fix typomiwi2007-01-231-1/+1
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* - Project moves to a new home. Change MASTER_SITES and WWWrafan2007-01-232-2/+2
| | | | | | PR: ports/108214 Submitted by: Thomas Abthorpe <thomas at goodking.ca> Approved by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
* Fix build.maho2007-01-191-1/+1
| | | | Submitted by: kris via pointyhat.
* Forgot to commit a patch. Fixes build.maho2007-01-191-0/+20
| | | | Submitted by: kris via pointyhat.
* * Migrate to gfortran.maho2007-01-172-13/+11
| | | | * Bump port revision.
* . change dependencies: shells/bash2 -> shells/bash;bsam2007-01-171-1/+2
| | | | | | | | | | | | | | | . bump PORTREVISION (RUN_DEPENDS changes); . for converters/konwert: - introduce PATCHLEVEL to be used instead of PORTREVISION at filenames; - update to new PATCHLEVEL=11. PR: 107000 [1], 107046 [2], 107106 [3], 107114 [4] Submitted by: bsam (me) Approved by: all maintainers timeout three and a half week: mij at bitchx.it [1] j.koopmann at seceidos.de [2] chuynh at biolateral.com.au [3] alexs at snark.rinet.ru [4]
* * Migrate to gfortran.maho2007-01-161-5/+4
| | | | | | | * Bump port revision. * fix build [1]. Submitted by: kris [1]
* - update to use new bsd.gnustep.mkdinoex2007-01-131-4/+3
| | | | Approved by: gurkan@linuks.mine.nu
* * Migrate to gfortran.maho2007-01-122-2/+7
| | | | * Bump port revision.
* Using gfortran42 only. not using gcc42.maho2007-01-121-3/+5
| | | | Bump portrevision.
* Using only gfortran42. not gcc42.maho2007-01-122-6/+10
| | | | Bump portrevision.
* * Add dummy knob WANT_FORTRAN for future gfortranmaho2007-01-092-127/+147
| | | | | migration. currently it is not buildable with gfrotran42. * Honor FC and FFLAGS.
* migrated to gfortran.maho2007-01-091-0/+3
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* Migrated to gfortran.maho2007-01-093-6/+13
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* The BioCocoa framework provides developers with the opportunity to adddinoex2006-12-305-0/+45
| | | | | | | | | support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE, Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and TNT files by writing only three lines of code. The framework is written in Cocoa (Objective-C). WWW: http://bioinformatics.org/biococoa/
* - Update to 1.0.1miwi2006-12-303-97/+98
| | | | | | | | - Update MASTER_SITES - Pass maintainership to submitter PR: ports/107246 Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
* Update to v0.15aaron2006-12-283-40/+40
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* Reset tonymaher@optusnet.com.au due to maintainer-timeouts and no responselinimon2006-12-265-5/+5
| | | | | | to email. Hat: portmgr
* - Update to 5.1.2miwi2006-12-2411-236/+308
| | | | | | | - Update maintainer mail adresse PR: ports/107118 Submitted by: M. L. Dodson <bdodson@houston.rr.com> (maintainer)
* - Update to 1.03rafan2006-12-193-105/+42
| | | | | | PR: ports/106300 Submitted by: chinsan Approved by: maintainer timeout (15 days)
* Reset dbader@ece.unm.edu due to timeouts and no response to email.linimon2006-12-132-2/+2
| | | | Hat: portmgr
* Reset whitekid@gmail.com after timeouts and no response to email.linimon2006-12-131-1/+1
| | | | Hat: portmgr
* - Update to 2.1.3gabor2006-12-104-33/+19
| | | | | | | | - Fix fetching - Remove old patch and use MAKE_ARGS instead - portlint(1) and whitespace Approved by: erwin (mentor)
* - Deprecategabor2006-12-103-0/+9
| | | | | | - Set EXPIRATION_DATE Approved by: erwin (mentor)
* - Local/Tools/Resources now globaldinoex2006-12-091-1/+0
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* - Respect X11BASErafan2006-12-091-0/+5
| | | | Approved by: portmgr (linimon)
* - Update to 0.14laszlof2006-12-074-56/+48
| | | | | Submitted by: Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw> Approved by: maintainer timeout (3 months)
* - Mark broken on amd64 < 6. We got followingrafan2006-12-041-0/+4
| | | | | | | | | | | | | | cc -O -pipe -fPIC -g -Wall -DACEDB4 -I. -I./wh -DFREEBSD -c -O -pipe -fPIC -g -Wall -DACEDB4 -c arraysub.c arraysub.c: In function `stackused': arraysub.c:54: error: unrecognizable insn: (insn 44 22 24 2 arraysub.c:53 (set (reg:SI 1 dx [66]) (subreg:SI (plus:DI (subreg:DI (reg:SI 7 sp) 0) (const_int -1 [0xffffffffffffffff])) 0)) -1 (nil) (nil)) arraysub.c:54: internal compiler error: in extract_insn, at recog.c:2083 Reported by: pointyhat via kris Approved by: Philip M. Gollucci (maintainer)
* Correct path to Compress::Zlib.pm after recent p5-Compress-Zlib update.demon2006-12-031-1/+1
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* - Respect X11BASErafan2006-12-031-1/+1
| | | | Approved by: maintainer (implicit)
* - Use features of bsd.wx.mk, especially USE_WXpav2006-12-011-4/+2
| | | | | PR: ports/101613 Submitted by: alepulver
* - Respect X11BASEmiwi2006-11-281-2/+2
| | | | | PR: ports/105891 Submitted by: trasz
* - Update to 1.91rafan2006-11-273-38/+5
| | | | | | | | - Unbreak on amd64 PR: ports/105414 Submitted by: rafan Approved by: maintainer timeout (15 days)
* - Upgrade to the latest beta and unbreak;thierry2006-11-224-230/+274
| | | | | | | | | - Add a regression-test target; - Fix plist for WITHOUT_SAMPLES. PR: ports/104685 Approved by: maintainer's time-out (1 month)
* - cleanup patchesdinoex2006-11-131-3/+0
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* - fix build on non i386 archsdinoex2006-11-101-2/+2
| | | | Submitted by: Gürkan Sengün
* Adun is a new extendible molecular simulation program that alsodinoex2006-11-1010-0/+607
| | | | | | | | includes data management and analysis capabilities. WWW: http://diana.imim.es/Adun Submitted by: Gürkan Sengün Reviewed by: dinoex
* - Update to 1.42miwi2006-10-313-121/+90
| | | | | | PR: ports/104635 Submitted by: Thomas Abthorpe <thomas@goodking.ca> Approved by: maintainer
* - Update to 34.t26.b3miwi2006-10-313-4/+7
| | | | | PR: ports/104508 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Distfile now checksums successfully.lawrance2006-10-151-4/+0
| | | | | | PR: ports/104341 Submitted by: Frank J. Laszlo <laszlof@vonostingroup.com> Approved by: portmgr (marcus)
* Chase the GNOME X11BASE to LOCALBASE move, and fix the build with themarcus2006-10-142-5/+7
| | | | | | | new freetype2 where needed. Submitted by: mezz, ahze, pav, and many others Approved by: portmgr (implicit, kris)
* - Add hmmer 5.09 applicationpav2006-10-104-10/+38
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* Chase pdf library and bump PORTREVISION.ale2006-10-091-1/+2
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* - Allow wxWidgets 2.6 alongside 2.4, this port works with bothpav2006-10-091-4/+3
| | | | | PR: ports/102168 Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 0.98dclsung2006-10-062-4/+4
| | | | | | PR: ports/103408 Submitted by: chinsan Approved by: maintainer (timeout)
* Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNAclsung2006-09-298-0/+105
| | | | | | | and EST Sequences. PR: ports/103651 Submitted by: Bob Zimmermann <rpz at cse.wustl.edu>
* Unbreak: molden has been updated on Aug 17, with the same DISTNAME.thierry2006-09-174-23/+35
| | | | Changelog at <http://www.cmbi.ru.nl/molden/HISTORY>.
* Fix build on amd64maho2006-09-172-4/+4
| | | | Submitted by: kris
* BROKEN on amd64 and ia64: Does not buildkris2006-09-171-0/+4
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* BROKEN: Size mismatch. Since this is unmaintained, deprecate and schedulekris2006-09-041-0/+4
| | | | for termination on 2006-12-01
* NO_CDROM and NO_PACKAGE are not appropriate herekris2006-09-031-3/+1
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* Schedule these broken ports for termination on 2006-12-01kris2006-09-032-0/+4
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* Folding@Home is a distributed computing project -- people from through out thepav2006-08-295-0/+61
| | | | | | | | | | | | | | world download and run software to band together to make one of the largest supercomputers in the world. Every computer makes the project closer to our goals. Folding@Home uses novel computational methods coupled to distributed computing, to simulate problems thousands to millions of times more challenging than previously achieved. WWW: http://folding.standford.edu PR: ports/101235 Submitted by: Yonatan <onatan@gmail.com>
* - s,INSTALLS_SHLIB,USE_LDCONFIG,gclsung2006-08-141-1/+1
| | | | | | | - these include astro/ audio/ biology/ chinese/ maintained by ports@ PR: ports/101916 Submitted by: Gea-Suan Lin <gslin_AT_gslin dot org>
* Mark as broken for i386 4.xedwin2006-08-111-1/+7
| | | | | PR: ports/101789 Submitted by: Scott Flatman <sf@slappy.org>
* Unmark BROKEN, it seems to be caused by a stale distfile on ftp-master.erwin2006-08-041-2/+0
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* Mark BROKEN: checksum mismatcherwin2006-08-041-0/+2
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* Mark broken due to checksum mismatcherwin2006-08-041-0/+2
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* - Update to 5.10pav2006-07-182-8/+8
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* - Fix pkg-plist [1]rafan2006-07-102-12/+19
| | | | | | - pet portlint(1) Noticed by: pointyhat via linimon [1]
* - Update to 2.4.3rafan2006-07-088-234/+147
| | | | | | | | - Pass maintainersip to submitter PR: 99901 Submitted by: Scott Flatman <sf slappy.org> Approved by: delphij (mentor, implicit)
* - Use the correct MASTER_SITE_SUBDIR, make it fetchablerafan2006-07-041-1/+1
| | | | | | PR: 99757 Submitted by: Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw> Approved by: delphij (mentor, implicit)
* Mark as BROKEN on sparc64 due to internal compiler error.linimon2006-07-041-1/+7
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* Update to 1.10 (maintained by others) and unbreak.maho2006-07-0311-268/+50
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* o Update to 0.99rc1maho2006-07-015-39/+203
| | | | | | | | | o add data dir to have working port[1] PR: 95121[1] Submitted by: Sangwoo Shim <sangwoos at gmail.com>[1] This commit is a result of hacks at the CodeFest Akihabara 2006 hosted by FSIJ.
* - Provide SSE optimized application as an optionpav2006-06-252-1/+12
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* - Instruct amd64 users to libmap libpthread.so.2 to libc_r.so.6pav2006-06-232-3/+15
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* SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculatedpav2006-06-207-0/+110
| | | | | | | | | | | | protein similarities that plays a key role in many bioinformatics methods. It contains about all currently published protein sequences and is continuously updated. The computational effort for keeping SIMAP up-to-date is constantly increasing. Please help to update SIMAP by calculating protein similarities on your computer. WWW: http://boinc.bio.wzw.tum.de/boincsimap/
* Re-add CONFIGURE_TARGET and fix libm detection.thierry2006-06-191-1/+5
| | | | | PR: ports/99072 (fu2) Submitted by: Josh Tolbert <hemi (at) puresimplicity.net> (maintainer)
* - Upgrade to to 1.9.9 and unbreak;thierry2006-06-184-146/+134
| | | | | | | - Take maintainership. PR: ports/99072 Submitted by: Josh Tolbert <hemi (at) puresimplicity.net>
* USE_SIZE was obsoleted in rev. 1.484 of bsd.port.mk more thanerwin2006-06-111-1/+0
| | | | | | 2 years ago. Clean out the last traces of it. With hat: portmgr
* - Update PORTREVISION to match latest release (see main web site)pav2006-06-113-8/+27
| | | | | | | - Update the port to add other architectures (amd64) PR: ports/98764 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 34.t25.d9pav2006-06-102-5/+5
| | | | | PR: ports/98761 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Update biology/ncbi-toolkit to the latest release.itetcu2006-06-063-5/+11
| | | | | | | | | | | | Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml Major changes include: blastall now uses the new engine by default, resulting in significant performance improvements and enabling query concatenation for all program types. PR: ports/98570 Submitted by: maintainer Approved by: lawrance (mentor, implict)
* - Add MASTER_SITEerwin2006-06-062-30/+31
| | | | | | | | - Use DATADIR PR: 97603 Submitted by: miwi Approved by: maintainer timeout
* - Update to 34.t25.d8 [1]erwin2006-06-062-5/+5
| | | | | | | | - While I'm here, pet portlint [2] PR: 98398 [1] Submitted by: miwi [1], self [2] Approved by: maintainer [1]
* - update to 34.t25.d7sem2006-05-253-77/+7
| | | | | | | - add MASTER_SITE_LOCAL as a second master site PR: ports/97310 Submitted by: maintainer
* BROKEN: Unfetchablekris2006-05-221-0/+2
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* - Update to 3.15sem2006-05-212-4/+4
| | | | | | PR: ports/96941 Submitted by: Paul Schmehl <pauls@utdallas.edu> Approved by: maintainer timeout
* - Updated from 0.07 to 0.12aaron2006-05-203-12/+25
| | | | | | | | | | | | | | | | | | | | | | Approved by: tobez (implicit) 0.08 20/Feb/2006 15:14 Improved referential integrity between nodes, taxa, and data. Implemented Fastnexus parser Node object silently implements Bio::Tree::NodeI interface if BioPerl is installed Tree object silently implements Bio::Tree::TreeI interface if BioPerl is installed Added convertor methods for XML and CIPRES Implemented more Matrix methods Implemented symbol tables in Bio::Phylo::Util::CONSTANT Implemented visit method for listable objects Implemented caching infrastructure for calculations Changed object-model to inside-out arrays Added Biodiversity measures code by Aki Mimoto Moved constants and exceptions to Bio::Phylo::Util::* Fixed memory leak due to circular references
* Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.aaron2006-05-145-0/+110
| | | | Approved by: tobez (implicit)
* - Update to 34.t25.d6sem2006-05-084-38/+80
| | | | | PR: ports/96063 Submitted by: maintainer
* Update to 21.u1.d1 (fixes fetch).lawrance2006-05-075-27/+18
| | | | Reported by: fenner's distfile survey
* - Satisfy portlintsem2006-05-071-4/+3
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* Add protomol 2.0.3, OO, component based, framework for molecularehaupt2006-05-065-0/+201
| | | | | | | dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com>
* Remove USE_REINPLACE from all categories starting with Bedwin2006-05-0421-22/+0
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* - Update to 1.89leeym2006-05-036-16/+60
| | | | | | | | | | - refine BROKEN to make portlint happier - patch to use on Scalar::Util instead of WeakRef - mark IGNORE under old perl which don't support weak reference PR: 96656 Submitted by: leeym Approved by: maintainer
* Bioperl-run contain modules that provides a PERL interface to variousgarga2006-05-035-0/+784
| | | | | | | | | | bioinformatics applications. This allows various applications to be used with common Bioperl objects. WWW: http://bioperl.org/ PR: ports/93675 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
* Bioperl-run contain modules that provides a PERL interface to variousgarga2006-05-035-0/+752
| | | | | | | | | | bioinformatics applications. This allows various applications to be used with common Bioperl objects. WWW: http://bioperl.org/ PR: ports/93674 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
* - Update to 1.0.0pav2006-04-263-40/+174
| | | | | | | | - Provide OPTIONS - Take maintainership PR: ports/94123 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
* BROKEN: Does not compilekris2006-04-231-0/+2
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* Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking aboutlinimon2006-04-055-5/+5
| | | | | | maintainer timeouts. Hat: portmgr
* Reset jeremy@external.org who has not responded to email asking aboutlinimon2006-04-051-1/+1
| | | | | | maintainer timeouts. Hat: portmgr
* - Update to 2006.02.13mnag2006-04-053-8/+8
| | | | | PR: 95281 Submitted by: maintainer
* Use SUB_FILES for pkg-messageedwin2006-04-014-1/+4
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* For EMBOSS:thierry2006-03-31