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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abyss	all: drop support for expired FreeBSD 14.0	2024-10-01 20:56:20 +02:00
ad2vcf
andi
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
bedtools
bfc
bifrost
bio-mocha
bioawk
biococoa
biolibc
biolibc-tools
bioparser
biosig	biology/biosig: fix build with libc++ 19	2024-10-11 19:36:10 +02:00
biosoup
biostar-tools
bolt-lmm	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
bowtie
bowtie2
btllib
bwa
canu	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
cd-hit
cdbfasta
checkm
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
ddocent
diamond
dsr-pdb	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
edlib
emboss
erminej
exonerate
fasda
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
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
gcta
gemma
generand
gff2ps
gffread
gkl
gmap
gperiodic
graphlan
groopm
haplohseq	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
hhsuite
hisat2
hmmer
htslib
hyphy
igv
infernal
iolib
iqtree	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
jalview
jellyfish
kallisto	biology/kallisto: Update to 0.51.1,1	2024-09-19 17:46:47 -05:00
kmcp
lamarc
libbigwig
libcombine
libgff
libgtextutils
libneurosim
libnuml
libsbml	biology/libsbml: Update to 5.20.4	2024-09-09 02:36:57 +08:00
libsedml
linux-foldingathome
locarna
mafft
mapm3
mashmap
megahit
metaeuk
migrate
minimap2
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
ncbi-toolkit	all: drop support for expired FreeBSD 14.0	2024-10-01 20:56:20 +02:00
ncbi-vdb
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
p5-TrimGalore
paml
pbbam	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
peak-classifier
pear-merger
phrap
phred
phyml
picard-tools
plink
pooler
primer3
prodigal
prodigy-lig	biology/prodigy-lig: update 1.1.1 → 1.1.2	2024-10-04 02:15:23 -07:00
protomol
psi88
py-bcbio-gff
py-biom-format
py-biopython
py-biosig
py-bx-python
py-crossmap
py-cutadapt
py-deeptools
py-deeptoolsintervals
py-dna-features-viewer
py-dnaio
py-ete3
py-Genesis-PyAPI
py-gffutils
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
py-multiqc
py-newick
py-ont-fast5-api
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-py2bit
py-pybigwig
py-pyfaidx
py-pyrodigal
py-pysam
py-PySCeS
py-python-libsbml
py-pywgsim
py-resdk
py-scikit-bio
py-valerius
py-xenaPython
pyfasta
python-nexus
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
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
scrm
seaview
seqan
seqan1
seqan3
seqan-apps
seqkit
seqtk
seqwish
sigviewer
slclust
smithwaterman
snpeff
spoa
sra-tools
stacks
star
stringtie
subread
tabixpp
taxonkit
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ucsc-userapps
ugene
unikmer
vcf2hap
vcf-split
vcflib
vcftools
velvet
viennarna
vsearch
vt
wfa2-lib
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