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Author SHA1 Message Date
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
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
Gabor Kovesdan
ac97872da3 - Deprecate 
- Set EXPIRATION_DATE

Approved by:	erwin (mentor)
 2006-12-10 12:37:38 +00:00
Dirk Meyer
cb4e8b9a8e - Local/Tools/Resources now global 2006-12-09 09:40:38 +00:00
Rong-En Fan
c1e393d3a9 - Respect X11BASE 
Approved by:	portmgr (linimon)
 2006-12-09 07:49:55 +00:00
Frank J. Laszlo
4ffcd931fe - Update to 0.14 
Submitted by:	Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw>
Approved by:	maintainer timeout (3 months)
 2006-12-07 15:43:27 +00:00
Rong-En Fan
146e6417d0 - Mark broken on amd64 < 6. We got following 
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)
 2006-12-04 04:13:30 +00:00
Dmitry Sivachenko
274e5c4ab3 Correct path to Compress::Zlib.pm after recent p5-Compress-Zlib update. 2006-12-03 12:45:59 +00:00
Rong-En Fan
365cb9a6e2 - Respect X11BASE 
Approved by:	maintainer (implicit)
 2006-12-02 20:34:11 +00:00
Pav Lucistnik
d750615763 - Use features of bsd.wx.mk, especially USE_WX 
PR:		ports/101613
Submitted by:	alepulver
 2006-12-01 07:39:02 +00:00
Martin Wilke
bdfb7058a1 - Respect X11BASE 
PR:		ports/105891
Submitted by:	trasz
 2006-11-27 22:03:22 +00:00
Rong-En Fan
47d8f620ab - Update to 1.91 
- Unbreak on amd64

PR:		ports/105414
Submitted by:	rafan
Approved by:	maintainer timeout (15 days)
 2006-11-27 02:35:16 +00:00
Thierry Thomas
dd746cb883 - Upgrade to the latest beta and unbreak; 
- Add a regression-test target;

- Fix plist for WITHOUT_SAMPLES.

PR:		ports/104685
Approved by:	maintainer's time-out (1 month)
 2006-11-21 22:35:28 +00:00
Dirk Meyer
1efa3fa64a - cleanup patches 2006-11-12 16:59:53 +00:00
Dirk Meyer
b8fd717fad - fix build on non i386 archs 
Submitted by:	Gürkan Sengün
 2006-11-10 14:51:56 +00:00
Dirk Meyer
1d8ba7db66 Adun is a new extendible molecular simulation program that also 
includes data management and analysis capabilities.

WWW: http://diana.imim.es/Adun
Submitted by:	Gürkan Sengün
Reviewed by:	dinoex
 2006-11-09 20:16:54 +00:00
Martin Wilke
58c1e960b2 - Update to 1.42 
PR:		ports/104635
Submitted by:	Thomas Abthorpe <thomas@goodking.ca>
Approved by:	maintainer
 2006-10-31 13:25:21 +00:00
Martin Wilke
37c6f45ce2 - Update to 34.t26.b3 
PR:		ports/104508
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-10-31 09:02:04 +00:00
Sam Lawrance
1969eb5f6b Distfile now checksums successfully. 
PR:		ports/104341
Submitted by:	Frank J. Laszlo <laszlof@vonostingroup.com>
Approved by:	portmgr (marcus)
 2006-10-14 16:13:49 +00:00
Joe Marcus Clarke
29747f458a Chase the GNOME X11BASE to LOCALBASE move, and fix the build with the 
new freetype2 where needed.

Submitted by:	mezz, ahze, pav, and many others
Approved by:	portmgr (implicit, kris)
 2006-10-14 08:54:54 +00:00
Pav Lucistnik
deff0d8ddd - Add hmmer 5.09 application 2006-10-10 11:31:42 +00:00
Alex Dupre
8e8d970bfa Chase pdf library and bump PORTREVISION. 2006-10-09 08:18:35 +00:00
Pav Lucistnik
bf619e630a - Allow wxWidgets 2.6 alongside 2.4, this port works with both 
PR:		ports/102168
Approved by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-10-09 07:16:37 +00:00
Cheng-Lung Sung
81bb3a52c4 - Update to 0.98d 
PR:		ports/103408
Submitted by:	chinsan
Approved by:	maintainer (timeout)
 2006-10-06 04:12:59 +00:00
Cheng-Lung Sung
3e9ed050ec Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA 
and EST Sequences.

PR:		ports/103651
Submitted by:	Bob Zimmermann <rpz at cse.wustl.edu>
 2006-09-29 04:05:55 +00:00
Thierry Thomas
41a8cea837 Unbreak: molden has been updated on Aug 17, with the same DISTNAME. 
Changelog at <http://www.cmbi.ru.nl/molden/HISTORY>.
 2006-09-17 13:41:56 +00:00
Maho Nakata
1a1223bfca Fix build on amd64 
Submitted by:	kris
 2006-09-17 11:51:56 +00:00
Kris Kennaway
64e99d9063 BROKEN on amd64 and ia64: Does not build 2006-09-17 01:32:58 +00:00
Kris Kennaway
2248301e36 BROKEN: Size mismatch. Since this is unmaintained, deprecate and schedule 
for termination on 2006-12-01
 2006-09-04 14:50:49 +00:00
Kris Kennaway
fa2fe3f774 NO_CDROM and NO_PACKAGE are not appropriate here 2006-09-03 00:34:47 +00:00
Kris Kennaway
15b247f443 Schedule these broken ports for termination on 2006-12-01 2006-09-02 16:51:10 +00:00
Pav Lucistnik
940da0dc4a Folding@Home is a distributed computing project -- people from through out the 
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>
 2006-08-28 22:33:45 +00:00
Cheng-Lung Sung
ab63f5bd0b - s,INSTALLS_SHLIB,USE_LDCONFIG,g 
- these include astro/ audio/ biology/ chinese/ maintained by ports@

PR:		ports/101916
Submitted by:	Gea-Suan Lin <gslin_AT_gslin dot org>
 2006-08-14 10:08:25 +00:00
Edwin Groothuis
0171dc55b4 Mark as broken for i386 4.x 
PR:		ports/101789
Submitted by:	Scott Flatman <sf@slappy.org>
 2006-08-10 23:02:49 +00:00
Erwin Lansing
ef6efc6dc9 Unmark BROKEN, it seems to be caused by a stale distfile on ftp-master. 2006-08-03 20:28:00 +00:00
Erwin Lansing
c5893d00f4 Mark BROKEN: checksum mismatch 2006-08-03 19:06:04 +00:00
Erwin Lansing
3bae54439d Mark broken due to checksum mismatch 2006-08-03 18:59:01 +00:00
Pav Lucistnik
61fa65e53c - Update to 5.10 2006-07-17 21:44:52 +00:00
Rong-En Fan
9e6a69437a - Fix pkg-plist [1] 
- pet portlint(1)

Noticed by:	pointyhat via linimon [1]
 2006-07-10 05:32:58 +00:00
Rong-En Fan
901b9f75cb - Update to 2.4.3 
- Pass maintainersip to submitter

PR:		99901
Submitted by:	Scott Flatman <sf slappy.org>
Approved by:	delphij (mentor, implicit)
 2006-07-08 03:36:36 +00:00
Rong-En Fan
4f1966845c - Use the correct MASTER_SITE_SUBDIR, make it fetchable 
PR:		99757
Submitted by:	Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw>
Approved by:	delphij (mentor, implicit)
 2006-07-04 03:43:16 +00:00
Mark Linimon
ba8be9a92f Mark as BROKEN on sparc64 due to internal compiler error. 2006-07-03 22:22:09 +00:00
Maho Nakata
cccc84b713 Update to 1.10 (maintained by others) and unbreak. 2006-07-03 04:41:35 +00:00
Maho Nakata
8db209b977 o Update to 0.99rc1 
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.
 2006-07-01 05:06:21 +00:00
Pav Lucistnik
eb9164cdb6 - Provide SSE optimized application as an option 2006-06-24 21:04:45 +00:00
Pav Lucistnik
ac3d6b8aa7 - Instruct amd64 users to libmap libpthread.so.2 to libc_r.so.6 2006-06-22 18:53:30 +00:00
Pav Lucistnik
15299a017f SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculated 
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/
 2006-06-19 20:32:08 +00:00
Thierry Thomas
57359d2a70 Re-add CONFIGURE_TARGET and fix libm detection. 
PR:		ports/99072 (fu2)
Submitted by:	Josh Tolbert <hemi (at) puresimplicity.net> (maintainer)
 2006-06-18 20:35:18 +00:00
Thierry Thomas
78ba726349 - Upgrade to to 1.9.9 and unbreak; 
- Take maintainership.

PR:		ports/99072
Submitted by:	Josh Tolbert <hemi (at) puresimplicity.net>
 2006-06-17 22:07:36 +00:00
Erwin Lansing
0ca34eb9ed USE_SIZE was obsoleted in rev. 1.484 of bsd.port.mk more than 
2 years ago. Clean out the last traces of it.

With hat:	portmgr
 2006-06-11 15:29:01 +00:00
Pav Lucistnik
e6e4d55131 - Update PORTREVISION to match latest release (see main web site) 
- Update the port to add other architectures (amd64)

PR:		ports/98764
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-06-11 09:13:43 +00:00
Pav Lucistnik
3181cf2cce - Update to 34.t25.d9 
PR:		ports/98761
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-06-09 19:18:08 +00:00
Ion-Mihai Tetcu
9da018b5cc Update biology/ncbi-toolkit to the latest release. 
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)
 2006-06-06 12:05:19 +00:00
Erwin Lansing
f85047fc66 - Add MASTER_SITE 
- Use DATADIR

PR:		97603
Submitted by:	miwi
Approved by:	maintainer timeout
 2006-06-06 10:07:55 +00:00
Erwin Lansing
f0dcdd522f - Update to 34.t25.d8 [1] 
- While I'm here, pet portlint [2]

PR:		98398 [1]
Submitted by:	miwi [1], self [2]
Approved by:	maintainer [1]
 2006-06-05 21:18:23 +00:00
Sergey Matveychuk
45d46bd0a5 - update to 34.t25.d7 
- add MASTER_SITE_LOCAL as a second master site

PR:		ports/97310
Submitted by:	maintainer
 2006-05-24 16:55:46 +00:00
Kris Kennaway
b8bfb594a1 BROKEN: Unfetchable 2006-05-21 21:40:02 +00:00
Sergey Matveychuk
2e790c2143 - Update to 3.15 
PR:		ports/96941
Submitted by:	Paul Schmehl <pauls@utdallas.edu>
Approved by:	maintainer timeout
 2006-05-20 18:52:19 +00:00
Aaron Dalton
e25d96e450 - Updated from 0.07 to 0.12 
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
 2006-05-19 23:18:32 +00:00
Aaron Dalton
29ad3c789c Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl. 
Approved by:	tobez (implicit)
 2006-05-13 16:48:15 +00:00
Sergey Matveychuk
edab74313c - Update to 34.t25.d6 
PR:		ports/96063
Submitted by:	maintainer
 2006-05-07 16:52:33 +00:00
Sam Lawrance
649566ad8c Update to 21.u1.d1 (fixes fetch). 
Reported by:	fenner's distfile survey
 2006-05-07 13:04:20 +00:00
Sergey Matveychuk
36778a1acd - Satisfy portlint 2006-05-06 21:20:59 +00:00
Emanuel Haupt
dfc2535ebe Add protomol 2.0.3, OO, component based, framework for molecular 
dynamics (MD) simulations.

PR:		95123
Submitted by:	Sangwoo Shim <sangwoos@gmail.com>
 2006-05-05 20:09:54 +00:00
Edwin Groothuis
72ad491a93 Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
Yen-Ming Lee
fb9e59f589 - Update to 1.89 
- 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
 2006-05-02 23:16:02 +00:00
Renato Botelho
8aaa665368 Bioperl-run contain modules that provides a PERL interface to various 
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>
 2006-05-02 21:31:43 +00:00
Renato Botelho
5d19d83aa6 Bioperl-run contain modules that provides a PERL interface to various 
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>
 2006-05-02 21:30:08 +00:00
Pav Lucistnik
dc8e5f28fa - Update to 1.0.0 
- Provide OPTIONS
- Take maintainership

PR:		ports/94123
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
 2006-04-25 22:09:29 +00:00
Kris Kennaway
87b2bd6cb6 BROKEN: Does not compile 2006-04-22 22:10:17 +00:00
Mark Linimon
54a45e213c Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking about 
maintainer timeouts.

Hat:	portmgr
 2006-04-05 06:13:46 +00:00
Mark Linimon
756130dd96 Reset jeremy@external.org who has not responded to email asking about 
maintainer timeouts.

Hat:	portmgr
 2006-04-05 05:46:33 +00:00
Marcus Alves Grando
843d1a4279 - Update to 2006.02.13 
PR:		95281
Submitted by:	maintainer
 2006-04-05 01:58:03 +00:00
Edwin Groothuis
c88ecfb4d6 Use SUB_FILES for pkg-message 2006-04-01 12:34:24 +00:00
Thierry Thomas
10570c91c8 For EMBOSS: 
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)
 2006-03-31 09:43:21 +00:00
Pav Lucistnik
763955a476 - Update to 34.t25.d5 
PR:		ports/94741
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-03-20 22:23:24 +00:00
Renato Botelho
c1c9dc017a - Update to 5.743 
- 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
 2006-03-19 12:59:16 +00:00
Renato Botelho
35642ebc86 Add lagan 1.2, efficient tools for large-scale multiple alignments of 
genomic DNA.

PR:		ports/93058
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-03-16 22:31:26 +00:00
Renato Botelho
81ba48cd37 Add mafft 5.734, multiple sequence alignments based on fast Fourier 
transform.

PR:		ports/93059
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-03-15 10:41:16 +00:00
Renato Botelho
1b3445b684 Add dotter 20021204 # last modified date in FTP server, a viewer for 
multiple sequence alignments.

PR:		ports/93055
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-03-15 10:35:24 +00:00
Renato Botelho
0694735737 Add blat 33, a fast tool for local sequence similarity searches. 
PR:		ports/93060
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-03-15 10:26:12 +00:00
Renato Botelho
bfe1c1f260 Add belvu 2.29, a viewer for multiple sequence alignments. 
PR:		ports/93056
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-03-15 10:24:57 +00:00
Maho Nakata
a8bac6a90f Update to 1.5 
Submitted by:	distfile survey by kris, fenner
 2006-03-15 08:10:49 +00:00
Ade Lovett
fe279f0df8 Bump PORTREVISION on glib12/gtk12 consumer ports to ease the upgrade path. 
Discussed with:	kris
Approved by:	portmgr (implicit)
 2006-03-07 08:28:06 +00:00
Ade Lovett
8503536d38 Conversion to a single libtool environment. 
Approved by:	portmgr (kris)
 2006-02-23 10:40:44 +00:00
Kris Kennaway
65fe00966b BROKEN: Configure fails 2006-02-20 01:46:03 +00:00
Herve Quiroz
cf01181180 Jalview is a multiple alignment editor written in Java. It is used widely in a 
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>
 2006-02-13 09:42:13 +00:00
Alexander Leidinger
d16f7bfb92 Reset maintainership to ports@ after ~4 months without any response to any 
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]
 2006-02-11 21:03:14 +00:00
Sam Lawrance
0e94382809 Update to 3.27. 
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)
 2006-02-10 09:45:28 +00:00
Sam Lawrance
f4cdc25a87 Update to 34.t25.d4. 
PR:		ports/93052
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-02-10 09:37:02 +00:00
Sam Lawrance
fed5ed01f9 Update to 2006.01.25. 
PR:		ports/93051
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-02-09 10:33:47 +00:00
Sam Lawrance
c70bfb8977 Put PORTEPOCH back. 
Reported by:	chkversion
 2006-02-09 01:17:59 +00:00
Sam Lawrance
c6f127a070 Update to 3.65. 
PR:		ports/92182
Submitted by:	"Choe, Cheng-Dae" <whitekid@gmail.com>
Approved by:	dbader@ece.unm.edu (maintainer, timeout 14 days)
 2006-02-08 14:45:45 +00:00
Joe Marcus Clarke
92cc33210c Remove CONFLICTS with nss. 2006-02-02 23:12:05 +00:00
Kris Kennaway
cbb7ba562c Add missing USE_ICONV 2006-01-26 04:11:16 +00:00
Edwin Groothuis
44855e0b04 SHA256ify (manually done and checked) 
Approved by:    krion@
 2006-01-22 09:54:26 +00:00
Edwin Groothuis
acd87b4ad8 SHA256ify 
Approved by:    krion@
 2006-01-22 08:34:46 +00:00
Edwin Groothuis
913a5a5cba Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry 
Approved by:    krion@
PR:             ports/88711 (related)
 2006-01-22 01:29:46 +00:00
Edwin Groothuis
e8d3c8300f Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry 2006-01-22 00:17:42 +00:00
Alexey Dokuchaev
cbb224e9a3 Utilize EXAMPLESDIR. 2006-01-20 09:56:18 +00:00
Alexey Dokuchaev
a6dbbc0318 - Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoid 
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
 2006-01-19 19:47:59 +00:00