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410 Commits

Author SHA1 Message Date
Maho Nakata
b8c46ab23d Delete biology/gaussian98. Maintain is too hard and 
gray in license
 2003-01-31 22:37:39 +00:00
Akinori MUSHA
4dce26edf6 Update to 0.4.0. 2003-01-29 10:45:59 +00:00
Mario Sergio Fujikawa Ferreira
365028dd1b add '-f' argument to rm so that the script always work even if a 
file is not there

Submitted by:	Frerich Raabe <frerich.raabe@gmx.de>
 2003-01-23 19:27:43 +00:00
Edwin Groothuis
b7eafb33b6 New Port: biology/act 
PR:		ports/35753
Submitted by:	Camson Huynh <chuynh@biolateral.com.au>
 2003-01-16 14:22:59 +00:00
Kris Kennaway
5da5198ae4 Add missing file 2003-01-14 05:30:42 +00:00
Kris Kennaway
ffd4e64c29 Add some missing files 2003-01-14 03:39:21 +00:00
Tilman Keskinoz
d022ce8307 Update to 3.8 
Approved by:	rmiya@cc.hirosaki-u.ac.jp (maintainer)
 2003-01-08 12:05:57 +00:00
Edwin Groothuis
191d7dac5e update biology/babel to properly output mm3 files. 
PR:		ports/42425
Submitted by:	Glenn Johnson <glennpj@charter.net>
 2003-01-03 08:52:41 +00:00
Ying-Chieh Liao
3220806664 upgrade to 3.7 
PR:		44957
Submitted by:	maintainer
 2003-01-02 03:57:58 +00:00
Ying-Chieh Liao
b5041aa484 add missing include 
PR:		46584
Submitted by:	Ports Fury
 2002-12-29 04:44:13 +00:00
Ying-Chieh Liao
c545891882 fix build on -current 
PR:		46459
Submitted by:	Ports Fury
 2002-12-22 12:51:20 +00:00
Mario Sergio Fujikawa Ferreira
88902156b6 Fix typo: distribfold.org -> distributedfolding.org 
Submitted by:	Matt Mills <alpha@vanity.com>
 2002-12-19 18:33:55 +00:00
Mario Sergio Fujikawa Ferreira
df92c7e01b o Update to 20021105 snapshot 
o Depend on compat4x on OSVERSION >= 500000 since these are 4.5-RELEASE
  binaries
o House a copy under MASTER_SITE_LOCAL: the local copy will be
  versioned, developer has yet to be convinced of the advantages
  of distributing versioned files

Approved by:	portmgr (knu)
 2002-12-19 01:17:07 +00:00
Mario Sergio Fujikawa Ferreira
8a51d4351d Mark BROKEN due to "Unknown problem" 
Submitted by:	maintainer
 2002-11-25 02:11:13 +00:00
Ying-Chieh Liao
5f94a921b1 unbroke by upgrade to 20021018 
drop maintainership

PR:		45466
Submitted by:	old maintainer
 2002-11-20 14:03:25 +00:00
Ying-Chieh Liao
545bf7ae46 add treepuzzle 5.1 
Maximum likelihood phylogeny reconstruction using quartets

PR:		45241
Submitted by:	Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>
 2002-11-20 08:54:10 +00:00
Maho Nakata
ce7f2b93cc 1. add a missing dependency on png and unbreak. 
2. change e-mail address of maho.
 2002-11-19 23:01:49 +00:00
Mario Sergio Fujikawa Ferreira
f0a1969d34 o Rollback PORTCOMMENT modifications while this feature's implementation 
is better studied
o Turn PORTCOMMENT variable in Makefile back into pkg-comment files

Approved by:	kris (portmgr hat),
		portmgr, re (silence)
 2002-11-10 16:48:51 +00:00
Tilman Keskinoz
7599b3caa6 Update WWW 2002-11-07 23:13:11 +00:00
Edwin Groothuis
2e9537a130 Updated to fix problems as stated in PR ports/42915 
PR:		ports/42915
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2002-11-07 13:45:17 +00:00
Adam Weinberger
c62fe39354 Fix PORTCOMMENTs that were killing INDEX builds. 
105 pointy hats to:	me
Approved by:		pat
 2002-11-07 03:10:58 +00:00
Adam Weinberger
d9611f9375 Use PORTCOMMENT in the Makefile, and whack the pkg-comment. 
Approved by:	pat
 2002-11-06 22:47:41 +00:00
Edwin Groothuis
f4aab86d3c Modify replace RE to match syntax of sed now ("\)" -> ")" 
Noticed by: bento
 2002-11-05 01:44:12 +00:00
Edwin Groothuis
37f2224fa6 PERL -> REINPLACE 
And some ports have USE_PERL5=yes now.
 2002-11-04 05:46:38 +00:00
Edwin Groothuis
6097f03e91 PERL -> REINPLACE 
Noticed on: bento
 2002-11-04 02:35:01 +00:00
Edwin Groothuis
558f2d386c PERL -> REINPLACE 
Noticed on: bento
 2002-11-04 01:56:21 +00:00
Edwin Groothuis
c3eddc377e Port needs perl to build. 
Seen on: bento
 2002-11-04 01:47:57 +00:00
Edwin Groothuis
6cf3dcffa8 Make biology/avida building on -current again 
PR:		ports/44819
Submitted by:	Oliver Lehmann <lehmann@ans-netz.de>
Approved by:	Jeremy Karlson <karlj000@unbc.ca>
 2002-11-03 23:40:02 +00:00
Patrick Li
516d846c10 Add another entry for MASTER_SITES and unbreak with latest version of bison 
PR:		ports/44711
Submitted by:	maintainer
 2002-10-29 22:27:17 +00:00
Tom Hukins
2284d53b36 Update CATEGORIES as per ports/44331. 
While I'm here, remove unnecessary whitespace spotted by portlint.

PR:		ports/44331
Submitted by:	Martin Klaffenboeck <martin.klaffenboeck@gmx.at>
 2002-10-21 10:59:11 +00:00
Mario Sergio Fujikawa Ferreira
ee31677712 o Update to snapshot 20021015 
o Fix an issue with the startup scripts
 2002-10-19 18:19:50 +00:00
Kris Kennaway
9883a05f7e Fix dependency on wxgtk 2002-10-19 09:50:53 +00:00
Akinori MUSHA
744ecfac33 CC, CXX, CFLAGS, PTHREAD_CFLAGS and PTHREAD_LIBS may contain `/' in 
them when using a non-default compiler/linker, so do not use `/' as
delimiter for s///. (I picked `|' instead)
 2002-10-10 12:59:36 +00:00
Mario Sergio Fujikawa Ferreira
72353480ab Connect distribfold to build after moving it from misc category 
Prompted by:	kris,
		Adam Weinberger <adam@vectors.cx>,
		Fernan Aguero <fernan@iib.unsam.edu.ar>,
		others
 2002-10-07 03:07:59 +00:00
Mario Sergio Fujikawa Ferreira
e6797a6f48 o New port distribfold version 0.1: distribfold.org distributed protein 
folding project
o One can start multiple instances of this port. Just install it
  using WITH_NCPU
 2002-10-07 03:07:13 +00:00
Akinori MUSHA
8dc9b4eb8b Use RUBY_MOD*. 2002-10-06 21:08:30 +00:00
Johann Visagie
f4e518bd9b - Unbreak fetching of distfiles. (Needs update as soon as freeze is over.) 
Submitted by:	kris, bento
Approved by:	Implicitly by first rule of ports freeze, I hope!
 2002-09-27 08:58:19 +00:00
Ying-Chieh Liao
460fa2aa9e add forgotten "USE_REINPLACE=yes" 
Submitted by:	maintainer
 2002-09-21 14:56:18 +00:00
Ying-Chieh Liao
6c06a9090d upgrade to 20020426 
PR:		39357
Submitted by:	maintainer
 2002-09-21 06:59:28 +00:00
Kris Kennaway
dc1db85872 BROKEN: Does not fetch 2002-09-20 20:45:20 +00:00
Kris Kennaway
ce1e6ce51e BROKEN: Does not build 2002-09-19 02:45:38 +00:00
Ying-Chieh Liao
47be6d4a10 add primer3 0.9 
Primer3 helps to choose primers for PCR reactions

PR:		35298
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2002-09-17 15:31:09 +00:00
Dirk Meyer
f593f06ed2 Flip is used to find/translate orfs. 
WWW: ftp://megasun.bch.umontreal.ca/pub/flip/
PR:		35332
Submitted by:	tonym@biolateral.com.au
 2002-09-10 14:04:06 +00:00
Dirk Meyer
ce85742f4f "Wise2 is package that is focused on comparing DNA sequences at 
the level of its conceptual translation, regardless of sequencing
error and introns."
 2002-09-10 13:58:40 +00:00
Maxim Sobolev
4715163d34 Chase new name of wxgtk shared library. 2002-09-09 14:21:08 +00:00
Kris Kennaway
8fa8041fe5 Remove USE_NEWGCC, which is no longer supported or required. 
Submitted by:	Tilman Linneweh <tilman@arved.de>
PR:		ports/40571
 2002-08-31 02:38:29 +00:00
Mario Sergio Fujikawa Ferreira
5dec55380d Deploy USE_GNOMENG infrastructure 
PR:		42187
Submitted by:	Edwin Groothuis <edwin@mavetju.org>
 2002-08-30 12:59:40 +00:00
Hye-Shik Chang
164aad7a64 o Fix examples directory path which is changed in last revision. 
Submitted by:	Glenn Johnson <glennpj@charter.net>
 2002-08-26 05:13:28 +00:00
Hye-Shik Chang
485faf1e84 o Fix RUN_DEPENDS path (PMW -> Pmw) 
o Fix DISTNAME which was broken by previous commit.
o Install example files

PR:		41977
Submitted by:	Glenn Johnson <glennpj@charter.net>
Approved by:	maintainer
 2002-08-25 08:37:53 +00:00
Kris Kennaway
56881e441f Prefer <limits.h> over <values.h> as the latter has been removed from 
-current.

Noticed by:	bento
 2002-08-23 03:36:33 +00:00