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freebsd-ports/biology
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Gerald Pfeifer 15945f8122 Update the default version of GCC in the Ports Collection from GCC 4.7.4 
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
2014-09-10 20:50:31 +00:00
..
ariadne Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
artemis Support stage 2014-01-20 23:06:48 +00:00
avida
babel Rename biology/ patch-xy patches to reflect the files they modify. 2014-07-28 14:22:16 +00:00
biococoa Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
biojava - add stage support 2014-06-01 10:37:22 +00:00
blat 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
boinc-simap Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
chemeq Stage support 2014-01-18 15:55:42 +00:00
clustalw Multiple ports: reset maintainers 2014-05-26 02:33:38 +00:00
consed update ports: 2014-08-23 18:04:58 +00:00
crux Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
emboss Remove indefinite articles and trailing periods from COMMENT, plus 2014-06-09 11:21:52 +00:00
fasta - Add staging support 2014-03-24 09:01:39 +00:00
fasta3 biology/fasta3: Checked new distfile and regenerated distinfo to unbreak 2014-03-02 10:58:50 +00:00
fastdnaml Support staging 2014-02-16 11:32:43 +00:00
fluctuate Support staging 2014-02-16 11:35:00 +00:00
garlic biology/garlic: Stage properly to unbreak 2014-07-17 10:13:06 +00:00
gff2ps Add staging support 2014-03-23 17:43:41 +00:00
gmap Fix MASTER_SITES 2014-09-05 09:25:45 +00:00
gperiodic Add staging support 2014-03-23 18:09:23 +00:00
grappa - Respect CC/CFLAGS 2013-12-20 13:27:13 +00:00
hmmer Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS. 2014-07-15 14:54:54 +00:00
iolib - I forgot to svn add a new patch 2014-05-31 18:03:08 +00:00
jalview Fix properties on pkg-plist 2014-01-21 23:18:05 +00:00
lagan
lamarc - rename AL2 to APACHE20 in Mk/bsd.licenses.db.mk 2013-12-30 20:55:18 +00:00
libsbml - Update to 5.10.2 2014-08-10 06:21:53 +00:00
linux-foldingathome Stagify. 2014-07-06 16:05:34 +00:00
mafft Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
mapm3 - Fix build with clang 2014-01-12 19:07:28 +00:00
migrate - Stagify; cleanup Makefile and reorder the knobs a bit 2014-01-29 12:08:29 +00:00
molden Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
mopac - Switch to USES=libtool, drop .la files 2014-08-06 16:05:49 +00:00
mrbayes Fix build on -current by un-clobbering LDFLAGS. Also, don't 2014-08-15 16:37:37 +00:00
mummer biology/mummer: Use OPSYS with OSVERSION 2014-07-19 22:00:16 +00:00
muscle Update to 3.8.31. 2014-06-17 21:36:06 +00:00
ncbi-toolkit Add staging support 2014-03-23 20:50:54 +00:00
njplot - add stage support 2014-06-01 11:26:39 +00:00
ortep3 Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
p5-AcePerl Fix build. Hopefully it doesn't break the app. 2014-08-22 00:33:16 +00:00
p5-Bio-ASN1-EntrezGene Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
p5-Bio-Das - support stage 2014-01-05 12:07:20 +00:00
p5-Bio-Das-Lite - fix pkg-plist 2014-01-30 07:34:25 +00:00
p5-Bio-GFF3 - Fix PLIST 2014-03-26 14:23:09 +00:00
p5-Bio-Glite - support stage 2014-01-05 12:07:20 +00:00
p5-Bio-Graphics Really fix. 2014-07-25 23:08:58 +00:00
p5-Bio-MAGETAB - update to 1.31 2014-05-16 13:33:02 +00:00
p5-Bio-NEXUS - Stage support 2014-01-31 12:47:06 +00:00
p5-Bio-Phylo - support stage 2014-01-05 12:07:20 +00:00
p5-Bio-SCF Remove all the bootstrap files (.bs) from the plists. 2014-06-10 12:14:12 +00:00
p5-bioperl biology/p5-bioperl: fix pkg-descr sidenote link 2014-08-04 04:32:38 +00:00
p5-bioperl-run biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagify 2014-08-04 08:54:10 +00:00
paml Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
phrap update ports: 2014-08-23 18:04:58 +00:00
phred update ports: 2014-08-23 18:04:58 +00:00
phylip The FreeBSD x11@ and graphics team proudly presents 2014-04-16 18:28:47 +00:00
phyml - Stage support 2014-01-31 12:32:55 +00:00
platon Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
plink Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
plinkseq - Switch to USES=libtool, drop .la files 2014-07-22 22:12:15 +00:00
povchem Rename biology/ patch-xy patches to reflect the files they modify. 2014-07-28 14:22:16 +00:00
primer3 Quote ${CC} and similar variables in MAKE_ARGS. 2014-05-20 19:32:39 +00:00
protomol Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
psi88 Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
py-biopython Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
pycogent Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
pyfasta Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
python-nexus Remove indefinite articles and trailing periods from COMMENT, plus 2014-06-09 11:21:52 +00:00
recombine - Support staging 2014-02-16 11:39:42 +00:00
ruby-bio Support stage 2014-04-07 13:01:26 +00:00
seaview Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
seqan Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
seqio Support staging 2014-02-16 11:42:09 +00:00
seqtools USES=execinfo 2014-08-04 23:06:21 +00:00
sim4 Support staging 2014-02-16 11:43:07 +00:00
ssaha biology/ssaha: undeprecate, this port fetches and builds fine. 2014-03-09 09:39:50 +00:00
t_coffee Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
tinker Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
treepuzzle
treeviewx Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
tRNAscan-SE Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
ugene Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
velvet Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
wise - Add staging support 2014-03-24 10:46:35 +00:00
xmolwt Add staging support 2014-03-24 11:06:56 +00:00
Makefile Second run at cleaning out non staged ports without pending PR 2014-09-02 12:45:01 +00:00