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644 Commits

Author SHA1 Message Date
Max Khon
626ca478fe - Switch to wxgtk2 
- USE_MESA -> USE_GL
 2003-11-09 19:04:36 +00:00
Eric Anholt
b1e4f642e5 LIB_DEPENDS on libglut for libglut rather than soon-to-disappear Mesa3. 2003-11-07 20:45:29 +00:00
Adam Weinberger
c479bf51a5 Update to 2.0.7. 2003-11-07 16:50:32 +00:00
Eric Anholt
e4a14e5699 Mark BROKEN: distfile has changed. 2003-11-06 23:15:06 +00:00
James E. Housley
0e9cd423cb ${MASTER_SITES} are slow. This patch adds a mirror site to help 
fetch work more frequently.  This patch patches the Makefile from
PORTSDIR}/biology

PR:		58130
Submitted by:	MAINTAINER
 2003-11-06 11:32:30 +00:00
Max Khon
14988eebf4 Make this port use wxgtk 2.4.2. 2003-11-05 10:26:00 +00:00
Max Khon
cfe5492411 Chase wxgtk library name (and version) change. 2003-11-04 20:52:58 +00:00
Mark Linimon
43233244ca Pet portlint. 2003-11-03 21:01:28 +00:00
Edwin Groothuis
a27bc39328 Date: Tue, 04 Nov 2003 00:42:55 +0900 
From: Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
Subject: Re: question about FreeBSD ports you maintain

Briefly, I have no time for maintaining ports.
So I wish to leave the maintainer position of these ports:

biology/fastdnaml
textproc/wv

Thanks you for maintaining the FreeBSD system.

                                        Best regards,
					Motomichi Matsuzaki
 2003-11-03 20:44:32 +00:00
Kris Kennaway
09b69954f2 Mark BROKEN (see bento logs). These ports are scheduled for removal 
after Feb 2 2004 if they are still broken at that time and no fixes
have been submitted by PR.
 2003-11-03 03:56:42 +00:00
Edwin Groothuis
df3c9e78bd ports with possibly unreachable MAINTAINERs 
*** addresses that seem to be dead:

PR:		ports/58694
Submitted by:	Oliver Eikemeier <eikemeier@fillmore-labs.com>
 2003-11-02 02:48:08 +00:00
Mark Linimon
817fa652d7 Chased new mastersite per distfile survey. Notified maintainer. 2003-10-26 08:19:46 +00:00
Ying-Chieh Liao
c634b4bb83 utilize SITE_PERL 
PR:		58166
Submitted by:	Cheng-Lung Sung <clsung@dragon2.net>
 2003-10-24 12:05:09 +00:00
Kris Kennaway
d4788043a6 Respect CC and CFLAGS 2003-10-23 00:01:04 +00:00
Sergey A. Osokin
958842c5c6 Cosmetic fix: use %%DOCSDIR%% macro. 
No functionally changes.

Submitted by:	Oleg Karachevtsev <ok@etrust.ru>
A part of PR:	57992
 2003-10-22 09:37:18 +00:00
Kirill Ponomarev
c05d3fc123 - Update to 0.5.2 
PR:		58304
Submitted by:	Clement Laforet <sheepkiller@cultdeadsheep.org>
 2003-10-20 22:41:04 +00:00
Kris Kennaway
19b417918e Don't remove share/java/classes system directory. 2003-10-19 02:26:52 +00:00
Mark Linimon
280fea9546 Fixes the checksum problem, but doesn't fix the port; adds a BROKEN 
line about how it fails.  Some other interested person will have
to take it from here.

PR:		56882
 2003-10-15 23:56:43 +00:00
Akinori MUSHA
586e37458f Update to 0.5.3. 2003-10-14 22:25:59 +00:00
Daichi GOTO
50e96887d2 update biology/nab: 4.5.1 -> 4.5.2 
PR:		57970
Submitted by:	M. L. Dodson <bdodson@scms.utmb.edu> (maintainer)
 2003-10-14 12:18:51 +00:00
Kris Kennaway
c68a93561d BROKEN: Broken pkg-plist 2003-10-13 06:31:57 +00:00
Kris Kennaway
c2b0bb508d BROKEN: Does not fetch 2003-10-12 22:31:49 +00:00
Edwin Groothuis
ec14a6f561 Port update (maintainer): biology/wise 
Fenner's porsurvey show wise no longer available at original
	site.  Original site readme shows it has moved so update
	the MASTER_SITES accordingly.

PR:		ports/57154
Submmited by:	Tony Maher <tonymaher@optushome.com.au>
 2003-09-24 11:32:44 +00:00
Sergey A. Osokin
f37f7775e3 Make portlint(1) happy by changing strip to ${STRIP_CMD} 
Submitted by:	Oleg Karachevtsev <ok@etrust.ru>
PR:		56998
 2003-09-24 09:37:11 +00:00
Edwin Groothuis
bdb4445a67 Update port: biology/gperiodic to 2.0.6 
- Update to version 2.0.6

PR:		 ports/56522
Submitted by:	 KATO Tsuguru <tkato@prontomail.com>
 2003-09-08 06:09:31 +00:00
Edwin Groothuis
ec3cd3ad7f new port:biology/lsysexp 
L-system Explorer is a program used for viewing and creating
	L-system fractals.

	The following features are supported:

	- Over 500 builtin L-systems, arranged into about 20 groups.
	- Ability to create and save custom L-systems and L-system groups.
	- Abilty to save images of L-systems (in PNG or JPEG format).
	- Multiple L-systems can be viewed at the same time.
	- Able to use custom colors and gradients.
	- Can also generate random gradients, or completely random colors.
	- Able to draw using lines, points, or a random combination of both.

PR:		iports/51400
Submitted by:	David Yeske <dyeske@yahoo.com>
 2003-09-03 02:23:23 +00:00
Maho Nakata
17cbc7c345 Silent changes to the port distfile which *not* have significant 
functional differences.
just changing very minor change of documatation, adding very minor
functionality and some cleanup for coding

Submitted by:	bento's log
 2003-09-01 22:00:00 +00:00
Kirill Ponomarev
c101866e9f - Add an end-of-string to each line of the input 
when parsing the input files

PR:		56043
Submitted by:	maintainer
 2003-08-28 04:51:02 +00:00
Akinori MUSHA
0f1f27c54b Update to 0.5.2. 2003-08-22 22:53:54 +00:00
Hye-Shik Chang
c76af54099 Fix build on python2.3 2003-08-20 10:40:37 +00:00
Norikatsu Shigemura
efb928619b o Main modification 
graphics/gd(based on 1.8.4)    -> graphics/gd1
  graphics/gd2(based on 2.0.15)  -> graphics/gd
  graphics/p5-GD(based on 1.41)  -> graphics/p5-GD1
  graphics/p5-GD2(based on 2.07) -> graphics/p5-GD
  japanese/gd                    -> japanese/gd1
  japanese/gd2                   -> japanese/gd
o Include some feature
  WITH_XPM(w/, w/o WITHOUT_X11)
o Chase this modification
o Fix build error [1]

PR:		ports/54540
Submitted by:	Ports Fury
Approved by:	maintainer (blanket)
Reported by:	bento via kris [1]
 2003-08-18 16:15:10 +00:00
Kris Kennaway
736746419e As announced on May 6, remove the broken p5-bioperl-devel port. 2003-08-08 03:31:11 +00:00
Kris Kennaway
616a6528af BROKEN: Checksum mismatch 2003-08-07 09:29:17 +00:00
Hye-Shik Chang
2b12324a99 Fix python version detection routines to cope with python 2.3's 
boolean representation.
 2003-08-01 22:04:57 +00:00
Maho Nakata
636cfee514 Somehow pkg-plist is removed... 
Pointy hat to: myself
 2003-08-01 03:31:42 +00:00
Maho Nakata
c99edb7512 a) Update to 1.7.3 
b) Maintainer timeout:
   This PR is submitted by Thu May 08 07:30:18 PDT 2003
   but no reply from the maintainer.

PR:		51971
Submitted by:	KATO Tsuguru <tkato@prontomail.com> aka Ports Fury
 2003-08-01 03:27:54 +00:00
Maho Nakata
7c5ae7045b Add USE_XLIB=yes to compile 
Submitted by:	kris via bento
 2003-07-31 08:06:09 +00:00
Akinori MUSHA
c78ef63727 Update to 0.5.1. 2003-07-29 06:44:28 +00:00
Maho Nakata
4dd4b89f44 A new port garlic, free molecular viewer and editor, free molecular 
visualization program, protein structure, DNA structure, PDB,
molecular rendering, biological macromolecule.
 2003-07-28 06:38:37 +00:00
Kirill Ponomarev
d5ad075240 - Update to version 2.0.5 
PR:		54899
Submitted by:	KATO Tsuguru <tkato@prontomail.com>
Approved by:	fjoe (mentor) (implicit)
 2003-07-27 16:00:31 +00:00
Maho Nakata
10c43988bd Some clean-up. 
a) ECHO-> ECHO_CMD
b) place of WITH_OPTIMIZED_FLAGS seems to be wrong.
c) fix errors reported from freshports.org
 2003-07-25 22:30:55 +00:00
Maho Nakata
aa86451d35 Duplicated the pre-extract:' and post-build:' 
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Pointy hat to:	myself
 2003-07-25 21:19:09 +00:00
Maho Nakata
7a5f7030ac a) Some corrupts with Makefile and pkg-plist. 
b) forgot to notice that drop maintainership to ports@

Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Pointy hat to:	myself
 2003-07-25 07:19:40 +00:00
Maho Nakata
d0d6c6466b a) Forgot to update distinfo 52498 
b) added LEGAL. author requests no distribution
   except from his FTP site
c) clean-ups for compiler optimization

Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Pointy hat to:	maho; partially :)
 2003-07-25 02:48:05 +00:00
Maho Nakata
7f03690b18 Update to 0.90 2003-07-24 07:06:17 +00:00
Maho Nakata
efc116207e enhancement, build and install the opengl viewer, moldenogl. 
update to 3.9, not 3.8, which is newer :)

Committed by maintainer timeout:
> Sat Apr  5 17:46:57 EST 2003 - edwin - informed maintainer

PR:		47177
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
 2003-07-19 04:17:06 +00:00
Maho Nakata
2b7927a921 honor CFLAGS and FFLAGS 
PR:		54396
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
 2003-07-19 03:58:51 +00:00
Maho Nakata
3c2eb776a2 Maintainer update of biology/tinker port to version 4.0. 
PR:		52498
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
 2003-07-19 03:48:44 +00:00
Yen-Ming Lee
fb228ea556 Add semi-colons(;) after declare statements that go in the povray scene file 
so that povchem works with povray-3.5.

Maintainer prefer not to depend on ImageMagick since users can use their
favorite picture viewer. display isn't the only one choice.

Drop maintainership.

PR:		54397
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Reviewed by:	Chen-hsiung Chan <frankch@waru.life.nthu.edu.tw>
 2003-07-14 06:50:15 +00:00
Norikatsu Shigemura
99a390f50b o Change library name from libgd to libgd1. 
o Do not install everything except headers and libraries
  (to avoid conflicting with graphics/gd2)
o Fix dependency on new libgd1(for many ports).

PR:		ports/54100
Submitted by:	Ports Fury
 2003-07-11 18:16:14 +00:00
Sergey A. Osokin
afa7efcce6 s/NOPORTSDOCS/NOPORTDOCS/ [1] 
Use %%PORTDOCS%%%%DOCSDIR%% in pkg-plist.

PR:		53911 [1]
Approved by:	maintainer
 2003-07-11 11:01:13 +00:00
Daichi GOTO
a1ab1ee112 update biology/nab: 4.4 -> 4.5.1 
PR:		52786
Submitted by:	M. L. Dodson <bdodson@scms.utmb.EDU> (maintainer)
 2003-07-08 11:50:36 +00:00
Akinori MUSHA
9d7ec05179 Update to 0.5.0. 2003-06-26 03:34:44 +00:00
Daichi GOTO
262d632dae update ports/biology/act to latest release (v2) 
PR:		49093
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2003-06-23 13:37:39 +00:00
Erwin Lansing
9a7422c0c5 - update to 1.83 
- give maintainership to submitter as the old maintainer's
  address bounces

PR:		52054
Submitted by:	Philip M. Gollucci <philip@p6m7g8.com>
Approved by:	maintainer bounces
 2003-06-17 18:39:47 +00:00
Kris Kennaway
93872f18cc Move inclusion of bsd.port.pre.mk later in the file for conditional BROKEN 
tag.  Early inclusion caused problems for some ports, so to be safe I'm
updating all of them.

Pointy hat to:	kris
 2003-06-04 22:43:38 +00:00
Adam Weinberger
0225134607 Assign MAINTAINER to ports@FreeBSD.org. 
PR:		ports/52534
Submitted by:	Christian Brueffer <chris@unixpages.org>
 2003-06-04 18:58:11 +00:00
Tim Vanderhoek
29763acb4a Upgrade to 2003.01.21. Appears to only add some more file export/print 
options.  Additional patches were necessary since the fltk port seems
to have been upgraded and thus also broken this port (which would
been already broken due to the checksum failure).
 2003-05-22 05:59:32 +00:00
Tim Vanderhoek
826bc61d7e Add back the WWW which was inexplicably deleted in a previous 
revision.  Make a few organisational improvements.  However, be
too lazy to move to pkg-message a note that really shouldn't
be necessary for the end user at all.
 2003-05-22 02:44:05 +00:00
Pete Fritchman
2fa167da9b - fix build under gcc 3.3 
- respect CC/CFLAGS

PR:		52013
Submitted by:	maintainer
 2003-05-19 01:48:33 +00:00
Kris Kennaway
257ef67bc8 Back out previous commit, the port was fixed a few days ago. 2003-05-18 21:52:02 +00:00
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
Ying-Chieh Liao
facc5fd919 change master site 
add mpich support

PR:		36468
Submitted by:	maintainer
 2002-03-29 08:15:13 +00:00
Pete Fritchman
142857d2b0 Respect CFLAGS/CC. 
PR:		36395
Submitted by:	maintainer
Reported by:	bento
 2002-03-28 22:50:15 +00:00
Johann Visagie
c6d9b64615 Add crimap 2.4, a tool for the creation of multilocus linkage maps. 
PR:		35198
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2002-03-27 14:42:56 +00:00
Johann Visagie
9e8dd630bc Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection. 
PR:		33853
Submitted by:	chuynh@biolateral.com.au
 2002-03-27 14:18:49 +00:00
Johann Visagie
11fd4f1a75 - Add a new patch 
- Bump $PORTREVISION

PR:		36206
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2002-03-27 14:01:57 +00:00
Maxim Sobolev
62f2687e21 Add USE_SUBMAKE, where it might be necessary. 2002-03-25 09:19:20 +00:00
Kris Kennaway
da58c0cc52 BROKEN: Does not build 2002-03-25 02:33:32 +00:00
Johann Visagie
5e52a21fed - Fix certain mistakes in FreeBSD patches 
- Bump PORTREVISION
- Poroblem originally reported by Fernan Aguero <fernan@iib.unsam.edu.ar> on
  FreeBSD-bio list

PR:		36169
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2002-03-22 08:23:22 +00:00
Akinori MUSHA
291dac941c Update to 0.3.5. 2002-03-12 23:12:03 +00:00
Daniel Harris
6c9fcf063c Fix WWW. 2002-03-08 20:50:08 +00:00
Patrick Li
672a625d5d Update to 2001.12.20 
PR:		35203
Submitted by:	maintainer
 2002-02-22 07:57:07 +00:00
Pete Fritchman
124f4dcb9e Pass maintainership to submitter and add a backup master site. 
PR:		35043
Submitted by:	Christian Brueffer <chris@unixpages.org>
 2002-02-20 06:53:44 +00:00
Patrick Li
719fbd8399 - Install documentation 
- Update WWW:

PR:		34889
Submitted by:	maintainer
 2002-02-13 02:54:31 +00:00
Akinori MUSHA
8fdfd13285 Use ${ECHO_CMD} instead of ${ECHO} where you mean the echo command; 
the ECHO macro is set to "echo" by default, but it is set to "true" if
make(1) is invoked with the -s option while ECHO_CMD is always set to
the echo command.

Use command macros where appropriate.
 2002-01-29 09:39:59 +00:00
Johann Visagie
a3a6a2eb07 Add t_coffee 1.37, a multiple DNA or protein sequence alignment package. 2002-01-25 14:58:16 +00:00
Johann Visagie
449211250e - Update to version of 2001-12-30 2002-01-25 13:33:00 +00:00
Johann Visagie
2b0b32622c - Update to version 1.82 2002-01-25 12:35:20 +00:00
Johann Visagie
35678fe414 - Update to version 0.7.2, somewhat overdue. :-) 2002-01-25 11:46:09 +00:00
FUJISHIMA Satsuki
8ea66910b1 o update to 3.7. 
differences from the PR:
 - this port requires Xlib so add USE_XLIB.
 - remove unnecessary PORTREVISION.

PR:		34196
Submitted by:	maintainer
 2002-01-23 19:59:19 +00:00
FUJISHIMA Satsuki
946f0b4771 o update to 0.7. 
PR:		34197
Submitted by:	maintainer
 2002-01-23 19:52:38 +00:00
FUJISHIMA Satsuki
56260aa14e update to 1.3.3. 
PR:		34180
Submitted by:	KATO Tsuguru <tkato@prontomail.com>
 2002-01-22 21:19:05 +00:00
Johann Visagie
ba0a0aded4 - Update to version 1.00a4 
PR:		33719
Submitted by:	Hye-Shik Chang <perky@fallin.lv>
 2002-01-22 10:54:02 +00:00
Trevor Johnson
cfa84869ca Update to 0.99.7. Use new DATADIR macro. Install documentation, 
including examples.  Add warning.
 2002-01-20 02:45:37 +00:00
Ying-Chieh Liao
ec822f7631 Upgrade tinker to the latest revision 
PR:		33425
Submitted by:	maintainer
 2002-01-19 15:15:16 +00:00
Johann Visagie
443693b9ae - Update to version 2.2.0 
- Update included EMBASSY package EMNU
- Fix a long-standing bug in Makefile that would preclude PKGMESSAGE from
  being generated properly
- Consider this an interim update merely to track the latest version - more
  work is required to activate the newly included "Jemboss" Java GUI
  interface
 2002-01-18 14:04:03 +00:00
Pete Fritchman
66cf3707e5 Update to 0.2. 
PR:		33218
Submitted by:	maintainer
 2001-12-29 06:36:25 +00:00
Kevin Lo
30d7b16772 Initial import of artemis 4.0 
Artemis is a  DNA sequence viewer and annotation tool.

PR: 32914
Submitted by: Camson <chuynh@biolateral.com.au>
 2001-12-22 14:39:40 +00:00
Akinori MUSHA
c93a735a7f Update to 0.3.3. 2001-12-21 21:25:16 +00:00
Pete Fritchman
74375be19f Add gff2ps 0.97b, converts gff-formated genomic data-sets to 
PostScript.

PR:		32920
Submitted by:	Camson Huynh <chuynh@biolateral.com.au>
 2001-12-19 10:03:26 +00:00
Pete Fritchman
e42a8c9a6e Add dna-qc 1993.07.26, a quality control algorithm for DNA 
sequencing projects.

PR:		32998
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-12-19 03:20:48 +00:00
Steve Price
bc08a589e7 Update to version 2001.10.12. 2001-12-16 19:36:48 +00:00
Ying-Chieh Liao
46d2f41bac fix pkg-plist 
PR:		32609
Submitted by:	Ports Fury
 2001-12-08 20:49:21 +00:00
Christian Weisgerber
9aee951f75 * Replace pkg-message about setting BABEL_DIR with a wrapper script 
that does.
* Remove misleading full path name from usage message.
* Improve fgets() usage.
* Add converters category.
* Improve pkg-comment and pkg-descr.
 2001-12-02 13:09:47 +00:00
Pete Fritchman
cdc0a86dc7 - update to 1.3.2 
- use DOCSDIR

PR:		32305
Submitted by:	KATO Tsuguru <tkato@prontomail.com>
 2001-11-28 20:52:44 +00:00
Akinori MUSHA
2bc9eb704d Update to 0.3.2. 2001-11-28 13:46:31 +00:00
Mario Sergio Fujikawa Ferreira
72dab870f3 Style police: WWW tags should either end in a file/script or TRAILING /; Fix the later case 2001-11-20 23:49:34 +00:00
Mario Sergio Fujikawa Ferreira
75ad5febcb Style police: WWW tags should either end in a file/script or TRAILING /; Fix the later case 2001-11-20 23:29:38 +00:00
FUJISHIMA Satsuki
fe5926b918 chase checksum for repacked distfile almost an year ago. 
Maintainer does not have previous distfile.
As the distfile for this port is not distributable, it is OK to me to change
distinfo now.

PR:		31010
Submitted by:	maintainer
 2001-11-06 13:32:44 +00:00
Akinori MUSHA
b98ad00ebf Add ruby-bio (BioRuby), an integrated environment for Bioinformatics 
written in Ruby.
 2001-10-24 06:21:52 +00:00