Tijl Coosemans c8eeb158e4 devel/automake: Update to 1.17 ... biology/libneurosim: Fix use of libltdl. dns/ddclient: Take out -Werror. lang/sdcc: - Patching ARCH is no longer needed. Remove it because it touched some configure.ac files and that causes other autotools files to appear out-of-date. - Run autoreconf in WRKSRC/device/lib/pic14 because aclocal.m4 and config.h.in appear out-of-date. net/rpki-client: Patch Makefile.in instead of Makefile.am to avoid autotools. sysutils/genimage: Run configure with --disable-silent-rules because upstream changed the default to silent and when silent rules are enabled it also runs make with --no-print-directory which is a gmake flag. Patch Makefile.am so it uses --no-print-directory depending on the actual verbosity instead of the default. PR: 280277 Exp-run by: antoine		2024-07-20 13:27:02 +02:00
..
abyss	biology/abyss: Move man pages to share/man	2024-03-03 10:04:08 +00:00
ad2vcf	biology/ad2vcf: Update to 0.1.6.19	2024-05-19 08:41:41 -05:00
artemis
atac-seq
augustus	*/*: chase SuiteSparse’s upgrade	2024-04-29 22:08:56 +02:00
avida
babel
bamtools
bamutil
barrnap
bbmap
bcf-score
bcftools	biology/bcftools: Move man pages to share/man	2024-03-02 18:38:43 +00:00
bedtools
bfc
bifrost	biology/bifrost: Update to 1.3.5	2024-03-18 09:29:43 -05:00
bio-mocha
bioawk
biococoa
biolibc	biology/biolibc: Update to 0.2.6.4	2024-05-19 08:40:24 -05:00
biolibc-tools	biology/biolibc-tools: Move man pages to share/man	2024-03-02 18:44:44 +00:00
bioparser
biosig	*/*: chase SuiteSparse’s upgrade	2024-04-29 22:08:56 +02:00
biosoup
biostar-tools	biology/biostar-tools: Update to 1.11	2024-06-03 06:38:30 -05:00
bolt-lmm	*/*: bump PORTREVISION after the upgrade to OpenBLAS	2024-06-21 19:49:24 +02:00
bowtie
bowtie2	biology/bowtie2: Update to 2.5.4	2024-05-24 06:33:53 -05:00
btllib	biology/btllib: update 1.7.1 → 1.7.2	2024-04-09 00:40:58 -07:00
bwa
canu
cd-hit
cdbfasta
checkm	biology/checkm: update 1.2.0 → 1.2.2	2024-04-23 01:40:35 -07:00
chip-seq
clustal-omega
clustalw
cufflinks	devel/boost: bump consumers after library update	2024-02-13 17:44:22 +03:00
cytoscape	biology/cytoscape: Broken on i386	2024-05-25 18:45:24 -07:00
ddocent
diamond	biology/diamond: Update to 2.1.9	2024-02-04 15:41:51 -04:00
dsr-pdb	devel/boost: bump consumers after library update	2024-02-13 17:44:22 +03:00
edlib
emboss
erminej
exonerate	biology/exonerate: Moved man to share/man	2024-02-22 14:23:45 +01:00
fasda	biology/fasda: Move man pages to share/man	2024-03-02 19:03:05 +00:00
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastq-trim	biology/fastq-trim: Move man pages to share/man	2024-03-02 19:08:45 +00:00
fastqc
fasttree
fastx-toolkit
figtree
flash
fluctuate
freebayes
garlic
gatk	biology/gatk: Fix fetch	2024-07-20 01:36:53 -07:00
gcta	biology/gcta: Unbreak fetch	2024-07-08 17:04:44 -05:00
gemma	*/*: bump PORTREVISION after the upgrade to OpenBLAS	2024-06-21 19:49:24 +02:00
generand	biology/generand: Move man pages to share/man	2024-03-02 19:14:06 +00:00
gff2ps
gffread
gmap
gperiodic
graphlan
groopm
haplohseq	devel/boost: bump consumers after library update	2024-02-13 17:44:22 +03:00
hhsuite	*/*: bump PORTREVISION after OpenMPI upgrade	2024-02-18 10:29:31 +01:00
hisat2
hmmer	biology/hmmer: Moved man to share/man	2024-02-22 14:23:46 +01:00
htslib	biology/htslib: Moved man to share/man	2024-01-27 13:37:30 +01:00
hyphy	biology/hyphy: Update to 2.5.62	2024-06-21 13:58:09 -03:00
igv
infernal	biology/infernal: Moved man to share/man	2024-02-22 14:23:47 +01:00
iolib	biology/iolib: Moved man to share/man	2024-02-22 14:23:48 +01:00
iqtree	biology/iqtree: Update to 2.3.5	2024-07-01 18:28:31 -03:00
jalview
jellyfish	biology/jellyfish: Move man pages to share/man	2024-03-02 19:17:36 +00:00
kallisto	biology/kallisto: Use EXTRACT_AFTER_ARGS to omit unused htslib dir	2024-05-05 09:47:05 -05:00
kmcp	all: Bump after lang/go121 update	2024-07-03 08:29:54 +00:00
lamarc
libbigwig
libcombine
libgff
libgtextutils
libneurosim	devel/automake: Update to 1.17	2024-07-20 13:27:02 +02:00
libnuml
libsbml	biology/libsbml: Fix build with libxml2 2.12.0+	2024-06-18 12:05:09 +08:00
libsedml
linux-foldingathome
locarna	biology/locarna: Move man pages to share/man	2024-03-03 10:04:08 +00:00
mafft	biology/mafft: Moved man to share/man	2024-02-22 14:23:49 +01:00
mapm3
mashmap	biology/mashmap: Broken on armv7	2024-01-12 17:57:41 -08:00
megahit
metaeuk	biology/metaeuk: update 6 → 7	2024-06-01 01:10:52 -07:00
migrate	biology/migrate: fix build on !x86	2024-07-09 12:04:31 +02:00
minimap2	biology/minimap2: Unbreak build on aarch64	2024-05-28 16:06:42 -05:00
mmseqs2
molden
mothur	biology/mothur: update 1.48.0 → 1.48.1	2024-05-16 01:56:44 -07:00
mrbayes
mummer
muscle
ncbi-blast+	devel/grpc: Update to 1.62.0	2024-03-09 22:05:20 +08:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: update 28.0.5 → 28.0.6	2024-07-06 18:27:07 -07:00
ncbi-entrez-direct	all: Bump after lang/go121 update	2024-07-03 08:29:54 +00:00
ncbi-toolkit
ncbi-vdb
ngs-sdk	biology/ngs-sdk: Attempt to fix build on i386	2024-04-28 00:10:02 -07:00
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
p5-TrimGalore	biology/p5-TrimGalore: Release to ports@	2024-04-05 19:12:17 -05:00
paml
pbbam
peak-classifier	biology/peak-classifier: Clean up USES=python	2024-04-05 08:43:40 +08:00
pear-merger
phrap
phred
phyml	biology/phyml: fix build on non-amd64	2024-06-16 17:25:18 +02:00
picard-tools
plink	*/*: bump PORTREVISION after the upgrade to OpenBLAS	2024-06-21 19:49:24 +02:00
pooler	biology/pooler: Moved man to share/man	2024-02-22 14:23:50 +01:00
primer3
prodigal
prodigy-lig	biology/prodigy-lig: update 1.1.0 → 1.1.1	2024-04-26 22:55:21 -07:00
protomol	graphics/tiff: Update to 4.6.0	2024-04-27 14:44:59 +02:00
psi88
py-bcbio-gff
py-biom-format	biology/py-biom-format: update 2.1.10 → 2.1.16	2024-07-13 11:06:57 -07:00
py-biopython	biology/py-biopython: Update to 1.83	2024-04-08 02:29:37 +00:00
py-biosig	biology/{,py-}biosig: update 2.5.2 → 2.6.0	2024-04-05 18:04:45 -07:00
py-bx-python	biology/py-bx-python: update 0.10.0 → 0.11.0	2024-02-12 15:07:35 -08:00
py-crossmap
py-cutadapt	biology/py-cutadapt: update to 4.9	2024-06-20 10:38:00 +02:00
py-deeptools
py-deeptoolsintervals
py-dna-features-viewer
py-dnaio	biology/py-dnaio: Update to 1.2.1	2024-07-04 09:15:39 +00:00
py-ete3
py-Genesis-PyAPI
py-gffutils	biology/py-gffutils: update 0.11.1 → 0.13	2024-06-16 18:20:35 -07:00
py-goatools
py-gtfparse
py-hits
py-htseq	biology/py-htseq: Fix build with python-3.11	2024-01-21 07:13:35 +00:00
py-libnuml
py-libsedml
py-loompy
py-macs2
py-macs3	all: drop support for FreeBSD 13.2 which reached EOL today	2024-07-01 22:27:23 +02:00
py-mrcfile	biology/py-mrcfile: update 1.5.0 → 1.5.1	2024-07-12 01:57:59 -07:00
py-multiqc	devel/py-pyyaml: Move devel/py-yaml to devel/py-pyyaml	2024-07-07 16:05:33 +08:00
py-newick	biology/py-newick: Add new port	2024-02-03 00:58:29 +00:00
py-ont-fast5-api
py-orange3-bioinformatics	devel/py-setuptools-scm: update to 8.0.4	2024-02-29 02:18:32 -05:00
py-orange3-single-cell
py-pandas-charm
py-py2bit
py-pybigwig
py-pyfaidx
py-pyrodigal	biology/py-pyrodigal: update 3.4.1 → 3.5.0	2024-07-18 01:22:46 -07:00
py-pysam	biology/py-pysam: update 0.22.0 → 0.22.1	2024-04-25 07:52:08 -07:00
py-PySCeS	biology/py-PySCeS: update 1.1.1 → 1.2.1	2024-05-26 14:57:06 -07:00
py-python-libsbml
py-pywgsim	biology/py-pywgsim: fix build	2024-06-07 11:11:35 +03:00
py-resdk	biology/py-resdk: update 21.1.0 → 21.2.0	2024-07-12 01:58:00 -07:00
py-scikit-bio	biology/py-scikit-bio: update 0.6.1 → 0.6.2	2024-07-12 22:17:53 -07:00
py-valerius
py-xenaPython
pyfasta
python-nexus	biology/python-nexus: Update to 2.9.0 and fix build with python-3.11	2024-02-03 00:58:29 +00:00
R-cran-Biobase
R-cran-BiocGenerics
R-cran-BiocManager	biology/R-cran-BiocManager: Update version 1.30.22=>1.30.23	2024-05-12 01:10:24 +02:00
rainbow
rampler
readseq
rna-seq
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
salmon	devel/onetbb: Update to 2021.13.0	2024-07-04 13:39:44 +02:00
sam2pairwise
samtools	biology/samtools: Move man pages to share/man	2024-03-02 19:40:58 +00:00
scrm	biology/scrm: Move man pages to share/man	2024-03-02 19:59:23 +00:00
seaview
seqan
seqan1
seqan3
seqan-apps
seqkit	all: Bump after lang/go121 update	2024-07-03 08:29:54 +00:00
seqtk
seqwish	biology/seqwish: update 0.7.9 → 0.7.10	2024-05-18 10:29:58 -07:00
sigviewer
slclust
smithwaterman
snpeff
spoa	biology/spoa: Broken on i386	2024-04-11 21:05:12 -07:00
sra-tools	cleanup: remove occurrences of WITH_DEBUG	2024-04-12 08:04:05 +02:00
stacks	biology/stacks: Unbreak build on aarch64	2024-05-28 16:17:25 -05:00
star	biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir	2024-05-05 09:58:47 -05:00
stringtie
subread
tabixpp
taxonkit	biology/taxonkit: update 0.16.0 → 0.17.0	2024-07-04 09:32:16 -07:00
treekin	biology/treekin: Move man pages to share/man	2024-03-02 20:02:27 +00:00
treepuzzle
trimadap
trimmomatic	biology/trimmomatic: Release to ports@	2024-04-05 19:12:17 -05:00
tRNAscan-SE
ucsc-userapps
ugene
unikmer	all: Bump after lang/go121 update	2024-07-03 08:29:54 +00:00
vcf2hap	biology/vcf2hap: Move man pages to share/man	2024-03-02 20:07:47 +00:00
vcf-split	biology/vcf-split: Move man pages to share/man	2024-03-02 20:04:57 +00:00
vcflib	biology/vcflib: add upstream reference for zig >= 0.11	2024-05-20 16:42:43 +02:00
vcftools	biology/vcftools: Move man pages to share/man	2024-03-02 20:35:56 +00:00
velvet
viennarna	biology/viennarna: Move man pages to share/man	2024-03-02 20:35:56 +00:00
vsearch	biology/vsearch: Update to 2.28.1	2024-05-01 08:41:05 -05:00
vt
wfa2-lib	biology/wfa2-lib: Update to 2.3.5	2024-04-22 07:42:04 -05:00
wise
Makefile	biology/pbseqan: Remove expired port	2024-05-05 13:35:44 +02:00