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339 Commits

Author SHA1 Message Date
Johann Visagie
8565b5de56 - Add installation of include files 
- Bump PORTREVISION

PR:		30660
Submitted by:	Tony Maher <tonym@biolateral.com.au> (MAINTAINER)
 2001-09-19 13:03:18 +00:00
Mario Sergio Fujikawa Ferreira
064782fb41 style fix: un"echo" commands 
Approved by:	MAINTAINER
 2001-09-13 03:50:40 +00:00
Mario Sergio Fujikawa Ferreira
dfd533edaa Update to 3.9 
PR:		30398
Submitted by:	MAINTAINER
 2001-09-13 01:13:52 +00:00
Andrey A. Chernov
5676988fbd Bump png major 2001-09-11 03:32:41 +00:00
Anton Berezin
8091bed6f3 Fix a buglet with the use of XFREE86_VERSION without including 
bsd.port.pre.mk first.

Spotted by:	Dan Langille <dan@langille.org>
 2001-09-06 22:36:38 +00:00
Anton Berezin
fc3d9f8482 Make biology/rasmol work at all color depths. 
PR:		30406
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
 2001-09-06 21:25:13 +00:00
Johann Visagie
5f3039ab60 - Update to version 1.00.a3 
- Use pkg-req to check the installed version of Python
 2001-09-06 12:42:36 +00:00
Johann Visagie
22c3e2138e - Update to version 3.1 
PR:		30176
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2001-08-29 12:00:08 +00:00
Johann Visagie
b77bfb26fc - Update to version 1.0.3 
PR:		30175
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2001-08-29 11:53:29 +00:00
Johann Visagie
3953bc07d2 - Update to version 1.2.4 2001-08-22 14:43:45 +00:00
Johann Visagie
4e8aeac440 - Update port to version 2.2g 2001-08-22 13:18:10 +00:00
Johann Visagie
8aff3a669c Add seqio 1.2.2, a set of C functions which can read/write 
biological sequence files.

PR:		29922
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-08-22 12:07:26 +00:00
Johann Visagie
2149e94178 - Update to version 3.6.a2.1 - since the distribution tarball hadn't been 
renamed between versions, this port failed checksum.
- Apply some whitespace edits and cut pkg-descr down to size to placate
  portlint.

Reported by:	Jason Stajich <jason@chg.mc.duke.edu>
Approved by:	No response from MAINTAINER
 2001-08-22 10:02:27 +00:00
Johann Visagie
db0bae3c16 - Move the (very) long list of manpages from the port Makefile to a separate 
file.

Inspired by:	nectar's treatment of security/heimdal
 2001-08-20 12:41:11 +00:00
Trevor Johnson
6113f46e0d Update to 0.95. 
Compile molecule_tools.cpp with -O0 on all architectures, not just
the Alpha, to avoid g++ pessimization.

Submitted by:	Matthew Emmerton <matt@gsicomp.on.ca>
 2001-08-20 11:12:44 +00:00
Kris Kennaway
7a82bf9bb9 Remove a patch turd from the pkg-plist 2001-08-20 06:47:56 +00:00
Johann Visagie
490da9f942 Add treeviewx 0.1.1, a phylogenetic tree viewer. 
PR:		29770
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-08-17 08:39:28 +00:00
Johann Visagie
133a08c54d Add p5-bioperl-devel 0.9.0, 
a collection of Perl modules for
bioinformatics (developer's release).
 2001-08-14 09:36:36 +00:00
Johann Visagie
767182618a Update to version 1.75 2001-08-13 11:27:36 +00:00
Johann Visagie
102c91c252 - Properly list run-time dependencies in RUN_DEPENDS in Makefile. 
- Deploy %%PERL_VER%% and %%PERL_ARCH%% pragmas consistently throughout
  pkg-plist.  (Ouch, that was embarrassing.)
- Bump PORTREVISION due to the above.
- Update my email address and the project's URL in pkg-descr.
 2001-08-13 10:26:44 +00:00
Ying-Chieh Liao
676731ee70 upgrade to 0.26 
drop maintainership
 2001-08-09 17:37:03 +00:00
Johann Visagie
f7b5a60b9b Add lamarc 2001.08.06, 
a package of programs for computing
population parameters.
 2001-08-07 08:17:58 +00:00
Johann Visagie
043c249d98 Add recombine 1.40, a program to fit population models across sites. 2001-08-06 14:49:53 +00:00
Johann Visagie
52619bca7a Add fluctuate 1.30, a program to fit population models. 2001-08-06 14:45:39 +00:00
Johann Visagie
cd0583a2a8 Add coalesce 1.50, a program to fit population models. 2001-08-06 14:41:58 +00:00
Johann Visagie
a4dc6fd25a Correct my email address. 2001-08-06 14:26:51 +00:00
Johann Visagie
199894f656 Add migrate 1.2, 
a program to estimate population sizes and
migration rates.
 2001-08-06 13:07:46 +00:00
Johann Visagie
8a04d259ee Update maintainer's email address. 
Approved by:	MAINTAINER
 2001-08-06 10:50:02 +00:00
Johann Visagie
e391dae637 - Update port to version 2.0.1 
- Add two new EMBASSY applications, MEME and HMMER.
 2001-08-03 11:32:42 +00:00
Mario Sergio Fujikawa Ferreira
2409be3f61 add USE_XLIB 
PR:		29330
Submitted by:	bento, Patrick Li <pat@databits.net>
 2001-07-30 21:05:54 +00:00
Steve Price
73d28d48ac This port require bison to build so add USE_BISON. 2001-07-25 17:57:49 +00:00
Johann Visagie
3ea351668d Remove obsolete pointer to online documentation. 2001-07-11 13:58:12 +00:00
Johann Visagie
ff28a890c2 Update package's URL; my email address. 2001-07-11 13:33:34 +00:00
Bill Fenner
8df1bc22f6 Update Tony Maher's email address. 2001-07-10 16:35:08 +00:00
Maxim Sobolev
ec7b561464 ${PREFIX}/share/${PORTNAME} --> ${DATADIR} 2001-07-10 13:54:22 +00:00
Johann Visagie
bb7cb3d31e Update to version 1.00.a2 2001-07-09 09:57:51 +00:00
Ying-Chieh Liao
a39c693c25 Add NOPORTDOCS support to pkg-plist 2001-07-08 18:15:34 +00:00
Johann Visagie
3bd1feafc5 Update to version 1.3.0 
PR:		28761
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-06 09:22:22 +00:00
Johann Visagie
7ddb2910c6 - General clean-up of port. 
- Install PDF and HTML documentation.
- Take over maintainership.

Approved by:	Silence from previous maintainer; no objections from -ports
 2001-07-05 08:58:12 +00:00
Johann Visagie
b4e642da75 - Update to version 0.7.1 
- Add a build-time message to inform the user of available options.
 2001-07-04 13:22:13 +00:00
Johann Visagie
819158bfa4 - Add %%PORTDOCS%% support to pkg-plist. 
- $INSTALL_MAN -> $INSTALL_DATA in Makefile where appropriate.

PR:		28668
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-04 12:16:13 +00:00
Johann Visagie
f046432f9c Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny 
Software.

PR:		28541
Submitted by:	dbader@eece.unm.edu
 2001-07-04 08:39:40 +00:00
Johann Visagie
9d8379b1a4 Add %%PORTDOCS%% support to pkg-plist, and tweak Makefile slightly to support 
it.

PR:		28665
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-04 08:12:21 +00:00
Johann Visagie
cd3cb2536e Add %%PORTDOCS%% suppor to pkg-plist. 
Change $PREFIX to $MAN1PREFIX as appropriate in Makefile.

PR:		28664
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-03 14:53:14 +00:00
Johann Visagie
61dd23d81d Add support for %%PORTDOCS%%. 
PR:		28670
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-03 13:15:39 +00:00
Johann Visagie
6d6802e97f Replace erroneous usage of INSTALL_MAN with INSTALL_DATA. 
PR:		28666
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-03 09:08:26 +00:00
Johann Visagie
fcd2e1988c Update to version 3.04 
PR:		28614
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2001-07-03 08:17:14 +00:00
Johann Visagie
78e80cc06c Update to version 1.82 
PR:		28609
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2001-07-03 08:10:28 +00:00
Johann Visagie
7ff0eaebd1 Use $FILESDIR rather than hard-coded path. 2001-06-29 15:04:06 +00:00
Johann Visagie
afc010f63a Updating my email address in my remaining ports. 
Prompted by:	vanilla
 2001-06-27 10:15:01 +00:00
Johann Visagie
4ff56da9dd Embarrassingly long overdue update to 0.7.0, including optional support for 
GUI (Tk) and CORBA extensions.
 2001-06-26 15:09:39 +00:00
Johann Visagie
d8c2a7d247 Update to version 2001.04.03; add installation of some documentation. 
Approved by:	MAINTAINER
 2001-06-20 14:25:54 +00:00
Johann Visagie
23164d0987 Update to 1.00.a1; change MAINTAINER to my new address. 
Many changes to port, including addition of CORBA functionality.

PR:		27957
Submitted by:	Johann Visagie <johann@egenetics.com>
Reviewed by:	nbm
 2001-06-15 13:25:56 +00:00
Johann Visagie
4ff0dd1679 Update to 1.13.3; remove bogus file. 
PR:		28119
Reviewed by:	nbm
 2001-06-15 12:11:33 +00:00
Kevin Lo
2d42c48665 - Update to version 1.2.6a 
- Fix WWW: line

PR: 28038
Submitted by: Ports Fury
 2001-06-12 13:35:56 +00:00
Mark Pulford
b20964040b Distfile was moved and renamed. 
PR:		28004
Submitted by:	Jeff Palmer <scorpio@drkshdw.org>
 2001-06-11 05:53:41 +00:00
David E. O'Brien
90eb686abd Use proper POSIX syntax for `chown'. 2001-06-01 06:05:18 +00:00
Kevin Lo
a7cfeee1e2 Update to version 1.13.1 
PR: 27768
Submitted by: MAINTAINER
 2001-05-30 14:34:56 +00:00
Maxim Sobolev
f58180f9a2 math/numpy was renamed to math/py-numeric. 
PR:		27594
Submitted by:	Chang, Hye-Shik <perky@python.or.kr>
 2001-05-29 12:50:07 +00:00
Ying-Chieh Liao
fa38289059 upgrade to 4.3.2 
PR:		27273
Submitted by:	maintainer
 2001-05-27 13:49:54 +00:00
James E. Housley
cd9bb0cadd Update the EMBOSS suite (biology/emboss) to version 1.12.0 
PR:		27179
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER
 2001-05-07 12:18:57 +00:00
James E. Housley
ef5b919982 Updata biology/fasta3 to version 33.t08.d4 
PR:		27176
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER
 2001-05-07 12:16:33 +00:00
Jimmy Olgeni
3e92e3a55e Update distfile checksum (PORTREVISION bumped) 
also:

* Change maintainer's email address.
* Remove support for older FreeBSD versions.

PR:		26710
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
 2001-04-20 14:01:35 +00:00
FUJISHIMA Satsuki
fbe7fb6566 activate IGNOREFILES. 2001-04-13 18:50:23 +00:00
FUJISHIMA Satsuki
6f40800400 Ignore checksum. The distfile changes day by day. 2001-04-13 14:47:28 +00:00
Steve Price
07d222c8d7 This port require X libraries to build/run. 2001-04-11 03:51:34 +00:00
Will Andrews
dbba8af644 Overhaul QT/KDE support: 
- bsd.port.mk update to use bsd.kde.mk for USE_{QT,KDE}*
- Cleanup corresponding ports for bsd.kde.mk update.
- Fix bsd.kde.mk: use correct kdelibs dependency, put qt at the bottom,
  introduce QT_NONSTANDARD variable for nonstandard configure setup.
- Update KDE2 to 2.1.1.  Two patches included in x11/kdelibs2 to fix the
  proxy authentication that was broken for 2.1.1.  Remove old patches.
- Potentially fix kdelibs build for alpha.
- Fix qt-designer 2.3.0 build.
- Ruby stuff left alone since it looks like black magic to me.  Should
  still work w/ compat shims for older USE_QT[,2] style.  Some others
  were also left alone for the same reason.

Reviewed by:	portmgr, ports (bsd.kde.mk+bsd.port.mk)
Submitted by:	David Faure <faure@kde.org> (proxy auth patches)
		Alex Zepeda <garbanzo@kde.org> (old patches removal)
 2001-04-03 08:14:43 +00:00
Michael Haro
5fda8a9c36 update to 3.03 
PR:		26094
Submitted by:	    maintainer
 2001-04-02 05:16:26 +00:00
Michael Haro
8f55984793 updated port biology/phylip from vers 3.5 to 3.6 
PR:		26146
Submitted by:	    "David A. Bader" <dbader@eece.unm.edu>
 2001-04-02 05:10:15 +00:00
Kevin Lo
177bea6922 - Update MASTER_SITES and WWW: line 
- Support CC/CFLAGS properly
- Support install macros
- Add PORTDOCS to pkg-plist

PR: 26228
Submitted by: Ports Fury
 2001-03-31 15:51:15 +00:00
Maxim Sobolev
12df99274b Update to 33.t08.d3. 
Submitted by:	maintainer
 2001-03-22 09:04:47 +00:00
Kevin Lo
57b28bc623 - Upgrade to version 1.70 
- Update WWW

PR: 25772
Submitted by: maintainer
 2001-03-13 14:50:13 +00:00
Jun Kuriyama
f40cd4a088 Upgrade to 0.4. 
Submitted by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp> (maintainer)
PR:		ports/25741
 2001-03-13 02:03:47 +00:00
FUJISHIMA Satsuki
1dd0f3b3d8 o update to 2.7.2. 
o pass maintainership to ports@.

PR:		25685
Submitted by:	maintainer
 2001-03-12 19:16:15 +00:00
FUJISHIMA Satsuki
0977aef0a8 pass maintainership to ports@. 
PR:		25685
Submitted by:	maintainer
 2001-03-12 18:57:34 +00:00
Kevin Lo
124e7fc8d8 Update to lastest version 
PR: 25726
Submitted by: maintainer
 2001-03-12 14:31:53 +00:00
Neil Blakey-Milner
5ff72b2dc1 Update the EMBOSS suite to v1.11.0 
PR:		25728
Submitted by:	johann@egenetics.com
 2001-03-12 10:33:50 +00:00
Neil Blakey-Milner
b1fd16c68d - A small bugfix lead to a rerelease without a version number change. 
- Bumped PORTREVISION.

Submitted by:	Johann Visagie <johann@egenetics.com>
PR:		25725
 2001-03-12 10:24:38 +00:00
Trevor Johnson
4e48a033b1 Update to 0.85. 2001-03-12 08:35:23 +00:00
Trevor Johnson
0922168ea3 Force -O0 on the Alpha. 
Submitted by:	steve
 2001-03-12 08:33:42 +00:00
FUJISHIMA Satsuki
fb08a99b1a fix WWW: 
PR:		25625
Submitted by:	maintainer
 2001-03-09 12:14:23 +00:00
FUJISHIMA Satsuki
f87f524546 update to 33.t08.d2. 
PR:		25609
Submitted by:	maintainer
 2001-03-08 14:39:10 +00:00
Ying-Chieh Liao
4b72e379d4 gd.2, not gd.1 
Submitted by:	bento
 2001-03-05 07:39:05 +00:00
Peter Pentchev
b561cf1b15 Change MASTER_SITE and FTP/WWW lines: caos.kun.nl is cmbi.kun.nl now. 
PR:		25422
Submitted by:	Marc van Woerkom <marc.vanwoerkom@science-factory.com>
 2001-03-04 17:26:37 +00:00
Vanilla I. Shu
68c2f99c63 Remove do-configure section, use PERL_CONFIGURE now. 2001-03-01 06:39:18 +00:00
Kevin Lo
46974dd506 Update to version 1.10.1 
PR: 25449
Submitted by: maintainer
 2001-02-28 15:58:11 +00:00
Ying-Chieh Liao
384048cae5 reimport biology/genpak 2001-02-28 02:46:51 +00:00
Ying-Chieh Liao
d87d30e484 module name conflict with print/gp, so remove it and I'll reimport it again 2001-02-28 02:43:22 +00:00
Ying-Chieh Liao
ca27237a16 add gp 
GP is a set of small utilities to manipulate DNA sequences
 2001-02-27 17:22:29 +00:00
Kevin Lo
9b3eb6afbe Update to version 1.10.0 
PR: 25228
Submitted by: MAINTAINER
 2001-02-20 15:51:34 +00:00
Trevor Johnson
27973117c6 The author (at my request) has gone back to a more FreeBSD-friendly 
way of naming the distfile.  Change the port accordingly.
 2001-02-19 23:32:42 +00:00
Trevor Johnson
dd43b8b9db Update to 0.84. 2001-02-19 15:53:46 +00:00
James E. Housley
9ac7f698c2 Update to version 2001-02-06 
PR:		25200
Submitted by:	Johann Visagie <johann@egenetics.com>
 2001-02-19 12:32:57 +00:00
Akinori MUSHA
9e04885221 Chase graphics/gd's shlib version bump. 2001-02-12 10:01:08 +00:00
James E. Housley
a3686c5ead - New port: biology/fasta3, which comprises the FASTA3 suite of DNA and 
protein sequence search programs
- FASTA3 updates only some of the elements of FASTA2, which is why I have
  submitted ports of both versions (as biology/fasta and biology/fasta3)

PR:		24716
Submitted by:	Johann Visagie <johann@egenetics.com>
 2001-02-11 16:28:59 +00:00
James E. Housley
c82fc94311 New port: biology/fasta, the FASTA2 suite of DNA and protein sequence 
search tools

PR:		24715
Submitted by:	Johann Visagie <johann@egenetics.com>
 2001-02-11 16:24:18 +00:00
FUJISHIMA Satsuki
d705c4a51d add gaussian98, an ab-initio molecular orbital calculation program. 
PR:             23577
Submitted by:   NAKATA, Maho <chat95@mbox.kyoto-inet.or.jp>
 2001-02-10 19:38:20 +00:00
Trevor Johnson
1491cd5a99 Update to 0.84a. Generate the plist. 2001-02-08 19:57:19 +00:00
Kevin Lo
f34ef8cc9c - Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1 
- Update the EMBASSY package EMNU from 1.0.2 to 1.0.3
- Merged the four pkg-plist* files into one

PR: 24717
Submitted by: MAINTAINER
 2001-01-29 15:48:01 +00:00
Ying-Chieh Liao
5c6705c3ff update from 3.7 to 3.8 
PR:		24371
Submitted by:	MAINTAINER
 2001-01-24 17:58:44 +00:00