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1575 commits

Author SHA1 Message Date
Baptiste Daroussin
2e34754bf6 Support stage 2014-01-20 23:10:10 +00:00
Baptiste Daroussin
090f15acf5 Support stage 2014-01-20 23:06:48 +00:00
Baptiste Daroussin
5221a9dd7a Support stage 2014-01-20 23:00:56 +00:00
Baptiste Daroussin
5da0c9a774 Support stage 
Conver USE_GMAKE
 2014-01-20 17:02:11 +00:00
Antoine Brodin
6eb2857024 Stage support 2014-01-18 15:55:42 +00:00
Alexey Dokuchaev
9dc680d0e8 - Update to version 1.13.0 and improve FreeBSD support; it also builds 
pretty cleanly with GCC v4.2, v4.6, and Clang (modulo a few warnings)
- Sadly, do not use PORTDOCS: since DOCSDIR is set to be inside DATADIR,
  and will get appended to PLIST after @dirrm %%DATADIR%%, which upsets
  sanity checking tools; instead, list the docs explicitly in DISTFILES
  and add them to pkg-plist (guarded by %%PORTDOCS%%)

Tested on:	i386 (only)
 2014-01-16 17:17:15 +00:00
Baptiste Daroussin
0adb5c3f94 Reduce over inclusion of bsd.port.mk 2014-01-15 22:52:28 +00:00
Baptiste Daroussin
b6b54b0a88 Reduce over inclusion of bsd.port.mk 2014-01-15 22:51:26 +00:00
Baptiste Daroussin
3b82ca9795 Reduce over inclusion of bsd.port.mk 2014-01-15 22:50:50 +00:00
Baptiste Daroussin
281fdcd544 Reduce over inclusion of bsd.port.mk 2014-01-15 22:50:18 +00:00
Baptiste Daroussin
06600f966f Reduce over inclusion of bsd.port.mk 2014-01-15 22:48:32 +00:00
Baptiste Daroussin
9d0066d3ff Support stage 
Reduce over inclusions of bsd.port.mk
Use BROKEN_${ARCH}
 2014-01-15 22:44:13 +00:00
Rene Ladan
50f8eaece1 Python cleanup: 
- USE_PYTHON* = 2.X -> USE_PYTHON* = 2
- USE_PYTHON* = 2.X+ -> USE_PYTHON* = yes
Reviewed by:	python (mva, rm)
Approved by:	portmgr-lurkers (mat)
 2014-01-13 21:00:02 +00:00
Thomas Zander
368c138aae - Fix build with clang 
- Stage support

PR:		ports/185655
Submitted by:	Tassilo Philipp <tphilipp@potion-studios.com> (maintainer)
Approved by:	thierry (mentor)
 2014-01-12 19:07:28 +00:00
Andrej Zverev
f09fca2358 - add stage support 
Approved by:	portmgr (blanket infrastructure)
 2014-01-06 09:57:19 +00:00
Andrej Zverev
2c6b14778c - add stage support 
Approved by:	portmgr (blanket infrastructure)
 2014-01-06 09:44:19 +00:00
Andrej Zverev
f41a84cc7d - support stage 2014-01-05 12:07:20 +00:00
Baptiste Daroussin
4be4ab0c7e Mark as broken: Invalid checksum, seems like the software was rerolled 2014-01-03 19:46:05 +00:00
Adam Weinberger
955d37365b Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
Olli Hauer
4fb1cfb1cd - rename AL2 to APACHE20 in Mk/bsd.licenses.db.mk 
- svn move Templates/Licenses/AL2 Templates/Licenses/APACHE20
- add APACHE10 and APACHE11 to Mk/bsd.licenses.db.mk
- add entry in UPDATING
- bulk change all ports AL2 => APACHE20

- math/openfst/pkg-plist: remove share/licenses/openfst-1.3.4

PR:		ports/184785
Submitted by:	ohauer
Reviewed by:	tabthorpe
Approved by:	portmgr (tabthorpe@)
 2013-12-30 20:55:18 +00:00
Antoine Brodin
b5fdf54ec6 Stage support 2013-12-30 18:27:32 +00:00
Antoine Brodin
9d9aec7824 Stage support 2013-12-30 18:08:14 +00:00
Tijl Coosemans
ec8db877f4 - USES=fortran gmake. 
- Add dependency on xproto.
- Fix build with new CFLAGS.
- Staging.
- New WWW.
 2013-12-29 14:30:20 +00:00
Rene Ladan
94066acc1a The hmmer binary was renamed upstream to indicate that it is now an 
archive file, adjust the port so that fetch and extract work again.
 2013-12-29 10:41:50 +00:00
William Grzybowski
1f6544c522 biology/seqtools: update to 4.24 
PR:		ports/185162
Submitted by:	maintainer
 2013-12-24 17:23:23 +00:00
Rene Ladan
652c8e10fe Several fixes: 
- install files as the BOINC user/group, this ensures that work units can
  be downloaded and sent
- try to remove ~boinc/projects if empty
- do not specify -o and -g parameters to ${INSTALL}, this ensures the
  package can be built as user
- only extract the hmmer binary from the hmmer distribution file, this
  ensures correct permissions when modifying app_info.xml as user
- Bump PORTREVISION

Reviewed by:	bapt
 2013-12-23 18:03:15 +00:00
Wen Heping
1fc27b753e - Fix build with clang/libc++. 
- Support staging.

PR:		184974
Submitted by:	tijl@
 2013-12-20 15:29:07 +00:00
Pawel Pekala
91571f28bb - Respect CC/CFLAGS 
PR:		ports/184857
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
 2013-12-20 13:27:13 +00:00
Tijl Coosemans
1555ae4f31 - biology/tinker: USES=fortran, staging. 
- Add CONFLICTS_INSTALL between hunspell and tinker.
  Both install bin/analyze.
 2013-12-18 18:27:04 +00:00
Tijl Coosemans
f0d679be01 USES=fortran, staging. 2013-12-18 17:24:51 +00:00
Tijl Coosemans
bd36806845 USES=fortran, staging, miscellaneous cleanups. 2013-12-18 16:23:08 +00:00
Tijl Coosemans
9eba83c71f Version 2013.12.12, USES=fortran, staging. 2013-12-17 21:55:24 +00:00
Tijl Coosemans
23f82b30c6 USES=fortran, fix LDFLAGS, staging. 2013-12-17 21:24:17 +00:00
Gerald Pfeifer
2291db64ec Fix the build with more standards-compliant compilers such as GCC 4.7. [1] 
On the way replace USE_GMAKE by USES=gmake.

PR:		184566 [1], 182136
Submitted by:	Christoph Moench-Tegeder <cmt@burggraben.net> [1]
Approved by:	maintainer (Jason Bacon <jwbacon@tds.net>) [1]
 2013-12-13 09:34:40 +00:00
Baptiste Daroussin
a2275161bd In preparation for making libtool generate libraries with a sane name, fix all 
LIB_DEPENDS in biology
 2013-12-11 14:43:51 +00:00
Baptiste Daroussin
732ab835ac Support stage 
USE_GMAKE -> USES=gmake
use USES=readline:port
 2013-12-10 17:54:12 +00:00
Baptiste Daroussin
67c403a63a Support stage 
USE_GMAKE -> USES=gmake
Respect CC
 2013-12-10 17:25:38 +00:00
Baptiste Daroussin
46c85cde39 Support stage 
Convert USE_GMAKE to USES=gmake
Add dependency on perl which the port need and was getting by chance
bump portrevision, dependencies has changed
 2013-12-10 17:21:46 +00:00
Adam Weinberger
6507f2bc7a Respect PORT_OPTIONS:MDOCS 
Clean up COMMENT
USES=gmake
 2013-12-09 01:28:41 +00:00
Wen Heping
7c42586279 - Fix build on head 2013-12-01 01:58:31 +00:00
Philippe Audeoud
ad6d50d019 - Update to 1.28 
Sponsored by:	OBS
 2013-11-28 15:05:08 +00:00
Philippe Audeoud
ee7ae13fca - Fix build with clang 
- Support STAGEDIR

PR:		ports/184242
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
 2013-11-27 16:07:51 +00:00
Philippe Audeoud
9a5536a62b - Fix build 
- Support STAGEDIR

PR:		ports/184238
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
 2013-11-27 13:16:47 +00:00
William Grzybowski
38592c3bf2 biology/lamarc: fix build on current 
PR:		ports/184219
Submitted by:	KATO Tsuguru <tkato432 yahoo.com>
 2013-11-26 15:37:05 +00:00
Baptiste Daroussin
51c60ddf7f Convert to USES=dos2unix 
While here stagify some of the ports
Modernize LIB_DEPENDS
Extract zip with bsdtar when possible
 2013-11-18 13:45:44 +00:00
William Grzybowski
75a509365b biology/seqtools: update to 4.23 
PR:		ports/183960
Submitted by:	maintainer
 2013-11-14 20:09:00 +00:00
Baptiste Daroussin
0169c8b869 Add stage support 
Use bsdtar to extract the distfile
Rip out USE_GMAKE
 2013-11-12 22:02:02 +00:00
Baptiste Daroussin
b2ac854afe Stage support 
drop USE_GMAKE
 2013-11-12 21:54:36 +00:00
William Grzybowski
20139c3cfa biology/seqtools: Tools for visualising sequence alignments 
Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.

Belvu is a multiple sequence alignment viewer and phylogenetic tool.

Dotter is a graphical dot-matrix program for detailed comparison
of two sequences.

WWW: http://www.sanger.ac.uk/resources/software/seqtools/

PR:		ports/183801
Submitted by:	Kurt Jaeger <fbsd-ports opsec.eu>
 2013-11-10 11:01:02 +00:00
Boris Samorodov
6807405893 . give maintainership to the submitter; 
. add one month to DEPRACATION_DATE;

while here: strip the indefinite article from COMMENT.

PR:		ports/183742
Submitted by:	Kurt Jaeger <fbsd-ports@opsec.eu> (assigned maintainer)
 2013-11-07 13:18:51 +00:00