Dimitry Andric 9e3c846ca0 biology/biosig: fix build with libc++ 19 ... With libc++ 19, biology/biosig fails to compile, with errors similar to: /usr/include/c++/v1/__math/special_functions.h:51:16: error: expected unqualified-id 51 | if (!__math::isfinite(__H_n)) { | ^ ./t230/../biosig-dev.h:932:22: note: expanded from macro 'isfinite' 932 | # define isfinite(a) (-INFINITY < (a) && (a) < INFINITY) | ^ This is because biosig attempts to define its own isfinite() macro, which it should not do. Stub out the incompatible definition. PR: 281976 Approved by: yuri (maintainer) MFH: 2024Q4 (cherry picked from commit 08d6ba6fa1)		2024-10-11 19:36:10 +02:00
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R-cran-Biobase	…
R-cran-BiocGenerics	…
R-cran-BiocManager	biology/R-cran-BiocManager: Update version 1.30.24=>1.30.25	2024-09-08 19:28:55 +02:00
abyss	all: drop support for expired FreeBSD 14.0	2024-10-01 20:56:20 +02:00
ad2vcf	biology/ad2vcf: Update to 0.1.6.19	2024-05-19 08:41:41 -05:00
andi	biology/andi: New ports: Efficient estimation of evolutionary distances	2024-09-07 14:31:10 -07:00
artemis	…
atac-seq	…
augustus	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
avida	…
babel	…
bamtools	*/*: Bump dependencioes after devel/jsoncpp update	2024-09-12 09:20:06 -07:00
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	biology/biosig: fix build with libc++ 19	2024-10-11 19:36:10 +02:00
biosoup	…
biostar-tools	biology/biostar-tools: Update to 1.11	2024-06-03 06:38:30 -05:00
bolt-lmm	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
bowtie	…
bowtie2	biology/bowtie2: Update to 2.5.4	2024-05-24 06:33:53 -05:00
btllib	biology/btllib: update 1.7.2 → 1.7.3	2024-07-27 13:19:18 -07:00
bwa	…
canu	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
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	…
coverm	biology/coverm: Broken on i386	2024-10-06 11:31:38 -07:00
cufflinks	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +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	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +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	…
fastani	biology/fastani: New port: Fast Whole-Genome Similarity (ANI) Estimation	2024-09-20 20:03:29 -07:00
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	…
fermi-lite	biology/fermi-lite: Add ONLY_FOR_ARCHS line	2024-09-19 14:05:26 -07:00
figtree	…
flash	…
fluctuate	…
freebayes	…
garlic	…
gatk	biology/gatk: Update COMMENT	2024-08-04 13:13:15 -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	…
gkl	biology/gkl: New port: Accelerated kernel library for genomics	2024-08-04 13:09:41 -07:00
gmap	…
gperiodic	…
graphlan	…
groopm	…
haplohseq	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +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	…
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	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
jalview	…
jellyfish	biology/jellyfish: Move man pages to share/man	2024-03-02 19:17:36 +00:00
kallisto	biology/kallisto: Update to 0.51.1,1	2024-09-19 17:46:47 -05:00
kmcp	all: Bump after lang/go121 update	2024-08-09 06:24:08 +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: Update to 5.20.4	2024-09-09 02:36:57 +08:00
libsedml	…
linux-foldingathome	biology/linux-foldingathome: Point MASTER_SITES to the new location	2024-08-12 14:58:05 +02:00
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	…
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: Add NOT_FOR_ARCHS for most 32-bit processors	2024-07-20 14:55:08 -05:00
mmseqs2	…
molden	…
mothur	all: drop support for expired FreeBSD 14.0	2024-10-01 20:56:20 +02:00
mrbayes	…
mummer	…
muscle	…
ncbi-blast+	devel/grpc: Update to 1.66.1	2024-09-16 04:09:34 +08:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: update 28.0.8 → 28.0.9	2024-10-06 11:08:26 -07:00
ncbi-entrez-direct	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
ncbi-toolkit	all: drop support for expired FreeBSD 14.0	2024-10-01 20:56:20 +02:00
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-DB-EMBL	…
p5-Bio-DB-NCBIHelper	…
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-Bio-Variation	…
p5-BioPerl	…
p5-BioPerl-Run	…
p5-TrimGalore	biology/p5-TrimGalore: Update to 0.6.10	2024-07-23 11:01:28 -04:00
p5-transdecoder	…
paml	…
pbbam	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
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 1.1.1 → 1.1.2	2024-10-04 02:15:23 -07:00
protomol	graphics/tiff: Update to 4.6.0	2024-04-27 14:44:59 +02:00
psi88	…
py-Genesis-PyAPI	…
py-PySCeS	biology/py-PySCeS: update 1.2.1 → 1.2.2	2024-08-03 01:27:31 -07:00
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 2.6.0 → 2.6.1	2024-08-05 07:37:01 -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-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	…
py-libnuml	…
py-libsedml	…
py-loompy	…
py-macs2	…
py-macs3	biology/py-macs3: Update to 3.0.2	2024-09-14 08:23:32 -05:00
py-mrcfile	biology/py-mrcfile: update 1.5.2 → 1.5.3	2024-07-26 01:57:55 -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	…
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 3.5.1 → 3.5.2	2024-09-05 01:48:51 -07:00
py-pysam	biology/py-pysam: update 0.22.0 → 0.22.1	2024-04-25 07:52:08 -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
rainbow	…
rampler	…
readseq	…
rna-seq	…
ruby-bio	…
rubygem-bio	…
rubygem-bio-executables	…
rubygem-bio-old-biofetch-emulator	…
rubygem-bio-shell	…
salmon	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
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	…
seqan-apps	…
seqan1	…
seqan3	…
seqkit	all: Bump after lang/go121 update	2024-08-09 06:24:08 +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	…
tRNAscan-SE	…
tabixpp	…
taxonkit	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
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
ucsc-userapps	…
ugene	…
unikmer	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
vcf-split	biology/vcf-split: Move man pages to share/man	2024-03-02 20:04:57 +00:00
vcf2hap	biology/vcf2hap: Move man pages to share/man	2024-03-02 20:07:47 +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: fix build without libomp	2024-08-04 14:00:47 +02:00
wise	all: drop support for expired FreeBSD 14.0	2024-10-01 20:56:20 +02:00
Makefile	biology/coverm: New port: Read coverage calculator for metagenomics	2024-10-04 20:09:27 -07:00