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Author SHA1 Message Date
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
Pav Lucistnik
59783a7d36 - Chase openbabel update 2007-05-24 22:21:26 +00:00
Florent Thoumie
d4f0d0048a - Welcome X.org 7.2 \o/. 
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
 2007-05-19 20:36:56 +00:00
Edwin Groothuis
4a1e6b5974 [patch] cleanup non-supported FreeBSD versions 
PR:		ports/111728
Submitted by:	Edwin Groothuis <edwin@mavetju.org>
Approved by:	maintainer timeout
 2007-05-02 07:15:46 +00:00
Edwin Groothuis
f42468ac8f [patch] cleanup non-supported FreeBSD versions 
PR:		ports/111726
Submitted by:	Edwin Groothuis <edwin@mavetju.org>
Approved by:	maintainer timeout
 2007-05-02 07:15:18 +00:00
Edwin Groothuis
4e8e11bf73 [patch] cleanup non-supported FreeBSD versions 
PR:		ports/111725
Submitted by:	Edwin Groothuis <edwin@mavetju.org>
Approved by:	maintainer timeout
 2007-05-02 07:14:50 +00:00
Edwin Groothuis
c817a83fdc [patch] cleanup non-supported FreeBSD versions 
PR:		ports/111724
Submitted by:	Edwin Groothuis <edwin@mavetju.org>
Approved by:	maintainer timeout
 2007-05-02 07:13:53 +00:00
Tong LIU
17b108023a Use my @FreeBSD.org address. 
Approved by:	delphij (mentor)
 2007-04-30 06:27:41 +00:00
Cheng-Lung Sung
f1b8c87794 - Update to 4.5 2007-04-24 10:24:51 +00:00
Martin Wilke
c3defe91a4 - Unbreak 
- Add backup MASTER_SITES

PR:		111963
Submitted by:	Jason Harris <jharris@widomaker.com>
 2007-04-21 15:26:54 +00:00
Kris Kennaway
30536eed17 BROKEN: Unfetchable 2007-04-20 08:03:12 +00:00
Edwin Groothuis
dd6b0c2e8c [patch] cleanup non-supported FreeBSD versions 
PR:		ports/111727
Submitted by:	Edwin Groothuis <edwin@mavetju.org>
Approved by:	Bob Zimmermann <rpz@cse.wustl.edu>
 2007-04-16 21:18:53 +00:00
Edwin Groothuis
3783392432 Remove always-true condition due to OSVERSION 2007-04-16 11:58:10 +00:00
Edwin Groothuis
aa0f192c42 - Remove unreachable OSVERSION code. 
- Make portlint happier
 2007-04-16 11:57:17 +00:00
Pav Lucistnik
0925dae118 - Fix after objformat removal 
Reported by:	pointyhat
 2007-03-28 17:31:59 +00:00
Martin Wilke
c3b46463f4 - Update to 1.5-beta2 
- Pass maintainership to submitter

PR:             110621
Submitted by:   Nemo Liu<nemoliu@gmail.com>
 2007-03-27 08:01:54 +00:00
Gabor Kovesdan
7a850f3a0c - MASTER_SITE is back, remove BROKEN 
PR:		ports/109954
Submitted by:	Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
 2007-03-16 21:16:36 +00:00
Mark Linimon
979cd8dcb7 Reset razi@genet.sickkids.on.ca due to maintainer-timeouts and no response to 
email.

Hat:		portmgr
 2007-03-14 08:18:21 +00:00
Mark Linimon
426a0cc0f1 Reset dbader@eece.unm.edu due to maintainer-timeouts. 
Hat:		portmgr
 2007-03-11 03:21:18 +00:00
Mark Linimon
74f43621e7 Reset dbader@eece.unm.edu due to maintainer-timeout. While here, fix fetch. 2007-03-11 03:20:27 +00:00
Mark Linimon
1fb31bef8c Reset chuynh@biolateral.com.au: address bounces. 
Hat:		portmgr
 2007-03-10 20:20:10 +00:00
Martin Wilke
d427c1e56d - Update to 4.96 
PR:             110080
Submitted by:   Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
 2007-03-09 11:26:16 +00:00
Martin Wilke
572ad4f218 - Update to 34.26.2 
PR:             110079
Submitted by:   Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
 2007-03-09 11:26:13 +00:00
Martin Wilke
92bc0115f8 - Release distfile was renamed. 
PR:             110078
Submitted by:   Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
 2007-03-08 13:17:26 +00:00
Kris Kennaway
bd7aa23ad2 BROKEN: Unfetchable 2007-02-27 04:55:59 +00:00
Dirk Meyer
86102784f5 - mark ignore on FreeBSD 5.x 
Approved by:	maintainer
 2007-02-19 03:39:29 +00:00
Kris Kennaway
de78dd974b Schedule these broken ports for removal on 2007-04-10 if they are still 
broken at that time and no fix has been submitted.
 2007-02-11 01:23:35 +00:00
Maho Nakata
6235387960 Update to 0.99rc6. 
PR:		108940
Submitted by:	CHAO Shin
 2007-02-09 00:11:54 +00:00
Kris Kennaway
4c7fb3a8cb BROKEN: Does not build 2007-02-05 00:08:52 +00:00
Kris Kennaway
ae994c8ea8 Use libtool port instead of included version to avoid objformat a.out botch 2007-02-01 02:42:05 +00:00
Dirk Meyer
e904a42961 - add category gnustep 
PR:		103931
Approved by:	pav
 2007-01-31 18:18:14 +00:00
Maho Nakata
9dba1af857 Build fix. 
Submitted by:	kris via pointyhat and pav.
 2007-01-29 02:13:52 +00:00
Ion-Mihai Tetcu
124ca189fb Update to 3.66 
PR:		ports/108434
Submitted by:	Marcelo Araujo
 2007-01-27 21:23:52 +00:00
Vasil Dimov
885510efe1 Fix master sites, un-deprecate and update biology/recombine to 1.41. 2007-01-25 12:22:50 +00:00
Vasil Dimov
b82ef03e30 Remove expired leaf port: 
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.
 2007-01-25 11:25:40 +00:00
Vasil Dimov
c4499324f3 Get rid of biology/coalesce dependency, it is deprecated and will be removed 
shortly.
 2007-01-25 11:10:43 +00:00
Vasil Dimov
4b65027977 Fix master site and un-deprecate 2007-01-25 11:01:25 +00:00
Martin Wilke
e52225d8c8 - Fix typo 2007-01-23 13:05:24 +00:00
Rong-En Fan
b06ef1af5b - Project moves to a new home. Change MASTER_SITES and WWW 
PR:		ports/108214
Submitted by:	Thomas Abthorpe <thomas at goodking.ca>
Approved by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
 2007-01-22 23:22:53 +00:00
Maho Nakata
4406ddf947 Fix build. 
Submitted by:	kris via pointyhat.
 2007-01-19 06:41:03 +00:00
Maho Nakata
0f3556420c Forgot to commit a patch. Fixes build. 
Submitted by:	kris via pointyhat.
 2007-01-19 02:19:06 +00:00
Maho Nakata
8599517b90 * Migrate to gfortran. 
* Bump port revision.
 2007-01-17 05:30:10 +00:00
Boris Samorodov
22f2e343c5 . change dependencies: shells/bash2 -> shells/bash; 
. 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]
 2007-01-16 18:21:00 +00:00
Maho Nakata
0189d58a25 * Migrate to gfortran. 
* Bump port revision.
* fix build [1].

Submitted by:	kris [1]
 2007-01-16 04:41:41 +00:00
Dirk Meyer
d7f59ea8de - update to use new bsd.gnustep.mk 
Approved by:	gurkan@linuks.mine.nu
 2007-01-13 03:57:25 +00:00
Maho Nakata
667bd5ea91 * Migrate to gfortran. 
* Bump port revision.
 2007-01-12 12:21:21 +00:00
Maho Nakata
709a18cca2 Using gfortran42 only. not using gcc42. 
Bump portrevision.
 2007-01-12 05:40:57 +00:00
Maho Nakata
5d7fcfc438 Using only gfortran42. not gcc42. 
Bump portrevision.
 2007-01-12 05:39:18 +00:00
Maho Nakata
602b708bfb * Add dummy knob WANT_FORTRAN for future gfortran 
migration. currently it is not buildable with gfrotran42.
* Honor FC and FFLAGS.
 2007-01-09 02:37:43 +00:00
Maho Nakata
8ae475f6a8 migrated to gfortran. 2007-01-09 01:48:41 +00:00
Maho Nakata
397f4ace33 Migrated to gfortran. 2007-01-09 01:47:06 +00:00
Dirk Meyer
5779dde040 The BioCocoa framework provides developers with the opportunity to add 
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/
 2006-12-30 09:20:54 +00:00
Martin Wilke
96867a420d - Update to 1.0.1 
- Update MASTER_SITES
- Pass maintainership to submitter

PR:		ports/107246
Submitted by:	Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
 2006-12-29 23:40:53 +00:00
Aaron Dalton
dda8ae5412 Update to v0.15 2006-12-27 18:58:26 +00:00
Mark Linimon
5977ae11ec Reset tonymaher@optusnet.com.au due to maintainer-timeouts and no response 
to email.

Hat:		portmgr
 2006-12-26 12:46:34 +00:00
Martin Wilke
5f0f9b3c0a - Update to 5.1.2 
- Update maintainer mail adresse

PR:		ports/107118
Submitted by:	M. L. Dodson <bdodson@houston.rr.com> (maintainer)
 2006-12-23 21:45:17 +00:00
Rong-En Fan
93e8068e88 - Update to 1.03 
PR:		ports/106300
Submitted by:	chinsan
Approved by:	maintainer timeout (15 days)
 2006-12-19 06:47:45 +00:00
Mark Linimon
e0cde90bd9 Reset dbader@ece.unm.edu due to timeouts and no response to email. 
Hat:		portmgr
 2006-12-13 13:20:20 +00:00
Mark Linimon
2db91e4f1f Reset whitekid@gmail.com after timeouts and no response to email. 
Hat:		portmgr
 2006-12-13 12:56:01 +00:00
Gabor Kovesdan
93e805e722 - Update to 2.1.3 
- Fix fetching
- Remove old patch and use MAKE_ARGS instead
- portlint(1) and whitespace

Approved by:	erwin (mentor)
 2006-12-10 12:39:32 +00:00