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Author SHA1 Message Date
Martin Wilke
21d58ada23 - Update MASTER_SITES and WWW: line 
- Support CC/CFLAGS properly
- Strip binary

PR:		123866
Submitted by:	Ports Fury
 2008-05-22 00:49:42 +00:00
Marcelo Araujo
2cba6cd79f - Include some ports in perl5 category. 
PR:		ports/123530
Submitted by:	Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:	araujo (myself)
Approved by:	flz (portmgr)
 2008-05-19 13:12:08 +00:00
Pav Lucistnik
48927e76ef - Update maintainer's email address 
Submitted by:	Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
 2008-05-17 16:52:34 +00:00
Pav Lucistnik
ee146516be - Try to fix fetch 
Submitted by:	Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
 2008-05-17 16:50:12 +00:00
Erwin Lansing
4ddb273770 Update to 1.23 2008-05-15 02:50:21 +00:00
Pav Lucistnik
0149bce295 NJplot is a tree drawing program able to draw any phylogenetic tree expressed 
in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP
package). NJplot is especially convenient for rooting the unrooted trees
obtained from parsimony, distance or maximum likelihood tree-building methods.

The package contains the following programs:
njplot      - draw phylogenetic trees and interactively modify them
newicktops  - non-interactive version rendering into a PostScript file
newicktotxt - non-interactive version rendering into a text file
unrooted    - draw unrooted circular trees

If you use NJplot in a published work, please cite the following reference:

Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for
biological sequence banks. Biochimie, 78, 364-369.

WWW: http://pbil.univ-lyon1.fr/software/njplot.html

PR:		ports/118438
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
 2008-05-14 14:07:01 +00:00
Pav Lucistnik
8c0e82e57e MUSCLE is multiple alignment software for protein and nucleotide sequences. 
The name stands for multiple sequence comparison by log-expectation.

A range of options is provided that give you the choice of optimizing
accuracy, speed, or some compromise between the two. Default parameters are
those that give the best average accuracy in the published tests. MUSCLE
can achieve both better average accuracy and better speed than CLUSTALW or
T-Coffee, depending on the chosen options.

Citation:

Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
and high throughput. Nucleic Acids Research 32(5): 1792-1797.

Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5(1): 113.

The NAR paper gives only a brief overview of the algorithm and
implementation details. For a full discussion of the method and many of
the non-default options that it offers, please see the BMC paper.

WWW: http://www.drive5.com/muscle/

PR:		ports/118460
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
 2008-05-14 13:51:50 +00:00
Dirk Meyer
944bce5e27 - add PORTSCOUT 2008-05-04 11:41:25 +00:00
OKAZAKI Tetsurou
8045c7b02c Update to version 34. 
Remove BROKEN.

PR:		123218
Submitted by:	maintainer
 2008-04-30 23:19:29 +00:00
Dirk Meyer
b079bde230 - update to 0.8.2 
- take maintainership
Approved by:	maintainer
 2008-04-29 17:46:12 +00:00
Martin Wilke
260898cd6e - Update to 2.0.6 
- Pass maintainership to submitter

PR:		123193
Submitted by:	Wen heping <wenheping@gmail.com>
 2008-04-29 12:58:52 +00:00
Mark Linimon
e3e5d56ef1 Reset aaron's port maintainerships due to many maintainer-timeouts. 2008-04-29 05:27:09 +00:00
Pav Lucistnik
98a58aed9f - Mark BROKEN on -CURRENT: error: 'linkat' redeclared as different kind of symbol 
Reported by:	pointyhat
 2008-04-25 22:53:23 +00:00
Martin Wilke
3e4ed01146 - Remove unneeded dependency from gtk12/gtk20 [1] 
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+

Thanks to all Helpers:
	Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
	ehaupt, nox, itetcu, flz, pav

PR:		116263
Tested on:	pointyhat
Approved by:	portmgr (pav)
 2008-04-19 17:56:05 +00:00
Edwin Groothuis
b9b294b8fc implement @dirrmtry macro for the pkg-plist 2008-04-19 00:24:21 +00:00
Jean Milanez Melo
cd98b10dae - Update mastersite. 
PR:		ports/122130
Submitted by:	Ganael Laplanche <ganael.laplanche@martymac.com>
 2008-04-18 15:36:54 +00:00
Pav Lucistnik
35e763ef1b - Replace SF with second working master site 
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2008-04-17 17:06:48 +00:00
Marcelo Araujo
4aaab89f57 - Take advantage of CPAN macro from bsd.sites.mk, change ${MASTER_SITE_PERL_CPAN} to CPAN. 
PR:		ports/122674
Submitted by:	Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:	araujo (myself)
Approved by:	portmgr (pav)
 2008-04-17 14:30:31 +00:00
Rong-En Fan
a8dd349ab1 - It seems that upstream removes their distfiles from sourceforge, so add 
the download site pointed by their webpage as first choice.

Noticed by:    pointyhat via pav
 2008-04-17 01:31:22 +00:00
Rong-En Fan
6098818ed4 - Update to 5.0.0 
PR:		ports/122437
Submitted by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
 2008-04-13 07:22:42 +00:00
Rong-En Fan
a0ab9c0e54 - Sort pkg-plist before updating to 5.0.0 
PR:		ports/122437
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2008-04-13 07:21:16 +00:00
Emanuel Haupt
deb298071b Change maintainers e-mail address. 
Requested over:		IRC
 2008-04-10 16:11:24 +00:00
Cheng-Lung Sung
1f16f8b132 - Update to 35.3.6 
PR:		ports/122607
Submitted by:	maintainer (Fernan Aguero)
 2008-04-10 08:09:10 +00:00
Philippe Audeoud
d369e5c287 - Chase the gsl shared lib bump. 
Approved by:	thierry (mentor)
 2008-04-08 13:53:22 +00:00
Rong-En Fan
e0dc7ba46f - Update maintainer's email 
- Mark as deprecated

PR:		ports/122474
Submitted by:	M. L. Dodson <mldodson at comcast.net> (maintainer with another email)
 2008-04-06 08:39:20 +00:00
Rong-En Fan
7e14529975 MAPMAKER/EXP is a linkage analysis package designed to help construct primary 
linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP
performs full multipoint linkage analysis (simultaneous estimation of all
recombination fractions from the primary data) for dominant, recessive, and co-
dominant (e.g.  RFLP-like) markers.  MAPMAKER/EXP is an experimental-cross-only
successor to the original MAPMAKER program.

MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map
genes controlling polygenic quantitative traits in F2 intercrosses and BC1
backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL
can be found in the technical report (included with MAPMAKER/QTL).

WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/

PR:		ports/122452
Submitted by:	Tassilo Philipp <tphilipp at potion-studios.com>
 2008-04-06 04:49:05 +00:00
Rong-En Fan
483203c167 - Update to 5.68 
- Remove gcc version restriction

PR:		ports/122435
Submitted by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
 2008-04-05 10:47:11 +00:00
Pav Lucistnik
1774725d03 - Update to 1.1.3 
PR:		ports/122374
Submitted by:	Wen heping <wenheping@gmail.com>
Patch revised:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2008-04-04 20:46:35 +00:00
Pav Lucistnik
3b18cc0258 - Chase fasta3 update 
Reported by:	pointyhat
 2008-04-01 22:24:51 +00:00
Rong-En Fan
0e77ef5912 - Update to 35.3.5 
- Switch to .tar.gz distfile so that we don't define our do-extract
- While I'm here, using substitution for version numbers in pkg-plist
  for easier upgrade

PR:		ports/121690
Submitted by:	Wen heping <wenheping at gmail.com>
Approved by:	maintainer timeout (2 weeks)
 2008-03-30 05:07:36 +00:00
Pietro Cerutti
3d12db1718 - Fix build with GCC 4.2 
Approved by:	miwi (mentor)
 2008-03-28 19:01:48 +00:00
Martin Wilke
6c0425c0a8 - Add missing dependens 
- Bump PORTREVISION

Submitted by:	pointyhat via pav
 2008-03-27 11:20:17 +00:00
Martin Wilke
cda30a295f - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG 
- Bump PORTREVISION

Approved by:	portmgr (xorg cleanup)
 2008-03-25 22:44:48 +00:00
Martin Wilke
270a2cb06b - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG 
- Bump PORTREVISION

Approved by:	portmgr (xorg cleanup)
 2008-03-24 13:03:55 +00:00
Martin Wilke
06aa815303 - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG 
- Bump PORTREVISION

Approved by:	portmgr (xorg cleanup)
 2008-03-23 23:03:18 +00:00
Martin Wilke
5afc678aac - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG 
- Bump PORTREVISION

Approved by:	portmgr (xorg cleanup)
 2008-03-23 16:44:09 +00:00
Beech Rintoul
5416e97007 - Remove USE_X_PREFIX 
- Bump portrevision

Approved by:	David Yeske <dyeske@gmail.com> (maintainer, implicit)
 2008-03-21 20:00:05 +00:00
Philippe Audeoud
7f65d2c4e1 - Update to 2.0.5 
- Add RESTRICTED due to non-commercial use licence.

PR:		ports/121794
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Approved by:	thierry and tabthorpe (mentors)
 2008-03-19 14:01:13 +00:00
Philippe Audeoud
5a299a59fb - Update to version 2.0.5 
- Add RESTRICTED due to a non-commercial use licence.

PR:		ports/121794
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Approved by:	thierry and tabthorpe (mentors)
 2008-03-19 13:31:52 +00:00
Martin Wilke
4459f0cf50 - Update to 1.07 2008-03-12 12:24:10 +00:00
Maho Nakata
be24b251f3 Fix pkg-plist 
Submitted by:	pav
 2008-03-10 00:57:15 +00:00
Maho Nakata
89a3cd0f56 Update to 1.0r2. 2008-03-07 02:38:09 +00:00
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
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