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freebsd-ports/biology
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Jan Beich af3cf39e99 biology/bedtools: unbreak with libc++ 8 
In file included from FileReader.cpp:1:
In file included from /usr/include/c++/v1/iostream:38:
In file included from /usr/include/c++/v1/ios:216:
In file included from /usr/include/c++/v1/__locale:15:
In file included from /usr/include/c++/v1/string:505:
In file included from /usr/include/c++/v1/string_view:176:
In file included from /usr/include/c++/v1/__string:57:
In file included from /usr/include/c++/v1/algorithm:640:
In file included from /usr/include/c++/v1/initializer_list:47:
In file included from /usr/include/c++/v1/cstddef:38:
../../../utils//gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^

PR:		236192
Approved by:	portmgr blanket
2019-03-04 06:55:08 +00:00
..
abyss New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end sequence assembler 2019-02-25 07:56:45 +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
bowtie Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
bowtie2 Update devel/tbb to version 2019.1 and bump dependent ports' revisions 2018-10-11 14:47:13 +00:00
bwa Multiple ports: 2018-01-31 01:07:07 +00:00
canu Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
cd-hit Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
cdbfasta Multiple ports: 2018-01-31 01:07:07 +00:00
checkm biology/checkm: Update 1.0.12 -> 1.0.13 2019-02-09 22:58:09 +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
clustalx Mark QT4 ports/functionality for removal on 2019-03-15 2018-12-02 15:41:47 +00:00
consed
cytoscape biology/cytoscape: Fix license 2018-08-12 06:29:51 +00:00
ddocent Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
diamond biology/diamond: Update to version 0.9.24 2018-12-31 19:00:00 +00:00
dsr-pdb biology/dsr-pdb: Correct typo 2019-02-05 19:01:59 +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 Multiple ports: 2018-01-31 01:07:07 +00:00
fastqc [new port] biology/fastqc: Quality control tool for high throughput sequence data 2017-11-30 22:54:29 +00:00
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 Return maho@'s ports to the pool after his commit bit expired. 2018-03-11 11:20:43 +00:00
gatk devel/gradle: Update to 5.0 2018-12-04 17:53:46 +00:00
gff2ps biology/gff2ps: update 0.98d to 0.98l 2018-12-19 17:34:29 +00:00
gmap Multiple ports: 2018-01-31 01:07:07 +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
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 2.4.16 -> 2.4.19 2019-02-23 21:23:51 +00:00
infernal Allow building on powerpc64. 2018-09-27 23:02:56 +00:00
iolib Remove the incorrect typedefs to fix build on tier-2. 2018-11-05 19:45:23 +00:00
iqtree biology/iqtree: Update to version 1.6.10 2019-02-21 14:33:43 +00:00
jalview
jellyfish Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
kallisto kallisto: Upgrade to 0.45.1, unbundle hstlib 2019-02-24 20:32:19 +00:00
lagan
lamarc biology/lamarc: Fix build with Clang 6 2018-08-25 03:13:37 +00:00
libgtextutils biology/libgtextutils: Unbreak for FreeBSD 12 2018-03-29 15:41:07 +00:00
libsbml Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +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
molden Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
mrbayes
mummer Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
muscle
ncbi-blast+ Update dns/libidn2 to 2.1.1 2019-02-09 23:25:36 +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 dns/libidn2 to 2.1.1 2019-02-09 23:25:36 +00:00
ngs-sdk biology/ngs-sdk: Update 2.9.3 -> 2.9.4 2019-02-23 21:55:55 +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 every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-NEXUS Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Phylo Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-SCF Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +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 [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming 2017-12-09 13:23:32 +00:00
paml biology/paml: Update to version 4.9i 2019-02-26 15:12:42 +00:00
pbbam biology/pbbam: Upgrade to 0.18.0 release 2019-02-19 23:03:41 +00:00
pbcopper biology/pbcopper: Upgrade to 0.4.1 release 2019-02-19 22:20:11 +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 - Update to 3.697 2018-01-01 08:40:22 +00:00
phyml Change 4 ports from net/mpich2 to net/mpich 2018-09-22 18:00:24 +00:00
plinkseq Multiple ports: 2018-01-31 01:07:07 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-biom-format Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-biopython - Update to 1.73 2018-12-22 04:54:51 +00:00
py-bx-python Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 1.18 2018-09-20 14:10:52 +00:00
py-fastTSNE New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNE 2018-12-15 08:58:05 +00:00
py-Genesis-PyAPI Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-gffutils New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework 2018-10-19 02:06:53 +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 biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2 2018-10-28 04:34:14 +00:00
py-pysam biology/py-pysam: Update 0.15.1 -> 0.15.2 2019-01-26 04:15:54 +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 biology/seqan-apps, biology/seqan: Update to 2.4.0 2018-03-10 06:21:37 +00:00
seqan-apps Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
seqan1
seqio - Switch to options helpers 2017-11-26 09:00:21 +00:00
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 Multiple ports: 2018-01-31 01:07:07 +00:00
smithwaterman biology/smithwaterman: Smith-waterman-gotoh alignment algorithm 2018-04-15 17:45:52 +00:00
stacks biology/stacks: Upgrade to 2.3 2019-01-12 15:53:00 +00:00
stringtie New port: biology/stringtie: Transcript assembly and quantification for RNA-seq 2018-07-11 21:32:39 +00:00
t_coffee Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
tabixpp biology/tabixpp: C++ wrapper to tabix indexer 2018-04-14 23:52:16 +00:00
treepuzzle
trimadap Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
trimmomatic Multiple ports: 2018-01-31 01:07:07 +00:00
tRNAscan-SE - Unbreak by adding missing pkg-plist 2018-09-28 00:12:48 +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 biology/unanimity: Upgrade to 3.4.1 2019-02-24 16:04:58 +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 - Convert to option helper install target (add OPTIONS_DEFINE=DOCS 2018-01-11 18:09:00 +00:00
wise
Makefile New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end sequence assembler 2019-02-25 07:56:45 +00:00