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483 Commits

Author SHA1 Message Date
Kris Kennaway
9c288e873f BROKEN on 5.1: bad C++ 2003-05-18 09:55:25 +00:00
Michael Landin
05b1705af9 - Update to latest release. 
- Better autoconf/automake so patches no longer needed
- Changed dependency. (now wxgtk-devel)

PR:		51741
Submitted by:	maintainer
Approved by: 	roberto(mentor)
 2003-05-14 13:09:11 +00:00
Kris Kennaway
cdb6ec2c28 BROKEN: Broken pkg-plist 2003-05-06 23:36:56 +00:00
Tilman Keskinoz
b2097beda0 Update to 2003.04.21 
PR:		51709
Submitted by:	Tony Maher <tonymaher@optushome.com.au>
 2003-05-05 12:24:08 +00:00
Pete Fritchman
42220eeb24 - unbreak on 4.x: add dependency on gdkpixbuf, fix Makefiles to compile with 
the correct libraries
- add a WITH_OPTIMIZED_CFLAGS knob

PR:		51614
Submitted by:	maintainer
 2003-05-03 18:27:53 +00:00
Maho Nakata
1132a00c6e Updated to 0.8.6. 
Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU>
Pkg-plist by: maho
 2003-05-03 03:45:31 +00:00
Mario Sergio Fujikawa Ferreira
c5e7423b03 Update to 20030425 snapshot 2003-04-25 18:01:46 +00:00
Joe Marcus Clarke
4fb7eb3a61 Remove USE_GNOMENG. 2003-04-18 04:54:11 +00:00
Edwin Groothuis
80f9519693 Update the biology/tinker Makefile so it builds on -current 
PR:		ports/50371
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
 2003-03-30 06:43:14 +00:00
Christian Weisgerber
3e8676b331 * Fix build with GCC3 (-CURRENT). 
* Honor CXX/CXXFLAGS.
* Use predefined DOCSDIR and EXAMPLESDIR variables.

Approved by:	maintainer timeout
 2003-03-25 12:28:57 +00:00
Ade Lovett
7e52725f2a Clear moonlight beckons. 
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
 2003-03-07 06:14:21 +00:00
Trevor Johnson
5e37fb828f Retire comment file. 2003-03-01 14:34:33 +00:00
Mario Sergio Fujikawa Ferreira
55dc9026c2 Update to 20030227 snapshot 2003-02-28 01:46:50 +00:00
Mario Sergio Fujikawa Ferreira
74740483d0 De-pkg-comment 2003-02-23 19:58:35 +00:00
Akinori MUSHA
57f9198bc7 De-pkg-comment. 2003-02-21 11:08:38 +00:00
Akinori MUSHA
7cc1393a93 De-pkg-comment. 2003-02-20 17:07:10 +00:00
Christian Weisgerber
9de6d7d1a0 Fix install and packaging list. 
Reported by:	kris
 2003-02-18 14:09:17 +00:00
Akinori MUSHA
a4542a306f De-pkg-comment. 2003-02-18 04:24:40 +00:00
Christian Weisgerber
97d4b58c28 Update to 1.83. 
PR:		48264
Submitted by:	David A. Bader <dbader@eece.unm.edu>
 2003-02-15 18:43:14 +00:00
Christian Weisgerber
5eb743da03 * Update to 3.13. 
PR:		48255
Submitted by:	David A. Bader <dbader@eece.unm.edu>

* Also honor CC/CFLAGS.
 2003-02-14 23:21:23 +00:00
Edwin Groothuis
6e497f06be Add dependency on security/p5-Digest-MD5 
Noticed on: bento
 2003-02-13 02:52:13 +00:00
Christian Weisgerber
aeefc83b6c Update to version 0.5.1. 
PR:		48047
Submitted by:	Ports Fury
 2003-02-11 18:13:27 +00:00
Kris Kennaway
1140e88185 Remove gaussian98 
Pointy hat to:	maho
 2003-02-05 09:01:06 +00:00
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
Hye-Shik Chang
0aedf7e003 o Remove redundant dependency on py-tkinter. 
o Bump PORTREVISION that I've missed on last commit.

Submitted by:	Glenn Johnson <glennpj@charter.net>
 2002-08-22 04:20:19 +00:00
Hye-Shik Chang
bf0c82e18c Add a dependecy to x11-toolkits/pmw 
PR:		41857
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Approved by:	maintainer
 2002-08-22 03:35:32 +00:00
Mario Sergio Fujikawa Ferreira
e3aab5688e New port L-Breeder version 1.0: Allows you to display and breed 
L-system forms

PR:		38725
Submitted by:	David Yeske <dyeske@yahoo.com>
 2002-08-21 00:01:59 +00:00
Christian Weisgerber
9f15c68bdd - Support CXXFLAGS properly. 
- Do not install .la file.

PR:		41732
Submitted by:	Ports Fury
 2002-08-17 19:16:55 +00:00
Christian Weisgerber
5852631db9 Update to version 3.6.a3. 
PR:		41412
Submitted by:	David A. Bader <dbader@eece.unm.edu>

Additional clean-up:
* Respect CC, CFLAGS, X11BASE.
* Use versioned DIST_SUBDIR.

Approved by:	maintainer
 2002-08-13 16:07:45 +00:00
Hye-Shik Chang
dc8e3f8160 Add pymol 0.82, Free and Open-Source molecular modeling system. 
PR:		40694
Submitted by:	Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
 2002-08-13 11:53:43 +00:00
Akinori MUSHA
efc8639c1f Update to 0.3.9. 2002-08-03 07:02:10 +00:00
Ying-Chieh Liao
e2e513a934 add libgenome 0.5.0 
Toolkit for developing bioinformatic related software in C++
 2002-07-30 10:57:06 +00:00
Ying-Chieh Liao
827fd8ad5f upgrade to 4.4 
PR:		40612
Submitted by:	maintainer
 2002-07-16 06:18:16 +00:00
Thomas Gellekum
b7ae6bf01c Use $PYNUMERIC in the dependencies. 2002-07-15 11:37:35 +00:00
Johann Visagie
72f20def8c - Add patch that will, for -CURRENT only, change: -pthread -> -lc_r 
- Bump $PORTREVISION

Prompted by:	Various questions from Rune Linding <linding@EMBL-Heidelberg.DE>
 2002-07-11 10:52:14 +00:00
Akinori MUSHA
e592f1eba6 Update to 0.3.8. 2002-07-07 18:21:43 +00:00
Johann Visagie
cd4c80ae90 - Update to version 2.4.1 
- Unmark BROKEN
- Start adding support for Jemboss Java-based GUI (not active yet)

PR:		40198 ; many private requests
Submitted by:	Tilman Linneweh <tilman@arved.de> (2.4.1 update)
 2002-07-05 10:09:32 +00:00
Mike Heffner
c31a69e966 Bump XForms lib. version. 2002-07-04 09:20:30 +00:00
Greg Lewis
10d07fbd22 Unbreak this port: 
. Fix dependencies to be in sync with the recent JDK ports renaming.
. Replace MASTER_SITES with a location that actually contains the
  source.
. Fix the packing list.

Note that there is a much newer version of this application available,
but that is beyond the scope of what I was trying to do (just fix the
JDK dependency), as is the last two items.
 2002-06-16 01:08:49 +00:00
Pete Fritchman
6e909e06e2 Correct MASTER_SITES. 
PR:		39016
Submitted by:	maintainer
 2002-06-08 00:40:10 +00:00
SADA Kenji
c814b1bf01 Note distribution term. 
Requested by:	maintainer
 2002-05-27 06:25:53 +00:00
SADA Kenji
6891ceb1b7 Back my last commit out. 
We couldn't update distinfo without inspecting distfile's changes.
PR:	ports/37476
Suggested by:	kris
 2002-05-23 08:56:36 +00:00
SADA Kenji
9a674d6c69 distfile has silently changed, 
so md5 has to be rewritten.
PR:	ports/37476
Submitted by:	maintainer
 2002-05-18 03:24:22 +00:00
Kris Kennaway
f2285e9ab6 BROKEN: Checksum is incorrect 2002-05-18 02:36:56 +00:00
Kris Kennaway
67ef0f1942 BROKEN: incorrect checksums 2002-05-17 09:24:32 +00:00
Kris Kennaway
9a31e4a0f0 Update to sim4-2002.03.03 to unbreak build. 
Noticed by:	bento
 2002-05-04 21:45:10 +00:00
Ying-Chieh Liao
3011ed52b9 upgrade to V110-1 
build with newer bison
remove BROKEN

PR:		37313
Submitted by:	maintainer
 2002-04-21 13:33:29 +00:00
Ying-Chieh Liao
9e3da593d2 add avida 1.6.0 
Avida is an auto-adaptive genetic system designed for ALife research

PR:		37268
Submitted by:	Jeremy Karlson <karlj000@unbc.ca>
 2002-04-20 15:17:46 +00:00
Akinori MUSHA
8210b67ce4 Update to 0.3.6. 2002-04-10 18:37:18 +00:00
Dirk Meyer
3e70b923da Swiss-PdbViewer is an application that provides a user friendly interface 
allowing to analyse several proteins at the same time. The proteins can be
superimposed in order to deduce structural alignments and compare their
active sites or any other relevant parts. Amino acid mutations, H-bonds,
angles and distances between atoms are easy to obtain thanks to the
intuitive graphic and menu interface.

Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated
homology modelling server developped at Glaxo Welcome Experimental Research
in Geneva. Working with these two programs greatly reduces the amount of work
necessary to generate models, as it is possible to thread a protein primary
sequence onto a 3D template and get an immediate feedback of how well the
threaded protein will be accepted by the reference structure before
submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various
tools to build into the density. In addition, various modelling tools are
integrated and command files for popular energy minimisation packages can be
generated.

Finally, as a special bonus, POV-Ray scenes can be generated from the
current view in order to make stunning ray-traced quality images.

WWW:  http://www.expasy.ch/spdbv/

PR:		33902
Submitted by:	chuynh@biolateral.com.au
 2002-04-02 16:18:53 +00:00
Kris Kennaway
556d50ff76 Remove #include <malloc.h> 2002-03-31 03:55:29 +00:00