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Piotr Kubaj 29410b915b biology/tabixpp: fix build on GCC architectures 
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -fPIC -c tabix.cpp -Ihtslib
In file included from /usr/local/include/htslib/hts.h:37,
                 from /usr/local/include/htslib/tbx.h:30,
                 from tabix.hpp:5,
                 from tabix.cpp:1:
/usr/local/include/htslib/kstring.h: In function 'int ks_resize(kstring_t*, size_t)':
/usr/local/include/htslib/kstring.h:149: error: 'SIZE_MAX' was not declared in this scope
tabix.cpp: In constructor 'Tabix::Tabix(std::string&)':
tabix.cpp:15: warning: 'bgzf_is_bgzf' is deprecated (declared at /usr/local/include/htslib/bgzf.h:263)
tabix.cpp:15: warning: 'bgzf_is_bgzf' is deprecated (declared at /usr/local/include/htslib/bgzf.h:263)
2020-11-23 16:13:15 +00:00
..
abyss biology/abyss: Update 2.2.4 -> 2.2.5 2020-09-27 06:59:05 +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 Bump devel/jsoncpp consumers after r540853. 2020-06-30 17:46:18 +00:00
bcftools biology/bcftools: Upgrade to 1.11 2020-11-05 20:34:03 +00:00
bedtools biology/bedtools: Upgrade to 2.29.2 2019-12-19 01:04:11 +00:00
bioawk biology/bioawk: BWK awk modified for biological data 2020-06-05 02:45:33 +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 Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64. 2020-09-27 07:41:33 +00:00
bowtie biology/bowtie: Unbreak build with GCC 10 2020-07-04 10:46:08 +00:00
bowtie2 biology/bowtie2: Upgrade to 2.4.2 2020-11-07 13:47:41 +00:00
bwa biology/bwa: fix build on recent current 2020-08-28 11:17:13 +00:00
canu biology/canu: Upgrade to 2.1 2020-09-14 22:27:37 +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
cufflinks biology/cufflinks: fix build on recent current 2020-08-28 18:24:04 +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 version 2.0.4 2020-08-30 16:14:22 +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 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 biology/fastp: Upgrade to 0.20.1 2020-04-09 16:17:02 +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 Add education virtual category 2020-11-20 07:16:06 +00:00
fluctuate
freebayes Fix build with -fno-common 2020-09-21 18:14:57 +00:00
garlic Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
gatk biology/gatk: Fix build 2020-09-08 19:25:36 +00:00
gcta biology/gcta: Switch eigen3 dep to USES framework 2020-11-08 14:31:00 +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 biology/gmap: enable on powerpc64le 2020-10-09 13:23:12 +00:00
gperiodic - Update WWW 2020-01-19 09:30:22 +00:00
graphlan biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed 2020-08-14 04:59:29 +00:00
grappa Extend expiration of ports broken with -fno-common 2020-08-30 09:47:49 +00:00
groopm biology/groopm: Remove python's 2.7 restriction placed here by mistake 2020-08-13 19:19:23 +00:00
hhsuite biology/hhsuite: Update 3.2.0 -> 3.3.0 2020-08-27 04:28:24 +00:00
hisat2
hmmer Also enable on powerpc64le. 2020-09-24 20:29:35 +00:00
htslib biology/htslib: Upgrade to 1.11.0 2020-11-05 20:30:50 +00:00
hyphy biology/hyphy: Update to version 2.5.23 2020-11-19 10:53:55 +00:00
igv Deprecate java/openjfx8-devel consumers 2020-03-19 09:33:13 +00:00
infernal Also enable on powerpc64le. 2020-09-24 20:38:59 +00:00
iolib
iqtree biology/iqtree: Update to version 2.0.6 2020-05-30 18:43:26 +00:00
jalview Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
jellyfish biology/htslib: Upgrade to 1.10.2 2020-08-03 17:40:04 +00:00
kallisto biology/kallisto: Revert to 0.46.1 2020-08-03 15:45:21 +00:00
lagan Extend expiration of ports broken with -fno-common 2020-08-30 09:47:49 +00:00
lamarc
libbigwig New port: biology/libbigwig: C library for handling bigWig files (containing genomic data) 2019-07-11 17:05:22 +00:00
libgtextutils
libsbml Convert REINPLACE_CMD to patch file 2020-09-29 18:23:04 +00:00
linux-foldingathome Update to 7.6.13 2020-05-09 13:21:29 +00:00
mafft
mapm3 biology/mapm3: Reformat patches. 2020-09-04 12:24:23 +00:00
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: fix build on powerpc64le 2020-10-19 10:30:11 +00:00
mrbayes - Swap back from net/openmpi3 to net/openmpi 2020-04-21 21:47:57 +00:00
mummer biology/mummer: fix build on powerpc64 elfv2 and powerpc64le 2020-10-25 23:03:14 +00:00
muscle biology/muscle: unbreak in -CURRENT 2020-01-17 16:49:03 +00:00
ncbi-blast+ biology/ncbi-blast+: Upgrade to 2.11.0 2020-11-16 18:25:03 +00:00
ncbi-cxx-toolkit biology/ncbi-cxx-toolkit: Fix build on 13 2020-09-27 04:57:44 +00:00
ncbi-toolkit Chase security/p11-kit update 2020-08-30 03:10:23 +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 Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113 2020-06-26 11:55:23 +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: fix the build with LLVM 11 2020-08-20 17:07:03 +00:00
pbbam biology/htslib: Upgrade to 1.10.2 2020-08-03 17:40:04 +00:00
pbseqan biology/unanimity and dependencies: Flag as no longer open source 2019-11-24 15:53:00 +00:00
pear-merger
phrap Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1). 2020-05-27 11:59:13 +00:00
phred Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
phylip Extend expiration of ports broken with -fno-common 2020-08-30 09:47:49 +00:00
phyml biology/phyml: fix build on recent current 2020-08-29 08:34:27 +00:00
picard-tools biology/picard-tools: Remove extraneous file 2020-08-30 14:06:54 +00:00
plink Allow building on powerpc64le. 2020-09-27 07:44:15 +00:00
pooler biology/pooler: Optimise DNA sequencing primer-set combinations 2020-11-15 18:50:17 +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 Unbreak bulk -a 2020-06-13 15:05:44 +00:00
protomol Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
psi88 biology/psi88: Unbreak build with GCC 10 2020-07-04 12:15:58 +00:00
py-biom-format biology/py-biom-format: Fix fetch and relax scipy requirement 2020-09-26 09:10:37 +00:00
py-biopython biology/py-biopython: Upgrade to 1.78 2020-10-16 19:12:43 +00:00
py-bx-python biology/py-bx-python: Update 0.8.8 -> 0.8.9 2020-06-26 04:17:11 +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 0.4.2 2020-05-24 15:23:15 +00:00
py-ete3 Update PyQt to 5.15.0, py-sip to 4.19.24 and qscintilla2 to 2.11.5 2020-10-05 15:50:03 +00:00
py-fastTSNE Drop dependency on devel/openmp 2020-03-08 21:56:36 +00:00
py-Genesis-PyAPI
py-gffutils Unbreak bulk -a 2020-07-14 07:59:28 +00:00
py-gtfparse biology/py-gtfparse: Update 1.2.0 -> 1.2.1 2020-08-07 04:13:00 +00:00
py-hits New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments 2020-05-16 03:11:05 +00:00
py-loompy biology/py-loompy: Update 2.0.17 -> 3.0.6 2020-06-16 02:26:08 +00:00
py-macs2 biology/py-macs2: Upgrade to 2.2.7.1 2020-04-14 12:13:55 +00:00
py-multiqc Unbreak bulk -a 2020-09-19 14:15:42 +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 Update Sphinx 2020-05-11 23:51:58 +00:00
py-pandas-charm Clean up some things 2020-05-30 00:57:02 +00:00
py-pyfaidx biology/py-pyfaidx: Update 0.5.5.2 -> 0.5.9.1 2020-09-13 19:05:30 +00:00
py-pysam biology/py-pysam: Update 0.16.0 -> 0.16.0.1 2020-11-15 19:26:37 +00:00
py-scikit-bio Add education virtual category 2020-11-20 07:16:06 +00:00
py-xenaPython biology/py-xenaPython: Update 1.0.10 -> 1.0.14 2020-11-11 05:27:43 +00:00
pyfasta Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
python-nexus
rainbow Update WWW 2020-03-31 23:18:09 +00:00
recombine Fix after gets(3) retirement using gets_s(3). 2019-09-02 05:00:43 +00:00
ruby-bio biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser 2020-05-05 14:22:09 +00:00
rubygem-bio Update to 2.0.1 2020-07-24 07:49:43 +00:00
rubygem-bio-executables Add rubygem-bio-executables 1.0.0 2020-07-24 07:08:00 +00:00
rubygem-bio-old-biofetch-emulator Add rubygem-bio-old-biofetch-emulator 1.0.0 2020-07-24 07:08:05 +00:00
rubygem-bio-shell Add rubygem-bio-shell 1.0.0 2020-07-24 07:08:11 +00:00
samtools biology/samtools: Upgrade to 1.11 2020-11-05 20:32:39 +00:00
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 5.0.3=>5.0.4 2020-06-22 17:34:44 +00:00
seqan
seqan-apps devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
seqan1 Fix some misspelled or duplicated LICENSE_* 2019-09-17 19:21:45 +00:00
seqio
seqtk
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 2.7.3a 2020-04-09 12:43:03 +00:00
stringtie biology/stringtie: fix build on GCC architectures 2020-02-23 10:52:44 +00:00
subread biology/subread: Add -fcommon for clang 11 2020-09-18 00:57:35 +00:00
tabixpp biology/tabixpp: fix build on GCC architectures 2020-11-23 16:13:15 +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 biology/ugene: prepare for Qt5-5.15 2020-05-19 18:00:02 +00:00
vcflib biology/htslib: Upgrade to 1.10.2 2020-08-03 17:40:04 +00:00
vcftools
velvet
viennarna biology/viennarna: Update 2.4.15 -> 2.4.16 2020-11-11 23:27:38 +00:00
vsearch biology/vsearch: Update to 2.15.0 2020-06-20 14:31:59 +00:00
vt biology/vt: Fix build with htslib 1.11 2020-11-09 00:35:58 +00:00
wise a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
Makefile biology/pooler: Optimise DNA sequencing primer-set combinations 2020-11-15 18:50:17 +00:00