Gerald Pfeifer 04d6f52202 Bump PORTREVISIONs for ports depending on the canonical version of GCC and ... lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some circumstances such as versions of FreeBSD or platforms). This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using using Mk/bsd.octave.mk which in turn has USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang, c++11-lang, c++0x, c11, or gcc-c++11-lib. PR: 216707		2017-04-01 15:23:30 +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	2017-04-01 15:23:30 +00:00
bowtie2	Update devel/tbb to 2017.5	2017-03-07 12:44:41 +00:00
bwa	Mark various ports broken on aarch64 and armv6.	2017-01-31 03:40:46 +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	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
diamond	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +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 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
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	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	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
molden	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
mopac	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +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+	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	Bump PORTREVISION for ports affected by the fix the last commit.	2017-01-31 16:21:45 +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	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
phyml
plink	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +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	2017-04-01 15:23:30 +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
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	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
seqio
seqtools	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +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
treeviewx	Mark the remaining ports depending on Google Code as DEPRECATED, with an	2017-03-03 16:00:19 +00:00
trimmomatic
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