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freebsd-ports/biology
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Jason W. Bacon df8230f473 ncbi-blast+: Unbreak build with gcc8 following gcc9 patch 
GCC 8 and 9 are incompatible in handling const variables with OpenMP
default(none).  All const variables default to shared even with default(none)
present.  8 errors out if a const variable is explicitly defined as shared and
9 requires an explicit definition.

Using an upstream trunk patch for now, which checks the compiler version.
Also discussing more portable approaches to avoid future issues.

Reported by:    jrm
2019-07-12 23:58:22 +00:00
..
abyss biology/abyss: fix build on big-endian architectures 2019-06-21 11:43:09 +00:00
artemis biology/artemis: Update 9 -> 17.0.1-11 2018-06-11 17:45:56 +00:00
avida Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
babel
bamtools Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
bcftools biology/bcftools: update to 1.9 2018-08-02 19:30:57 +00:00
bedtools biology/bedtools: unbreak with libc++ 8 2019-03-04 06:55:08 +00:00
biococoa Move Objective-C ports to the v2 GNUstep ABI. 2019-02-03 15:37:58 +00:00
bolt-lmm biology/bolt-lmm: Mixed model association testing and variance component analysis 2019-05-26 03:36:49 +00:00
bowtie Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
bowtie2 biology/bowtie2: Clarify CPU-specificity 2019-04-24 17:41:27 +00:00
bwa
canu biology/canu: Fix build on powerpc64 and aarch64 2019-04-18 12:15:56 +00:00
cd-hit biology/cd-hit: Upgrade to 4.8.1 2019-03-14 23:59:47 +00:00
cdbfasta
checkm Bump a few PORTREVISIONs after r498529 2019-04-10 06:18:31 +00:00
chemeq
clustal-omega biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw 2018-05-21 22:15:26 +00:00
clustalw biology/clustalw: Fix license, take maintainership 2018-05-21 01:13:40 +00:00
consed
cufflinks biology/cufflinks: Fix build on i386 by removing the hard-coded -m64 2019-05-29 07:02:28 +00:00
cytoscape biology/cytoscape: Fix license 2018-08-12 06:29:51 +00:00
ddocent biology/ddocent: Upgrade to 2.7.8 2019-05-04 15:09:10 +00:00
diamond biology/diamond: Update to version 0.9.24 2018-12-31 19:00:00 +00:00
dsr-pdb devel/boost-*: update to 1.70.0 2019-04-12 06:36:31 +00:00
emboss
exonerate New port: biology/exonerate: Generic tool for sequence alignment 2018-07-13 07:02:16 +00:00
fasta
fasta3
fastahack biology/fastahack: Utility for indexing and sequence extraction from FASTA files 2018-04-16 14:50:46 +00:00
fastdnaml
fastool
fastp biology/fastp: Remove redundant USE_GCC 2019-05-20 23:41:08 +00:00
fastqc
fasttree Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
fastx-toolkit biology/fastx-toolkit: Fix build on FreeBSD 12 2018-05-16 15:13:43 +00:00
figtree New port: biology/figtree: Graphical viewer of phylogenetic trees 2019-02-03 21:14:38 +00:00
fluctuate
freebayes Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
garlic
gatk devel/gradle: Update to 5.0 2018-12-04 17:53:46 +00:00
gemma biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC 2019-05-18 22:41:15 +00:00
gff2ps biology/gff2ps: update 0.98d to 0.98l 2018-12-19 17:34:29 +00:00
gmap Enable workaround for building on powerpc64. 2019-06-21 11:15:08 +00:00
gperiodic
graphlan New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees 2019-02-03 20:13:26 +00:00
grappa
groopm biology/groopm fails to build with python3 2019-01-07 09:44:42 +00:00
hhsuite biology/hhsuite: Fix build on platforms where SIMD instruction set doesn't exist or isn't detected. 2019-05-22 02:50:56 +00:00
hisat2 New port: biology/hisat2: Program for mapping next-generation sequencing reads 2019-01-11 16:02:05 +00:00
hmmer vec_splats function is not supported by base GCC. Add USES=compiler:c11 2019-02-18 01:30:24 +00:00
htslib biology/htslib: update to 1.9 2018-08-02 19:27:13 +00:00
hyphy Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
igv biology/igv: Update 2.5.2 -> 2.5.3 2019-06-01 20:49:20 +00:00
infernal Allow building on powerpc64. 2018-09-27 23:02:56 +00:00
iolib - Fix build in head i386 2019-04-01 19:33:15 +00:00
iqtree biology/iqtree: Update to version 1.6.11 2019-06-24 21:47:34 +00:00
jalview
jellyfish biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64 2019-05-13 16:23:35 +00:00
kallisto biology/kallisto: Upgrade to 0.46.0 2019-06-12 15:24:55 +00:00
lagan
lamarc biology/lamarc: Fix build with Clang 6 2018-08-25 03:13:37 +00:00
libbigwig New port: biology/libbigwig: C library for handling bigWig files (containing genomic data) 2019-07-11 17:05:22 +00:00
libgtextutils biology/libgtextutils: Unbreak for FreeBSD 12 2018-03-29 15:41:07 +00:00
libsbml Use USES=pathfix 2019-06-22 21:48:14 +00:00
linux-foldingathome biology/linux-foldingathome: reset maintainer by request 2018-07-27 02:19:43 +00:00
mafft
mapm3
migrate Mark broken on armvX and mips. 2018-03-18 13:48:07 +00:00
minimap2 biology/minimap2: Upgrade to 2.17 2019-05-05 14:56:07 +00:00
molden Related to revision 499061 bump ports with USES=fortran to have them 2019-04-22 13:16:33 +00:00
mopac Related to revision 499061 bump ports with USES=fortran to have them 2019-04-22 13:16:33 +00:00
mothur biology/mothur: Update 1.42.2 -> 1.42.3 2019-06-28 04:02:22 +00:00
mrbayes Update devel/readline to 8.0 2019-04-09 14:04:49 +00:00
mummer Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
muscle
ncbi-blast+ ncbi-blast+: Unbreak build with gcc8 following gcc9 patch 2019-07-12 23:58:22 +00:00
ncbi-cxx-toolkit Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
ncbi-toolkit Update security/nettle to 3.5.1 2019-07-09 17:13:07 +00:00
ngs-sdk Mark this port as not buildable on powerpc64: 2019-06-25 12:17:04 +00:00
p5-AcePerl Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-ASN1-EntrezGene Update to 1.73 2018-10-10 10:23:10 +00:00
p5-Bio-Cluster Add p5-Bio-Cluster 1.7.3 2019-02-20 20:46:37 +00:00
p5-Bio-Coordinate Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Das Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Das-Lite Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-FeatureIO Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-GFF3 Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Glite Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Graphics Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-MAGETAB Fix typo 2019-04-23 14:11:50 +00:00
p5-Bio-NEXUS Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Phylo Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-SCF - Add LICENSE 2019-03-30 09:01:08 +00:00
p5-BioPerl Update to 1.007005 (1.7.5) 2019-02-22 19:54:12 +00:00
p5-BioPerl-Run Update to 1.007003 2019-02-20 20:46:58 +00:00
p5-transdecoder Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
p5-TrimGalore biology/p5-TrimGalore: Upgrade to 0.6.1 2019-03-24 21:44:17 +00:00
paml biology/paml: Update to version 4.9i 2019-02-26 15:12:42 +00:00
pbbam devel/boost-*: update to 1.70.0 2019-04-12 06:36:31 +00:00
pbcopper devel/boost-*: update to 1.70.0 2019-04-12 06:36:31 +00:00
pbseqan biology/pbseqan: Mark deprecated 2019-02-20 01:53:35 +00:00
pear-merger Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
phrap Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
phred Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
phylip
phyml - Update to 3.3.20190321 2019-05-20 09:17:29 +00:00
plinkseq
primer3 biology/primer3: Fix build with Clang 6 2018-08-25 03:35:46 +00:00
prodigal New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes 2019-02-03 18:08:14 +00:00
prodigy-lig New port: biology/prodigy-lig: Prediction of protein-small molecule binding affinities 2019-02-03 18:49:23 +00:00
protomol biology/protomol: Fix doubled USES overwriting the old value 2018-08-25 03:47:25 +00:00
psi88 Related to revision 499061 bump ports with USES=fortran to have them 2019-04-22 13:16:33 +00:00
py-biom-format Bump a few PORTREVISIONs after r498529 2019-04-10 06:18:31 +00:00
py-biopython - Update WWW 2019-07-08 09:32:08 +00:00
py-bx-python biology/py-bx-python: Update 0.8.2 -> 0.8.4 2019-06-19 08:08:31 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 2.3 2019-04-27 01:26:17 +00:00
py-dnaio biology/py-dnaio: Read and write FASTQ and FASTA 2019-03-24 19:40:26 +00:00
py-fastTSNE devel/openmp: phase out 2019-05-08 16:05:53 +00:00
py-Genesis-PyAPI Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-gffutils Bump a few PORTREVISIONs after r498529 2019-04-10 06:18:31 +00:00
py-gtfparse Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-loompy biology/py-loompy: Update 2.0.16 -> 2.0.17 2019-02-02 21:38:48 +00:00
py-macs2 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-orange3-bioinformatics Fix Qt5 symbol version scripts to put the catch-all clause first. When 2019-01-16 11:13:44 +00:00
py-orange3-single-cell Fix Qt5 symbol version scripts to put the catch-all clause first. When 2019-01-16 11:13:44 +00:00
py-pyfaidx Bump a few PORTREVISIONs after r498529 2019-04-10 06:18:31 +00:00
py-pysam biology/py-pysam: Update 0.15.1 -> 0.15.2 2019-01-26 04:15:54 +00:00
py-xenaPython New port: biology/py-xenaPython: API for Xena Hub to access genetic information shared through the hub 2019-04-12 17:01:10 +00:00
pycogent Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
pyfasta - Update WWW 2019-02-07 09:30:40 +00:00
python-nexus - Update to 1.63 2018-09-22 08:54:58 +00:00
rainbow biology/rainbow: Efficient clustering and assembling of short reads 2018-04-02 16:50:46 +00:00
recombine
ruby-bio
rubygem-bio Update to 1.5.2 2018-09-21 18:08:24 +00:00
samtools biology/samtools: update to 1.9 2018-08-02 19:28:36 +00:00
seaview biology/seaview: Fix build with Clang 6 2018-09-08 09:01:35 +00:00
seqan
seqan-apps devel/boost-*: update to 1.70.0 2019-04-12 06:36:31 +00:00
seqan1
seqio
seqtk biology/seqtk: Tool for processing sequences in FASTA/FASTQ format 2018-04-03 20:57:05 +00:00
seqtools biology/seqtools: fix build on current, if lld is lld7 2019-01-07 19:54:40 +00:00
sim4
slclust
smithwaterman biology/smithwaterman: Smith-waterman-gotoh alignment algorithm 2018-04-15 17:45:52 +00:00
stacks biology/stacks: Remove obsolete pkg-message regarding web interface 2019-05-10 21:15:42 +00:00
star biology/star: Force newer GCC on platforms with GCC 4.2 base 2019-05-02 00:39:51 +00:00
stringtie New port: biology/stringtie: Transcript assembly and quantification for RNA-seq 2018-07-11 21:32:39 +00:00
t_coffee Related to revision 499061 bump ports with USES=fortran to have them 2019-04-22 13:16:33 +00:00
tabixpp biology/tabixpp: C++ wrapper to tabix indexer 2018-04-14 23:52:16 +00:00
treekin New port: biology/treekin: Efficient computation of RNA folding dynamics 2019-06-15 20:37:06 +00:00
treepuzzle
trimadap biology/trimadap: Mark only for amd64 and i386 2019-05-11 00:18:24 +00:00
trimmomatic
tRNAscan-SE biology/tRNAscan-SE: Update to 2.0.3 2019-06-08 01:31:18 +00:00
ugene Fix Qt5 symbol version scripts to put the catch-all clause first. When 2019-01-16 11:13:44 +00:00
unanimity Clean up plist 2019-04-25 13:25:50 +00:00
vcflib Mark these ports as broken on aarch64. 2018-06-22 00:03:08 +00:00
vcftools biology/vcftools: Update to 0.1.16, a security release 2018-08-04 01:29:29 +00:00
velvet
viennarna biology/viennarna: Make it less/not prone to failures due to hardcoded C++ library name 2019-06-24 19:30:15 +00:00
vsearch biology/vsearch: Update to 2.13.4 2019-05-11 13:42:33 +00:00
wise
Makefile New port: biology/libbigwig: C library for handling bigWig files (containing genomic data) 2019-07-11 17:05:22 +00:00