Robert Clausecker 8e2ec289a2 biology/phyml: fix build on non-x86 ... - only initialise x86-only fields on x86. - make code compatible with platforms where char is unsigned Obtained from: 9c55b683c8 MFH: 2023Q2		2023-05-08 10:25:50 +02:00
..
abyss	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
ad2vcf
artemis
atac-seq	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
augustus	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
avida
babel
bamtools
bamutil
barrnap	biology/barrnap: Update descr	2022-11-24 19:12:18 -08:00
bbmap
bcf-score	biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics	2023-02-25 08:27:46 -06:00
bcftools	biology/bcftools: Update to 1.17	2023-02-24 17:30:58 -06:00
bedtools	biology/bedtools: Update to 2.31.0	2023-04-28 20:03:07 -05:00
bfc
bio-mocha	biology/bio-mocha: Update to 1.16	2023-01-05 17:21:03 -06:00
bioawk
biococoa	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
biolibc	biology/biolibc: Update to 0.2.4	2022-12-11 14:06:23 -06:00
biolibc-tools	biology/biolibc-tools: Update to 0.1.4.1	2022-12-13 18:11:56 -06:00
bioparser
biosig	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
biosoup	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
biostar-tools	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
bolt-lmm	*/*: bump all direct Boost cunsumers	2023-04-27 21:25:55 +03:00
bowtie
bowtie2	biology/bowtie2: Update to 2.5.1	2023-01-21 16:30:48 -06:00
bwa
canu	*/*: Refactor java/openjdk7 removal	2023-04-04 13:10:53 -05:00
cd-hit
cdbfasta
checkm	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
clustal-omega
clustalw
cufflinks	*/*: bump all direct Boost cunsumers	2023-04-27 21:25:55 +03:00
cytoscape	biology/cytoscape: Broken on armv6, armv7	2022-12-10 23:41:04 -08:00
ddocent	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
diamond	biology/diamond: Update to 2.1.6	2023-03-18 12:49:03 -03:00
dsr-pdb	*/*: bump all direct Boost cunsumers	2023-04-27 21:25:55 +03:00
edlib
emboss	biology/emboss: Ignore with mysql 8.0	2023-02-01 04:39:38 -06:00
erminej
exonerate
fasda	biology/fasda: Fast and simple differential analysis	2022-12-12 11:17:22 -06:00
fasta
fasta3
fastahack
fastdnaml
fastool
fastp	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
fastq-trim	biology/fastq-trim: Update to 0.1.2	2022-12-11 15:24:05 -06:00
fastqc	biology/fastqc: Update to 0.12.1	2023-03-04 18:17:20 -06:00
fasttree
fastx-toolkit	biology/fastx-toolkit: Unbreak build on 14-CURRENT	2023-03-07 11:28:13 -06:00
figtree
flash
fluctuate
freebayes	biology/freebayes: Drop redundant tabixpp dep	2023-01-22 10:42:34 -06:00
garlic
gatk	biology/gatk: Update 4.2.6.1 -> 4.3.0.0	2022-11-26 20:06:47 -08:00
gcta	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
gemma	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
generand
gff2ps
gffread
gmap
gperiodic	accessibility/at-spi2-core: update to 2.46.0	2023-03-02 06:23:10 +01:00
graphlan
groopm	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
haplohseq	*/*: bump all direct Boost cunsumers	2023-04-27 21:25:55 +03:00
hhsuite	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
hisat2
hmmer	biology/hmmer: Update to 3.3.2	2022-10-11 15:13:01 -05:00
htslib	biology/htslib: fix build on armv7	2023-04-18 23:55:29 +02:00
hyphy	biology/hyphy: Update to 2.5.50	2023-04-19 13:30:57 -03:00
igv	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
infernal	biology/infernal: Update to 1.1.4	2022-10-12 11:15:54 +01:00
iolib
iqtree	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
jalview	biology/jalview: Update 2.11.1.4 -> 2.11.2.5	2022-10-11 23:58:18 -07:00
jellyfish	biology/jellyfish: Bump PORTREVISION for biology/htslib update	2023-01-05 19:24:44 -06:00
kallisto	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
kmcp	all: Bump PORTREVISION after lang/go{119,120} update	2023-04-08 10:13:25 -05:00
lamarc	biology/lamarc: Refactor after wxgtk28 removal	2022-12-31 04:54:58 +01:00
libbigwig
libcombine	biology/libcombine: Update 0.2.19 -> 0.2.20	2022-12-08 03:11:24 -08:00
libgff
libgtextutils
libneurosim
libnuml
libsbml	biology/libsbml: Update WWW and clean up pkg-descr	2023-04-06 01:29:43 +08:00
libsedml
linux-foldingathome
mafft
mapm3
megahit	biology/megahit: Add cmake patch to respect ports build flags	2022-11-24 08:10:13 -06:00
metaeuk	biology/metaeuk: Fix build on systems withour OpenMP enabled	2022-12-10 01:51:02 -08:00
migrate
minimap2	biology/minimap2: Update to 2.25	2023-04-29 09:53:40 -05:00
mmseqs2
molden	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
mothur
mrbayes
mummer
muscle
ncbi-blast+	devel/grpc: Update to 1.54.0 (should be part of 8f17596cf5)	2023-04-20 02:53:02 +08:00
ncbi-cxx-toolkit	graphics/proj: Update to 9.2.0	2023-03-09 13:42:31 +01:00
ncbi-entrez-direct	all: Bump PORTREVISION after lang/go{119,120} update	2023-04-08 10:13:25 -05:00
ncbi-toolkit	*/*: Bump PORTREVISION for consumers of libunistring	2022-10-22 11:36:07 +02:00
ncbi-vdb	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
ngs-sdk
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL
p5-Bio-DB-NCBIHelper
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-Bio-Variation
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder	biology/p5-transdecoder: Update to 5.7.0	2023-01-30 16:30:54 -06:00
p5-TrimGalore
paml	biology/paml: Update to 4.10.6	2022-11-12 22:35:29 -04:00
pbbam	biology/pbbam: Bump PORTREVISION for biology/htslib update	2023-01-05 19:25:09 -06:00
pbseqan
peak-classifier	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
pear-merger
phrap
phred
phyml	biology/phyml: fix build on non-x86	2023-05-08 10:25:50 +02:00
picard-tools	*/*: Refactor java/openjdk7 removal	2023-04-04 13:10:53 -05:00
plink	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
pooler	biology/pooler: update to 1.86	2022-12-19 08:56:15 +01:00
primer3
prodigal
prodigy-lig	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
protomol
psi88	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-bcbio-gff	biology/py-bcbio-gff: Update to 0.7.0	2023-03-16 17:32:06 -05:00
py-biom-format	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-biopython	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-biosig	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-bx-python	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-crossmap	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-cutadapt	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
py-deeptools	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-deeptoolsintervals	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
py-dna-features-viewer	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-dnaio	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
py-ete3	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
py-Genesis-PyAPI	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
py-gffutils	biology/py-gffutils: Update 0.11.0 → 0.11.1	2023-03-12 01:02:31 -08:00
py-goatools	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-gtfparse	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-hits	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
py-libnuml	biology/py-libnuml: Allow build with swig 4.1.0+	2023-04-19 02:05:12 +08:00
py-libsedml	biology/py-libsedml: Allow build with swig 4.1.0+	2023-04-19 02:05:12 +08:00
py-loompy	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-macs2	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-mrcfile	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-multiqc	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-ont-fast5-api	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-orange3-bioinformatics	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
py-orange3-single-cell	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
py-pandas-charm	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-py2bit	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
py-pybigwig	biology/py-pybigwig: Update to 0.3.21	2023-04-01 16:10:15 -05:00
py-pyfaidx	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
py-pyrodigal	biology/py-pyrodigal: Update 2.0.3 → 2.1.0	2023-03-19 09:42:53 -07:00
py-pysam	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
py-PySCeS	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-python-libsbml	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
py-pywgsim	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
py-resdk	biology/py-resdk: Update 16.0.0 → 17.0.0	2023-04-27 01:36:47 -07:00
py-scikit-bio	www/py-cachecontrol: Fix port	2023-05-08 07:55:57 +08:00
py-valerius	biology/py-valerius: New port: Python bioinformatics tools	2022-10-03 21:06:22 -07:00
py-xenaPython	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
pyfasta	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
python-nexus	*/*: rename CHEESESHOP to PYPI in MASTER_SITES	2023-01-11 18:58:34 +03:00
rainbow
rampler	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
readseq
recombine
rna-seq	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
ruby-bio	Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby	2023-01-14 17:08:33 -06:00
rubygem-bio	Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby	2023-01-14 17:08:33 -06:00
rubygem-bio-executables	Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby	2023-01-14 17:08:33 -06:00
rubygem-bio-old-biofetch-emulator	Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby	2023-01-14 17:08:33 -06:00
rubygem-bio-shell	Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby	2023-01-14 17:08:33 -06:00
sam2pairwise
samtools	biology/samtools: Update to 1.17	2023-02-24 17:27:21 -06:00
scrm
seaview
seqan
seqan1
seqan3	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
seqan-apps
seqio
seqkit	all: Bump PORTREVISION after lang/go{119,120} update	2023-04-08 10:13:25 -05:00
seqtk
sigviewer	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
sim4
slclust
smithwaterman
snpeff	biology/snpeff: Update to 5.1	2022-12-19 12:50:00 -06:00
spoa	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
sra-tools	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
stacks
star	biology/star: Bump PORTREVISION for biology/htslib update	2023-01-05 19:27:16 -06:00
stringtie
subread
tabixpp	biology/tabixpp: Deprecate	2023-01-22 11:01:57 -06:00
taxonkit	biology/taxonkit: Update 0.14.1 → 0.14.2	2023-04-14 22:02:19 -07:00
treekin	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
treepuzzle
trimadap
trimmomatic
tRNAscan-SE	biology/tRNAscan-SE: Update to 2.0.11	2022-10-12 12:45:24 +01:00
ucsc-userapps
ugene
unikmer	all: Bump PORTREVISION after lang/go{119,120} update	2023-04-08 10:13:25 -05:00
vcf2hap
vcf-split	biology/vcf-split: Update to 0.1.5-4	2022-12-11 14:11:33 -06:00
vcflib	biology/vcflib: Update to 1.0.7	2023-02-09 09:35:32 -06:00
vcftools
velvet
viennarna
vsearch	biology/vsearch: Update to 2.22.1	2022-09-21 11:24:14 -05:00
vt	biology/vt: Bump PORTREVISION for biology/htslib update	2023-01-05 19:19:19 -06:00
wfa2-lib	*/*: Sunset 12.3-RELEASE from ports tree	2023-03-30 18:59:51 -05:00
wise
Makefile	biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics	2023-02-25 08:27:46 -06:00