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Commit Graph

1709 Commits

Author SHA1 Message Date
Adam Weinberger
b5e31c70a1 Rename biology/ patch-xy patches to reflect the files they modify. 2014-07-28 14:22:16 +00:00
Wen Heping
aa18ea4cb6 - Update to 1.6.924 [1]
- Reset maintainer to perl@

PR:		192088 [1]
Submitted by:	Kurt Jaeger<pi@FreeBSD.org> [1]
2014-07-27 07:27:17 +00:00
Mathieu Arnold
6800031748 Really fix.
Sponsored by:	Absolight
2014-07-25 23:08:58 +00:00
Mathieu Arnold
3c328a52a2 Fix build.
Sponsored by:	Absolight
2014-07-25 15:06:46 +00:00
Kurt Jaeger
f5a09e89e1 biology/p5-Bio-Graphics: 2.37 -> 2.38 2014-07-24 09:48:03 +00:00
Baptiste Daroussin
64620e9118 Reset maintainership for ports not staged with no pending PR
With hat:	portmgr
2014-07-23 16:44:27 +00:00
Dmitry Marakasov
646f175619 - Switch to USES=libtool, drop .la files
- Fix shebangs

Approved by:	portmgr blanket
2014-07-22 22:12:15 +00:00
John Marino
4fa4056388 biology/mummer: Use OPSYS with OSVERSION
I don't think selecting clang as a function of OSVERSION is generally
desired, but if it's going to happen, make sure FreeBSD-specific
conditions are limited to FreeBSD by comparing OPSYS first.
2014-07-19 22:00:16 +00:00
John Marino
dbb41fc2bf biology/garlic: Stage properly to unbreak
The main problem was the WRKDIR is not within STAGEDIR.  Fix this while
moving all the directory creation steps into one.  While here
set TAR to use switches as outlined in its man page.

Also, the permission setting in stagedir is not necessary, so it's simply
been removed.
2014-07-17 10:13:06 +00:00
Adam Weinberger
44eaadcb75 Add OPTIONS_DEFINE=DOCS for ports with %%PORTDOCS%% in the plist.
Where possible, correct a few instances where PORTDOCS was being used
to flag stuff in EXAMPLESDIR. For some ports, mostly those owned by
ruby@, PORTDOCS is applied to pretty much everything whether it's
documentation or example.
2014-07-15 23:11:12 +00:00
Adam Weinberger
e7e692da08 Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS.
While here, use OPTIONS helpers and re-enable manpage installation.
2014-07-15 14:54:54 +00:00
John Marino
74a0052cf9 biology/platon: Unbreak by hosting known distfiles elsewhere
The distfiles are regenerated often, too frequently to be suitable for
ports.  Fonz has decided to host the tarball of a known version to
restore this unmaintained port.

PR:		191685
Submitted by:	Fonz
2014-07-13 11:27:44 +00:00
Kurt Jaeger
c633e61a10 biology/seqtools: 4.26 -> 4.27 2014-07-12 18:56:03 +00:00
Adam Weinberger
55550f84bb Use gcc on all platforms.
PR:		191692
Submitted by:	maintainer
2014-07-10 22:29:52 +00:00
Vanilla I. Shu
1dc5f0c755 Stagify.
Approved by:	portmgr@ (blanket)
2014-07-06 16:05:34 +00:00
Adam Weinberger
ea1babb4f7 Missed a NOPORTDOCS. 2014-07-05 00:15:40 +00:00
Adam Weinberger
0cf8ed500c Remove NOPORTDOCS and NOPORTEXAMPLES from unstaged ports. Stage a couple while
we're here. Remove any other references to NOPORT*.

Approved by:	portmgr (blanket for modernization)
2014-07-04 23:46:52 +00:00
Martin Wilke
bd48d39657 - Chase database/sqlite3 slib bump
Approved by:	portmgr (myself)
2014-06-27 17:21:06 +00:00
Martin Wilke
2a912e1c5e Fix compilation on 10+ (clang)
Fix format of WWW entry in pkg-descr

PR:		190798
2014-06-27 14:14:01 +00:00
Wen Heping
f47ad7b877 - Mark BROKEN
Approved by:	portmgr@(implicit)
2014-06-26 14:38:10 +00:00
Antoine Brodin
063f95149a Put HOME in MAKE_ARGS to handle pverride of HOME in MAKE_ENV from bsd.port.mk 2014-06-25 08:55:55 +00:00
Baptiste Daroussin
3078c82f53 Use MAKE_CMD instead of GMAKE
With hat:	portmgr
2014-06-24 22:02:32 +00:00
Baptiste Daroussin
7984527ad4 Mark as broken: no distinfo provided 2014-06-22 22:07:25 +00:00
Baptiste Daroussin
8fa661c2d9 Mark as broken: no distinfo provided
With hat:	portmgr
2014-06-22 22:06:01 +00:00
Raphael Kubo da Costa
26b977f43a Fix shebang line in Perl and Python scripts.
PR:		191146
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
2014-06-20 12:54:29 +00:00
Antoine Brodin
6ae01531e3 Mark BROKEN: Fails to configure
===>  Configuring for p5-bioperl-run-1.6.1_4
Invalid prerequisite condition '0/processing XML data/Bio::Tools::Run::EMBOSSacd' for XML::Twig at /usr/local/lib/perl5/site_perl/5.16/Module/Build/Base.pm line 1702.
*** [do-configure] Error code 25

Reported by:	pkg-fallout
With hat:	portmgr
2014-06-19 21:31:16 +00:00
John Marino
af93a9e79e biology/blast: Deprecate for removal after 4 September 2014
This unstaged port will be removed for legal reasons.

PR:		190626
Submitted by:	Muhammad Rahman
Approved by:	portmgr (implicit)
2014-06-19 11:55:50 +00:00
Raphael Kubo da Costa
fa8c84c90c Update to 1.2.10.
PR:		191129
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
2014-06-17 21:39:44 +00:00
Raphael Kubo da Costa
53828d5f20 Update to 3.8.31.
PR:		191130
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
2014-06-17 21:36:06 +00:00
John Marino
d0bb05930a Reset the 99 ports still listed under sylvio@
Sylvio's last commit was 17 months ago, a full 5 months after all of his
ports could have been reset per policy.  Given the push to complete
staging (48 ports are still unstaged, something like 70+ have already
been staged by other committers) and given that PRs are automatically
assigned but never addressed, it's better just to reset all the ports and
PRs so that it's clear to others that these ports are free to maintain.

Approved by:	portmgr (implicit)
2014-06-11 18:55:29 +00:00
Mathieu Arnold
61de712f46 Remove all the bootstrap files (.bs) from the plists.
Starting with perl 5.20, they're not installed any more if empty,
and on FreeBSD, they're (always ?) empty.

PR:		190681
Submitted by:	mat
Exp-Run by:	antoine
Sponsored by:	Absolight
2014-06-10 12:14:12 +00:00
Jimmy Olgeni
37e782dfbc Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.

CR:		D196
Approved by:	portmgr (bapt)
2014-06-09 11:21:52 +00:00
Jimmy Olgeni
55dc0f983a Remove all space characters from Makefile assignments.
No functional changes included.

CR:		D193 (except math/sedumi)
Approved by:	portmgr (bapt)
2014-06-08 19:51:27 +00:00
Vanilla I. Shu
6ba77a1bb9 Stagify, remove BROKEN. 2014-06-07 01:54:41 +00:00
Martin Wilke
031596f908 - Update to 6.6.0
- Stage support

PR:		190508
Submitted by:	Muhammad Moinur Rahman
2014-06-05 03:28:06 +00:00
Antoine Brodin
9f6d625880 Unbreak 2014-06-04 20:08:15 +00:00
Martin Wilke
015670c696 - Update to 4.5.2
- Pass maintainership to submitter

PR:		190564
2014-06-04 06:28:56 +00:00
Baptiste Daroussin
2afa67184c Update to 0.5.1 snapshot 20100824
For the story when moved to google code the project released a version 0.5 which was newer than the 0.5.1 from earlier hosting
To be consistent named it 0.5.1s20100824 (following what debian did)
Switch treeviewx to use unicode version of wx
Add a patch from Ubuntu to fix loading trees.
2014-06-03 14:51:29 +00:00
Olli Hauer
e1858b091a - add stage support
- adjust BSDn license
2014-06-01 11:42:17 +00:00
Olli Hauer
684d78ae77 - add stage support 2014-06-01 11:33:57 +00:00
Olli Hauer
f5e4f15bd6 - add stage support
- add OPTION for X11
- bump PORTREVISION
2014-06-01 11:26:39 +00:00
Olli Hauer
e3fe4137a9 - add stage support 2014-06-01 11:05:43 +00:00
Olli Hauer
c3fa596129 - add stage support 2014-06-01 10:54:33 +00:00
Olli Hauer
b2efa85d17 - add stage support 2014-06-01 10:37:22 +00:00
Danilo Egea Gondolfo
3a22921826 - I forgot to svn add a new patch 2014-05-31 18:03:08 +00:00
Danilo Egea Gondolfo
2e8ad31ad5 - Update from 1.13.5 to 1.13.7
- Add libtool to USES
- Take maintainership
2014-05-31 17:57:06 +00:00
Jonathan Chu
e4d4ffc175 Add DOCS and EXAMPLE options to biology/mafft
PR:		ports/190161
Submitted by:	"Reed A. Cartwright" <cartwright@asu.edu> (maintainer)
Approved by:	swills (maintainer)
2014-05-31 04:18:18 +00:00
Wen Heping
2699b52547 - Update to 1.6.923
- Add STAGE support

PR:		190342
Submitted by:	Muhammad Moinur Rahman <5u623l20@gmail.com>
2014-05-30 15:46:05 +00:00
John Marino
a7ff4d0e9c biology/embassy: specify post-extraction with ${TAR}
It's possible that EXTRACT_CMD won't be predefined in the near future
in order to support distfiles in multiple formats.  We know the post-
extraction tool needs to be tar, so let's specify it directly.

This port needs staging. It doesn't like like a quick job so I'm leaving
that to the listed maintainer.

Approved by:	infrastructure improvements blanket
Approved by:	portmgr (implicit) (to skip stage check)
2014-05-29 10:47:58 +00:00
Baptiste Daroussin
f0a8714b3a Convert to USES=dos2unix
With hat:	portmgr
2014-05-26 06:55:07 +00:00