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811 Commits

Author SHA1 Message Date
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