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freebsd-ports/biology
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John Marino ed9f597563 biology/segan: Limit GCC to 4.8 while waiting for update 
Due to questionable c++, GCC 4.9 and newer cannot build seqan.  An update
has been in the works that will enable clang compilers and all versions
of GCC to build seqan, but it is not quite ready yet.  While waiting for
it, limit the version of GCC used to 4.8.

PR:	196851
2015-03-21 11:53:27 +00:00
..
ariadne misc/otter & biology/ariadne: Not jobs safe 2015-01-21 18:39:11 +00:00
artemis - Add empty directory to plist 2015-03-11 14:41:53 +00:00
avida Cleanup plist 2014-12-20 17:27:08 +00:00
babel Rename biology/ patch-xy patches to reflect the files they modify. 2014-07-28 14:22:16 +00:00
biococoa Cleanup plist 2014-10-20 07:10:48 +00:00
biojava - add stage support 2014-06-01 10:37:22 +00:00
blat Update to upstream version 36 2015-01-01 18:17:53 +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 Cleanup plist 2014-10-20 07:10:48 +00:00
emboss Fix packaging as a user (pkg already takes care of credentials) 2015-03-18 21:52:19 +00:00
fasta - Add staging support 2014-03-24 09:01:39 +00:00
fasta3 Cleanup plist 2014-10-20 07:10:48 +00:00
fastdnaml Cleanup plist 2014-10-20 07:10:48 +00:00
fluctuate Support staging 2014-02-16 11:35:00 +00:00
garlic Cleanup plist 2014-10-20 07:10:48 +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 Cleanup plist 2014-10-20 07:10:48 +00:00
htslib biology/htslib: update 1.1 -> 1.2.1 2015-03-06 12:45:22 +00:00
iolib - Update to 1.13.10 2015-03-04 13:17:46 +00:00
jalview Cleanup plist 2014-10-20 07:10:48 +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
libsbml - Convert USE_PYTHON -> USES leftovers missed in the previous commits 2015-01-04 08:23:23 +00:00
linux-foldingathome Cleanup plist 2014-12-20 17:27:08 +00:00
mafft Cleanup plist 2014-10-20 07:10:48 +00:00
mapm3 - Fix build with clang 2014-01-12 19:07:28 +00:00
migrate - Update to 3.6.6 2015-01-31 06:35:24 +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 - Upadate biology/mopac to version 1.15 2014-12-16 22:10:23 +00:00
mrbayes Fix build on -current by un-clobbering LDFLAGS. Also, don't 2014-08-15 16:37:37 +00:00
mummer Cleanup plist 2014-10-20 07:10:48 +00:00
muscle Update to 3.8.31. 2014-06-17 21:36:06 +00:00
ncbi-blast+ Add a run dependency used by update_blastdb.pl 2015-03-06 10:39:31 +00:00
ncbi-toolkit Cleanup plist 2014-10-20 07:10:48 +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 - Simplify MASTER_SITES 2015-03-17 03:09:25 +00:00
p5-Bio-ASN1-EntrezGene Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Das Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Das-Lite Remove TEST dependency on p5-Test-Simple when the version in core is 2015-02-26 16:54:41 +00:00
p5-Bio-GFF3 Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Glite Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Graphics Some OCD cleanups on some of the perl@ ports. 2015-03-12 23:00:02 +00:00
p5-Bio-MAGETAB Some OCD cleanups on some of the perl@ ports. 2015-03-12 23:00:02 +00:00
p5-Bio-NEXUS Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Phylo - Update to 0.58 2014-12-07 04:41:47 +00:00
p5-Bio-SCF Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-bioperl Some OCD cleanups on some of the perl@ ports. 2015-03-12 23:00:02 +00:00
p5-bioperl-run For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME to 2015-03-20 20:07:50 +00:00
paml - Pass maintainership to submitter 2015-01-19 12:11:25 +00:00
phrap - Fix various distinfo errors 2014-10-16 08:55:30 +00:00
phred update ports: 2014-08-23 18:04:58 +00:00
phylip - Update to version 3.696 2014-11-02 14:13:59 +00:00
phyml Convert to USES=autoreconf 2014-12-28 19:14:13 +00:00
platon Unbreak by upgrading to March 5, 2015 "release" from upstream. 2015-03-08 23:13:21 +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 - Update to 0.10 2014-10-12 03:16:10 +00:00
povchem Cleanup plist 2014-12-20 17:27:08 +00:00
primer3 Quote ${CC} and similar variables in MAKE_ARGS. 2014-05-20 19:32:39 +00:00
protomol Bump portrevision after png update 2014-12-25 20:54:41 +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 biology/py-biopython: 2015-01-19 20:21:12 +00:00
pycogent - Convert ports from benchmarks/ and biology/ to new USES=python 2014-10-19 07:38:11 +00:00
pyfasta - Convert ports from benchmarks/ and biology/ to new USES=python 2014-10-19 07:38:11 +00:00
python-nexus - Convert ports from benchmarks/ and biology/ to new USES=python 2014-10-19 07:38:11 +00:00
recombine - Support staging 2014-02-16 11:39:42 +00:00
ruby-bio Cleanup plist 2014-10-20 07:10:48 +00:00
samtools biology/samtools: update 1.1 -> 1.2 2015-03-06 12:53:58 +00:00
seaview biology/seaview: UNBREAK 2015-03-16 12:07:49 +00:00
seqan biology/segan: Limit GCC to 4.8 while waiting for update 2015-03-21 11:53:27 +00:00
seqio Support staging 2014-02-16 11:42:09 +00:00
seqtools biology/seqtools: 4.31 -> 4.32 2015-02-12 12:04:09 +00:00
sim4 Support staging 2014-02-16 11:43:07 +00:00
ssaha Cleanup plist 2014-12-20 17:27:08 +00:00
t_coffee Remove Authors from pkg-descr 2015-03-02 23:09:43 +00:00
tinker Update from 7.1.1 to 7.1.2. 2015-03-11 13:44:21 +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 Unipro UGENE to version 1.16.0 (documentation was also rerolled). 2015-02-24 11:42:53 +00:00
velvet Designatate 4 ports as unsafe for parallel building 2015-01-19 17:43:57 +00:00
wise Cleanup plist 2014-12-20 17:27:08 +00:00
xmolwt devel/glib12 x11-toolkits/gtk12: 2014-09-13 15:11:27 +00:00
Makefile Remove expired ports: 2015-01-01 01:13:11 +00:00