cpet/freebsd-ports
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
2016Q3
freebsd-ports/biology
History
Dirk Meyer 937d324155 MFH: r418829 
- update libgd to 2.2.2
- new MASTER_SITES
- add security patch
PR:		210913
Submitted by:	Piotr Kubaj
Security: CVE-2015-8874
Security: CVE-2016-3074
Security: http://www.openwall.com/lists/oss-security/2016/07/12/4

Approved by:	portmgr (feld)
2016-07-20 21:30:03 +00:00
..
ariadne - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
artemis
avida
babel
bcftools biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1 2016-05-26 20:28:55 +00:00
bedtools
biococoa
biojava - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
blat - Fix trailing whitespace in pkg-messages 2016-05-19 11:09:14 +00:00
bowtie
bowtie2 biology/bowtie2: 2.2.7 -> 2.2.8 2016-05-13 20:12:44 +00:00
bwa
cd-hit
cdbfasta
chemeq - Add LICENSE 2016-04-10 11:24:32 +00:00
clustalw Remove useless WRKSRC definitions. 2016-05-25 15:43:34 +00:00
consed Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
crux Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
diamond biology/diamond: update 0.8.6 -> 0.8.9 2016-06-30 01:37:22 +00:00
emboss MFH: r418829 2016-07-20 21:30:03 +00:00
fasta
fasta3 - Fix trailing whitespace in pkg-messages 2016-05-19 11:09:14 +00:00
fastdnaml
fastool
fasttree
fastx-toolkit Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
fluctuate
garlic
gff2ps Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
gmap
gperiodic
grappa - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
hmmer
htslib biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1 2016-05-26 20:28:55 +00:00
iolib - Update to 1.14.8 2016-05-01 01:03:48 +00:00
jalview - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
jellyfish Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
lagan - Fix trailing whitespace in pkg-messages 2016-05-19 11:09:14 +00:00
lamarc
libgtextutils
libsbml Upgrade from 5.12.0 to 5.13.0. Release-announcement available here: 2016-04-16 01:54:15 +00:00
linux-foldingathome
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 - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
mopac
mrbayes
mummer
muscle
ncbi-blast+ Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
ncbi-toolkit - Add missing dependency, fixing build 2016-06-24 09:04:45 +00:00
p5-AcePerl Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-ASN1-EntrezGene - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-Bio-Das Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-Das-Lite Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-GFF3 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-Glite Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-Graphics Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-MAGETAB Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-NEXUS - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-Bio-Phylo - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-Bio-SCF Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-bioperl - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-bioperl-run Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-transdecoder Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
paml - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
phrap
phred
phylip Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
phyml Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
platon Deprecate ports broken for more than 6 months 2016-06-03 16:44:58 +00:00
plink Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
plinkseq many ports: mark broken on powerpc64 2016-04-21 16:43:14 +00:00
primer3
protomol Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
psi88 - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
py-biom-format - Fix run-time dependency issues 2016-06-11 09:25:04 +00:00
py-biopython - Update to 1.66 2016-04-17 03:55:01 +00:00
pycogent Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
pyfasta - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
python-nexus - Update to 1.35 2016-06-08 07:39:05 +00:00
recombine
ruby-bio Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +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 4.5.4.8=>4.6 2016-06-10 11:06:42 +00:00
seqan - Do install cmake and pkgconfig modules 2016-05-27 16:10:36 +00:00
seqan1 - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
seqan-apps - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
seqio
seqtools biology/seqtools: 4.41.1 -> 4.42.1 2016-04-22 16:27:25 +00:00
sim4
slclust Remove unneeded usage of: 2016-06-06 15:25:42 +00:00
ssaha - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
t_coffee Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
tinker
treepuzzle
treeviewx
trimmomatic
tRNAscan-SE Prevent collision with getline(3) 2016-05-13 18:38:34 +00:00
ugene During the exp-run in bug 208158, it was found that biology/ugene gives 2016-05-07 19:38:53 +00:00
vcftools
velvet
wise - Switch to options helpers 2016-06-21 09:05:06 +00:00
xmolwt - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
Makefile biology/seqan: update 1.3.1 -> 2.1.1 2016-05-10 01:05:23 +00:00