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freebsd-ports/biology
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Sunpoet Po-Chuan Hsieh c2d1a14c7c - Update to 7.31.0 
- Bump PORTREVISION for ftp/curl shlib change
- Add TEST_DEPENDS
- Convert to new options framework
- Adjust options:
  - Add COOKIES
  - Add CYASSL, NSS, POLARSSL, THREADED_RESOLVER, TLS_SRP [1]
  - Add GSSAPI and SPNEGO [2]
  - Remove KERBEROS4
  - Rename LIBIDN to IDN
  - Remove TRACKMEMORY [1]
- Sort option handler
- Add SLAVEDIRS: ftp/curl-hiphop
- Cosmetic change
- Cleanup Makefile header
- While I'm here, fix typo (PORTREVSION) in x11-wm/ede/Makefile

Changes:	http://curl.haxx.se/changes.html
PR:		ports/172325 (-exp run), ports/177369 (based on) [1]
Submitted by:	Hirohisa Yamaguchi <umq@ueo.co.jp> [1], hrs (via email) [2]
Exp run by:	miwi
2013-07-11 16:26:26 +00:00
..
adun
ariadne . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 14:10:02 +00:00
artemis Decommissioning java 1.5 (EOLed since October 2009): 2012-12-10 11:25:27 +00:00
avida - Fix build with clang 2013-06-04 08:26:03 +00:00
babel . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 19:01:47 +00:00
biococoa - cleanup comments 2012-10-13 13:39:56 +00:00
biojava Remove hardcoded extract dependency on diablo-jdk16, directly use USE_ZIP 2012-12-11 07:26:38 +00:00
blast - Take maintainership 2012-10-01 14:55:55 +00:00
blat . remove pkg-plist (along with the previous commit). 2013-06-19 18:44:32 +00:00
boinc-simap Use bsd.port.options.mk instead of bsd.port.{pre|post}.mk 2013-04-29 12:20:35 +00:00
chemeq . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 20:01:30 +00:00
clustalw
consed
crux - adoption of optionsNG 2013-03-18 06:48:55 +00:00
dotter - Mark broken checksum mismatch 2013-03-25 01:41:31 +00:00
embassy Convert from USE_MOTIF to USES=motif 2013-07-09 21:49:35 +00:00
emboss Convert from USE_MOTIF to USES=motif 2013-07-09 21:49:35 +00:00
fasta Fix some PORT_OPTIONS conversions 2013-06-30 20:53:06 +00:00
fasta3 - Take maintainership 2012-10-01 14:55:55 +00:00
fastdnaml . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 13:35:55 +00:00
finchtv - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
fluctuate . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 12:43:28 +00:00
garlic Fix typos in COMMENT 2012-07-25 06:32:06 +00:00
genpak
gff2ps . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 18:56:37 +00:00
gmap
gperiodic . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 19:05:47 +00:00
grappa
hmmer - Take maintainership 2012-10-01 14:55:55 +00:00
iolib - Update to 7.31.0 2013-07-11 16:26:26 +00:00
jalview Decommissioning java 1.5 (EOLed since October 2009): 2012-12-10 11:25:27 +00:00
lagan - Update to version 2.0 2012-11-15 07:04:29 +00:00
lamarc . trim Makefile headers; 2013-06-19 15:39:18 +00:00
libgenome . add license (GPLv2); 2013-06-19 18:53:54 +00:00
libsbml - adoption of optionsNG 2013-03-18 06:50:12 +00:00
linux-foldingathome
mafft Mark as broken on sparc64: depends on thread-local storage, which is not 2012-09-08 08:30:39 +00:00
mapm3
migrate - Update to 3.5.1 2013-05-26 07:49:47 +00:00
molden - Update to 5.0.6 2013-04-26 06:57:37 +00:00
mopac . NOPORTEXAMPLES -> PORT_OPTIONS:MEXAMPLES; 2013-06-19 18:38:46 +00:00
mrbayes
mummer
muscle Fix typos in COMMENT 2012-07-24 07:19:21 +00:00
ncbi-toolkit Convert from USE_MOTIF to USES=motif 2013-07-09 21:49:35 +00:00
njplot Convert from USE_MOTIF to USES=motif 2013-07-10 07:33:24 +00:00
ortep3 . introdice optionsNG to the port; 2013-06-19 20:06:59 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Das Cleanup supporting perl version 5.8 and 5.10, 2012-12-17 15:39:36 +00:00
p5-Bio-Das-Lite
p5-Bio-GFF3 - Update to 1.5 2012-12-16 04:22:15 +00:00
p5-Bio-Glite For perl@ owned ports: 2013-03-29 00:44:53 +00:00
p5-Bio-Graphics Add missing item to pkg-plist reported by QAT but not reported by poudriere. 2013-03-03 15:22:43 +00:00
p5-Bio-MAGETAB For perl@ owned ports: 2013-03-29 00:44:53 +00:00
p5-Bio-NEXUS For perl@ owned ports: 2013-03-29 00:44:53 +00:00
p5-Bio-Phylo - Update to 0.52 [1] 2013-02-16 14:58:51 +00:00
p5-Bio-SCF - Trim Makefile headers 2013-06-01 14:22:35 +00:00
p5-bioperl - Avoid of using SITE_PERL 2013-06-07 06:51:42 +00:00
p5-bioperl-run
paml - Trim Makefile headers 2013-06-01 14:22:35 +00:00
phd2fasta Remove unneeded escaping 2013-04-26 16:23:13 +00:00
phrap
phred
phylip Fix some screw ups introduced in r319847. 2013-06-24 18:09:52 +00:00
phyml - Update to 20121109. 2013-02-04 10:07:30 +00:00
platon
plink Add new ports biology/plink [1] and biology/plinkseq [2]: 2012-09-27 09:59:25 +00:00
plinkseq Fix build with protobuf-2.5.0 2013-03-21 14:09:22 +00:00
povchem - remove empty files 2013-02-15 08:57:19 +00:00
primer3 - Take maintainership 2012-10-01 14:55:55 +00:00
protomol - adoption of optionsNG 2013-03-18 06:54:39 +00:00
psi88 . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 19:54:13 +00:00
py-biopython - update to 1.60 2012-09-25 08:06:42 +00:00
pycogent - Update to 1.5.3 2012-10-08 03:17:02 +00:00
pyfasta - Trim Makefile headers 2013-06-01 14:22:35 +00:00
pymol Switch from libglut to freeglut and retire libglut. Libglut hasn't been 2012-08-04 22:52:02 +00:00
python-nexus
rasmol Convert to USES=imake 2013-06-28 18:32:25 +00:00
recombine . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 19:15:14 +00:00
ruby-bio - adoption of optionsNG 2013-03-18 06:55:42 +00:00
seaview - Update to 4.4.1 2013-03-26 01:08:40 +00:00
seqan - convert USE_CMAKE to USES 2013-03-22 20:06:14 +00:00
seqio Remove stale (since r321246) pkg-plist file. 2013-06-19 21:04:36 +00:00
sim4 . add license (GPLv2); 2013-06-19 16:36:53 +00:00
ssaha - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
t_coffee - Update to 9.03. 2013-01-14 08:04:38 +00:00
tinker - Update to 6.2.05 2013-05-29 05:25:49 +00:00
treepuzzle
treeviewx - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
tRNAscan-SE . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 19:20:25 +00:00
ugene Unbreak on 7.X and i386 systems. 2013-02-25 13:00:15 +00:00
velvet
wise Fix build by adding an explicit dep on pkgconf 2013-05-03 20:48:34 +00:00
xdrawchem - Strip header at request of original creator 2013-01-27 05:55:20 +00:00
xmolwt Use optionsNG for DOCS. 2013-06-19 19:07:35 +00:00
Makefile Add Unipro UGENE, a free open-source crowss-platform bioinformatics software. 2013-02-23 04:50:48 +00:00