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2008-01-04Fix build on !i386Tilman Keskinoz1-9/+5
PR: 118922 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=205000
2007-12-15- Update to 2.0Pav Lucistnik15-406/+60
PR: ports/117713 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> Notes: svn path=/head/; revision=203771
2007-12-15MrBayes is a program for the Bayesian estimation of phylogeny.Martin Wilke5-0/+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 Notes: svn path=/head/; revision=203737
2007-12-14MUMmer is a modular system for the rapid whole genome alignment of finishedMartin Wilke5-0/+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 Notes: svn path=/head/; revision=203638
2007-12-04- Mark BROKEN outside i386: does not compilePav Lucistnik1-0/+4
Reported by: pointyhat Approved by: portmgr (hat) Notes: svn path=/head/; revision=202901
2007-10-28- Allow build with AMD64Martin Wilke2-2/+5
- Fix pkg-plist - Bump PORTREVISION PR: 117435 Submitted by: "M. L. Dodson" <mldodson@comcast.net> (maintainer) Notes: svn path=/head/; revision=202239
2007-10-24- Update to 1.1.0Cheng-Lung Sung3-74/+86
PR: ports/117369 Submitted by: Motomichi Matsuzaki <mzaki_AT_e-mail dot ne dot jp> Approved by: maintainer (Mauricio Herrera Cuadra) Notes: svn path=/head/; revision=201876
2007-10-23- Update to 2.1.2bMartin Wilke5-37/+20
PR: 117336 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Notes: svn path=/head/; revision=201859
2007-10-17Migration from bison 1.x to 2.xAde Lovett1-1/+2
PR: 117086 Tested by: -exp runs Notes: svn path=/head/; revision=201613
2007-10-08- Update to 2.1Martin Wilke7-18/+196
PR: 116017 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Notes: svn path=/head/; revision=201095
2007-10-05- Sort category MakefilesAndrew Pantyukhin1-2/+2
Inspired by: Jason Harris <jharris@widomaker.com> Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles Notes: svn path=/head/; revision=200970
2007-10-04- Fix typo in WWWPav Lucistnik1-1/+1
Notes: svn path=/head/; revision=200799
2007-10-04Remove always-false/true conditions based on OSVERSION 500000Edwin Groothuis1-1/+1
Notes: svn path=/head/; revision=200767
2007-10-02Mark as broken on gcc4.2.Mark Linimon1-1/+7
Notes: svn path=/head/; revision=200623
2007-10-02Mark as broken with gcc4.2.Mark Linimon1-0/+4
Notes: svn path=/head/; revision=200622
2007-09-23biology/linux-foldingathome needs to run as root?Edwin Groothuis3-6/+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 Notes: svn path=/head/; revision=199937
2007-09-08Welcome bsd.perl.mk. Add support for constructs such as USE_PERL5=5.8.0+.Mark Linimon7-39/+5
Drop support for antique perl. Work done by: gabor Sponsored by: Google Summer of Code 2007 Hat: portmgr Notes: svn path=/head/; revision=199069
2007-09-07- Update to 1.06Martin Wilke2-12/+5
- Remove 4.X cruft Notes: svn path=/head/; revision=199031
2007-09-03- Update to version 2.3Ion-Mihai Tetcu4-46/+57
PR: ports/116019 Submitted by: KATO Tsuguru Notes: svn path=/head/; revision=198681
2007-09-02- Chase x11-toolkits/pmw renamed to x11-toolkits/py-PmwRong-En Fan1-2/+2
PR: 115302 Notes: svn path=/head/; revision=198632
2007-08-09Replace IGNORE with ONLY_FOR_ARCHS for this binary port.Kris Kennaway1-9/+2
Submitted by: maintainer Notes: svn path=/head/; revision=197358
2007-08-02Fix pkg-plistLars Engels1-0/+1
Spotted by: pav Approved by: miwi (mentor) Notes: svn path=/head/; revision=196987
2007-07-31Update to 2.0.10Lars Engels4-22/+22
PR: 114738 Submitted by: KATO Tsuguru <tkato432 (AT) yahoo.com> Approved by: miwi (mentor) Notes: svn path=/head/; revision=196859
2007-07-22- cleanup after gnustep-make-2.0.1Dirk Meyer1-1/+0
Approved by: maintainer (implicit) Notes: svn path=/head/; revision=196074
2007-07-14Now we use USE_FORTRAN=yes to use FORTRAN compiler.Maho Nakata1-7/+2
Notes: svn path=/head/; revision=195563
2007-07-12Now we use USE_FORTRAN=yes to use FORTRAN compiler.Maho Nakata1-4/+2
Notes: svn path=/head/; revision=195449
2007-07-12Now we use USE_FORTRAN=yes to use FORTRAN compiler.Maho Nakata2-9/+2
Notes: svn path=/head/; revision=195448
2007-07-12Now we use USE_FORTRAN=yes to use FORTRAN compiler.Maho Nakata1-5/+1
Notes: svn path=/head/; revision=195447
2007-07-08- Runs on 7.0-CURRENT with compat6xPav Lucistnik1-0/+4
Reported by: Rene Ladan <r.c.ladan@gmail.com> Notes: svn path=/head/; revision=195216
2007-07-08- Update to version 9Rong-En Fan3-1313/+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) Notes: svn path=/head/; revision=195215
2007-07-05dyeske at yahoo dot com -> dyeske at gmail dot comEdwin Groothuis4-6/+6
Notes: svn path=/head/; revision=195037
2007-06-29chase math/gsl lib versionYing-Chieh Liao1-2/+2
Notes: svn path=/head/; revision=194427
2007-06-19Bump to v0.16.Aaron Dalton3-6/+53
PR: 111719 Submitted by: araujo@bsdmail.org Notes: svn path=/head/; revision=193895
2007-06-18- Fix the build with GCC 4.2Alexey Dokuchaev2-7/+32
- Remove BROKEN tag Reported by: pointyhat (logs) Notes: svn path=/head/; revision=193835
2007-05-31- Fix typos.Martin Wilke1-3/+3
Reported by: stas@ Notes: svn path=/head/; revision=192436
2007-05-30- Update to 1.43Martin Wilke4-92/+167
PR: 111817 Submitted by: "P.BandieraPaiva" <paiva@unifesp.br> Approved by: maintainer Notes: svn path=/head/; revision=192382
2007-05-26BROKEN: UnfetchableKris Kennaway1-0/+2
Notes: svn path=/head/; revision=191940
2007-05-26BROKEN with gcc 4.2Kris Kennaway1-1/+7
Notes: svn path=/head/; revision=191937
2007-05-25- update for gnustep-make-2.0.0Dirk Meyer2-71/+79
Approved by: gurkan (maintainer) Notes: svn path=/head/; revision=191722
2007-05-25- update for gnustep-make-2.0.0Dirk Meyer1-1/+1
Notes: svn path=/head/; revision=191718
2007-05-25swap MASTER_SITES to improve fetchiness on pointyhat which is blocked from ↵Edwin Groothuis1-4/+2
dasher.wustl.edu Notes: svn path=/head/; revision=191699
2007-05-25BROKEN: UnfetchableKris Kennaway1-0/+2
Notes: svn path=/head/; revision=191691
2007-05-24- Chase openbabel updatePav Lucistnik1-2/+2
Notes: svn path=/head/; revision=191646
2007-05-19- Welcome X.org 7.2 \o/.Florent Thoumie35-20/+40
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}. - Bump PORTREVISION for ports intalling files in ${X11BASE}. Notes: svn path=/head/; revision=191544
2007-05-02[patch] cleanup non-supported FreeBSD versionsEdwin Groothuis1-7/+2
PR: ports/111728 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout Notes: svn path=/head/; revision=191382
2007-05-02[patch] cleanup non-supported FreeBSD versionsEdwin Groothuis1-7/+1
PR: ports/111726 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout Notes: svn path=/head/; revision=191381
2007-05-02[patch] cleanup non-supported FreeBSD versionsEdwin Groothuis1-6/+2
PR: ports/111725 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout Notes: svn path=/head/; revision=191380
2007-05-02[patch] cleanup non-supported FreeBSD versionsEdwin Groothuis1-7/+1
PR: ports/111724 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout Notes: svn path=/head/; revision=191379
2007-04-30Use my @FreeBSD.org address.Tong LIU1-1/+1
Approved by: delphij (mentor) Notes: svn path=/head/; revision=191183
2007-04-24- Update to 4.5Cheng-Lung Sung3-14/+13
Notes: svn path=/head/; revision=190798
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