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freebsd-ports/biology
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Mathieu Arnold bebf3178ae Mark the remaining ports depending on Google Code as DEPRECATED, with an 
EXPIRATION_DATE at the end of April 2017.

In the past six months, about a third of the ports marked BROKEN because
they were hosted on Google Code have been fixed.  The remaining must not
be of use to anyone.

With hat:	portmgr
Sponsored by:	Absolight
2017-03-03 16:00:19 +00:00
..
ariadne Cleanup $() variables in ports Makefiles. 2016-07-20 15:33:20 +00:00
artemis ${RM} already has -f. 2016-10-21 12:51:40 +00:00
avida Mark various ports as broken on armv6: invokes x86 asm. 2017-02-26 12:56:41 +00:00
babel
bcftools biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1 2016-05-26 20:28:55 +00:00
bedtools biology/bedtools is not jobs safe 2016-08-22 04:32:18 +00:00
biococoa
biojava - Mark it BROKEN 2016-10-28 01:49:40 +00:00
blat biology/blat: Fix build on DF (taken from dports) 2016-12-18 04:46:53 +00:00
bowtie Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-11-20 09:38:08 +00:00
bowtie2 biology/bowtie2: update to 2.3.0 2017-02-27 14:08:30 +00:00
bwa Mark various ports broken on aarch64 and armv6. 2017-01-31 03:40:46 +00:00
cd-hit biology/cd-hit: Update to bug-fix release 4.6.6 2016-12-20 16:48:12 +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 Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
diamond biology/diamond: Update to version 0.8.36. 2017-02-12 14:04:57 +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 Convert LICENSE= "GPLxx # or later" to "GPLxx+" 2016-01-12 16:20:31 +00:00
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 2016-11-20 09:38:08 +00:00
fastx-toolkit Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
fluctuate - Switch to options helpers 2015-11-19 00:51:15 +00:00
garlic
gff2ps Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
gmap Mark various ports as broken on armv6: invokes x86 asm. 2017-02-26 12:56:41 +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 - Update maintainer mail address 2015-12-11 08:48:56 +00:00
htslib Use USES=pathfix where applicable. 2016-10-21 15:21:13 +00:00
iolib Fix USE_GITHUB's GH_TAGNAME usage. 2017-02-28 08:33:44 +00:00
jalview - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
jellyfish Remove BROKEN_FreeBSD_9 2017-01-01 03:45:12 +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 Cleanup no longer needed CHMOD usage after r424898. 2016-11-02 22:45:14 +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 biology/molden: Unbreak port, regenerate checksums, increment PORTREVISION. 2017-02-11 02:06:03 +00:00
mopac Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
mrbayes
mummer
muscle Mark various leaf ports broken on aarch64, and, where appropriate, other 2016-11-11 09:31:02 +00:00
ncbi-blast+ biology/ncbi-blast+: Add MAKE_JOBS_UNSAFE 2016-12-22 16:49:16 +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 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 Bump PORTREVISION for ports affected by the fix the last commit. 2017-01-31 16:21:45 +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 - Add LICENSE_FILE 2016-12-18 15:25:22 +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 Bump PORTREVISION for ports affected by the fix the last commit. 2017-01-31 16:21:45 +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 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
plink Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
plinkseq biology/plinkseq: unbreak with clang 4.0 2017-02-27 14:09:25 +00:00
primer3
protomol biology/protomol: Support build with C++11 (taken from dports) 2016-12-18 05:34:42 +00:00
psi88 Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
py-biom-format Update email address to jrm@FreeBSD.org for ports that I maintain 2016-09-23 21:42:02 +00:00
py-biopython - Update to 1.68 2016-09-23 01:54:45 +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 1.42 2017-03-01 07:00:37 +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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +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 4.5.4.8=>4.6 2016-06-10 11:06:42 +00:00
seqan - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1] 2016-09-14 19:38:58 +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
seqan-apps Mark a few more ports that create large logfiles broken on armv6. 2017-02-26 15:38:10 +00:00
seqio
seqtools Remove BROKEN_FreeBSD_9 2017-01-01 03:45:12 +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 2016-11-20 09:38:08 +00:00
t_coffee Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
tinker Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
treepuzzle
treeviewx Mark the remaining ports depending on Google Code as DEPRECATED, with an 2017-03-03 16:00:19 +00:00
trimmomatic Trimmomatic performs a variety of useful trimming tasks for illumina 2016-03-17 08:21:14 +00:00
tRNAscan-SE Prevent collision with getline(3) 2016-05-13 18:38:34 +00:00
ugene - Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL 2017-01-09 13:16:49 +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 Move devel/rubygem-bio to biology/rubygem-bio 2017-02-05 04:26:56 +00:00