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Author SHA1 Message Date
Mark Linimon
e0cde90bd9 Reset dbader@ece.unm.edu due to timeouts and no response to email. 
Hat:		portmgr
 2006-12-13 13:20:20 +00:00
Mark Linimon
2db91e4f1f Reset whitekid@gmail.com after timeouts and no response to email. 
Hat:		portmgr
 2006-12-13 12:56:01 +00:00
Gabor Kovesdan
93e805e722 - Update to 2.1.3 
- Fix fetching
- Remove old patch and use MAKE_ARGS instead
- portlint(1) and whitespace

Approved by:	erwin (mentor)
 2006-12-10 12:39:32 +00:00
Gabor Kovesdan
ac97872da3 - Deprecate 
- Set EXPIRATION_DATE

Approved by:	erwin (mentor)
 2006-12-10 12:37:38 +00:00
Dirk Meyer
cb4e8b9a8e - Local/Tools/Resources now global 2006-12-09 09:40:38 +00:00
Rong-En Fan
c1e393d3a9 - Respect X11BASE 
Approved by:	portmgr (linimon)
 2006-12-09 07:49:55 +00:00
Frank J. Laszlo
4ffcd931fe - Update to 0.14 
Submitted by:	Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw>
Approved by:	maintainer timeout (3 months)
 2006-12-07 15:43:27 +00:00
Rong-En Fan
146e6417d0 - Mark broken on amd64 < 6. We got following 
cc -O -pipe  -fPIC  -g -Wall -DACEDB4  -I. -I./wh -DFREEBSD -c -O -pipe  -fPIC  -g -Wall -DACEDB4 -c arraysub.c
arraysub.c: In function `stackused':
arraysub.c:54: error: unrecognizable insn:
(insn 44 22 24 2 arraysub.c:53 (set (reg:SI 1 dx [66])
        (subreg:SI (plus:DI (subreg:DI (reg:SI 7 sp) 0)
	                (const_int -1 [0xffffffffffffffff])) 0)) -1 (nil)
			    (nil))
arraysub.c:54: internal compiler error: in extract_insn, at recog.c:2083

Reported by:	pointyhat via kris
Approved by:	Philip M. Gollucci (maintainer)
 2006-12-04 04:13:30 +00:00
Dmitry Sivachenko
274e5c4ab3 Correct path to Compress::Zlib.pm after recent p5-Compress-Zlib update. 2006-12-03 12:45:59 +00:00
Rong-En Fan
365cb9a6e2 - Respect X11BASE 
Approved by:	maintainer (implicit)
 2006-12-02 20:34:11 +00:00
Pav Lucistnik
d750615763 - Use features of bsd.wx.mk, especially USE_WX 
PR:		ports/101613
Submitted by:	alepulver
 2006-12-01 07:39:02 +00:00
Martin Wilke
bdfb7058a1 - Respect X11BASE 
PR:		ports/105891
Submitted by:	trasz
 2006-11-27 22:03:22 +00:00
Rong-En Fan
47d8f620ab - Update to 1.91 
- Unbreak on amd64

PR:		ports/105414
Submitted by:	rafan
Approved by:	maintainer timeout (15 days)
 2006-11-27 02:35:16 +00:00
Thierry Thomas
dd746cb883 - Upgrade to the latest beta and unbreak; 
- Add a regression-test target;

- Fix plist for WITHOUT_SAMPLES.

PR:		ports/104685
Approved by:	maintainer's time-out (1 month)
 2006-11-21 22:35:28 +00:00
Dirk Meyer
1efa3fa64a - cleanup patches 2006-11-12 16:59:53 +00:00
Dirk Meyer
b8fd717fad - fix build on non i386 archs 
Submitted by:	Gürkan Sengün
 2006-11-10 14:51:56 +00:00
Dirk Meyer
1d8ba7db66 Adun is a new extendible molecular simulation program that also 
includes data management and analysis capabilities.

WWW: http://diana.imim.es/Adun
Submitted by:	Gürkan Sengün
Reviewed by:	dinoex
 2006-11-09 20:16:54 +00:00
Martin Wilke
58c1e960b2 - Update to 1.42 
PR:		ports/104635
Submitted by:	Thomas Abthorpe <thomas@goodking.ca>
Approved by:	maintainer
 2006-10-31 13:25:21 +00:00
Martin Wilke
37c6f45ce2 - Update to 34.t26.b3 
PR:		ports/104508
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-10-31 09:02:04 +00:00
Sam Lawrance
1969eb5f6b Distfile now checksums successfully. 
PR:		ports/104341
Submitted by:	Frank J. Laszlo <laszlof@vonostingroup.com>
Approved by:	portmgr (marcus)
 2006-10-14 16:13:49 +00:00
Joe Marcus Clarke
29747f458a Chase the GNOME X11BASE to LOCALBASE move, and fix the build with the 
new freetype2 where needed.

Submitted by:	mezz, ahze, pav, and many others
Approved by:	portmgr (implicit, kris)
 2006-10-14 08:54:54 +00:00
Pav Lucistnik
deff0d8ddd - Add hmmer 5.09 application 2006-10-10 11:31:42 +00:00
Alex Dupre
8e8d970bfa Chase pdf library and bump PORTREVISION. 2006-10-09 08:18:35 +00:00
Pav Lucistnik
bf619e630a - Allow wxWidgets 2.6 alongside 2.4, this port works with both 
PR:		ports/102168
Approved by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-10-09 07:16:37 +00:00
Cheng-Lung Sung
81bb3a52c4 - Update to 0.98d 
PR:		ports/103408
Submitted by:	chinsan
Approved by:	maintainer (timeout)
 2006-10-06 04:12:59 +00:00
Cheng-Lung Sung
3e9ed050ec Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA 
and EST Sequences.

PR:		ports/103651
Submitted by:	Bob Zimmermann <rpz at cse.wustl.edu>
 2006-09-29 04:05:55 +00:00
Thierry Thomas
41a8cea837 Unbreak: molden has been updated on Aug 17, with the same DISTNAME. 
Changelog at <http://www.cmbi.ru.nl/molden/HISTORY>.
 2006-09-17 13:41:56 +00:00
Maho Nakata
1a1223bfca Fix build on amd64 
Submitted by:	kris
 2006-09-17 11:51:56 +00:00
Kris Kennaway
64e99d9063 BROKEN on amd64 and ia64: Does not build 2006-09-17 01:32:58 +00:00
Kris Kennaway
2248301e36 BROKEN: Size mismatch. Since this is unmaintained, deprecate and schedule 
for termination on 2006-12-01
 2006-09-04 14:50:49 +00:00
Kris Kennaway
fa2fe3f774 NO_CDROM and NO_PACKAGE are not appropriate here 2006-09-03 00:34:47 +00:00
Kris Kennaway
15b247f443 Schedule these broken ports for termination on 2006-12-01 2006-09-02 16:51:10 +00:00
Pav Lucistnik
940da0dc4a Folding@Home is a distributed computing project -- people from through out the 
world download and run software to band together to make one of the largest
supercomputers in the world. Every computer makes the project closer to our
goals.
Folding@Home uses novel computational methods coupled to distributed computing,
to simulate problems thousands to millions of times more challenging than
previously achieved.

WWW: http://folding.standford.edu

PR:		ports/101235
Submitted by:	Yonatan <onatan@gmail.com>
 2006-08-28 22:33:45 +00:00
Cheng-Lung Sung
ab63f5bd0b - s,INSTALLS_SHLIB,USE_LDCONFIG,g 
- these include astro/ audio/ biology/ chinese/ maintained by ports@

PR:		ports/101916
Submitted by:	Gea-Suan Lin <gslin_AT_gslin dot org>
 2006-08-14 10:08:25 +00:00
Edwin Groothuis
0171dc55b4 Mark as broken for i386 4.x 
PR:		ports/101789
Submitted by:	Scott Flatman <sf@slappy.org>
 2006-08-10 23:02:49 +00:00
Erwin Lansing
ef6efc6dc9 Unmark BROKEN, it seems to be caused by a stale distfile on ftp-master. 2006-08-03 20:28:00 +00:00
Erwin Lansing
c5893d00f4 Mark BROKEN: checksum mismatch 2006-08-03 19:06:04 +00:00
Erwin Lansing
3bae54439d Mark broken due to checksum mismatch 2006-08-03 18:59:01 +00:00
Pav Lucistnik
61fa65e53c - Update to 5.10 2006-07-17 21:44:52 +00:00
Rong-En Fan
9e6a69437a - Fix pkg-plist [1] 
- pet portlint(1)

Noticed by:	pointyhat via linimon [1]
 2006-07-10 05:32:58 +00:00
Rong-En Fan
901b9f75cb - Update to 2.4.3 
- Pass maintainersip to submitter

PR:		99901
Submitted by:	Scott Flatman <sf slappy.org>
Approved by:	delphij (mentor, implicit)
 2006-07-08 03:36:36 +00:00
Rong-En Fan
4f1966845c - Use the correct MASTER_SITE_SUBDIR, make it fetchable 
PR:		99757
Submitted by:	Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw>
Approved by:	delphij (mentor, implicit)
 2006-07-04 03:43:16 +00:00
Mark Linimon
ba8be9a92f Mark as BROKEN on sparc64 due to internal compiler error. 2006-07-03 22:22:09 +00:00
Maho Nakata
cccc84b713 Update to 1.10 (maintained by others) and unbreak. 2006-07-03 04:41:35 +00:00
Maho Nakata
8db209b977 o Update to 0.99rc1 
o add data dir to have working port[1]

PR:		95121[1]
Submitted by:	Sangwoo Shim <sangwoos at gmail.com>[1]

This commit is a result of hacks at the CodeFest Akihabara 2006 hosted by FSIJ.
 2006-07-01 05:06:21 +00:00
Pav Lucistnik
eb9164cdb6 - Provide SSE optimized application as an option 2006-06-24 21:04:45 +00:00
Pav Lucistnik
ac3d6b8aa7 - Instruct amd64 users to libmap libpthread.so.2 to libc_r.so.6 2006-06-22 18:53:30 +00:00
Pav Lucistnik
15299a017f SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculated 
protein similarities that plays a key role in many bioinformatics methods. It
contains about all currently published protein sequences and is continuously
updated.

The computational effort for keeping SIMAP up-to-date is constantly increasing.
Please help to update SIMAP by calculating protein similarities on your
computer.

WWW: http://boinc.bio.wzw.tum.de/boincsimap/
 2006-06-19 20:32:08 +00:00
Thierry Thomas
57359d2a70 Re-add CONFIGURE_TARGET and fix libm detection. 
PR:		ports/99072 (fu2)
Submitted by:	Josh Tolbert <hemi (at) puresimplicity.net> (maintainer)
 2006-06-18 20:35:18 +00:00
Thierry Thomas
78ba726349 - Upgrade to to 1.9.9 and unbreak; 
- Take maintainership.

PR:		ports/99072
Submitted by:	Josh Tolbert <hemi (at) puresimplicity.net>
 2006-06-17 22:07:36 +00:00
Erwin Lansing
0ca34eb9ed USE_SIZE was obsoleted in rev. 1.484 of bsd.port.mk more than 
2 years ago. Clean out the last traces of it.

With hat:	portmgr
 2006-06-11 15:29:01 +00:00
Pav Lucistnik
e6e4d55131 - Update PORTREVISION to match latest release (see main web site) 
- Update the port to add other architectures (amd64)

PR:		ports/98764
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-06-11 09:13:43 +00:00
Pav Lucistnik
3181cf2cce - Update to 34.t25.d9 
PR:		ports/98761
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-06-09 19:18:08 +00:00
Ion-Mihai Tetcu
9da018b5cc Update biology/ncbi-toolkit to the latest release. 
Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
Major changes include:
 blastall now uses the new engine by default, resulting
 in significant performance improvements and enabling
 query concatenation for all program types.

PR:		ports/98570
Submitted by:	maintainer
Approved by:	lawrance (mentor, implict)
 2006-06-06 12:05:19 +00:00
Erwin Lansing
f85047fc66 - Add MASTER_SITE 
- Use DATADIR

PR:		97603
Submitted by:	miwi
Approved by:	maintainer timeout
 2006-06-06 10:07:55 +00:00
Erwin Lansing
f0dcdd522f - Update to 34.t25.d8 [1] 
- While I'm here, pet portlint [2]

PR:		98398 [1]
Submitted by:	miwi [1], self [2]
Approved by:	maintainer [1]
 2006-06-05 21:18:23 +00:00
Sergey Matveychuk
45d46bd0a5 - update to 34.t25.d7 
- add MASTER_SITE_LOCAL as a second master site

PR:		ports/97310
Submitted by:	maintainer
 2006-05-24 16:55:46 +00:00
Kris Kennaway
b8bfb594a1 BROKEN: Unfetchable 2006-05-21 21:40:02 +00:00
Sergey Matveychuk
2e790c2143 - Update to 3.15 
PR:		ports/96941
Submitted by:	Paul Schmehl <pauls@utdallas.edu>
Approved by:	maintainer timeout
 2006-05-20 18:52:19 +00:00
Aaron Dalton
e25d96e450 - Updated from 0.07 to 0.12 
Approved by:	tobez (implicit)

0.08 20/Feb/2006 15:14
                       Improved referential integrity between nodes,
                                taxa, and data.
                       Implemented Fastnexus parser
                       Node object silently implements Bio::Tree::NodeI
                       		interface if BioPerl is installed
                       Tree object silently implements Bio::Tree::TreeI
                       		interface if BioPerl is installed
                       Added convertor methods for XML and CIPRES
                       Implemented more Matrix methods
                       Implemented symbol tables in Bio::Phylo::Util::CONSTANT
                       Implemented visit method for listable objects
                       Implemented caching infrastructure for calculations
                       Changed object-model to inside-out arrays
                       Added Biodiversity measures code by Aki Mimoto
                       Moved constants and exceptions to Bio::Phylo::Util::*
                       Fixed memory leak due to circular references
 2006-05-19 23:18:32 +00:00
Aaron Dalton
29ad3c789c Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl. 
Approved by:	tobez (implicit)
 2006-05-13 16:48:15 +00:00
Sergey Matveychuk
edab74313c - Update to 34.t25.d6 
PR:		ports/96063
Submitted by:	maintainer
 2006-05-07 16:52:33 +00:00
Sam Lawrance
649566ad8c Update to 21.u1.d1 (fixes fetch). 
Reported by:	fenner's distfile survey
 2006-05-07 13:04:20 +00:00
Sergey Matveychuk
36778a1acd - Satisfy portlint 2006-05-06 21:20:59 +00:00
Emanuel Haupt
dfc2535ebe Add protomol 2.0.3, OO, component based, framework for molecular 
dynamics (MD) simulations.

PR:		95123
Submitted by:	Sangwoo Shim <sangwoos@gmail.com>
 2006-05-05 20:09:54 +00:00
Edwin Groothuis
72ad491a93 Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
Yen-Ming Lee
fb9e59f589 - Update to 1.89 
- refine BROKEN to make portlint happier
- patch to use on Scalar::Util instead of WeakRef
- mark IGNORE under old perl which don't support weak reference

PR:		96656
Submitted by:	leeym
Approved by:	maintainer
 2006-05-02 23:16:02 +00:00
Renato Botelho
8aaa665368 Bioperl-run contain modules that provides a PERL interface to various 
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.

WWW: http://bioperl.org/

PR:		ports/93675
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
 2006-05-02 21:31:43 +00:00
Renato Botelho
5d19d83aa6 Bioperl-run contain modules that provides a PERL interface to various 
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.

WWW: http://bioperl.org/

PR:		ports/93674
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
 2006-05-02 21:30:08 +00:00
Pav Lucistnik
dc8e5f28fa - Update to 1.0.0 
- Provide OPTIONS
- Take maintainership

PR:		ports/94123
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
 2006-04-25 22:09:29 +00:00
Kris Kennaway
87b2bd6cb6 BROKEN: Does not compile 2006-04-22 22:10:17 +00:00
Mark Linimon
54a45e213c Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking about 
maintainer timeouts.

Hat:	portmgr
 2006-04-05 06:13:46 +00:00
Mark Linimon
756130dd96 Reset jeremy@external.org who has not responded to email asking about 
maintainer timeouts.

Hat:	portmgr
 2006-04-05 05:46:33 +00:00
Marcus Alves Grando
843d1a4279 - Update to 2006.02.13 
PR:		95281
Submitted by:	maintainer
 2006-04-05 01:58:03 +00:00
Edwin Groothuis
c88ecfb4d6 Use SUB_FILES for pkg-message 2006-04-01 12:34:24 +00:00
Thierry Thomas
10570c91c8 For EMBOSS: 
This patch brings EMBOSS up to date with the current version.

	i.   The patches included in files/ are bugfixes for files in
	     EMBOSS-3.0.0 that appeared after the release. They are
   	     documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README

	     This is just 'for the record' so that we remember to remove these
	     patches in the next update.

	ii.  EMBOSS is now installed by default in LOCALBASE/emboss
	     This is to avoid CONFLICTS with other ports that install files
	     with the same names. Installing EMBOSS to another PREFIX is also
	     possible.

	iii. now EMBASSY and EMBOSS both store their distfiles in the same
	     DIST_SUBDIR

	iv.  use built-in PKGMESSAGE and SUB_FILES instead of doing it the old
	     (manual) way

	For EMBASSY:

	This update brings embassy in sync with the update of EMBOSS to 3.0.0.

	Things that changed from previous version of the port:

	i.  embassy now installs by default in $LOCALBASE/emboss (the
	    new default PREFIX for emboss as well).

	ii. changed DIST_SUBDIR so that all the distfiles are put together with
	    emboss. This makes sense(TM)

	iii. incorporated new EMBASSY apps (this accounts for the changes in
	     OPTIONS and pkg-plist)

	iv.  removed obsoleted patches

	Finally, I included a sample text that could go in UPDATING.

PR:		93053
Submitted by:	Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
 2006-03-31 09:43:21 +00:00
Pav Lucistnik
763955a476 - Update to 34.t25.d5 
PR:		ports/94741
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-03-20 22:23:24 +00:00
Renato Botelho
c1c9dc017a - Update to 5.743 
- Add a MASTER_SITE backup since oficial one just have last version and make
  it fetchable again

Submitted by:	maintainer by email
Reported by:	krismail
 2006-03-19 12:59:16 +00:00
Renato Botelho
35642ebc86 Add lagan 1.2, efficient tools for large-scale multiple alignments of 
genomic DNA.

PR:		ports/93058
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-03-16 22:31:26 +00:00
Renato Botelho
81ba48cd37 Add mafft 5.734, multiple sequence alignments based on fast Fourier 
transform.

PR:		ports/93059
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-03-15 10:41:16 +00:00
Renato Botelho
1b3445b684 Add dotter 20021204 # last modified date in FTP server, a viewer for 
multiple sequence alignments.

PR:		ports/93055
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-03-15 10:35:24 +00:00
Renato Botelho
0694735737 Add blat 33, a fast tool for local sequence similarity searches. 
PR:		ports/93060
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-03-15 10:26:12 +00:00
Renato Botelho
bfe1c1f260 Add belvu 2.29, a viewer for multiple sequence alignments. 
PR:		ports/93056
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-03-15 10:24:57 +00:00
Maho Nakata
a8bac6a90f Update to 1.5 
Submitted by:	distfile survey by kris, fenner
 2006-03-15 08:10:49 +00:00
Ade Lovett
fe279f0df8 Bump PORTREVISION on glib12/gtk12 consumer ports to ease the upgrade path. 
Discussed with:	kris
Approved by:	portmgr (implicit)
 2006-03-07 08:28:06 +00:00
Ade Lovett
8503536d38 Conversion to a single libtool environment. 
Approved by:	portmgr (kris)
 2006-02-23 10:40:44 +00:00
Kris Kennaway
65fe00966b BROKEN: Configure fails 2006-02-20 01:46:03 +00:00
Herve Quiroz
cf01181180 Jalview is a multiple alignment editor written in Java. It is used widely in a 
variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain
database) and is also available as a general purpose alignment editor.

WWW: http://www.jalview.org

PR:		93054
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
 2006-02-13 09:42:13 +00:00
Alexander Leidinger
d16f7bfb92 Reset maintainership to ports@ after ~4 months without any response to any 
PR.

Thanks for contributing.

Since the acroread7 port is a somewhat important port for our users, I
will hand it over to emulation@ if no _active_ *committer* takes it
before the ports freeze.

While I'm here:
 - fix a little nit in the csound port (I think the intention was to
   create no backup file instead of creating one with a "-e" extension)
 - set ARCH to i386 in the amd64 case for the acroread7 port. This
   is a work-around to be able to install everything when a dependency
   is not already installed (ARCH is read-only in sub-makes, so the
   dependencies can't change it). This should be removed when the
   dependencies are fixed or converted to use bsd.linux-rpm.mk. [1]

Not objected to by:	portmgr (explicit: krion; silence: rest)
Maintainer timeout:	~4 months
Submitted by:		Sangwoo Shim <sangwoos@gmail.com> [1]
PR:			87985 [1]
 2006-02-11 21:03:14 +00:00
Sam Lawrance
0e94382809 Update to 3.27. 
Use GCC 3.3 on systems with 3.4, due to an internal compiler error.

PR:		ports/93050
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-02-10 09:45:28 +00:00
Sam Lawrance
f4cdc25a87 Update to 34.t25.d4. 
PR:		ports/93052
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-02-10 09:37:02 +00:00
Sam Lawrance
fed5ed01f9 Update to 2006.01.25. 
PR:		ports/93051
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-02-09 10:33:47 +00:00
Sam Lawrance
c70bfb8977 Put PORTEPOCH back. 
Reported by:	chkversion
 2006-02-09 01:17:59 +00:00
Sam Lawrance
c6f127a070 Update to 3.65. 
PR:		ports/92182
Submitted by:	"Choe, Cheng-Dae" <whitekid@gmail.com>
Approved by:	dbader@ece.unm.edu (maintainer, timeout 14 days)
 2006-02-08 14:45:45 +00:00
Joe Marcus Clarke
92cc33210c Remove CONFLICTS with nss. 2006-02-02 23:12:05 +00:00
Kris Kennaway
cbb7ba562c Add missing USE_ICONV 2006-01-26 04:11:16 +00:00
Edwin Groothuis
44855e0b04 SHA256ify (manually done and checked) 
Approved by:    krion@
 2006-01-22 09:54:26 +00:00
Edwin Groothuis
acd87b4ad8 SHA256ify 
Approved by:    krion@
 2006-01-22 08:34:46 +00:00
Edwin Groothuis
913a5a5cba Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry 
Approved by:    krion@
PR:             ports/88711 (related)
 2006-01-22 01:29:46 +00:00
Edwin Groothuis
e8d3c8300f Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry 2006-01-22 00:17:42 +00:00
Alexey Dokuchaev
cbb224e9a3 Utilize EXAMPLESDIR. 2006-01-20 09:56:18 +00:00
Alexey Dokuchaev
a6dbbc0318 - Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoid 
unnecessary PORTEPOCH bump)
- Update MASTER_SITES and WWW line, provide backup download site
- Come up with better port description
- Reset maintainer to ports@
- Uphold CXX and CXXFLAGS
- Clean up Makefile slightly
- Don't install yet another copy of GPL and texts in French
- Add SHA256 hash to distinfo
 2006-01-19 19:47:59 +00:00
Pav Lucistnik
7dc0abbf54 - Remove expired ports 2006-01-14 21:16:35 +00:00
Pav Lucistnik
52e61d2411 - Update to 2.0.20060101 
PR:		ports/91715
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-01-14 19:36:19 +00:00
Pav Lucistnik
5825fa4ce6 - Update to 2005.12.06 
PR:		ports/91714
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2006-01-14 19:34:43 +00:00
Pav Lucistnik
366702a54e - Chase openbabel update 2006-01-14 12:43:12 +00:00
Kris Kennaway
314f18d79c BROKEN: Broken dependency 2006-01-14 09:38:11 +00:00
Sergey Matveychuk
b4d2ac42d7 - Update graphics/libglut to 6.4.1. 
- Shared lib version and PORTREVISION bumb for all affected ports.

While I'm here:
- Remove USE_MESA knob where it was (35 ports).
  It marked as depricated for 2 years.

PR:		ports/90247
Submitted by:	Ermal Lu?i <eri--@albabsd.org>
 2006-01-12 12:54:32 +00:00
Edwin Groothuis
8a256d14e0 Fix maintainer address 
From: Tony Maher <anthony.maher@uts.edu.au>
    To: Edwin Groothuis <edwin@FreeBSD.org>
    Subject: Re: ports/91537: maths/xgobi - download site moved/maintainer addressupdate

    Actually I need  modify all my ports to use OptusNet rather than
    Biolateral.  Is there an easy way to do this or should I submit a
    separate 1-line patch and PR for each port?

    biology/crimap
    biology/dna-qc
    biology/flip
    biology/primer3
    biology/seqio
    biology/wise
    math/xgobi
    net/generic-nqs

Submitted by:	Tony Maher <anthony.maher@uts.edu.au>
 2006-01-09 03:25:03 +00:00
Trevor Johnson
f449b89dca Hash with SHA-256. 2006-01-07 20:00:08 +00:00
Pav Lucistnik
3527239417 - Remove symlinks that belong to mtree 
Approved by:	maintainers
 2006-01-05 22:31:12 +00:00
Edwin Groothuis
4e74668975 possible fix to unbreak biology/L-Breeder 
L-Breeder is currently marked unfetchable:
	http://people.freebsd.org/~fenner/portsurvey/biology.html#L-Breeder

	So I tried to investigate the problem and I'm now submitting
	my homework so it doesn't get lost.

	This is what I noticed:

	i) L-Breeder upstream sources have "stagnated for some time,
	but now a new simplified version is available" (sic, from
	the web site)

	So, the fetch issue is resolved. And the pkg-descr is also
	updated to reflect the new home page. However:

	ii) L-Breeder is now called LBreeder. I have changed PORTNAME
	to reflect this, although I don't know if this is the right
	thing to do. Should the port be moved to biology/LBreeder?
	Or perhaps just leaving PORTNAME pointing to the old name
	and then work inside the Makefile to point the build/install
	to the correct name?

	iii) the sources have been reorganized so I have to update
	the port's Makefile to reflect this. The attached patch
	works for me under FreeBSD-4.11 (although it's possible
	that I may have missed a dependency if I already have a
	required library installed in my box. Sorry, I don't have
	a tinderbox-like setup to test builds)

	iv) the program does not have a version number, nor did I
	find one by looking inside the sources. To avoid changing
	too much the port I just left PORTVERSION at 1.0 and bumped
	PORTREVISION to 6

	Finally, do note that I am not a user of LBreeder, so I
	cannot test the program myself. I just noticed that by
	calling the executable I get a black X screen, that I can
	quit by pressing 'q' as documented in Readme.txt, but I
	can't tell myself if this is the expected behaviour. Nor
	do I know how to use the example files. Caveat emptor.

PR:		ports/90073
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:	maintainer timeout
 2006-01-02 21:29:30 +00:00
Tim Bishop
b9073575f7 - New upstream version; two patches incorporated. 
PR:		90140
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:	clement (mentor)
 2005-12-10 14:04:33 +00:00
Emanuel Haupt
f9f998fd02 Update to 1.3.1 
PR:		90029
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2005-12-06 21:23:04 +00:00
Tim Bishop
ef117d6358 - Update to 2005.13.07 to make fetchable again 
PR:		89976
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:	clement (mentor)
 2005-12-06 15:13:17 +00:00
Tim Bishop
f5b55cca3b - Update to 3.18 to make fetchable again 
- Mark broken on 6.x upwards

PR:		89977
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:	clement (mentor)
 2005-12-06 15:10:08 +00:00
Marcus Alves Grando
690b4fde8e Update to 0.5.1 
Unbroken >= 502126
Add SHA256

PR:		89980
Submitted by:	maintainer
 2005-12-06 02:00:55 +00:00
Tim Bishop
ce480365f5 - Fix fetch problems 
PR:		89971
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:	clement (mentor)
 2005-12-05 16:57:26 +00:00
Edwin Groothuis
b6d6a6eb9e Add conflicts: 
CONFLICTS= p5-bioperl-1.[02468]*

Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>, Mauricio Herrera Cuadra <arareko@yahoo.com>
 2005-12-04 22:12:48 +00:00
Edwin Groothuis
9c69af1094 Add conflicst: 
CONFLICTS=     p5-bioperl-1.[13579]*

Submitted by:	Mauricio Herrera Cuadra <arareko@yahoo.com>,Fernan Aguero <fernan@iib.unsam.edu.ar>
 2005-12-04 22:11:44 +00:00
Edwin Groothuis
ede129019c Fix port: biology/p5-bioperl-devel 
This patch adds a LATEST_LINK line in the Makefile to avoid
      duplication with the 'p5-bioperl' port in the packages/Latest
      directory.

PR:		ports/89916
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
 2005-12-04 06:24:05 +00:00
Simon Barner
083e22eece - Re-add p5-bioperl-devel, development version of biology/p5-bioperl 
(A collection of Perl modules for bioinformatics)

PR:		ports/89497
Submitted by:	Mauricio Herrera Cuadra <arareko@yahoo.com>
 2005-12-02 21:40:12 +00:00
Simon Barner
01d9e8ebe5 - Unbreak by updating to 4.4 
- Add dependecy to MESA

PR:		ports/89795
Submitted by:	Johan van Selst <johans@stack.nl>
 2005-12-01 14:42:44 +00:00
Bill Fenner
ac94c20eb3 Add the right MASTER_SITE_SUBDIR, so that this port is fetchable from 
20 sites instead of just 1.
 2005-11-26 03:40:59 +00:00
Pav Lucistnik
4e4ebe662e - Add SHA256 2005-11-24 00:04:00 +00:00
Pav Lucistnik
75d9276aa1 - Drop old povchem.c checksum 
- Add SHA256, SIZE
 2005-11-24 00:02:29 +00:00
Pav Lucistnik
bc1673d0ae - BROKEN: Size mismatch 2005-11-23 23:59:57 +00:00
Kris Kennaway
8295c21a0e BROKEN: Size mismatch 2005-11-16 04:37:44 +00:00
Ade Lovett
54a0b86543 Mass-conversion to the USE_AUTOTOOLS New World Order. The code present 
in bsd.autotools.mk essentially makes this a no-op given that all the
old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in
exactly the same way as USE_AUTOTOOLS itself.

Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME
team -- all GNOME 2.12.x ports use it.

Preliminary documentation can be found at:
	http://people.FreeBSD.org/~ade/autotools.txt

which is in the process of being SGMLized before introduction into the
Porters Handbook.

Light blue touch-paper.  Run.
 2005-11-15 06:52:12 +00:00
Renato Botelho
a9178a7bf6 - Mark it as DEPRECATED - master site disapeared 
- Set EXPIRATION_DATE

PR:		ports/88003
Submitted by:	Jean Milanez Melo <jmelo@freebsdbrasil.com.br>
Approved by:	maintainer timeout (17 days)
 2005-11-11 14:40:32 +00:00
Renato Botelho
67c234358e - Mark it as DEPRECATED - master site disapeared 
- Set EXPIRATION_DATE

PR:		ports/88002
Submitted by:	Jean Milanez Melo <jmelo@freebsdbrasil.com.br>
Approved by:	maintainer timeout (17 days)
 2005-11-11 14:40:25 +00:00
Renato Botelho
8669a508d3 - Mark it as DEPRECATED (mastersite disapeared) 
- Set EXPIRATION_DATE

PR:		ports/88000
Submitted by:	Jean Milanez Melo <jmelo@freebsdbrasil.com.br>
Approved by:	maintainer timeout (16 days)
 2005-11-11 14:29:09 +00:00
Mark Linimon
34da9bdf57 With portmgr hat on, reset maintainership of knu's ports since he has 
been inactive more than 6 months.  We hope to see him back sometime.
 2005-11-11 01:18:01 +00:00
Marcus Alves Grando
23d07b2cdb Update to 1.41 
Take MAINTAINER
Add SHA256

PR:		88792
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
 2005-11-11 01:15:35 +00:00
Marcus Alves Grando
12417fc462 Update to 3.14b 
Update MASTER_SITES
Add SHA256
Remove extra TABS

PR:		88007
Submitted by:	Jean Milanez Melo <jmelo@freebsdbrasil.com.br>
Approved by:	maintainer timeout, 14 days
 2005-11-10 01:21:42 +00:00
Kris Kennaway
b1cf59535c Remove expired ports 2005-11-05 09:07:44 +00:00
Joe Marcus Clarke
235c907ae5 Bump PORTREVISION to chase the glib20 shared library update. 2005-11-05 05:22:06 +00:00
Sam Lawrance
94cbb85aef Mark DEPRECATED since upstream is unmaintained and mastersite is gone. 
PR:		ports/88004
Submitted by:	Jean Milanez Melo <jmelo@freebsdbrasil.com.br>
Approved by:	Tony Maher <anthony.maher@uts.edu.au> (maintainer)
 2005-10-29 14:09:33 +00:00
Kris Kennaway
585033d00e BROKEN: Unfetchable 2005-10-28 06:38:35 +00:00
Emanuel Haupt
2cb934bb50 Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser for 
NCBI Entrez Gene.

PR:		87423
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
Approved by:	novel (mentor) (implicit)
 2005-10-15 20:09:50 +00:00
Sergey Matveychuk
6c2583cf18 - Update to 20050605 
PR:		ports/87266
Submitted by:	maintainer
 2005-10-11 22:33:34 +00:00
Sergey Matveychuk
53f6cba83b - Update to 3.13. It fixes fetching. 
PR:		ports/87264
Submitted by:	maintainer
 2005-10-11 20:44:38 +00:00
Maho Nakata
9f13557fd3 Update to 0.9.8 2005-10-10 09:08:22 +00:00
Trevor Johnson
2ca0f2bd92 Checking MACHINE_ARCH is deprecated. 2005-09-23 16:21:45 +00:00
Herve Quiroz
ab8ee8cdcc Update to version 7 
PR:		86196
Submitted by:	Tony Maher <anthony.maher@uts.edu.au>
Approved by:	maintainer
 2005-09-20 14:59:28 +00:00
Volker Stolz
a15a746cf2 Don't strip static libraries on installation ;) 
(Unbreaks e.g. biology/nclever)
 2005-09-14 09:24:04 +00:00
Renato Botelho
4eafa9b940 Add p5-Bio-Das 1.02, client-side library for Distributed Genome 
Annotation System.

PR:		ports/76379
Submitted by:	Razi Khaja <razi@genet.sickkids.on.ca>
 2005-09-01 13:09:32 +00:00
Kris Kennaway
0d8f47d8f7 This port is scheduled for deletion on 2005-09-22 if it is still broken 
at that time and no PRs have been submitted to fix it.
 2005-07-23 02:53:43 +00:00
Patrick Li
9480dee06a - Update to 1.0.0 
- Make DATADIR/EXAMPLESDIR/DOCSDIR safe
- Don't hardcode ${CPIO}

PR:		ports/82154
Submitted by:	George Hartzell <hartzell@alerce.com>
Approved by:	maintainer
 2005-06-13 04:31:34 +00:00
Oliver Lehmann
fbecb83eab change the libtool version to use from 1.3 to 1.5 2005-05-31 16:41:49 +00:00
Pav Lucistnik
68c58ff3ec - Update to 2.10.0 
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2005-05-29 18:26:25 +00:00
Pav Lucistnik
947a8e30b5 - Update to 2.10.0 
PR:		ports/81579
Submitted by:	"Choe, Cheng-Dae" <whitekid@gmail.com>
Approved by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2005-05-29 18:26:05 +00:00
Max Khon
d164e5eed2 Finish repo copy of wxgtk 2.4.2 ports to wxgtk24* 2005-05-12 16:39:59 +00:00
Jean-Yves Lefort
9f491ad439 - Fix the packing list [1] 
- Add a run dependency on ucpp
- Correct the NABHOME used in pre-install

PR:		ports/80457
Submitted by:	maintainer
Reported by:	pointyhat [1]
 2005-04-29 22:14:29 +00:00
Jean-Yves Lefort
b37b345fdb - Update to 5.0 
- Cleanups

PR:		ports/80372
Submitted by:	maintainer
 2005-04-28 19:01:41 +00:00
Tilman Keskinoz
3fd9de655e Bump PORTEPOCH. 3.6 < 3.62 
Pointyhat to:	arved
 2005-04-22 12:08:12 +00:00
Tilman Keskinoz
4b5bb63afb Upgrade to 3.62 
PR:		79234
Submitted by:	David A. Bader <dbader@ece.unm.edu>
 2005-04-21 13:45:15 +00:00
Yen-Ming Lee
5da6643360 - update grappa to 2.0 
- utilize PLIST_FILES
- unbreak it on 4.x
- update maintainer's email

PR:		79241
Submitted by:	David A. Bader <dbader@ece.unm.edu>
 2005-04-15 18:48:57 +00:00
David E. O'Brien
c3d8037aeb At Kris's request, back out the MACHINE_ARCH spelling correction until 
after 5.4-RELEASE.
 2005-04-12 03:26:56 +00:00
Florent Thoumie
8f8e8eb20c - Change maintainer's email address. 2005-04-11 20:34:36 +00:00
Florent Thoumie
0cde76ebca - ARCH is defined in bsd.port.pre.mk 2005-04-11 11:26:40 +00:00
David E. O'Brien
f2fc2d60ae Assist getting more ports working on AMD64 by obeying the 
Ports Collection documentation and use 'ARCH' rather than 'MACHINE_ARCH'.
 2005-04-11 08:04:41 +00:00
Thierry Thomas
ad720f7433 Upgrade to 0.5 and take maintainership. 
Remark: still broken on FreeBSD-5.x.

PR:		ports/79304
Submitted by:	Fernan Aguero (new maintainer)
Approved by:	Tony Maher (previous maintainer)
 2005-04-08 22:45:42 +00:00
Kris Kennaway
8f10413ffa Try to unbreak on amd64 and ia64 
Approved by:    portmgr (self)
 2005-03-26 22:20:19 +00:00
Kris Kennaway
03f424f513 BROKEN: Unfetchable 
Approved by:    portmgr (self)
 2005-03-26 21:59:50 +00:00
Maho Nakata
3b43fb872d Fix build on amd64 
Submitted by:	kris via pointy hat
Approved by:	portmgr (marcus)
 2005-03-24 01:06:40 +00:00
Herve Quiroz
2ed22f8f65 - Add 'java' category 
- Remove incorrect (and unneeded) JAVA_RUN statement

PR:		78761
Submitted by:	me
 2005-03-20 14:43:55 +00:00
Pav Lucistnik
320a3ff48e - Fix man page damage I did last night 
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
 2005-03-20 11:47:59 +00:00
Pav Lucistnik
807384d668 - Update to 2.2.10 from 20041020 
- Transfer maintainership

PR:		ports/67735
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:	old maintainer indirectly in
http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2004-June/035351.html
 2005-03-19 21:32:13 +00:00
Alexey Dokuchaev
44ff373a2a From the PR: 
I've added PORTREVISION to the port and set it to the release
  date as in the lang/gcc* ports.  Since the distinfo file is not
  used, this would help users know when they have to update their
  ports.

  Although newer release might be made, the idea is to bump
  PORTREVISION for important feature releases on when significant
  bugs are fixed.

  Other minor (cosmetic) changes also applied.

PR:		ports/78963
Sumbitted by:	maintainer
 2005-03-18 13:01:07 +00:00
Joe Marcus Clarke
b3458f652e Bump PORTREVISION to chase the glib20 shared lib version change. 2005-03-12 10:54:27 +00:00
Sergey Matveychuk
5282793c25 - biology/act is redundant after biology/artemis update 
PR:             ports/76217
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:	maintainer timeout (2 monthes)
 2005-03-12 08:07:23 +00:00
Sergey Matveychuk
0dc38c05ba - Update to version 6 
- Pass maintainership to submitter

PR:		ports/76219
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:	maintainer timeout (2 monthes)
 2005-03-12 08:01:19 +00:00
Thierry Thomas
142b74833b Add finchtv 1.3.0, a chromatogram trace viewer. 
PR:		70271
Submitted by:	Fernan Aguero <fernan (at) iib.unsam.edu.ar>
 2005-03-11 21:16:16 +00:00
Kirill Ponomarev
4b76311e47 Fix build on 4.x 
PR:		ports/77697
Submitted by:	Sam Lawrance <boris at brooknet.com.au>
 2005-02-19 06:38:25 +00:00
Kris Kennaway
11ea174ccb As previously announced, remove ports that have reached their expiry date, 
and the handful of ports that depended on them.
 2005-02-18 23:44:49 +00:00
Kirill Ponomarev
413ef4bf43 Update to version 2.0.3 
PR:		ports/77676
Submitted by:	Sam Lawrance <boris at brooknet.com.au>
 2005-02-18 13:45:42 +00:00
Kirill Ponomarev
10571886d6 Readd mistakenly removed patch to honour CC/CFLAGS. 2005-02-18 13:41:09 +00:00
Kirill Ponomarev
a8944ffbf8 Update to version 1.40 
PR:		ports/77675
Submitted by:	Sam Lawrance <boris at brooknet.com.au>
 2005-02-18 13:39:34 +00:00
Kirill Ponomarev
0b4743610c Fix unfetchable tarball, it was renamed and relocated on original 
server.

PR:		ports/77674
Submitted by:	Sam Lawrance <boris at brooknet.com.au>
 2005-02-18 12:58:07 +00:00
Sergey Matveychuk
73d0a2892a - Add (or fix) CONFLICTS line. The ports install bin/digest. 
Approved by:	portmgr (krion)
 2005-02-11 21:11:51 +00:00
Maho Nakata
d8a8a937f0 update to 0.97 2005-02-07 08:39:51 +00:00
Mark Linimon
d4bb9bdf92 With portmgr hat on, reset maintainership of this port. All of wjv's 
other ports were reset a couple of months ago; this one appears to have
been missed.
 2005-01-22 04:43:18 +00:00
Maho Nakata
a8fdc546a8 o update to 4.3 
o unbreak
o due to no fix for long period, drop maintainership to ports.
 2005-01-20 03:44:55 +00:00
Akinori MUSHA
ad31ad2bd2 Update to 0.6.2. 2004-12-25 17:52:46 +00:00
Kris Kennaway
b70e8b7e1d This port is scheduled to be removed on 2005-02-18 if it is still 
broken at that time, and a fix has not been submitted to GNATS.
 2004-12-18 23:02:35 +00:00
Kirill Ponomarev
f4bbeec3cb Update to version 2.0.8 
PR:		ports/75106
Submitted by:	Ports Fury
 2004-12-18 18:48:13 +00:00
Sergey Matveychuk
88de31623a - Update to 2004.12.16 
PR:		ports/75205
Submitted by:	maintainer
 2004-12-18 15:14:42 +00:00
Mark Linimon
4aa015434f Clean up wording of IGNORE output. 2004-12-17 08:01:21 +00:00
Mark Linimon
600b5645fd Unquote the IGNORE string. 2004-12-17 07:43:11 +00:00
Mark Linimon
020f0ea235 With portmgr hat on, switch from BROKEN to ignore. It does indeed build. 2004-12-17 06:43:46 +00:00
Pav Lucistnik
b5e176497d - Fix OPTIONS handling 
Pointy hat to:	sem
 2004-12-11 23:32:32 +00:00
Sergey Matveychuk
5e2edc3f15 Not a real update with the last patch. 
The real update here.
 2004-12-11 03:58:19 +00:00
Sergey Matveychuk
fd116809ac - This update brings seaview to the latest release (dated 09.24.04 
in the FTP site).

- While here add a modeline for vi, and fix a tab (cosmetic)

- Make portlint happy.

PR:		ports/74897
Submitted by:	maintainer
 2004-12-11 03:49:29 +00:00
Pav Lucistnik
487872e2c3 - Add some sites I found with Google, as old master site don't have this 
version anymore

Reported by:	pointyhat via krion
 2004-12-09 13:33:55 +00:00
Kris Kennaway
0a01282986 BROKEN: Broken distinfo file 2004-12-04 01:45:38 +00:00
Hye-Shik Chang
5a37bd265f Fix build on Python 2.4 
Spotted by:	kris
 2004-12-02 05:51:25 +00:00
Kirill Ponomarev
39a1da7133 Update MASTER_SITES and WWW: line 
PR:		ports/74421
Submitted by:	Ports Fury
 2004-11-26 19:45:59 +00:00
Sergey Matveychuk
883e920692 [new port] biology/embassy 
PR:		ports/74330
Submitted by:	Fernan Aguero <fernan(at)iib.unsam.edu.ar>
 2004-11-26 16:34:22 +00:00
Sergey Matveychuk
626e4b86a8 - Update to 2.9.0 
- Pass maintainership to submitter

PR:             ports/74333
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>
 2004-11-26 01:11:43 +00:00