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freebsd-ports/biology
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Rene Ladan a91d5178df Remove expired ports: 
2017-08-23 games/plee-the-bear: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-umicons: Broken for more than 6 months
2017-08-23 lang/bigloo: Broken for more than 6 months
2017-08-23 audio/linux-neroaaccodec: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-dark-glass: Broken for more than 6 months
2017-08-23 misc/fortune-mod-ferengi_rules_of_acquisition: Broken for more than 6 months
2017-08-23 misc/fortune-mod-culmea-culmilor: Broken for more than 6 months
2017-08-23 misc/xyzcmd: Broken for more than 6 months
2017-08-23 russian/fortuneru: Broken for more than 6 months
2017-08-23 security/bdc: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-icosx: Broken for more than 6 months
2017-08-23 devel/insight: Broken for more than 6 months
2017-08-23 devel/gdb66: Broken for more than 6 months
2017-08-23 biology/biojava: Broken for more than 6 months
2017-08-23 games/xroach: Broken for more than 6 months
2017-08-23 11:33:26 +00:00
..
ariadne Cleanup $() variables in ports Makefiles. 2016-07-20 15:33:20 +00:00
artemis - Fix shebangs 2017-04-21 16:28:25 +00:00
avida Mark some ports failing on power64. In cases where the error message 2017-05-13 03:35:51 +00:00
babel
bcftools Update math/gsl to 2.4 2017-07-03 20:38:11 +00:00
bedtools Mark some ports failing on armv6, for errors classified as "clang". 2017-05-27 15:07:11 +00:00
biococoa Update GNUstep core libraries. 2017-08-21 13:26:28 +00:00
blat - Update WWW 2017-06-10 09:01:19 +00:00
bowtie - Fix shebangs 2017-04-22 09:25:44 +00:00
bowtie2 Update devel/tbb to 2017.5 2017-03-07 12:44:41 +00:00
bwa Mark some ports failing on armv6, for errors classified as "???". 2017-05-26 20:02:44 +00:00
cd-hit Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
cdbfasta Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/ 2017-01-20 20:33:30 +00:00
chemeq biology/chemeq: fix build on GCC (taken from dports) 2016-12-18 04:22:26 +00:00
clustalw Remove useless WRKSRC definitions. 2016-05-25 15:43:34 +00:00
consed - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with 2016-09-05 19:23:42 +00:00
crux Mark some ports failing on armv6, for errors classified as "???". 2017-05-26 20:02:44 +00:00
diamond biology/diamond: Update to version 0.9.10 2017-08-15 20:45:08 +00:00
emboss - update libgd to 2.2.2 2016-07-20 09:33:31 +00:00
fasta ${RM} already has -f. 2016-10-21 12:51:40 +00:00
fasta3 - Fix trailing whitespace in pkg-messages 2016-05-19 11:09:14 +00:00
fastdnaml
fastool Never set WRKSRC when using USE_GITHUB. 2017-01-03 18:12:13 +00:00
fasttree Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
fastx-toolkit
fluctuate
garlic
gff2ps
gmap Mark some ports failing on power64. In cases where the error message 2017-05-13 03:35:51 +00:00
gperiodic Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
grappa - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
hmmer Begin deorbit burn of ia64. We have not attempted to build packages for 2017-06-25 00:29:09 +00:00
htslib Use USES=pathfix where applicable. 2016-10-21 15:21:13 +00:00
iolib Mark some ports failing on power64. In cases where the error message 2017-05-13 03:35:51 +00:00
jalview - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
jellyfish Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
lagan - Fix trailing whitespace in pkg-messages 2016-05-19 11:09:14 +00:00
lamarc biology/lamarc: Fix build on DF (taken from dports) 2016-12-18 04:34:33 +00:00
libgtextutils Use USES=pathfix where applicable. 2016-10-21 15:21:13 +00:00
libsbml - Update to 5.15.0 2017-05-18 02:22:18 +00:00
linux-foldingathome - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with 2016-09-05 19:23:42 +00:00
mafft - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
mapm3 - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
migrate - Switch to options helpers 2016-04-17 10:15:59 +00:00
molden Chase next distfile update. Upstream contacted whether we would be allowed to host a distfile copy. 2017-07-13 21:56:29 +00:00
mopac Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
mrbayes Update devel/readline to 7.0 patch 3 2017-06-27 13:46:53 +00:00
mummer
muscle Mark various leaf ports broken on aarch64, and, where appropriate, other 2016-11-11 09:31:02 +00:00
ncbi-blast+ Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
ncbi-toolkit Remove libjpeg.so.11 compatibility link that was added in r374303 to 2016-12-08 16:39:11 +00:00
njplot biology/njplot: Add site in MASTER_SITES because package builders are 2016-11-28 15:19:42 +00:00
p5-AcePerl Move -fPIC to where Linux puts it so it is limited to a single library. 2017-02-13 22:43:58 +00:00
p5-Bio-ASN1-EntrezGene - Add LICENSE 2016-12-18 15:25:13 +00:00
p5-Bio-Coordinate - Add p5-Bio-Coordinate 1.007001 2016-12-19 15:54:39 +00:00
p5-Bio-Das - Add LICENSE 2016-12-18 15:25:18 +00:00
p5-Bio-Das-Lite
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics Remove outdated PERL_LEVEL check 2017-06-01 23:50:28 +00:00
p5-Bio-MAGETAB
p5-Bio-NEXUS - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-Bio-Phylo - Add LICENSE_FILE 2016-12-18 15:25:22 +00:00
p5-Bio-SCF
p5-BioPerl Remove outdated PERL_LEVEL check 2017-06-01 23:50:33 +00:00
p5-BioPerl-Run Bump PORTREVISION for ports affected by the fix the last commit. 2017-01-31 16:21:45 +00:00
p5-transdecoder Never set WRKSRC when using USE_GITHUB. 2017-01-03 18:12:13 +00:00
paml Cleanup no longer needed CHMOD usage after r424898. 2016-11-02 22:45:14 +00:00
phrap
phred
phylip
phyml Update WWW 2017-05-30 15:22:06 +00:00
plink Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
plinkseq Mark some ports failing on power64. In cases where the error message 2017-05-13 03:35:51 +00:00
primer3
protomol Revision bump of all ports with USE_GL after consolidation of mesa-libs 2017-05-23 05:03:14 +00:00
psi88 Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
py-biom-format biology/py-biom-format: Update to version 2.1.6 2017-04-29 13:59:15 +00:00
py-biopython - update to 1.70 2017-08-18 12:57:06 +00:00
py-bx-python bx-python is a python library and associated set of scripts to allow for rapid 2017-05-06 06:07:03 +00:00
py-pysam - Update to 0.11.2.2 2017-06-10 02:03:39 +00:00
pycogent - Update to 1.9 [1] 2016-08-08 11:21:04 +00:00
pyfasta - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
python-nexus - Update to 1.53 2017-07-23 08:15:07 +00:00
recombine When there is a do-install target, do not use a post-install target, do 2016-07-19 11:04:13 +00:00
ruby-bio - Update to 1.5.1 2017-05-07 15:44:34 +00:00
rubygem-bio Update to 1.5.1 2017-02-06 23:03:17 +00:00
samtools biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1 2016-05-26 20:28:55 +00:00
seaview biology/seaview: Update version 4.6.1=>4.6.2 2017-07-21 17:33:10 +00:00
seqan - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1] 2016-09-14 19:38:58 +00:00
seqan-apps It is possible that r441426 will fix the build problem on armv6. Give 2017-05-21 23:37:34 +00:00
seqan1 When there is a do-install target, do not use a post-install target, do 2016-07-19 11:04:13 +00:00
seqio
seqtools Mark some ports failing on power64. In cases where the error message 2017-05-21 21:55:08 +00:00
sim4
slclust Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/ 2017-01-20 20:33:30 +00:00
ssaha Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
t_coffee Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
tinker Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
treepuzzle
trimmomatic
tRNAscan-SE Prevent collision with getline(3) 2016-05-13 18:38:34 +00:00
ugene Revision bump of all ports with USE_GL after consolidation of mesa-libs 2017-05-23 05:03:14 +00:00
vcftools Assume "pkg-config zlib" works after 9.x reached EOL 2017-01-03 17:06:49 +00:00
velvet
wise Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
xmolwt Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
Makefile Remove expired ports: 2017-08-23 11:33:26 +00:00