Steve Wills fb44dca45d Fix math/openblas and bump dependent ports ... * Fix build on i386 [1] * Fix science/code_saturne build with new openblas [2] * Avoid installing private headers [3] * Prevent build from optimizing for host by correcting build confg [4] * Bump portrevision of dependent ports [5] This is correcting issues from r523749 [1][2][4] and r515970 [3] PR: 231371 Reported by: build cluster [1] Reported by: Dima Pasechnik <dimpase+freebsd@gmail.com> [2] Reported by: many [5] Reviewed by: mat, bapt Approved by: implicit, since this is a build fix		2020-01-30 14:17:44 +00:00
..
abyss	biology/abyss: Broken on i386	2020-01-18 19:46:26 +00:00
artemis	Clean up after java/openjdk6 and java/openjdk6-jre removal	2019-11-26 21:46:12 +00:00
avida	biology/avida: unbreak on powerpc64	2019-10-23 16:25:10 +00:00
babel
bamtools	devel/jsoncpp: Update 1.8.1 -> 1.9.2	2020-01-13 21:38:35 +00:00
bcftools	math/gsl: update to 2.6	2019-10-25 23:41:34 +00:00
bedtools	biology/bedtools: Upgrade to 2.29.2	2019-12-19 01:04:11 +00:00
biococoa
bolt-lmm	Fix math/openblas and bump dependent ports	2020-01-30 14:17:44 +00:00
bowtie	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
bowtie2	Update devel/tbb to 2020.0 and bump dependent ports' revisions [1]	2019-12-26 16:25:22 +00:00
bwa
canu	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
cd-hit	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
cdbfasta
checkm	biology/checkm: Update 1.0.17 -> 1.0.18	2019-08-19 08:25:29 +00:00
clustal-omega
clustalw
consed	Mark a few ports BROKEN, unfetchable	2019-11-06 12:48:32 +00:00
cufflinks	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
cytoscape	Clean up after java/openjdk6 and java/openjdk6-jre removal	2019-11-26 21:46:12 +00:00
ddocent	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
diamond	biology/diamond: Update to v0.9.29	2019-11-20 17:14:29 +00:00
dsr-pdb	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
emboss	Sprinkle more USES=xorg	2019-11-07 20:19:59 +00:00
exonerate
fasta	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
fasta3	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
fastahack	biology/fastahack: Upgrade to 1.0.0	2019-10-06 21:34:32 +00:00
fastdnaml
fastool
fastp	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
fastqc	biology/fastqc: Upgrade to 0.11.8	2019-09-21 02:44:54 +00:00
fasttree	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
fastx-toolkit
figtree
fluctuate
freebayes	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
garlic	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
gatk	biology/gatk: Update 4.1.3.0 -> 4.1.4.1	2020-01-20 02:12:37 +00:00
gemma	Fix math/openblas and bump dependent ports	2020-01-30 14:17:44 +00:00
gff2ps
gmap	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
gperiodic	- Update WWW	2020-01-19 09:30:22 +00:00
graphlan
grappa
groopm	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
haplohseq	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
hhsuite	devel/openmp: update to 9.0.0	2019-09-21 18:59:57 +00:00
hisat2
hmmer	biology/hmmer: update to 3.3	2020-01-29 05:55:12 +00:00
htslib
hyphy	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
igv
infernal	biology/infernal: update to 1.1.3	2020-01-27 17:57:14 +00:00
iolib
iqtree	biology/iqtree: Update to version 1.6.12	2019-08-27 01:19:11 +00:00
jalview	Clean up after java/openjdk6 and java/openjdk6-jre removal	2019-11-26 21:46:12 +00:00
jellyfish	Drop C++11 workaround for GCC < 6 after r449590	2019-09-14 22:01:13 +00:00
kallisto	biology/kallisto: Upgrade to 0.46.1	2019-11-06 00:18:14 +00:00
lagan	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
lamarc
libbigwig
libgtextutils
libsbml
mafft
mapm3
migrate
minimap2
molden	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
mopac	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
mothur	biology/mothur: Update 1.42.3 -> 1.43.0	2019-10-05 17:04:42 +00:00
mrbayes	Mark a few ports BROKEN, unfetchable	2019-11-06 12:48:32 +00:00
mummer	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
muscle	biology/muscle: unbreak in -CURRENT	2020-01-17 16:49:03 +00:00
ncbi-blast+	biology/ncbi-blast+: Upgrade to 2.10.0	2019-12-26 16:21:17 +00:00
ncbi-cxx-toolkit	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
ncbi-toolkit	biologi/ncbi-toolkit: Remove dependency on libXp	2019-09-28 10:52:57 +00:00
ngs-sdk	biology/ngs-sdk: Update 2.10.1 -> 2.10.2	2020-01-17 07:05:29 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene	Update *_DEPENDS	2020-01-08 18:36:30 +00:00
p5-Bio-Cluster	Update *_DEPENDS	2019-12-08 16:57:18 +00:00
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL	Add p5-Bio-DB-EMBL 1.7.4	2019-12-08 16:49:19 +00:00
p5-Bio-DB-NCBIHelper	Add p5-Bio-DB-NCBIHelper 1.7.6	2019-12-08 16:49:25 +00:00
p5-Bio-FeatureIO
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-Bio-Variation	Update to 1.7.5	2020-01-08 18:36:35 +00:00
p5-BioPerl	Update to 1.007007 (1.7.7)	2019-12-08 16:57:23 +00:00
p5-BioPerl-Run	Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago	2020-01-08 18:36:40 +00:00
p5-transdecoder	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
p5-TrimGalore	biology/p5-TrimGalore: Upgrade to 0.6.5	2019-11-26 16:20:12 +00:00
paml	biology/paml: Update to version 4.9j	2019-11-22 15:32:40 +00:00
pbbam	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
pbcopper	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
pbseqan	biology/unanimity and dependencies: Flag as no longer open source	2019-11-24 15:53:00 +00:00
pear-merger
phrap
phred	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
phylip	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
phyml	biology/phyml: disable -march=native	2019-12-06 13:04:41 +00:00
plinkseq	Mark a few ports BROKEN, unfetchable	2019-11-06 12:48:32 +00:00
primer3
prodigal	biology/prodigal: Eliminate a very old version from the portscout discovery process	2019-10-12 15:40:21 +00:00
prodigy-lig	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
protomol	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
psi88	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-biom-format	- Limit python version (does not build with 3.7+)	2019-11-08 12:12:42 +00:00
py-biopython	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-bx-python	biology/py-bx-python: Update 0.8.4 -> 0.8.6	2019-11-23 05:53:50 +00:00
py-cutadapt	biology/py-cutadapt: Upgrade to 2.7	2019-11-23 14:45:53 +00:00
py-dnaio	biology/py-dnaio: Upgrade to 0.4.1	2019-11-23 14:40:00 +00:00
py-fastTSNE	devel/openmp: update to 9.0.0	2019-09-21 18:59:57 +00:00
py-Genesis-PyAPI
py-gffutils	biology/py-gffutils: Update 0.9 -> 0.10	2019-12-31 05:16:09 +00:00
py-gtfparse	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-loompy	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-macs2	biology/py-macs2: Upgrade to 2.2.6	2020-01-11 14:20:00 +00:00
py-multiqc	biology/py-multiqc: Upgrade to 1.8	2019-11-26 16:25:08 +00:00
py-orange3-bioinformatics	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-orange3-single-cell	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-pyfaidx
py-pysam	biology/py-pysam: Update 0.15.3 -> 0.15.4	2020-01-23 02:53:09 +00:00
py-xenaPython
pyfasta	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
python-nexus
rainbow
recombine	Fix after gets(3) retirement using gets_s(3).	2019-09-02 05:00:43 +00:00
ruby-bio
rubygem-bio
samtools	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
seaview	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
seqan
seqan1	Fix some misspelled or duplicated LICENSE_*	2019-09-17 19:21:45 +00:00
seqan-apps	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
seqio
seqtk
seqtools	Mark a few ports BROKEN, unfetchable	2019-11-06 12:48:32 +00:00
sim4
slclust
smithwaterman
stacks	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
star	biology/star: Upgrade to 2.7.2d	2019-10-06 22:18:31 +00:00
stringtie
t_coffee	Mark a few ports BROKEN, unfetchable	2019-11-06 12:48:32 +00:00
tabixpp
tophat	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
treekin	Fix math/openblas and bump dependent ports	2020-01-30 14:17:44 +00:00
treepuzzle
trimadap
trimmomatic	Clean up after java/openjdk6 and java/openjdk6-jre removal	2019-11-26 21:46:12 +00:00
tRNAscan-SE	biology/tRNAscan-SE: update to 2.0.5	2020-01-13 17:36:57 +00:00
ugene	Mark a few ports BROKEN, unfetchable	2019-11-06 12:48:32 +00:00
vcflib
vcftools
velvet
viennarna	biology/viennarna: Update 2.4.13 -> 2.4.14	2020-01-06 04:17:48 +00:00
vsearch
wise	a-b: Add missing USES={gnome,php,sdl,xorg}	2019-11-08 09:27:56 +00:00
Makefile	Remove expired ports:	2020-01-27 15:34:18 +00:00