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freebsd-ports/biology
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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
..
ariadne Stage support 2013-11-12 21:54:36 +00:00
artemis Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
avida - Fix build with clang 2013-11-27 16:07:51 +00:00
babel Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
biococoa Update BioCocoa to the latest release. 2013-10-08 18:34:45 +00:00
biojava Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
blast Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
blat Add stage support 2013-11-12 22:02:02 +00:00
boinc-simap Use value of BOINC_CLIENT_HOME in pkg-message 2013-09-24 12:00:40 +00:00
chemeq Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
clustalw Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
consed Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
crux In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
embassy In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +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 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
fasta3 Update to version 36.3.6d 2013-10-29 19:32:15 +00:00
fastdnaml Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
finchtv Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
fluctuate Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +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 Respect PORT_OPTIONS:MDOCS 2013-12-09 01:28:41 +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 Support stage 2013-12-10 17:25:38 +00:00
hmmer Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
iolib In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
jalview Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
lagan - Fix build 2013-11-27 13:16:47 +00:00
lamarc biology/lamarc: fix build on current 2013-11-26 15:37:05 +00:00
libgenome Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
libsbml In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +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 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
mapm3 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
migrate Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
molden Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +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 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +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 Fix NO_STAGE attribution 2013-09-22 18:05:04 +00:00
ortep3 In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
p5-AcePerl 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-ASN1-EntrezGene 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-Das 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-Das-Lite 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-GFF3 - Update to 1.8 2013-11-02 19:55:32 +00:00
p5-Bio-Glite 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-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 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-Phylo 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-SCF Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
p5-bioperl Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
p5-bioperl-run Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
paml Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
phd2fasta Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
phrap Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
phred Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +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 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
platon Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
plink Fix the build with more standards-compliant compilers such as GCC 4.7. [1] 2013-12-13 09:34:40 +00:00
plinkseq In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +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 In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
psi88 Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
py-biopython Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
pycogent Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
pyfasta Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +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 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
rasmol Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
recombine Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
ruby-bio Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
seaview In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
seqan Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
seqio Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
seqtools biology/seqtools: update to 4.23 2013-11-14 20:09:00 +00:00
sim4 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
ssaha Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
t_coffee Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
tinker Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
treepuzzle - Remove NO_STAGE as these have been tested to be safe 2013-09-25 00:54:08 +00:00
treeviewx Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
tRNAscan-SE Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
ugene - Install official UGENE documentation (PDF) 2013-11-01 15:20:28 +00:00
velvet Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
wise Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +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