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Commit Graph

1020 Commits

Author SHA1 Message Date
Wesley Shields
a8dc52d3dc - Roll back to 4.6 as 4.7 is the development version and is constantly being
re-rolled.
- Move post-patch target into files/patch-xwin.c to remove sed invocation.
- Respect NOPORTDATA and DATADIR.
- Bring files/patch-aa back (to preserve history) and retire patch-makefile.
- Fixup files/patch-xwin.c so it applies cleanly to this version.
2008-11-11 02:21:28 +00:00
Wesley Shields
69d100db8c Mark as broken since it has been re-rolled for the 4th(?) time. 2008-11-07 20:21:13 +00:00
Wesley Shields
f481e858d9 Distfile was re-rolled. The changes were to fix some bugs in the code.
While I'm here, make it respect NOPORTDOCS.
2008-11-07 00:33:32 +00:00
Wesley Shields
05d80caef1 Update to 4.7
PR:		ports/128476
Submitted by:	fulvio ciriaco <oivulf@gmail.com>
2008-11-04 21:55:39 +00:00
Dmitry Marakasov
c3fd0b3811 - Update to 2.8.1
PR:		128057
Submitted by:	Christian Sturm <athaba at inode dot at>
2008-10-23 14:13:37 +00:00
Rong-En Fan
1153c04ff7 - Unbreak
PR:		ports/128193
Submitted by:	Mauricio Herrera Cuadra <mauricio at arareko.net> (maintainer)
2008-10-21 15:24:46 +00:00
Martin Wilke
41618ec344 - Update to 1.48
PR:		127776
Submitted by:	Wen heping <wenheping@gmail.com>
Approved by:	maintainer
2008-10-11 15:26:33 +00:00
Martin Wilke
8e93b103e5 - Update to 4.1
- Pass maintainership to submitter

PR:		127683
Submitted by:	Wen heping <wenheping@gmail.com>
2008-09-30 08:54:55 +00:00
Pietro Cerutti
a434890f03 - Respect PORTDOCS/PORTEXAMPLES
Reported by:	QA Tindie
Approved by:	portmgr
2008-09-09 13:43:15 +00:00
Mark Linimon
775e8df21c Reset sf@slappy.org due to maintainer-timeouts and no response to email.
Hat:	portmgr
2008-09-03 02:57:44 +00:00
Pietro Cerutti
d59f739097 - Fix build
Reported by:	QA Tindie
2008-08-27 16:21:06 +00:00
Pietro Cerutti
4bfca18721 - Update to 3.68 2008-08-27 15:19:32 +00:00
Maho Nakata
7b319c494e Add -lf2c, this is the correct dependency. Bump portrevision. 2008-08-22 22:20:05 +00:00
Rong-En Fan
741aa71483 Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.

To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.

To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.

Changes to Mk/*:
 - Add runtime detection magic in bsd.port.mk
 - Remove CONFIGURE_TARGET hack in various bsd.*.mk
 - USE_GNOME=gnometarget is now an no-op

Changes to individual ports, other than removing the CONFIGURE_TARGET hack:

= pkg-plist changed (due to the ugly CONFIGURE_TARGET prefix in * executables)
  - comms/gnuradio
  - science/abinit
  - science/elmer-fem
  - science/elmer-matc
  - science/elmer-meshgen2d
  - science/elmerfront
  - science/elmerpost

= use x86_64 as ARCH
  - devel/g-wrap

= other changes
  - print/magicfilter
    GNU_CONFIGURE -> HAS_CONFIGURE since it's not generated by autoconf

Total # of ports modified:  1,027
Total # of ports affected: ~7,000 (set GNU_CONFIGURE to yes)

PR:		126524 (obsoletes 52917)
Submitted by:	rafan
Tested on:	two pointyhat 7-amd64 exp runs (by pav)
Approved by:	portmgr (pav)
2008-08-21 06:18:49 +00:00
Boris Samorodov
62b0d58228 Unbreak building for 8-x.
Submitted by:	Steve Kargl <sgk at troutmask.apl.washington.edu> at ports@ ML
2008-08-15 17:42:47 +00:00
Dirk Meyer
40b08a8d1c - update PORTSCOUT 2008-08-12 17:13:44 +00:00
Martin Wilke
e3fe8b1b7e - Update to 1.47
PR:		125912
Submitted by:	Wen heping <wenheping@gmail.com>
Approved by:	maintainer timeout
2008-08-11 22:06:31 +00:00
Philip M. Gollucci
1d2b2aee59 - Update to 2.1.3
Approved by:    gabor (mentor)
2008-07-31 16:18:42 +00:00
Pav Lucistnik
efa63f6ba4 - Remove USE_GCC where it can be satisfied with base compiler on following
FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT
2008-07-25 14:34:52 +00:00
Pav Lucistnik
29e60de039 - Remove duplicates from MAKE_ENV after inclusion of CC and CXX in default MAKE_ENV 2008-07-25 09:08:42 +00:00
Pav Lucistnik
32fefb3036 - Delete biology/nab port after being marked DEPRECATED for three months
PR:		ports/125891
Submitted by:	M. L. Dodson <mldodson@comcast.net> (maintainer)
2008-07-24 12:17:12 +00:00
Philip M. Gollucci
b43083409f Update my ports to my freebsd address
Approved by:    araujo (mentor)
2008-07-23 02:43:55 +00:00
Ion-Mihai Tetcu
30eddc16be - respect NOPORTEXAMPLES/NOPORTDOCS and fix plist
- bump PORTREVISION

Prompted by:	QA Tindy run
2008-07-12 06:28:25 +00:00
Marcelo Araujo
1a3f2abbec - Update to 2.1.2c.
- Pass maintainership to submitter.

PR:		ports/125497
Submitted by:	Philip M. Gollucci <pgollucci@p6m7g8.com>
2008-07-11 17:24:16 +00:00
Dirk Meyer
16d144d7a3 - extened PORTSCOUT 2008-07-08 17:32:52 +00:00
Pav Lucistnik
d0a749618d - Mark BROKEN: missing cpan dependency (interactive loop) 2008-07-07 22:57:49 +00:00
Beech Rintoul
5c8688edc5 - Bump portrevision after openbabel update 2008-07-07 05:14:23 +00:00
Felippe de Meirelles Motta
53ee713129 - Update to 1.5.2.
PR:		ports/124648
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
Reviewed by:	lippe
Approved by:	gabor (mentor, implicit)
2008-07-06 23:27:12 +00:00
Beech Rintoul
63a004d6f2 - Update to 1.45
PR:		ports/125134
Submitted by:	Wen heping <wenheping@gmail.com>
Approved by:	Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
2008-07-04 02:53:15 +00:00
Dirk Meyer
52cce0f680 - extend PORTSCOUT 2008-06-24 14:47:46 +00:00
Felippe de Meirelles Motta
7de163573f - Fix plist files installation.
- Bump PORTREVISION.

Reported by:	QA Tindy
Approved by:	gabor (mentor, implicit)
2008-06-21 02:46:21 +00:00
Felippe de Meirelles Motta
702ce22305 SSAHA is a software tool for very fast matching and alignment of DNA
sequences. It stands for Sequence Search and Alignment by Hashing
Algorithm. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.

WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/

PR:		ports/124525
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:	gabor (mentor, implicit)
2008-06-21 00:01:57 +00:00
Pav Lucistnik
fef2d1e552 - Fix fetch, update WWW 2008-06-18 19:12:59 +00:00
Pietro Cerutti
3eb1dc51ee - Fix build depends
- Bump port revision

Reported by:	pointyhat via pav
2008-06-09 13:01:30 +00:00
Edwin Groothuis
6527ef2070 Bump portrevision due to upgrade of devel/gettext.
The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)
2008-06-06 13:08:29 +00:00
Pietro Cerutti
301fc1156b - Update to 3.67
- Sanitize Makefile a little bit
2008-06-03 23:31:14 +00:00
Dirk Meyer
de7503e8c6 - cleanup FreeBSD 5.x 2008-06-01 19:22:24 +00:00
Martin Wilke
18a0ba7f1e - Update to 1.09 2008-05-31 13:46:14 +00:00
Edwin Groothuis
ea7995670b Teach the building cluster that these ports are not to be build 2008-05-25 23:05:10 +00:00
Edwin Groothuis
5081af2c64 New port: biology/consed viewing and editing workbench for sequence
assembly

	Consed is a tool for viewing, editing, and finishing sequence
	assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-24 07:04:45 +00:00
Edwin Groothuis
c65af41a3b New port: biology/consed viewing and editing workbench for sequence
assembly

	Consed is a tool for viewing, editing, and finishing sequence
	assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-24 07:03:23 +00:00
Edwin Groothuis
f30ad7580d New port: biology/consed viewing and editing workbench for sequence
assembly

	Consed is a tool for viewing, editing, and finishing sequence
	assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-24 07:01:56 +00:00
Edwin Groothuis
69ef603a61 New port: biology/consed viewing and editing workbench for sequence
assembly

	Consed is a tool for viewing, editing, and finishing sequence assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-24 07:00:37 +00:00
Mathieu Arnold
6c28dcfa2f Update to 1.08 2008-05-23 12:22:21 +00:00
Martin Wilke
21d58ada23 - Update MASTER_SITES and WWW: line
- Support CC/CFLAGS properly
- Strip binary

PR:		123866
Submitted by:	Ports Fury
2008-05-22 00:49:42 +00:00
Marcelo Araujo
2cba6cd79f - Include some ports in perl5 category.
PR:		ports/123530
Submitted by:	Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:	araujo (myself)
Approved by:	flz (portmgr)
2008-05-19 13:12:08 +00:00
Pav Lucistnik
48927e76ef - Update maintainer's email address
Submitted by:	Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
2008-05-17 16:52:34 +00:00
Pav Lucistnik
ee146516be - Try to fix fetch
Submitted by:	Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
2008-05-17 16:50:12 +00:00
Erwin Lansing
4ddb273770 Update to 1.23 2008-05-15 02:50:21 +00:00
Pav Lucistnik
0149bce295 NJplot is a tree drawing program able to draw any phylogenetic tree expressed
in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP
package). NJplot is especially convenient for rooting the unrooted trees
obtained from parsimony, distance or maximum likelihood tree-building methods.

The package contains the following programs:
njplot      - draw phylogenetic trees and interactively modify them
newicktops  - non-interactive version rendering into a PostScript file
newicktotxt - non-interactive version rendering into a text file
unrooted    - draw unrooted circular trees

If you use NJplot in a published work, please cite the following reference:

Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for
biological sequence banks. Biochimie, 78, 364-369.

WWW: http://pbil.univ-lyon1.fr/software/njplot.html

PR:		ports/118438
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-14 14:07:01 +00:00