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1388 Commits

Author SHA1 Message Date
Wen Heping
a8874c7021 - Fix fetch 
Reported by:	QAT@
 2010-12-21 00:12:22 +00:00
Wen Heping
0c58bca1ec - Update to 0.33 2010-12-16 08:19:56 +00:00
Philip M. Gollucci
7823a28b14 - Update to 0.32 
With Hat:       perl@
Changes:        http://search.cpan.org/dist/Bio-Phylo/Changes
 2010-12-12 21:29:40 +00:00
Philip M. Gollucci
8563ed7899 - fix fetch: wget is not required for fetching 
Reported by:    QAT
 2010-12-12 08:10:05 +00:00
Ade Lovett
4a8684e352 Sync to new bsd.autotools.mk 2010-12-04 07:34:27 +00:00
Wen Heping
01c6777188 - Update to 0.4.1 2010-12-02 13:42:09 +00:00
Alexey Dokuchaev
d2da4dcb85 Improve port description. 
Approved by:	maintainer timeout since December 2009
 2010-11-29 08:17:34 +00:00
Philip M. Gollucci
c24f9508d3 - Also remove them from pkg-plist lists not from me that crept in 2010-11-24 06:19:46 +00:00
Wen Heping
fabc490448 - Update to 0.31 2010-11-22 08:50:39 +00:00
Wen Heping
5c243d5c84 - Update to 2.1 2010-11-22 00:15:25 +00:00
Wen Heping
4cfe377eb9 - Update to 0.30 
PR:		ports/152205
Submitted by:	Gea-Suan Lin <gslin@gslin.org>
 2010-11-17 06:24:38 +00:00
Steven Kreuzer
1783398c20 Fix plist. 
Reported by:	QAT
 2010-11-16 23:55:41 +00:00
Wen Heping
f77bbf6dfe - Update to 2.15 
Changelog: http://search.cpan.org/src/LDS/Bio-Graphics-2.15/Changes

PR:		ports/152189
Submitted by:	Gea-Suan Lin <gslin@gslin.org>
 2010-11-16 08:07:27 +00:00
Wen Heping
dbe1b3c46b - Update to 1.5.0 2010-11-10 08:52:26 +00:00
Philippe Audeoud
3ccd369106 - Update to 0.28 2010-11-09 14:15:44 +00:00
Pav Lucistnik
b48012ad65 - Unbreak build: CPP is now part of MAKE_ENV 
Reported by:	pointyhat
 2010-11-08 15:05:11 +00:00
Wen Heping
aa13d40cda - Update to 2.10 
Changelog: http://search.cpan.org/src/RPETTETT/Bio-Das-Lite-2.10/Changes
 2010-11-04 06:24:22 +00:00
Rene Ladan
0fe3bfd649 - Unbreak by removing some old and adding some new master sites 
- Bump PORTREVISION
PR:		ports/151733
Submitted by:	Chris Petrik [c.petrik.sosa gmail.com]
 2010-10-30 23:51:30 +00:00
Wen Heping
a9e02fc8e4 - Update to 0.4.0 2010-10-26 00:34:36 +00:00
Wen Heping
8d82354698 - Update to 0.26 
- Reset maintainer to perl@
 2010-10-25 10:59:25 +00:00
Wen Heping
67d49aa254 - Update to 0.22 2010-10-22 09:29:44 +00:00
Frederic Culot
02a06c807c Update my MAINTAINER address to culot@FreeBSD.org. 
Approved by:	sahil@ (mentor)
 2010-10-20 05:53:20 +00:00
Wen Heping
891ffdbfa0 - Update to 2.14 
ChangeLog: http://search.cpan.org/src/LDS/Bio-Graphics-2.14/Changes
 2010-10-19 10:42:43 +00:00
Ade Lovett
6abd00a86b Punt autoconf267->autoconf268 2010-10-16 11:52:47 +00:00
Wen Heping
34df475911 - Update to 4.2.0 2010-10-08 02:06:53 +00:00
Ade Lovett
7e80cde328 Round one migration of ports from automake{19,110} to automake111 2010-10-05 19:57:56 +00:00
Sunpoet Po-Chuan Hsieh
40d054297f - Add an additional MASTER_SITES 
PR:		ports/151112
Submitted by:	gjb (maintainer)
Approved by:	pgollucci (mentor)
 2010-10-01 01:06:46 +00:00
Erwin Lansing
ea28b70614 Mark BROKEN: does not fetch. 2010-09-30 08:53:18 +00:00
Wen Heping
025752cd44 - Update to 2.13 2010-09-26 08:32:26 +00:00
Wen Heping
c0d7b4a1e1 - Update to 0.76 2010-09-25 08:14:02 +00:00
Martin Matuska
ddcc0de921 Change dependency on old p5-Compress-Zlib, p5-IO-Compress-Base, 
p5-IO-Compress-Zlib and p5-IO-Compress-Bzip2 modules to p5-IO-Compress.
Explicitly depend on p5-IO-Compress only if PERL_LEVEL < 500903
Bump PORTREVISION
 2010-09-21 07:56:43 +00:00
Mark Linimon
033923e0f5 Also broken on sparc64 (and, by implication, ia64). 
Hat:		portmgr
 2010-09-17 09:17:05 +00:00
Maho Nakata
893f4b14c0 Update to 1.3r1.3913. 
Actually the version number is from SVN, and maho@ manually
checked out from SVN.
The source archive is not distributed as tar ball.
 2010-09-16 21:48:04 +00:00
Wen Heping
aa10f7a2b8 - Update to 4.1.0 2010-09-16 03:31:29 +00:00
Ade Lovett
8262a7b51d Autotools update. Read ports/UPDATING 20100915 for details. 
Approved by:	portmgr (for Mk/bsd.port.mk part)
Tested by:	Multiple -exp runs
 2010-09-15 18:35:24 +00:00
Wen Heping
0d034d05fe - Update to 4.4c 2010-09-08 00:16:45 +00:00
Wen Heping
40365a66b5 - Update to 0.75 
- Reset maintainer to perl@
 2010-09-07 07:15:24 +00:00
Wen Heping
a751729898 - Update to 1.13 
PR:		ports/150317
Submitted by:	Frederic Culot <frederic@culot.org>
 2010-09-07 07:00:17 +00:00
Bernhard Froehlich
cc72c8c922 - Update MAINTAINER to submitters new mail address 
PR:		ports/150274
Submitted by:	Glen Barber <glen dot j dot barber at gmail dot com> (maintainer)
Approved by:	beat (co-mentor, implicit)
 2010-09-04 15:32:58 +00:00
Sahil Tandon
4da3929a92 - Update to 2.10.0 
- Add LICENSE
- Mark MAKE_JOBS_SAFE
- Eliminate unnecessary patch
- Note new homepage in pkg-descr
- Pass maintainership to submitter

PR:		ports/149827
Submitted by:	C-S <c-s@c-s.li>
 2010-08-21 00:28:49 +00:00
Greg Larkin
f657360287 - Update USE_PYTHON in Makefile to reflect upstream Python 
dependency version requirement

PR:		ports/149251
Submitted by:	glarkin
Approved by:	wen (via email)
 2010-08-18 14:09:34 +00:00
Andrej Zverev
0429d94053 Update to 1.12: 
- dependency on MooseX::FollowPBP added
- dependency on Moose::Policy removed

PR:		ports/149612
Submitted by:	Frederic Culot <frederic@culot.org>
 2010-08-18 12:05:38 +00:00
Li-Wen Hsu
b3866733aa - Update to 2.1.5 
- Pass maintainership to submitter

PR:		ports/149247
Submitted by:	C-S <c-s AT c-s.li>
 2010-08-04 06:30:07 +00:00
Baptiste Daroussin
a28a217ede Fix typo in maintainer mail address 
Submitted by:	Frederic Culot <frederic _at_ culot.org> (maintainer)
Approved by:	jadawin@ (co-mentor)
 2010-08-02 16:06:38 +00:00
Baptiste Daroussin
3cf9a14670 - Update to 1.12.4 
- Add libcurl as dependency
- Submitter is now maintainer

PR:		ports/149079
Submitted by:	Frederic Coulot <frederic _at_ coulot.org> (maintainer)
Approved by:	jadawin@ (co-mentor)
 2010-08-02 15:09:21 +00:00
Pav Lucistnik
39b767908d - Update the libmap instructions for amd64/8 
Submitted by:	Rick van der Zwet <info@rickvanderzwet.nl>
 2010-07-29 08:30:24 +00:00
Wen Heping
08ad71435d - Update to 1.54 
PR:		ports/148274
Submitted by:	Ju Pengfei <jupengfei@gmail.com>
Approved by:	maintainer
Feature safe:	yes
 2010-07-02 02:57:19 +00:00
Wen Heping
bd3021c9eb - Update to 2.11 
Feature safe:	yes
 2010-06-30 07:41:06 +00:00
Wen Heping
9c661b3e8e - Update to 1.17 
Feature safe:	yes
 2010-06-30 07:36:25 +00:00
Wen Heping
fd6b71cb08 - Update to 1.16 
Feature safe:	yes
 2010-06-24 00:24:22 +00:00
Wen Heping
c58b91a232 - Update to 2.04 
- Pass maintainership to perl@
Feature safe:	yes
 2010-06-22 03:28:49 +00:00
Erwin Lansing
8c6092e5ec BROKEN should not be quoted. 
No functional change.
 2010-06-13 08:40:06 +00:00
Wen Heping
a6a89abfbe - Update to 1.15 2010-06-12 06:18:36 +00:00
Anton Berezin
914f231c85 Update to 1.10. 
Changes:	http://search.cpan.org/dist/Bio-MAGETAB/Changes
 2010-06-10 16:56:04 +00:00
Philip M. Gollucci
aaeac0d126 - Update to 1.4.0 
- Sort pkg-plist
- seperate NOPORTDOCS and NOPORTEXAMPLES
 2010-06-08 00:18:54 +00:00
Dirk Meyer
da5e61df79 LICENSE GPLv2 2010-06-05 19:53:32 +00:00
Dirk Meyer
bad8a42899 LICENSE LGPL21 2010-06-05 06:14:28 +00:00
Wen Heping
e7bd8df79f - Update to 1.4.1 2010-06-01 06:57:30 +00:00
Ade Lovett
8d837132c7 Bounce PORTREVISION for gettext-related ports. Have fun, ya'll. 2010-05-31 02:01:56 +00:00
Sylvio Cesar Teixeira
51df349544 - Update to 3.1.6 
PR:		ports/147194
Submitted by:	Glen Barber <glen.j.barber@gmail.com> (maintainer)
 2010-05-30 23:46:55 +00:00
Dirk Meyer
ca8e128e62 - drop USE_GNUSTEP_PREFIX 2010-05-30 12:28:39 +00:00
Wen Heping
b77703b9d2 - Update to 4.0.1 2010-05-24 07:19:35 +00:00
Dirk Meyer
cf38b673c9 - fix build for gnustep-base 1.21.0 2010-05-23 20:51:27 +00:00
Wen Heping
a5713553a7 - Update to 1.12.2 
- Reset maintainer
 2010-05-21 06:19:18 +00:00
Wen Heping
af88609ea3 - Update to 2.09 2010-05-18 08:27:03 +00:00
Wen Heping
744e974fb0 - Update to 2.0.8 2010-05-14 13:05:15 +00:00
Wen Heping
14923d1dc1 - Update to 2.0.7 
- Set maintainer to perl@
 2010-05-10 02:36:57 +00:00
Sylvio Cesar Teixeira
b5dabfb20d - Update to 3.1.4 
PR:		ports/146411
Submitted by:	Glen Barber <glen.j.barber@gmail.com> (maintainer)
 2010-05-09 13:59:34 +00:00
Wen Heping
b6ad2f761a - Update to 1.00 
- Set maintainer to perl@
 2010-05-08 08:35:32 +00:00
Greg Larkin
44b546fe8c - Removed BROKEN because file fetches and checksums correctly 
- Added another MASTER_SITES for redundancy

PR:		ports/144733
Submitted by:	Fernan Aguero <fernan.aguero@gmail.com> (maintainer)
 2010-04-28 22:37:11 +00:00
Wen Heping
d78cf9ae49 - Update to 2.04 2010-04-20 08:48:47 +00:00
Wen Heping
4834e5f360 - Update to 4.4a 
- Update my mail address to FreeBSD
 2010-04-20 08:42:04 +00:00
Dirk Meyer
2e236823ab - update to 0.81 
- fix build on amd64
 2010-04-14 05:01:48 +00:00
Wen Heping
1c40ab037b - Update to 6.2.0 
Submitted by:	Wen Heping(myself)
Approved by:	maintainer(via Email)
 2010-04-07 01:21:36 +00:00
Wen Heping
cf68531462 - Update to 2.03 2010-04-02 09:06:35 +00:00
Mark Linimon
686a04b74a Mark various ports as broken or ignore on powerpc. 
While here, remove remnants of alpha.
 2010-04-01 05:16:19 +00:00
Wen Heping
9d69e4497a - Update to 2.02 2010-03-30 01:22:56 +00:00
Wen Heping
6905d4a0d8 - Bump PORTREVISION to chase the update of math/gsl 2010-03-29 01:12:27 +00:00
Dirk Meyer
de78af3ac5 - update to 1.4.1 
Reviewed by:	exp8 run on pointyhat
Supported by:	miwi
 2010-03-28 06:47:48 +00:00
Wen Heping
4440f60cd8 - Update to 3.1.3 
- Pass maintainership to submitter

PR:		ports/144992
Submitted by:	Glen Barber <glen.j.barber@gmail.com>
 2010-03-24 06:46:44 +00:00
Pietro Cerutti
c6a2501ef2 - Chase x11-toolkits/fltk update 2010-03-23 21:14:39 +00:00
Sylvio Cesar Teixeira
f1cd5913ef - Update to 3.22 
Approved by: 	itetcu (mentor)
 2010-03-21 17:18:20 +00:00
Wen Heping
7ac145c021 - Update to 0.3.9 2010-03-19 08:32:48 +00:00
Wen Heping
6f315dae4d - Update to 2.01 2010-03-10 01:35:57 +00:00
Wen Heping
d3c411d05d - Update to 0.21 2010-03-09 07:34:48 +00:00
Wen Heping
22c4a3da76 - Update to 0.18 
- Adopt

Feature safe:	yes
 2010-03-03 13:44:19 +00:00
Wen Heping
69518f2f86 p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XML 
over HTTP primarily for biological-data).

WWW: http://search.cpan.org/dist/Bio-Das-Lite/

Feature safe:	yes
 2010-03-01 09:16:25 +00:00
Wen Heping
eeba40ae35 - Update to 0.7 
Feature safe:	yes
 2010-02-24 01:30:46 +00:00
Philip M. Gollucci
b339872c92 - Reset more ports I don't use anymore 2010-02-10 21:47:48 +00:00
Edwin Groothuis
8658684e4b Update to 3.1.2 2010-02-10 09:47:48 +00:00
Wen Heping
22c4fef9a0 - Update to 2.00 2010-02-10 06:10:33 +00:00
Dirk Meyer
ca9c60461c - update to jpeg-8 2010-02-05 11:46:55 +00:00
Wen Heping
49bdce58bc - Update to 0.99 
- Update my mail address to FreeBSD
 2010-02-03 08:25:35 +00:00
Martin Wilke
53fc8b212a - Update to 3.1.1 
PR:		143437
Submitted by:	Ports Fury
 2010-02-02 22:42:47 +00:00
Philip M. Gollucci
bc7c753e14 - use $SUB_FILES to dynamically adjust pkg-message 
PR:             ports/142408
Submitted by:   Sevan Janiyan <venture37@geeklan.co.uk>
Approved by:    fernan@iib.unsam.edu.ar (maintainer)
 2010-01-31 03:42:20 +00:00
Jun Kuriyama
326d89e098 - Remove unneeded dependencies which is in perl-5.8.9 dist 
(part 19; last!).

Approved by:	portmgr (itetcu)
 2010-01-29 14:52:21 +00:00
Philip M. Gollucci
f6af25aa4a - actually remove old patch 
Reported by:	QAT
 2010-01-17 00:16:34 +00:00
Philip M. Gollucci
c49b8e0836 - Fix on amd64 
PR:             ports/142472
Submitted by:   Edmund Sumbar <esumbar@ualberta.ca>
 2010-01-16 17:54:38 +00:00
Jun Kuriyama
cbffb3af9d - Remove unneeded dependencies which is in perl-5.8.9 dist from ports 
maintained by (perl|ports|kuriyama)@FreeBSD.org.

- Targets are: Test::Simple, Digest::MD5, Locale-Maketext,
  ExtUtils::MakeMaker, ExtUtils::ParseXS, File::Temp, Getopt::Long,
  Encode, Digest, Pod::Parser, File::Spec.
 2010-01-16 14:45:49 +00:00
Philip M. Gollucci
3781ecad36 - SUB_FILES += pkg-message 
PR:             ports/142407
Submitted by:   Sevan Janiyan <venture37@geeklan.co.uk>
Approved by:    Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2010-01-09 23:51:26 +00:00
Wen Heping
d938c73fdc - Update to 1.03 
- Update my mail address to FreeBSD
 2010-01-09 01:21:21 +00:00
Philip M. Gollucci
8086ac7032 - SBU_FILES += pkg-message 
PR:             ports/142409
Submitted by:   Sevan Janiyan <venture37@geeklan.co.uk>
 2010-01-08 01:30:20 +00:00
Wen Heping
959567bbb7 - Update to 1.995 2010-01-07 02:27:20 +00:00
Wen Heping
43d8e24a17 - Update to 1.53 
PR:		ports/142221
Submitted by:	Wen Heping (myself)
Approved by:	maintainer
 2010-01-06 00:29:25 +00:00
Wen Heping
47dea29df8 python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees) 
reader for python.

WWW:    http://simon.net.nz/articles/python-nexus
 2009-12-29 13:39:14 +00:00
Wen Heping
4beee06b6b - Fix fetch error 2009-12-27 03:05:03 +00:00
Wen Heping
a70e97a715 - Update to 0.3.7 2009-12-24 03:14:34 +00:00
Martin Wilke
3cb69b845f - Update to 7.1.11 
PR:		141812
Submitted by:	Ports Fury
 2009-12-22 11:25:15 +00:00
Wen Heping
ac98d03ccc - Update to 0.3.5 2009-12-21 03:29:55 +00:00
Doug Barton
2fadfa2cfb For ports maintained by ports@FreeBSD.org, remove names and/or 
e-mail addresses from the pkg-descr file that could reasonably
be mistaken for maintainer contact information in order to avoid
confusion on the part of users looking for support. As a pleasant
side effect this also avoids confusion and/or frustration for people
who are no longer maintaining those ports.
 2009-12-21 02:19:12 +00:00
Wen Heping
46e3211a5d - Update to 1.1.4 
Submitted by:	Wen Heping (myself)
Approved by:	maintainer (via Email)
 2009-12-18 02:55:57 +00:00
Wen Heping
eb83a3ad9d - Update to 1.4 
- Update my mail address to FreeBSD
 2009-12-17 06:51:53 +00:00
Wen Heping
e514f1a729 - Update to 0.3.4 2009-12-16 12:48:04 +00:00
Philip M. Gollucci
89c63fe984 - Turn over a bunch of p5- ports that change infrequently to perl@ 
so more people can look at them.
 2009-12-13 18:07:49 +00:00
Wen Heping
d64a5ae397 - Update to 1.994 2009-12-11 08:02:53 +00:00
Wen Heping
5a07a83836 - Update to 0.3.3 2009-12-06 08:47:36 +00:00
Wen Heping
ad74a3628a - Update to 1.993 2009-12-04 11:53:48 +00:00
Wen Heping
e2b9177a1b - Update to 1.6.1 
Approved by:	maintainer (via Email)
 2009-12-04 11:50:10 +00:00
Max Brazhnikov
7cb3294da7 Chase math/gsl update, 
bump PORTREVISION
 2009-12-01 20:33:45 +00:00
Wen Heping
564d9e9ea8 - Update to 2.0.12 
- Update my mail address to FreeBSD
 2009-11-29 01:16:36 +00:00
Sylvio Cesar Teixeira
ba072d1713 - Update my mail address to FreeBSD 
Approved by:	miwi (mentor)
 2009-11-27 22:52:30 +00:00
Pav Lucistnik
38eb8c5339 - Mark MAKE_JOBS_UNSAFE 
Reported by:	pointyhat
 2009-11-20 22:53:09 +00:00
Wen Heping
40efa7ff9b - Update to 1.992 
- Update my mail address to FreeBSD
 2009-11-20 05:10:17 +00:00
Martin Wilke
0625d15cec - broken checksum mismatch 2009-11-19 12:43:06 +00:00
Pav Lucistnik
ed9c0642a6 - Mark MAKE_JOBS_UNSAFE 
Reported by:	pointyhat
 2009-11-18 22:39:55 +00:00
Wen Heping
695ed5163e pyfasta is a python module for fast, memory-efficient, pythonic 
access to fasta sequence files.

WWW:    http://bitbucket.org/brentp/biostuff/src/
 2009-11-18 05:53:17 +00:00
Wen Heping
fad82e7fd4 - Update to 21.1.1 2009-11-18 05:33:10 +00:00
Dmitry Marakasov
8dbd1070da Velvet is a de novo genomic assembler specially designed for short read 
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).

Citation:

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)

WWW: http://www.ebi.ac.uk/~zerbino/velvet/

PR:		140147
Submitted by:	Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
 2009-11-07 01:23:59 +00:00
Pav Lucistnik
975c364f32 - Annotate that 8.x no longer needs libmap hack 
Reported by:	rene
 2009-10-01 07:34:28 +00:00
Wen Heping
9c55d004d3 - Update to 4.0.0 
- Update my mail address to FreeBSD

PR:		ports/137652
Submitted by:	wenheping@gmail.com(myself)
Approved by:	miwi(mentor)
Feature safe:	yes
 2009-09-23 01:06:29 +00:00
Jason Evans
97df6db5cb Update to Crux 1.2.0. 
Feature safe:	yes
 2009-09-19 17:58:13 +00:00
Renato Botelho
3905d8ced0 UNBREAK: Probably was a temporary failure, checksums are ok now. 
Feature safe:	yes
 2009-09-16 15:57:18 +00:00
Martin Wilke
d583c2c02f -Update to 3.69 
PR:		138813
Submitted by:	Ports Fury
Feature safe:	yes
 2009-09-16 14:27:00 +00:00
Gerald Pfeifer
27ab5137ce Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now 
implies lang/gcc44 up from lang/gcc43.

Approved by:	portmgr
 2009-09-13 00:08:01 +00:00
Philippe Audeoud
64f2f2465b - Update to 1.14 2009-09-08 12:08:12 +00:00
Martin Wilke
2f12ae5444 - Update to 138038 
PR:		138038
Submitted by:	Wen Heping <wenheping@gmail.com>
Approved by:	maintainer
 2009-09-04 20:41:25 +00:00
Martin Wilke
4e4a5fc43b - Update to 0.982 
PR:		138264
Submitted by:	Wen Heping <wenheping@gmail.com> (maintainer)
 2009-08-28 23:36:45 +00:00
Martin Wilke
ab94a3bda7 Bio::SCF module allows you to read and update (in a restricted 
way) SCF chromatographic sequence files. It is an interface to
Roger Staden's io-lib. See the installation directions for further
instructions.

WWW:	http://search.cpan.org/dist/Bio-SCF/

PR:		ports/138263
Submitted by:	Wen Heping <wenheping at gmail.com>
 2009-08-28 23:36:09 +00:00
Martin Wilke
4afd96b25b Io_lib is a library of file reading and writing code to provide a 
general purpose trace file (and Experiment File) reading interface.
The programmer simply calls the (eg) read_reading to create a "Read"
C structure with the data loaded into memory. It has been compiled
and tested on a variety of unix systems, MacOS X and MS Windows.

WWW:	http://staden.sourceforge.net/

PR:		ports/138254
Submitted by:	Wen Heping <wenheping at gmail.com>
 2009-08-28 23:34:20 +00:00
Marcelo Araujo
7c7ff787ef - Update to 3.21. 
- Reset maintainer to submitter.

PR:		ports/138192
Submitted by:	Sylvio Cesar <scjamorim@bsd.com.br>
 2009-08-28 14:52:05 +00:00
Martin Wilke
15df496943 - Update to 1.12 
PR:		138230
Submitted by:	Wen Heping <wenheping@gmail.com>
 2009-08-27 20:34:58 +00:00
Max Brazhnikov
677abde4b7 Update to 35.4.9 
PR:		ports/137991
Submitted by:	Fernan Aguero (maintainer)
 2009-08-23 15:47:37 +00:00
Martin Wilke
cb1a940d17 Bio::NEXUS package provides an object-oriented, Perl-based 
applications programming interface (API) to the NEXUS file
format of Maddison, et al., 1997 (Syst. Biol. 46:590-621).
NEXUS is a powerful and extensible format designed for use
in evolutionary analysis, including the analysis of molecular
sequence data as well as classical morphological and life-history
data. NEXUS is the input or output format for software such as
PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and
so on.  This package also contains the demonstration applications
nexplot.pl (plot character data with a tree) and nextool.pl
(allowing programmatic editing, e.g., selecting particular
clades or subsets of data).

WWW: http://search.cpan.org/dist/Bio-NEXUS/

PR:		ports/137983
Submitted by:	Wen Heping <wenheping at gmail.com>
 2009-08-22 20:39:51 +00:00
Martin Wilke
17b7bfd60c - BROKEN checksum mismatch 2009-08-22 08:45:12 +00:00
Dmitry Marakasov
c926af277e - Switch SourceForge ports to the new File Release System: categories starting with B,C 2009-08-22 00:15:15 +00:00
Martin Wilke
a3c70c3529 - Fix fetch 
PR:		137840
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2009-08-17 15:38:37 +00:00
Martin Wilke
654825e7a9 - Update MASTER_SITES 
PR:		137750
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2009-08-14 08:33:22 +00:00
Martin Wilke
a69f9725b4 - Update to 4.3 
PR:		137625
Submitted by:	Wen Heping <wenheping@gmail.com> (maintainer)
 2009-08-13 17:00:04 +00:00
Erwin Lansing
9f3d7499d2 Fix PKGORIGIN 
Submitted by:	pointyhat
 2009-08-08 13:26:13 +00:00
Pav Lucistnik
4b4b7f19aa - Relax check on bioperl version; people keep forgetting to update this check 
when updating bioperl port

Reported by:	pointyhat
 2009-08-02 20:00:08 +00:00
Pav Lucistnik
55f1f70c83 - Unbreak fetch 
Submitted by:	maintainer
 2009-08-02 19:59:03 +00:00
Jeremy Messenger
789d75c728 -Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22. 
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.

It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.

With help:	marcus and kwm
Pointyhat-exp:	a few times by pav
Tested by:	pgollucci, "Romain Tartière" <romain@blogreen.org>, and
		a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by:	marcus
Approved by:	portmgr
 2009-08-02 19:36:34 +00:00
Dirk Meyer
eca78ec61b - bump all port that indirectly depends on libjpeg and have not yet been bumped or updated 
Requested by:	edwin
 2009-07-31 13:57:52 +00:00
Philip M. Gollucci
20cfadf5f7 Utilize %%SITE_PERL%% and %%PERL_ARCH%% in pkg-plists 
PR:             ports/136771
Exp Run by:     pav
Approved by:    portmgr (pav)
 2009-07-30 23:04:49 +00:00
Philip M. Gollucci
c10f314307 - lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checks 
PR:             ports/135398
Tested by:      2 -exp runs by pav
Approved by:    portmgr (pav)
 2009-07-22 16:27:08 +00:00
Dmitry Marakasov
442b6b908d PhyML is a software that estimates maximum likelihood phylogenies from 
alignments of nucleotide or amino acid sequences. It provides a wide range of
options that were designed to facilitate standard phylogenetic analyses. The
main strengths of PhyML lies in the large number of substitution models coupled
to various options to search the space of phylogenetic tree topologies, going
from very fast and efficient methods to slower but generally more accurate
approaches. It also implements two methods to evaluate branch supports in a
sound statistical framework (the non-parametric bootstrap and the approximate
likelihood ratio test). PhyML was designed to process moderate to large data
sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
can analyzed. In practice however, the amount of memory required to process a
data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided that
they are short. Also, PhyML can handle long sequences provided that they are
not numerous. With most standard personal computers, the "comfort zone" for
PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

WWW: http://code.google.com/p/phyml/

PR:		136877
Submitted by:	Ben Allen <ben@sysadminschronicles.com>
 2009-07-21 01:10:13 +00:00
Dirk Meyer
3bbc108312 - update to jpeg7 
Tested by:	pav on pointyhat
 2009-07-18 11:11:29 +00:00
Pav Lucistnik
1c7ddf4d89 - Flip MAKE_JOBS_SAFE to MAKE_JOBS_UNSAFE 
Reported by:	pointyhat
 2009-07-07 22:11:07 +00:00
Dirk Meyer
3c52fc9aaf - fix PORTSCOUT 2009-07-06 07:29:12 +00:00
Martin Wilke
ea40d68db0 - Update to 1.97 
PR:		136310
Submitted by:	Wen Heping <wenheping@gmail.com> (maintainer)
 2009-07-05 22:24:00 +00:00
Dirk Meyer
0c1ab4538d - cleanup ADDITIONAL_LIB_DIRS 2009-07-05 10:37:52 +00:00
Martin Wilke
5da99a81fe p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This 
is a beta release. All functions have now been implemented and most
have test suites; the exceptions include the modules involved in
export of MAGE-TAB documents, which are still a little experimental in
nature. The API is mostly finalised (and fully documented), but some
details may yet change where necessary to improve usability.

WWW: http://search.cpan.org/dist/Bio-MAGETAB/

PR:		ports/136021
Submitted by:	Wen Heping <wenheping at gmail.com>
 2009-07-01 09:03:28 +00:00
Martin Wilke
42c9c3189b PyCogent is a software library for genomic biology. It is a fully integrated 
and thoroughly tested framework for: controlling third-party applications;
devising workflows; querying databases; conducting novel probabilistic
analyses of biological sequence evolution; and generating publication quality
graphics. It is distinguished by many unique built-in capabilities (such as
true codon alignment) and the frequent addition of entirely new methods for
the analysis of genomic data.

WWW:	http://pycogent.sourceforge.net/

PR:		ports/135863
Submitted by:	Wen Heping <wenheping at gmail.com>
 2009-06-22 12:46:56 +00:00
Jason Evans
55a6878d0e Update to Crux 1.1.0. 
Fix the ATLAS/LAPACK build option.
 2009-06-21 06:18:51 +00:00
Dmitry Marakasov
8ef55a9903 - Update to 6.0.0 
- Unbreak

PR:		135376
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2009-06-16 22:42:34 +00:00
Jason Evans
91fb724efd Change CONFIGURE_ENV --> USE_CSTD. [1] 
Add missing pkg-plist entry for Parsing.so. [2]

Change RUN_DEPENDS --> LIB_DEPENDS for optional math/atlas dependency.

Submitted by:	[1] erwin
Reported by:	[2] QAT
 2009-06-10 01:25:02 +00:00
Dmitry Marakasov
33e3d901d4 Convert most of remaining ports that depend on xorg-libraries to 
modular xorg.

- supply corresponding USE_XORG for all imake-using ports that need it
- USE_IMAKE no longer implies USE_XLIB in absence of USE_XORG
- retire USE_X_PREFIX which is not really used anywhere after the
  above change
- a few minor nits like whitespace and SF macro

Tested by:	2 tinderbox runs by pav
Approved by:	portmgr (pav)
 2009-06-09 15:33:28 +00:00
Ion-Mihai Tetcu
e110a3719d - Update to 35.4.7 [1] 
- Obey PREFIX [2]

Submitted by:	maintainer [1] [2]
Reported by:	QATty [2]
 2009-06-09 07:53:37 +00:00
Jason Evans
5fe3fa6b36 Add the biology/crux port. 2009-06-08 23:49:59 +00:00
Martin Wilke
81100672d4 - Update lang/python26 and make Python 2.6.2 to the default Python version 
Tested by:	3 pointyhat runs
Thanks to:	pav, gahr, lwhsu, mva, amdmi3
 2009-06-08 22:30:55 +00:00
Philippe Audeoud
1740ae715c - Update to 1.11 2009-06-08 09:30:07 +00:00
Martin Wilke
f128ddfb8e 2009-05-31 biology/p5-bioperl-devel: no longer under development 
2009-05-31 biology/p5-bioperl-run-devel: no longer under development
2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead
2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either
 2009-06-05 20:38:36 +00:00
Martin Wilke
6592db2fc9 - Update to 1.95 
PR:		135141
Submitted by:	Wen Heping <wenheping@gmail.com> (maintainer)
 2009-06-02 21:34:06 +00:00
Dirk Meyer
c0ed6c1d56 - fix build for custom LOCALBASE in UL subdir 
Reported by:	QAT
 2009-06-02 02:33:05 +00:00
Dirk Meyer
a5f4286578 - fix build for custom LOCALBASE 
Reported by: 	QAT
 2009-06-01 10:55:07 +00:00
Martin Wilke
043ce69d39 LibSBML is an open-source programming library to help you read, write, 
manipulate, translate, and validate SBML files and data streams. It is
not an application itself (though it does come with example programs),
but rather a library you can embed in your own applications.

LibSBML understands all Levels and Versions of SBML, as well as the
SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
ISO C and C++ but can be used from all the languages listed in the
right-hand box.

WWW: http://www.sbml.org/

PR:		ports/135022
Submitted by:	Wen Heping <wenheping at gmail.com>
 2009-05-28 23:36:10 +00:00
Dirk Meyer
2cb071c749 - fix build with gnustep-make-2.2.0 2009-05-21 12:00:17 +00:00
Philip M. Gollucci
abf5b5ffc0 - Mark most of my ports MAKE_JOBS_SAFE=yes 
Tested by: several builds in P6 TB
 2009-05-16 06:27:56 +00:00
Ion-Mihai Tetcu
f5acd5e443 Fix LIB_DEPENDS on devel/readline: its sh lib version was bumped recently from 
5 to 6.

Forgotten by:	araujo@
Reported by:	QAT
 2009-05-12 11:28:17 +00:00
Martin Wilke
472002308b - Update to 1.94 
Approved by:	maintainer implicit
 2009-05-01 14:54:30 +00:00
Martin Wilke
8fd8309d5d - Update to 1.7 
- Pass maintainership to submitter

PR:		134056
Submitted by:	Wen Heping <wenheping@gmail.com>
 2009-05-01 09:33:42 +00:00
Martin Wilke
37e6f38c5e - Update to 1.93 
PR:		133342
Submitted by:	Wen Heping <wenheping@gmail.com> (maintainer)
 2009-04-04 17:45:12 +00:00
Martin Wilke
9de0881042 Bio::Glite is an interface to G-language Genome Analysis Environment 
through its REST web service (http://www.g-language.org). This module
allows almost everything G-language GAE can do, without installing
all necessary tookits and modules.

Advantage of this module over the standard installation of
G-language GAE package is:
   1. Easy installation from CPAN
   2. Extremely light-weight (less than 1000 lines of code)
   3. Does not require much CPU/RAM (all calculation is done on
the cloud)

Disadvantages includes:
   1. Slower analysis speed
   2. Internet connection is required
   3. No other software interfaces such as the G-language Shell

WWW: http://search.cpan.org/dist/Bio-Glite/

PR:		ports/133273
Submitted by:	Wen Heping <wenheping at gmail.com>
 2009-04-02 18:24:59 +00:00
Martin Wilke
ba4d5fa369 - Update to 2009.03.01 
PR:		133099
Submitted by:	Fernan Aguero <fernan.aguero@gmail.com>
Approved by:	maintainer
 2009-03-28 16:59:39 +00:00
Martin Wilke
7050620d4e - Update to 1.91 
PR:		133065
Submitted by:	Wen Heping <wenheping@gmail.com> (maintainer)
 2009-03-25 17:38:35 +00:00
Max Brazhnikov
eecc33021e bump PORTREVISION after cmake update 2009-03-24 19:13:32 +00:00
Martin Wilke
d29d4fb924 - Mark BROKEN does not compile 
Submitted by:	maintainer via private mail
 2009-03-23 21:56:39 +00:00
Martin Wilke
61dcb2fc1f - Update to 1.6.1 
PR:		132122
Submitted by:	Wen Heping <wenheping@gmail.com>
Approved by:	maintainer
 2009-03-19 20:54:05 +00:00
Martin Wilke
8a8dc13abc - Mark DEPRECATED (no longer under development) 
PR:		132122
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
 2009-03-19 19:29:34 +00:00
Boris Samorodov
0263b9d868 Welcome to the new linux ports infrastructure which allows using 
both current (fc4) and future linux (f8) distributions at one
ports tree.

The patch contains full changes to ports/Mk files and all ports involved.
But only infrastructure is changed. The resulting packages are the same as
before. Hence no need to bump PORTREVISIONs.

The idea was taken from bsd.gnome.mk and others.

More than 130 ports are switched to follow a new linux infrastructure
introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new
bsd.linux-apps.mk.

Thanks for all who was involved and helped me with this work.
And help from Alexander Leidinger was incredible.

Other changes are coming. Stay tuned!

PR:		ports/132510
Submitted by:	bsam (me)
Exp-run by:	portmgr (pav)
 2009-03-19 17:28:51 +00:00
Martin Wilke
0e6dd759f8 - Update to 1.90 
PR:		132659
Submitted by:	Wen heping <wenheping@gmail.com> (maintainer)
 2009-03-19 16:34:47 +00:00
Martin Wilke
edf86f42ee - Update to 0.1.24 
PR:		132527
Submitted by:	Wen Heping <wenheping@gmail.com>
Approved by:	maintainer
 2009-03-14 15:17:06 +00:00
Martin Wilke
f73ab4694c p5-Bio-Graphics is a simple GD-based renderer (diagram drawer) 
for DNA and protein sequences.

WWW: http://search.cpan.org/dist/Bio-Graphics/

PR:		ports/132088
Submitted by:	Wen Heping <wenheping at gmail.com>
 2009-03-10 18:50:49 +00:00
Sergey Skvortsov
9b79570fe6 Rename PERL_VER to PERL_VERSION. 
Pointed by:	pav
 2009-03-07 19:51:02 +00:00
Sergey Skvortsov
0f24c25f5a Remove variable PERL_VER from the ports tree at all - because 
it is obsolete since Perl 5.6.0.
 2009-03-05 17:56:24 +00:00
Martin Wilke
e0f3b63065 - Update to 4.2b 
PR:		132249
Submitted by:	Wen Heping <wenheping@gmail.com>
 2009-03-02 19:02:48 +00:00
Renato Botelho
58d4bedcf4 - Update to 1.6.0 
PR:		ports/131989
Submitted by:	maintainer
 2009-02-23 19:31:43 +00:00
Dmitry Marakasov
6aa54f51cd - Add forgotten patch 2009-02-23 16:13:19 +00:00
Dmitry Marakasov
bb0af38121 - Update to 35.4.4 
PR:		132007
Submitted by:	Fernan Aguero <fernan at iib dot unsam dot edu dot ar> (maintainer)
 2009-02-23 16:12:23 +00:00
Dirk Meyer
10f3be8676 - update PORTSCOUT 2009-02-15 16:45:58 +00:00