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* Umark BROKEN, stale distfile removed from ftp-master.erwin2008-01-271-2/+0
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* - Update to 2.4.2 (fix fetch problems)miwi2008-01-262-4/+4
| | | | Submitted by: pointyhat via pav
* Mark BROKEN: does not fetcherwin2008-01-261-0/+2
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* - Update to 2.4.1miwi2008-01-214-15/+46
| | | | | PR: 119719 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* Fix build on !i386arved2008-01-041-9/+5
| | | | | | PR: 118922 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* - Update to 2.0pav2007-12-1615-406/+60
| | | | | PR: ports/117713 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
* MrBayes is a program for the Bayesian estimation of phylogeny.miwi2007-12-155-0/+60
| | | | | | | | | | | | | | | Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. WWW: http://mrbayes.csit.fsu.edu/ PR: ports/118542 Submitted by: mzaki at biol.s.u-tokyo.ac.jp
* MUMmer is a modular system for the rapid whole genome alignment of finishedmiwi2007-12-155-0/+79
| | | | | | | | | | | or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher
* - Mark BROKEN outside i386: does not compilepav2007-12-051-0/+4
| | | | | Reported by: pointyhat Approved by: portmgr (hat)
* - Allow build with AMD64miwi2007-10-292-2/+5
| | | | | | | | - Fix pkg-plist - Bump PORTREVISION PR: 117435 Submitted by: "M. L. Dodson" <mldodson@comcast.net> (maintainer)
* - Update to 1.1.0clsung2007-10-243-74/+86
| | | | | | PR: ports/117369 Submitted by: Motomichi Matsuzaki <mzaki_AT_e-mail dot ne dot jp> Approved by: maintainer (Mauricio Herrera Cuadra)
* - Update to 2.1.2bmiwi2007-10-245-37/+20
| | | | | PR: 117336 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* Migration from bison 1.x to 2.xade2007-10-171-1/+2
| | | | | PR: 117086 Tested by: -exp runs
* - Update to 2.1miwi2007-10-087-18/+196
| | | | | PR: 116017 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* - Sort category Makefilessat2007-10-061-2/+2
| | | | | Inspired by: Jason Harris <jharris@widomaker.com> Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles
* - Fix typo in WWWpav2007-10-041-1/+1
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* Remove always-false/true conditions based on OSVERSION 500000edwin2007-10-041-1/+1
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* Mark as broken on gcc4.2.linimon2007-10-021-1/+7
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* Mark as broken with gcc4.2.linimon2007-10-021-0/+4
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* biology/linux-foldingathome needs to run as root?edwin2007-09-233-6/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | (also: update to 5.0.4) Upon installing FoldingAtHome I ran the software from a user account only to find that I was stuck in a loop of trying to enter configuration options. Shortly thereafter I realized that it was trying to write to /usr/local/share/foldingathome, and therefore requires being run as root to write there unless one changes permissions there. Seing as this isn't installed with a startup script for daemonization, and running as root seems a little excessive for this application, should this be adapted to run from a user account or set up to be able to start at boot? And from maintainer: This diff updates the port to version 5.04, and adds support to running as normal user using ~/.fah directory. PR: ports/113335 Submitted by: James Snyder <jbsnyder@fanplastic.org> Approved by: maintainer
* Welcome bsd.perl.mk. Add support for constructs such as USE_PERL5=5.8.0+.linimon2007-09-087-39/+5
| | | | | | | | Drop support for antique perl. Work done by: gabor Sponsored by: Google Summer of Code 2007 Hat: portmgr
* - Update to 1.06miwi2007-09-072-12/+5
| | | | - Remove 4.X cruft
* - Update to version 2.3itetcu2007-09-034-46/+57
| | | | | PR: ports/116019 Submitted by: KATO Tsuguru
* - Chase x11-toolkits/pmw renamed to x11-toolkits/py-Pmwrafan2007-09-021-2/+2
| | | | PR: 115302
* Replace IGNORE with ONLY_FOR_ARCHS for this binary port.kris2007-08-091-9/+2
| | | | Submitted by: maintainer
* Fix pkg-plistlme2007-08-031-0/+1
| | | | | Spotted by: pav Approved by: miwi (mentor)
* Update to 2.0.10lme2007-08-014-22/+22
| | | | | | PR: 114738 Submitted by: KATO Tsuguru <tkato432 (AT) yahoo.com> Approved by: miwi (mentor)
* - cleanup after gnustep-make-2.0.1dinoex2007-07-231-1/+0
| | | | Approved by: maintainer (implicit)
* Now we use USE_FORTRAN=yes to use FORTRAN compiler.maho2007-07-141-7/+2
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* Now we use USE_FORTRAN=yes to use FORTRAN compiler.maho2007-07-121-4/+2
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* Now we use USE_FORTRAN=yes to use FORTRAN compiler.maho2007-07-122-9/+2
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* Now we use USE_FORTRAN=yes to use FORTRAN compiler.maho2007-07-121-5/+1
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* - Runs on 7.0-CURRENT with compat6xpav2007-07-081-0/+4
| | | | Reported by: Rene Ladan <r.c.ladan@gmail.com>
* - Update to version 9rafan2007-07-083-1313/+1505
| | | | | | | | | - Don't install CVS directories which are going to be removed in next release PR: ports/113831 Submitted by: Thomas Abthorpe <thomas at goodking.ca> Approved by: maintainer timeout (20 days)
* dyeske at yahoo dot com -> dyeske at gmail dot comedwin2007-07-064-6/+6
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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:thierry2006-03-3122-1458/+7820
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
* - Update to 34.t25.d5pav2006-03-212-4/+4
| | | | | PR: ports/94741 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 5.743garga2006-03-194-44/+13
| | | | | | | | - Add a MASTER_SITE backup since oficial one just have last version and make it fetchable again Submitted by: maintainer by email Reported by: krismail
* Add lagan 1.2, efficient tools for large-scale multiple alignments ofgarga2006-03-176-0/+136
| | | | | | | genomic DNA. PR: ports/93058 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Add mafft 5.734, multiple sequence alignments based on fast Fouriergarga2006-03-156-0/+119
| | | | | | | transform. PR: ports/93059 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Add dotter 20021204 # last modified date in FTP server, a viewer forgarga2006-03-154-0/+63
| | | | | | | multiple sequence alignments. PR: ports/93055 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Add blat 33, a fast tool for local sequence similarity searches.garga2006-03-156-0/+100
| | | | | PR: ports/93060 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Add belvu 2.29, a viewer for multiple sequence alignments.garga2006-03-154-0/+54
| | | | | PR: ports/93056 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Update to 1.5maho2006-03-154-211/+229
| | | | Submitted by: distfile survey by kris, fenner
* Bump PORTREVISION on glib12/gtk12 consumer ports to ease the upgrade path.ade2006-03-071-1/+1
| | | | | Discussed with: kris Approved by: portmgr (implicit)
* Conversion to a single libtool environment.ade2006-02-234-2/+8
| | | | Approved by: portmgr (kris)
* BROKEN: Configure failskris2006-02-201-0/+2
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* Jalview is a multiple alignment editor written in Java. It is used widely in ahq2006-02-137-0/+137
| | | | | | | | | | variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) and is also available as a general purpose alignment editor. WWW: http://www.jalview.org PR: 93054 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Reset maintainership to ports@ after ~4 months without any response to anynetchild2006-02-121-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | PR. Thanks for contributing. Since the acroread7 port is a somewhat important port for our users, I will hand it over to emulation@ if no _active_ *committer* takes it before the ports freeze. While I'm here: - fix a little nit in the csound port (I think the intention was to create no backup file instead of creating one with a "-e" extension) - set ARCH to i386 in the amd64 case for the acroread7 port. This is a work-around to be able to install everything when a dependency is not already installed (ARCH is read-only in sub-makes, so the dependencies can't change it). This should be removed when the dependencies are fixed or converted to use bsd.linux-rpm.mk. [1] Not objected to by: portmgr (explicit: krion; silence: rest) Maintainer timeout: ~4 months Submitted by: Sangwoo Shim <sangwoos@gmail.com> [1] PR: 87985 [1]
* Update to 3.27.lawrance2006-02-103-10/+18
| | | | | | | Use GCC 3.3 on systems with 3.4, due to an internal compiler error. PR: ports/93050 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Update to 34.t25.d4.lawrance2006-02-1011-167/+155
| | | | | PR: ports/93052 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Update to 2006.01.25.lawrance2006-02-092-10/+9
| | | | | PR: ports/93051 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Put PORTEPOCH back.lawrance2006-02-091-0/+1
| | | | Reported by: chkversion
* Update to 3.65.lawrance2006-02-083-73/+17
| | | | | | PR: ports/92182 Submitted by: "Choe, Cheng-Dae" <whitekid@gmail.com> Approved by: dbader@ece.unm.edu (maintainer, timeout 14 days)
* Remove CONFLICTS with nss.marcus2006-02-031-1/+1
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* Add missing USE_ICONVkris2006-01-261-0/+1
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* SHA256ify (manually done and checked)edwin2006-01-222-1/+5
| | | | Approved by: krion@
* SHA256ifyedwin2006-01-2230-0/+41
| | | | Approved by: krion@
* Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtryedwin2006-01-224-12/+12
| | | | | Approved by: krion@ PR: ports/88711 (related)
* Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtryedwin2006-01-221-1/+1
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* Utilize EXAMPLESDIR.danfe2006-01-201-3/+3
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* - Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoiddanfe2006-01-205-0/+57
| | | | | | | | | | | unnecessary PORTEPOCH bump) - Update MASTER_SITES and WWW line, provide backup download site - Come up with better port description - Reset maintainer to ports@ - Uphold CXX and CXXFLAGS - Clean up Makefile slightly - Don't install yet another copy of GPL and texts in French - Add SHA256 hash to distinfo
* - Remove expired portspav2006-01-1517-462/+0
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* - Update to 2.0.20060101pav2006-01-152-2/+4
| | | | | PR: ports/91715 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 2005.12.06pav2006-01-154-44/+60
| | | | | PR: ports/91714 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Chase openbabel updatepav2006-01-141-3/+2
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* BROKEN: Broken dependencykris2006-01-141-0/+2
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* - Update graphics/libglut to 6.4.1.sem2006-01-123-4/+7
| | | | | | | | | | | - Shared lib version and PORTREVISION bumb for all affected ports. While I'm here: - Remove USE_MESA knob where it was (35 ports). It marked as depricated for 2 years. PR: ports/90247 Submitted by: Ermal Lu?i <eri--@albabsd.org>
* Fix maintainer addressedwin2006-01-096-6/+6
| | | | | | | | | | | | | | | | | | | | | From: Tony Maher <anthony.maher@uts.edu.au> To: Edwin Groothuis <edwin@FreeBSD.org> Subject: Re: ports/91537: maths/xgobi - download site moved/maintainer addressupdate Actually I need modify all my ports to use OptusNet rather than Biolateral. Is there an easy way to do this or should I submit a separate 1-line patch and PR for each port? biology/crimap biology/dna-qc biology/flip biology/primer3 biology/seqio biology/wise math/xgobi net/generic-nqs Submitted by: Tony Maher <anthony.maher@uts.edu.au>
* Hash with SHA-256.trevor2006-01-081-0/+1
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* - Remove symlinks that belong to mtreepav2006-01-061-2/+0
| | | | Approved by: maintainers
* possible fix to unbreak biology/L-Breederedwin2006-01-039-107/+60
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | L-Breeder is currently marked unfetchable: http://people.freebsd.org/~fenner/portsurvey/biology.html#L-Breeder So I tried to investigate the problem and I'm now submitting my homework so it doesn't get lost. This is what I noticed: i) L-Breeder upstream sources have "stagnated for some time, but now a new simplified version is available" (sic, from the web site) So, the fetch issue is resolved. And the pkg-descr is also updated to reflect the new home page. However: ii) L-Breeder is now called LBreeder. I have changed PORTNAME to reflect this, although I don't know if this is the right thing to do. Should the port be moved to biology/LBreeder? Or perhaps just leaving PORTNAME pointing to the old name and then work inside the Makefile to point the build/install to the correct name? iii) the sources have been reorganized so I have to update the port's Makefile to reflect this. The attached patch works for me under FreeBSD-4.11 (although it's possible that I may have missed a dependency if I already have a required library installed in my box. Sorry, I don't have a tinderbox-like setup to test builds) iv) the program does not have a version number, nor did I find one by looking inside the sources. To avoid changing too much the port I just left PORTVERSION at 1.0 and bumped PORTREVISION to 6 Finally, do note that I am not a user of LBreeder, so I cannot test the program myself. I just noticed that by calling the executable I get a black X screen, that I can quit by pressing 'q' as documented in Readme.txt, but I can't tell myself if this is the expected behaviour. Nor do I know how to use the example files. Caveat emptor. PR: ports/90073 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: maintainer timeout
* - New upstream version; two patches incorporated.tdb2005-12-105-39/+9
| | | | | | PR: 90140 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Approved by: clement (mentor)
* Update to 1.3.1ehaupt2005-12-072-3/+3
| | | | | PR: 90029 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 2005.13.07 to make fetchable againtdb2005-12-063-6/+31
| | | | | | PR: 89976 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Approved by: clement (mentor)
* - Update to 3.18 to make fetchable againtdb2005-12-062-6/+11
| | | | | | | | - Mark broken on 6.x upwards PR: 89977 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Approved by: clement (mentor)
* Update to 0.5.1mnag2005-12-063-23/+6
| | | | | | | | Unbroken >= 502126 Add SHA256 PR: 89980 Submitted by: maintainer
* - Fix fetch problemstdb2005-12-062-3/+5
| | | | | | PR: 89971 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Approved by: clement (mentor)
* Add conflicts:edwin2005-12-051-1/+1
| | | | | | CONFLICTS= p5-bioperl-1.[02468]* Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>, Mauricio Herrera Cuadra <arareko@yahoo.com>
* Add conflicst:edwin2005-12-051-0/+2
| | | | | | CONFLICTS= p5-bioperl-1.[13579]* Submitted by: Mauricio Herrera Cuadra <arareko@yahoo.com>,Fernan Aguero <fernan@iib.unsam.edu.ar>
* Fix port: biology/p5-bioperl-develedwin2005-12-041-0/+2
| | | | | | | | | This patch adds a LATEST_LINK line in the Makefile to avoid duplication with the 'p5-bioperl' port in the packages/Latest directory. PR: ports/89916 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
* - Re-add p5-bioperl-devel, development version of biology/p5-bioperlbarner2005-12-036-0/+2586
| | | | | | | (A collection of Perl modules for bioinformatics) PR: ports/89497 Submitted by: Mauricio Herrera Cuadra <arareko@yahoo.com>
* - Unbreak by updating to 4.4barner2005-12-014-25/+22
| | | | | | | - Add dependecy to MESA PR: ports/89795 Submitted by: Johan van Selst <johans@stack.nl>
* Add the right MASTER_SITE_SUBDIR, so that this port is fetchable fromfenner2005-11-261-0/+1
| | | | 20 sites instead of just 1.
* - Add SHA256pav2005-11-2416-0/+16
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* - Drop old povchem.c checksumpav2005-11-241-1/+4
| | | | - Add SHA256, SIZE
* - BROKEN: Size mismatchpav2005-11-241-0/+2
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* BROKEN: Size mismatchkris2005-11-161-0/+2
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* Mass-conversion to the USE_AUTOTOOLS New World Order. The code presentade2005-11-152-2/+2
| | | | | | | | | | | | | | | | | in bsd.autotools.mk essentially makes this a no-op given that all the old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in exactly the same way as USE_AUTOTOOLS itself. Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME team -- all GNOME 2.12.x ports use it. Preliminary documentation can be found at: http://people.FreeBSD.org/~ade/autotools.txt which is in the process of being SGMLized before introduction into the Porters Handbook. Light blue touch-paper. Run.
* - Mark it as DEPRECATED - master site disapearedgarga2005-11-111-0/+3
| | | | | | | | - Set EXPIRATION_DATE PR: ports/88003 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: maintainer timeout (17 days)
* - Mark it as DEPRECATED - master site disapearedgarga2005-11-111-0/+3
| | | | | | | | - Set EXPIRATION_DATE PR: ports/88002 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: maintainer timeout (17 days)
* - Mark it as DEPRECATED (mastersite disapeared)garga2005-11-111-0/+3
| | | | | | | | - Set EXPIRATION_DATE PR: ports/88000 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: maintainer timeout (16 days)
* With portmgr hat on, reset maintainership of knu's ports since he haslinimon2005-11-111-1/+1
| | | | been inactive more than 6 months. We hope to see him back sometime.
* Update to 1.41mnag2005-11-115-44/+87
| | | | | | | | Take MAINTAINER Add SHA256 PR: 88792 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
* Update to 3.14bmnag2005-11-102-9/+11
| | | | | | | | | | Update MASTER_SITES Add SHA256 Remove extra TABS PR: 88007 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: maintainer timeout, 14 days
* Remove expired portskris2005-11-057-110/+0
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* Bump PORTREVISION to chase the glib20 shared library update.marcus2005-11-054-3/+4
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* Mark DEPRECATED since upstream is unmaintained and mastersite is gone.lawrance2005-10-291-0/+3
| | | | | | PR: ports/88004 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: Tony Maher <anthony.maher@uts.edu.au> (maintainer)
* BROKEN: Unfetchablekris2005-10-281-0/+2
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* Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser forehaupt2005-10-165-0/+61
| | | | | | | | NCBI Entrez Gene. PR: 87423 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Approved by: novel (mentor) (implicit)
* - Update to 20050605sem2005-10-125-20/+36
| | | | | PR: ports/87266 Submitted by: maintainer
* - Update to 3.13. It fixes fetching.sem2005-10-124-167/+61
| | | | | PR: ports/87264 Submitted by: maintainer
* Update to 0.9.8maho2005-10-103-318/+363
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* Checking MACHINE_ARCH is deprecated.trevor2005-09-241-1/+1
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* Update to version 7hq2005-09-203-47/+160
| | | | | | PR: 86196 Submitted by: Tony Maher <anthony.maher@uts.edu.au> Approved by: maintainer
* Don't strip static libraries on installation ;)vs2005-09-141-1/+2
| | | | (Unbreaks e.g. biology/nclever)
* Add p5-Bio-Das 1.02, client-side library for Distributed Genomegarga2005-09-015-0/+158
| | | | | | | Annotation System. PR: ports/76379 Submitted by: Razi Khaja <razi@genet.sickkids.on.ca>
* This port is scheduled for deletion on 2005-09-22 if it is still brokenkris2005-07-231-0/+2
| | | | at that time and no PRs have been submitted to fix it.
generated by cgit (git 2.34.1) at 2024-12-29 03:33:01 +0800