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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
avida
babel
bamtools
bcftools
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
bowtie2
bwa
canu
cd-hit
cdbfasta
checkm biology/checkm: Update 1.0.12 -> 1.0.13 2019-02-09 22:58:09 +00:00
chemeq
clustal-omega
clustalw
clustalx
consed
cytoscape
ddocent
diamond
dsr-pdb biology/dsr-pdb: Correct typo 2019-02-05 19:01:59 +00:00
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastqc
fasttree
fastx-toolkit
figtree New port: biology/figtree: Graphical viewer of phylogenetic trees 2019-02-03 21:14:38 +00:00
fluctuate
freebayes
garlic
gatk
gff2ps
gmap
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
hyphy
igv biology/igv: Update 2.4.16 -> 2.4.19 2019-02-23 21:23:51 +00:00
infernal
iolib
iqtree biology/iqtree: Update to version 1.6.10 2019-02-21 14:33:43 +00:00
jalview
jellyfish
kallisto kallisto: Upgrade to 0.45.1, unbundle hstlib 2019-02-24 20:32:19 +00:00
lagan
lamarc
libgtextutils
libsbml
linux-foldingathome
mafft
mapm3
migrate
molden
mopac
mrbayes
mummer
muscle
ncbi-blast+ Update dns/libidn2 to 2.1.1 2019-02-09 23:25:36 +00:00
ncbi-cxx-toolkit
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
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster Add p5-Bio-Cluster 1.7.3 2019-02-20 20:46:37 +00:00
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
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-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
p5-TrimGalore
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
phrap
phred
phylip
phyml
plinkseq
primer3
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
psi88
py-biom-format
py-biopython
py-bx-python
py-cutadapt
py-fastTSNE
py-Genesis-PyAPI
py-gffutils
py-gtfparse
py-loompy biology/py-loompy: Update 2.0.16 -> 2.0.17 2019-02-02 21:38:48 +00:00
py-macs2
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
py-pysam biology/py-pysam: Update 0.15.1 -> 0.15.2 2019-01-26 04:15:54 +00:00
pycogent
pyfasta - Update WWW 2019-02-07 09:30:40 +00:00
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools
seaview
seqan
seqan1
seqan-apps
seqio
seqtk
seqtools biology/seqtools: fix build on current, if lld is lld7 2019-01-07 19:54:40 +00:00
sim4
slclust
smithwaterman
stacks biology/stacks: Upgrade to 2.3 2019-01-12 15:53:00 +00:00
stringtie
t_coffee
tabixpp
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
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
vcftools
velvet
wise
Makefile New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end sequence assembler 2019-02-25 07:56:45 +00:00