Mark Linimon f5d9ceebea Mark as BROKEN on powerpc64: ... utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error: 'get_deleter' declared as a 'virtual' field This may have something to do with compiler:openmp in USES. However, it has broken for more than 6 months at this point. Approved by: portmgr (tier-2 blanket)		2020-05-17 02:25:16 +00:00
..
abyss	Drop dependency on devel/openmp	2020-03-08 21:56:36 +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	Return theraven's ports to the pool after safekeeping his commit bit.	2020-03-05 20:49:05 +00:00
bolt-lmm	Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.	2020-05-06 16:11:14 +00:00
bowtie
bowtie2	Update devel/tbb to 2020.2 and bump dependent port's revisions	2020-04-01 14:14:51 +00:00
bwa
canu	Mark as BROKEN on powerpc64:	2020-05-17 02:25:16 +00:00
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks	biology/cufflinks: Update 2.2.1-83 -> 2.2.1-89	2020-03-31 06:42:22 +00:00
cytoscape	Clean up after java/openjdk6 and java/openjdk6-jre removal	2019-11-26 21:46:12 +00:00
ddocent
diamond	biology/diamond: Update to version 0.9.32	2020-04-24 23:04:14 +00:00
dsr-pdb	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
emboss	- update libgd to 2.3.0	2020-05-04 21:31:39 +00:00
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp	biology/fastp: Upgrade to 0.20.1	2020-04-09 16:17:02 +00:00
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
gatk	Preserve Gradle 6.2.2 for biology/gatk	2020-05-06 13:11:49 +00:00
gcta	Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.	2020-05-06 16:11:14 +00:00
gemma	Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas	2020-05-06 16:39:12 +00:00
gff2ps
gmap
gperiodic	- Update WWW	2020-01-19 09:30:22 +00:00
graphlan	Deprecate a few ports	2020-02-23 15:25:53 +00:00
grappa
groopm	Deprecate a few ports	2020-02-23 15:25:53 +00:00
haplohseq	Deprecate some ports using deprecated version of python	2020-03-08 17:01:46 +00:00
hhsuite	biology/hhsuite: fix build on powerpc64 elfv2	2020-05-11 19:33:32 +00:00
hisat2
hmmer	biology/hmmer: update to 3.3	2020-01-29 05:55:12 +00:00
htslib
hyphy	biology/hyphy: Update to version 2.5.12	2020-05-03 02:08:19 +00:00
igv	Deprecate java/openjfx8-devel consumers	2020-03-19 09:33:13 +00:00
infernal	biology/infernal: update to 1.1.3	2020-01-27 17:57:14 +00:00
iolib
iqtree	biology/iqtree: Update to version 2.0.4	2020-05-02 20:32:33 +00:00
jalview	Clean up after java/openjdk6 and java/openjdk6-jre removal	2019-11-26 21:46:12 +00:00
jellyfish	biology/jellyfish: Patch for clang 10	2020-03-07 19:25:54 +00:00
kallisto	kallisto: Patch for build with GCC	2020-04-01 23:35:38 +00:00
lagan
lamarc
libbigwig
libgtextutils
libsbml	Clean up Makefile	2020-02-08 19:01:40 +00:00
linux-foldingathome	Update to 7.6.13	2020-05-09 13:21:29 +00:00
mafft
mapm3
migrate
minimap2
molden	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
mopac
mothur	Update devel/gmake to 4.3.	2020-05-09 19:24:49 +00:00
mrbayes	- Swap back from net/openmpi3 to net/openmpi	2020-04-21 21:47:57 +00:00
mummer
muscle	biology/muscle: unbreak in -CURRENT	2020-01-17 16:49:03 +00:00
ncbi-blast+	Bump PORTREVISION for security/nettle shlib change	2020-05-16 10:51:32 +00:00
ncbi-cxx-toolkit	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
ncbi-toolkit	Bump PORTREVISION for security/nettle shlib change	2020-05-16 10:51:32 +00:00
ngs-sdk	biology/ngs-sdk: Update 2.10.4 -> 2.10.5	2020-04-04 20:09:00 +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	Cosmetic change	2020-04-02 12:01:30 +00:00
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	Cosmetic change	2020-04-02 12:01:35 +00:00
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
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	Mark BROKEN: fails to build	2020-03-10 14:17:19 +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
phylip	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
phyml	- Swap back from net/openmpi3 to net/openmpi	2020-04-21 21:51:56 +00:00
plink	Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas	2020-05-06 16:39:12 +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
protomol	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
psi88
py-biom-format	Deprecate a few ports	2020-02-23 15:25:53 +00:00
py-biopython
py-bx-python	biology/py-bx-python: Update 0.8.6 -> 0.8.8	2020-02-15 20:08:30 +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-ete3	New port: biology/py-ete3: Framework for the analysis and visualization of trees	2020-05-16 00:13:09 +00:00
py-fastTSNE	Drop dependency on devel/openmp	2020-03-08 21:56:36 +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
py-hits	New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments	2020-05-16 03:11:05 +00:00
py-loompy
py-macs2	biology/py-macs2: Upgrade to 2.2.7.1	2020-04-14 12:13:55 +00:00
py-multiqc	biology/py-multiqc: Upgrade to 1.8	2019-11-26 16:25:08 +00:00
py-orange3-bioinformatics
py-orange3-single-cell	Update Sphinx	2020-05-11 23:51:58 +00:00
py-pandas-charm	New port: biology/py-pandas-charm: Library for getting character matrices into and out of pandas	2020-05-16 00:14:16 +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-scikit-bio	biology/py-scikit-bio: Fix license	2020-05-16 02:29:20 +00:00
py-xenaPython
pyfasta
python-nexus
rainbow	Update WWW	2020-03-31 23:18:09 +00:00
recombine
ruby-bio	biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser	2020-05-05 14:22:09 +00:00
rubygem-bio
samtools
scrm	Add compiler:c++11-lang to USES to fix build on GCC-based systems:	2020-05-15 07:30:34 +00:00
seaview	biology/seaview: Update version 5.0=>5.0.2	2020-03-22 16:54:04 +00:00
seqan
seqan1
seqan-apps	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
seqio
seqtk
sim4
slclust
smithwaterman
stacks
star	biology/star: Upgrade to 2.7.3a	2020-04-09 12:43:03 +00:00
stringtie	biology/stringtie: fix build on GCC architectures	2020-02-23 10:52:44 +00:00
tabixpp
tophat	Deprecate some ports using deprecated version of python	2020-03-08 17:01:46 +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	- Resurrect and unbreak by updating to version 34.0	2020-05-10 15:42:32 +00:00
vcflib
vcftools
velvet
viennarna	- update libgd to 2.3.0	2020-05-04 21:31:39 +00:00
vsearch	biology/vsearch: Upgrade to 2.14.2	2020-02-19 22:34:36 +00:00
wise	a-b: Add missing USES={gnome,php,sdl,xorg}	2019-11-08 09:27:56 +00:00
Makefile	New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments	2020-05-16 03:11:05 +00:00