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934 Commits

Author SHA1 Message Date
Martin Wilke
4ba46d9017 - File was rerolled for a small bugfix. 
Submitted by:	pointyhat via pav/erwin
 2008-02-27 07:34:21 +00:00
Pav Lucistnik
147258bf29 - Restore clustalw symlink, other ports rely on it 
Reported by:	pointyhat
Pointy hat to:	pav
 2008-02-26 19:53:40 +00:00
Martin Wilke
a8719d91a6 - Update to 2.4.3 
Submitted by:	Ports Fury
 2008-02-25 22:34:13 +00:00
Pav Lucistnik
0289b4966d - Update to 2.0.3 2008-02-25 22:05:06 +00:00
Erwin Lansing
074c4e0cb5 Umark BROKEN, stale distfile removed from ftp-master. 2008-01-27 11:26:35 +00:00
Martin Wilke
61d80b7972 - Update to 2.4.2 (fix fetch problems) 
Submitted by:	pointyhat via pav
 2008-01-25 20:49:45 +00:00
Erwin Lansing
b2a161bb02 Mark BROKEN: does not fetch 2008-01-25 20:05:06 +00:00
Martin Wilke
31b078b9f7 - Update to 2.4.1 
PR:		119719
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
 2008-01-20 21:56:24 +00:00
Tilman Keskinoz
5f2b0bacf1 Fix build on !i386 
PR:		118922
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Approved by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2008-01-04 15:14:52 +00:00
Pav Lucistnik
0650f5cb0f - Update to 2.0 
PR:		ports/117713
Submitted by:	Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
 2007-12-15 18:47:00 +00:00
Martin Wilke
565d0310d5 MrBayes is a program for the Bayesian estimation of phylogeny. 
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
 2007-12-15 15:13:41 +00:00
Martin Wilke
9326ebd9c8 MUMmer is a modular system for the rapid whole genome alignment of finished 
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
 2007-12-14 20:54:47 +00:00
Pav Lucistnik
311b7c9239 - Mark BROKEN outside i386: does not compile 
Reported by:	pointyhat
Approved by:	portmgr (hat)
 2007-12-04 23:08:55 +00:00
Martin Wilke
7a4a4aba6d - Allow build with AMD64 
- Fix pkg-plist
- Bump PORTREVISION

PR:		117435
Submitted by:	"M. L. Dodson" <mldodson@comcast.net> (maintainer)
 2007-10-28 21:42:23 +00:00
Cheng-Lung Sung
87b89dd102 - Update to 1.1.0 
PR:		ports/117369
Submitted by:	Motomichi Matsuzaki <mzaki_AT_e-mail dot ne dot jp>
Approved by:	maintainer (Mauricio Herrera Cuadra)
 2007-10-24 01:38:51 +00:00
Martin Wilke
e3afa3a02b - Update to 2.1.2b 
PR:		117336
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
 2007-10-23 23:07:19 +00:00
Ade Lovett
dbd39ca660 Migration from bison 1.x to 2.x 
PR:		117086
Tested by:	-exp runs
 2007-10-17 10:13:01 +00:00
Martin Wilke
ec5ba85483 - Update to 2.1 
PR:		116017
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
 2007-10-08 13:04:51 +00:00
Andrew Pantyukhin
123d815215 - Sort category Makefiles 
Inspired by:	Jason Harris <jharris@widomaker.com>
Howto:		http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles
 2007-10-05 23:33:27 +00:00
Pav Lucistnik
2ee0a30a1b - Fix typo in WWW 2007-10-04 07:28:40 +00:00
Edwin Groothuis
13fcaf3ba2 Remove always-false/true conditions based on OSVERSION 500000 2007-10-04 00:15:01 +00:00
Mark Linimon
f6f8204621 Mark as broken on gcc4.2. 2007-10-02 09:10:48 +00:00
Mark Linimon
c05e24ab65 Mark as broken with gcc4.2. 2007-10-02 09:08:37 +00:00
Edwin Groothuis
e713c30f0c biology/linux-foldingathome needs to run as root? 
(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
 2007-09-23 05:45:41 +00:00
Mark Linimon
9839011ec3 Welcome bsd.perl.mk. Add support for constructs such as USE_PERL5=5.8.0+. 
Drop support for antique perl.

Work done by:	gabor
Sponsored by:	Google Summer of Code 2007
Hat:		portmgr
 2007-09-08 01:12:10 +00:00
Martin Wilke
3adc6ca3f2 - Update to 1.06 
- Remove 4.X cruft
 2007-09-07 14:45:12 +00:00
Ion-Mihai Tetcu
68b24c81a3 - Update to version 2.3 
PR:		ports/116019
Submitted by:	KATO Tsuguru
 2007-09-03 09:24:30 +00:00
Rong-En Fan
f9d985eff0 - Chase x11-toolkits/pmw renamed to x11-toolkits/py-Pmw 
PR:		115302
 2007-09-02 07:16:05 +00:00
Kris Kennaway
f3b72565d6 Replace IGNORE with ONLY_FOR_ARCHS for this binary port. 
Submitted by:	maintainer
 2007-08-09 01:00:45 +00:00
Lars Engels
3ffecf2926 Fix pkg-plist 
Spotted by:	pav
Approved by:	miwi (mentor)
 2007-08-02 20:25:01 +00:00
Lars Engels
f830ac44dd Update to 2.0.10 
PR:		114738
Submitted by:	KATO Tsuguru <tkato432 (AT) yahoo.com>
Approved by:	miwi (mentor)
 2007-07-31 21:08:54 +00:00
Dirk Meyer
fb9a1ceccf - cleanup after gnustep-make-2.0.1 
Approved by:	maintainer (implicit)
 2007-07-22 20:50:58 +00:00
Maho Nakata
269ae10910 Now we use USE_FORTRAN=yes to use FORTRAN compiler. 2007-07-14 09:51:49 +00:00
Maho Nakata
041f7e315b Now we use USE_FORTRAN=yes to use FORTRAN compiler. 2007-07-12 06:49:37 +00:00
Maho Nakata
eb0ab15198 Now we use USE_FORTRAN=yes to use FORTRAN compiler. 2007-07-12 06:41:22 +00:00
Maho Nakata
9cfd2bb219 Now we use USE_FORTRAN=yes to use FORTRAN compiler. 2007-07-12 06:33:38 +00:00
Pav Lucistnik
5ce82a190b - Runs on 7.0-CURRENT with compat6x 
Reported by:	Rene Ladan <r.c.ladan@gmail.com>
 2007-07-08 11:56:59 +00:00
Rong-En Fan
4f02991a02 - Update to version 9 
- 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)
 2007-07-08 11:47:58 +00:00
Edwin Groothuis
1fa9e4844d dyeske at yahoo dot com -> dyeske at gmail dot com 2007-07-05 23:39:06 +00:00
Ying-Chieh Liao
b9ba1ad61e chase math/gsl lib version 2007-06-29 05:46:43 +00:00
Aaron Dalton
9cec3ba81e Bump to v0.16. 
PR:		111719
Submitted by:	araujo@bsdmail.org
 2007-06-19 20:15:58 +00:00
Alexey Dokuchaev
8049a87680 - Fix the build with GCC 4.2 
- Remove BROKEN tag

Reported by:	pointyhat (logs)
 2007-06-18 21:35:50 +00:00
Martin Wilke
b7bc246771 - Fix typos. 
Reported by:    stas@
 2007-05-31 03:49:14 +00:00
Martin Wilke
884af2b045 - Update to 1.43 
PR:		111817
Submitted by:	"P.BandieraPaiva" <paiva@unifesp.br>
Approved by:	maintainer
 2007-05-30 06:57:20 +00:00
Kris Kennaway
709f1961ae BROKEN: Unfetchable 2007-05-26 21:03:05 +00:00
Kris Kennaway
add90dd319 BROKEN with gcc 4.2 2007-05-26 20:38:49 +00:00
Dirk Meyer
0e0e859328 - update for gnustep-make-2.0.0 
Approved by:	gurkan (maintainer)
 2007-05-25 06:04:44 +00:00
Dirk Meyer
13b3264699 - update for gnustep-make-2.0.0 2007-05-25 05:55:36 +00:00
Edwin Groothuis
9291d1b365 swap MASTER_SITES to improve fetchiness on pointyhat which is blocked from dasher.wustl.edu 2007-05-25 01:41:55 +00:00
Kris Kennaway
fe3a568be3 BROKEN: Unfetchable 2007-05-25 01:19:17 +00:00