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freebsd-ports/biology
History
Gerald Pfeifer 1cd277bdce Update the default version of GCC used in the Ports Collection from 
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
2014-03-10 20:55:20 +00:00
..
ariadne Stage support 2013-11-12 21:54:36 +00:00
artemis Support stage 2014-01-20 23:06:48 +00:00
avida - Fix build with clang 2013-11-27 16:07:51 +00:00
babel Support stage 2014-01-15 22:44:13 +00:00
biococoa Update BioCocoa to the latest release. 2013-10-08 18:34:45 +00:00
biojava Unbreak 2014-03-08 16:39:01 +00:00
blast Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
blat Convert b* to USES=zip 2014-03-07 15:52:40 +00:00
boinc-simap Drop maintainership BOINC ports, old machine running them gave up. 2014-02-04 17:54:29 +00:00
chemeq Stage support 2014-01-18 15:55:42 +00:00
clustalw - Fix build with clang/libc++. 2013-12-20 15:29:07 +00:00
consed Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
crux Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
embassy Reduce over inclusion of bsd.port.mk 2014-01-15 22:48:32 +00:00
emboss In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
fasta Reduce over inclusion of bsd.port.mk 2014-01-15 22:50:18 +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
finchtv Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
fluctuate Support staging 2014-02-16 11:35:00 +00:00
garlic Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
genpak Deprecate a few unmaintained ports (leaf ports, non staged and unmaintained since more than 12 years) 2014-03-08 22:26:21 +00:00
gff2ps Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
gmap Support stage 2013-12-10 17:21:46 +00:00
gperiodic - Remove manual creation and removal of share/applications, as it's now in the mtree (categories starting with [bce]) 2013-10-22 13:57:35 +00:00
grappa - Respect CC/CFLAGS 2013-12-20 13:27:13 +00:00
hmmer Stage support 2013-12-30 18:08:14 +00:00
iolib Support stage 2014-01-20 17:02:11 +00:00
jalview Fix properties on pkg-plist 2014-01-21 23:18:05 +00:00
lagan - Fix build 2013-11-27 13:16:47 +00:00
lamarc - rename AL2 to APACHE20 in Mk/bsd.licenses.db.mk 2013-12-30 20:55:18 +00:00
libgenome biology/libgenome: Fix build on dragonfly 2014-02-05 23:47:48 +00:00
libsbml Convert b* to USES=zip 2014-03-07 15:52:40 +00:00
linux-foldingathome Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
mafft Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +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 used in the Ports Collection from 2014-03-10 20:55:20 +00:00
mopac In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
mrbayes Support stage 2013-12-10 17:54:12 +00:00
mummer Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
muscle Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
ncbi-toolkit Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
njplot Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
ortep3 Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
p5-AcePerl - Stage support 2014-02-10 06:56:52 +00:00
p5-Bio-ASN1-EntrezGene - add stage support 2014-01-06 09:57:19 +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 - Update to 1.9 2014-01-23 03:28:37 +00:00
p5-Bio-Glite - support stage 2014-01-05 12:07:20 +00:00
p5-Bio-Graphics Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
p5-Bio-MAGETAB - Update to 1.28 2013-11-28 15:05:08 +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 - add stage support 2014-01-06 09:44:19 +00:00
p5-bioperl Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
p5-bioperl-run Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
paml Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
phd2fasta Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
phrap Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
phred Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
phylip Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
phyml - Stage support 2014-01-31 12:32:55 +00:00
platon Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
plink Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
plinkseq Convert to dos2unix 2014-03-07 11:37:35 +00:00
povchem Convert to USES=dos2unix 2013-11-18 13:45:44 +00:00
primer3 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
protomol Reduce over inclusion of bsd.port.mk 2014-01-15 22:51:26 +00:00
psi88 Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
py-biopython Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
pycogent Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
pyfasta Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
pymol In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
python-nexus - Convert to PYDISTUTILS_AUTOPLIST 2014-01-31 12:30:39 +00:00
rasmol Deprecate a few unmaintained ports (leaf ports, non staged and unmaintained since more than 12 years) 2014-03-08 22:26:21 +00:00
recombine - Support staging 2014-02-16 11:39:42 +00:00
ruby-bio Reduce over inclusion of bsd.port.mk 2014-01-15 22:52:28 +00:00
seaview - Stage support 2014-02-27 08:46:42 +00:00
seqan Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
seqio Support staging 2014-02-16 11:42:09 +00:00
seqtools Fix old makeplist bug. 2014-02-12 14:03:25 +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 used in the Ports Collection from 2014-03-10 20:55:20 +00:00
tinker Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
treepuzzle - Remove NO_STAGE as these have been tested to be safe 2013-09-25 00:54:08 +00:00
treeviewx Stage support 2013-12-30 18:27:32 +00:00
tRNAscan-SE biology/tRNAscan-SE: Fix hardcoded perl path 2014-02-05 23:44:50 +00:00
ugene Update to version 1.13.1. 2014-03-07 07:39:20 +00:00
velvet Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
wise biology/wise: Add dragonfly support 2014-02-05 23:42:06 +00:00
xmolwt Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
Makefile biology/seqtools: Tools for visualising sequence alignments 2013-11-10 11:01:02 +00:00