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Joseph Mingrone 6ac077207c
biology/iqtree: Update to 2.4.0 
Refer to the release notes for information about a bug that may impact
past results.

PR:		284746
Release Notes:	https://github.com/iqtree/iqtree2/releases/tag/v2.4.0
Sponsored by:	The FreeBSD Foundation

Co-authored-by:	Alven <alster@vinterdalen.se>
2025-02-12 11:08:27 -04:00
..
abyss Mk/bsd.commands.mk: Use absolute path to define GMAKE 2024-12-29 12:34:56 +01:00
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 Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
atac-seq all: remove support for expired FreeBSD 13.3 2025-01-01 17:09:59 +01:00
augustus */*: bump PORTREVISION after the upgrade to Suitesparse 2025-01-11 11:02:35 +01:00
avida
babel
bamtools */*: Bump dependencioes after devel/jsoncpp update 2024-09-12 09:20:06 -07:00
bamutil
barrnap
bbmap biology/bbmap: Update to 39.15 2025-01-16 06:35:49 -06:00
bcf-score */*: bump PORTREVISION after the upgrade to Suitesparse 2025-01-11 11:02:35 +01:00
bcftools biology/bcftools: Update to 1.21 2024-10-09 17:23:09 -05:00
bedtools
bfc
bifrost biology/bifrost: Update to 1.3.5 2024-03-18 09:29:43 -05:00
bio-mocha biology/bio-mocha: Update to 1.20 2024-10-09 17:23:10 -05:00
bioawk
biococoa
biolibc biology/biolibc: Update to 0.2.6.4 2024-05-19 08:40:24 -05:00
biolibc-tools
bioparser
biosig */*: bump PORTREVISION after the upgrade to Suitesparse 2025-01-11 11:02:35 +01:00
biosoup
biostar-tools biology/biostar-tools: Update to 2.0 2024-11-07 18:44:28 -06:00
bolt-lmm */*: bump PORTREVISION after OpenBLAS upgrade 2025-01-28 17:42:55 +01:00
bowtie
bowtie2 biology/bowtie2: Update to 2.5.4 2024-05-24 06:33:53 -05:00
btllib biology/btllib: update 1.7.3 → 1.7.5 2024-12-05 10:11:11 -08:00
bwa biology/bwa: small improvements 2025-01-06 17:29:54 +01:00
canu Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
cd-hit
cdbfasta
checkm biology/checkm: update 1.2.2 → 1.2.3 2024-12-14 22:50:29 -08:00
chip-seq
clustal-omega
clustalw
coverm lang/rust: Bump revisions after 1.84.0 2025-01-20 12:06:50 +01:00
cufflinks devel/boost: bump consu,ers after update Boost to 1.86 release 2024-11-20 13:05:25 +03:00
cytoscape Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
ddocent Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
diamond biology/diamond: Update to 2.1.11 2025-01-25 10:35:27 -04:00
dsr-pdb devel/boost: bump consu,ers after update Boost to 1.86 release 2024-11-20 13:05:25 +03:00
edlib
emboss
erminej Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
exonerate biology/exonerate: remove maintainer (email address gone) 2024-10-28 13:41:54 +01:00
fasda
fasta
fasta3
fastahack
fastani biology/fastani: Broken where OpenMP isn't available; Update WWW 2024-11-02 23:47:52 -07:00
fastdnaml
fastool
fastp biology/fastp: Update to 0.24.0 2024-11-16 07:10:58 -06:00
fastq-trim
fastqc Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
fasttree biology/fasttree: Update to 2.1.11 2024-12-03 08:55:06 -06:00
fastx-toolkit
fermi-lite biology/fermi-lite: enable on powerpc64le 2025-01-29 17:56:29 +01:00
figtree Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
flash
fluctuate
freebayes
garlic
gatk biology/gatk: Fix build breakage after gradle update to 8.12.1 2025-02-06 07:05:37 -08:00
gcta */*: bump PORTREVISION after OpenBLAS upgrade 2025-01-28 17:42:55 +01:00
gemma */*: bump PORTREVISION after OpenBLAS upgrade 2025-01-28 17:42:55 +01:00
generand
gff2ps
gffread
gkl Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
gmap
gperiodic
graphlan
groopm
haplohseq devel/boost: bump consu,ers after update Boost to 1.86 release 2024-11-20 13:05:25 +03:00
hhsuite
hisat2
hmmer biology/hmmer: update to 3.4 2024-10-28 13:41:48 +01:00
htslib biology/htslib: Update to 1.21 2024-10-09 17:23:08 -05:00
hyphy biology/hyphy: Update to 2.5.68 2025-01-28 16:48:19 -04:00
igv Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
infernal biology/infernal: update 1.1.4 → 1.1.5 2025-01-30 08:35:31 +01:00
iolib
iqtree biology/iqtree: Update to 2.4.0 2025-02-12 11:08:27 -04:00
jalview Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
jellyfish
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 biology/libbigwig: update 0.4.7 → 0.4.8 2025-01-18 01:52:23 -08:00
libcombine
libgff
libgtextutils
libneurosim devel/automake: Update to 1.17 2024-07-20 13:27:02 +02:00
libnuml
libsbml textproc/xerces-c3: Update to 3.3.0 2024-10-25 23:56:41 +08:00
libsedml
linux-foldingathome biology/linux-foldingathome: Point MASTER_SITES to the new location 2024-08-12 14:58:05 +02:00
locarna
mafft
mapm3
mashmap
mca-calling biology/mca-calling: Core tools for mCA event calling 2024-10-24 08:32:05 -05:00
megahit
metaeuk biology/metaeuk: builds now fine on powerpc64le 2025-01-29 17:56:26 +01:00
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 biology/mmseqs2: Update to 17.b804.f 2025-01-25 07:24:31 -06:00
molden all: return jmd's ports to the pool after safekeeping their commit bit. 2024-11-28 17:10:52 +01:00
mothur biology/mothur: update 1.48.1 → 1.48.2 2024-11-04 23:25:49 -08:00
mrbayes
mummer biology/mummer: update 4.0.0 → 4.0.1 2025-02-08 00:07:06 -08:00
muscle
ncbi-blast+ devel/grpc: Update to 1.70.1 2025-02-08 05:34:57 +08:00
ncbi-cxx-toolkit biology/ncbi-cxx-toolkit: update 28.0.11 → 28.0.12 2025-01-07 01:29:09 -08:00
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
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: Update to 0.6.10 2024-07-23 11:01:28 -04:00
paml
pbbam devel/boost: bump consu,ers after update Boost to 1.86 release 2024-11-20 13:05:25 +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 Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
plink */*: bump PORTREVISION after OpenBLAS upgrade 2025-01-28 17:42:55 +01:00
pooler biology/pooler: Update to 1.89 2025-02-01 01:36:31 +00:00
preseq preseq: Not for 32-bit platforms 2024-11-24 07:50:11 -06:00
primer3
prodigal
prodigy-lig biology/prodigy-lig: update 1.1.2 → 1.1.3 2024-10-15 08:33:52 -07:00
protomol graphics/tiff: Update to 4.6.0 2024-04-27 14:44:59 +02:00
psi88
py-bcbio-gff biology/py-bcbio-gff: Update to 0.7.1 2025-01-16 06:55:42 -06:00
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 0.11.0 → 0.13.0 2024-12-15 06:55:17 -08:00
py-crossmap
py-cutadapt biology/py-cutadapt: Update to 5.0 2025-01-10 16:35:23 +01:00
py-deeptools
py-deeptoolsintervals
py-dna-features-viewer
py-dnaio biology/py-dnaio: Update to 1.2.3 2024-12-20 07:40:26 +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 biology/py-gtfparse: Fix fetch 2024-12-05 19:44:23 -08:00
py-hits
py-htseq py-htseq: New maintainer 2024-11-28 06:22:44 -06:00
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 biology/py-multiqc: Add missing py-natsort RUN_DEPEND 2024-12-12 08:52:37 -06:00
py-newick
py-ont-fast5-api
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-py2bit
py-pybigwig
py-pyfaidx
py-pyrodigal biology/py-pyrodigal: update 3.5.2 → 3.6.3 2024-11-12 00:32:35 -08:00
py-pysam biology/py-pysam: update 0.22.1 → 0.23.0 2025-02-06 07:05:43 -08:00
py-PySCeS biology/py-PySCeS: update 1.2.1 → 1.2.2 2024-08-03 01:27:31 -07:00
py-python-libsbml biology/py-python-libsbml: update 5.20.1 → 5.20.4 2024-11-12 02:18:13 -08:00
py-pywgsim biology/py-pywgsim: fix build 2024-06-07 11:11:35 +03:00
py-resdk biology/py-resdk: update 21.2.0 → 21.2.1 2024-11-10 19:54:22 -08:00
py-scikit-bio biology/py-scikit-bio: update 0.6.2 → 0.6.3 2025-01-13 19:26:05 -08:00
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 Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
rna-seq
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
salmon devel/boost: bump consu,ers after update Boost to 1.86 release 2024-11-20 13:05:25 +03:00
sam2pairwise
samtools biology/samtools: Update to 1.21 2024-10-09 17:23:09 -05:00
scrm
seaview biology/seaview: unbreak the port's build against FLTK 1.3.10 2025-02-05 16:37:24 +00:00
seqan
seqan-apps
seqan1
seqan3
seqkit biology/seqkit: update 2.8.2 → 2.9.0 2024-11-04 17:26:42 -08:00
seqtk
seqwish biology/seqwish: Broken on 13 2024-12-19 22:05:53 -08:00
sigviewer
slclust
smithwaterman
snpeff Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
spoa biology/spoa: Broken on i386 2024-04-11 21:05:12 -07:00
sra-tools biology/sra-tools: Update to 3.2.0 2025-01-29 14:16:40 -06:00
stacks biology/stacks: fix build without libomp 2025-01-22 12:27:04 +01:00
star biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir 2024-05-05 09:58:47 -05:00
stringtie
subread biology/subread: Update to 2.0.8 2025-01-19 06:46:51 -06:00
tabixpp
taxonkit biology/taxonkit: update 0.17.0 → 0.18.0 2024-11-04 17:26:41 -08:00
treekin */*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS 2025-01-24 13:18:28 +01:00
treepuzzle
trimadap biology/trimadap: drop not necessary powerpc64le knob 2025-01-29 17:56:25 +01:00
trimmomatic Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
tRNAscan-SE
ucsc-userapps biology/ucsc-userapps: Update to v474 2024-11-28 09:59:20 -06:00
ugene
unikmer biology/unikmer: Update WWW 2025-01-05 20:01:04 -08:00
vcf-split
vcf2hap
vcflib biology/vcflib: Update to 1.0.12 2024-11-25 08:49:37 -06:00
vcftools
velvet
viennarna */*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS 2025-01-24 13:18:28 +01:00
vsearch biology/vsearch: Update to 2.29.2 2024-12-29 14:59:05 -06:00
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/ncbi-vdb: Remove expired port 2025-01-01 11:59:57 +01:00