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
Kevin Lo
dba8433b08
Upgrade to version 1.9.0
...
PR: 24597
Submitted by: MAINTAINER
2001-01-24 11:36:37 +00:00
Maxim Sobolev
2b1a883dc4
Massive style enforcement - use ^I instead of spaces for variables identation.
2001-01-16 17:33:20 +00:00
Will Andrews
e40046b15d
Clean up inefficient perl invocations; use multiple REs in the same call.
2001-01-07 17:49:52 +00:00
Kevin Lo
3e1c5c9fe6
Update to 1.2.6
...
PR: 23756
Submitted by: Ports Fury
2000-12-22 16:19:26 +00:00
Dmitry Sivachenko
0aafce6a70
Remove trailing period and package name from the pkg-comment.
2000-12-18 20:32:55 +00:00
Steve Price
7314b99412
Update to version 5.79.
...
PR: 23345
Submitted by: Jeremy Shaffner <jeremy@external.org>
2000-12-11 03:10:04 +00:00
Peter Pentchev
bcd08c1529
Update distfiles' checksums after the distfiles have been rerolled yet
...
again without changing names or versions. Also add a new MASTER_SITE.
PR: 23262
Submitted by: Johann Visagie <johann@egenetics.com>
2000-12-04 13:00:07 +00:00
Peter Pentchev
37d9887c8d
Distfile tarballs were rerolled without notice due to a minor bug.
...
PR: 23193
Submitted by: Johann Visagie <johann@egenetics.com>
2000-11-30 20:13:30 +00:00
James E. Housley
c318e4acb5
- Update port biology/emboss from 1.7.0 to 1.8.0
...
PR: 23130
Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
2000-11-28 01:43:39 +00:00
James E. Housley
824b95bb92
Make nolonger support :U. Fix to compensate for that.
...
Submitted by: fenner
Approved by: MAINTAINER
2000-11-19 03:06:48 +00:00
James E. Housley
fcf874293c
They made changes to the "blast" program.
...
Submitted by: MAINTAINER
2000-11-15 00:54:09 +00:00
James E. Housley
d1b418e214
- This is a fairly extensive rework of this port.
...
- "EMBASSY" applications are third party tools which have been adapted to
function as part of EMBOSS, but which are not included with the base EMBOSS
distribution for licensing or other reasons. This new version of the
EMBOSS port now contains the three current EMBASSY applications as well,
and during installation the user is presented with a dialog(1) menu to
PR: 22818
Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
2000-11-13 13:49:46 +00:00
James E. Housley
7e4beec5d7
- This is a fairly extensive rework of this port.
...
- "EMBASSY" applications are third party tools which have been adapted to
function as part of EMBOSS, but which are not included with the base EMBOSS
distribution for licensing or other reasons. This new version of the
EMBOSS port now contains the three current EMBASSY applications as well,
and during installation the user is presented with a dialog(1) menu to
choose which of these should be isntalled.
PR: 22818
Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
2000-11-13 13:48:49 +00:00
Satoshi Asami
7112ba2b40
Change motif to a normal dependency. REQUIRES_MOTIF is now called
...
USE_MOTIF and generates a LIB_DEPENDS to x11-toolkits/open-motif. As
before, it implies USE_XPM (and therefore USE_XLIB). Motif-dummy is
removed from PKG_IGNORE_DEPENDS, whose sole resident is now XFree86-3.
Most of the simple ".if defined(HAVE_MOTIF)"s are removed to always
have USE_MOTIF. ftp/moxftp will define USE_MOTIF unless
WANT_ATHENA_VERSION (new variable) is defined. I merged the X cases
in cad/mars, so USE_MOTIF is used iff WITHOUT_X11 is not defined.
I will remove x11-toolkits/Motif-dummy (which has been repo copied to
open-motif) in a few days.
2000-11-07 23:28:20 +00:00