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Hiroki Tagato a6233e5a2f */*: switch dependency from devel/py-lxml5 to devel/py-lxml 
Currently, there are two versions of python XML processing library
which conflict each other in the ports tree, namely:
- devel/py-lxml5 (now at version 5.4.0)
- devel/py-lxml  (now at version 6.0.1)

To avoid the situation that some ports depend on py-lxml5 and some
others do on py-lxml (by switching dependencies individually), this
commit switches the dependencies from py-lxml5 to py-lxml at once.

Additional note: There are still two ports (textproc/py-rdflib and
www/py-draftjs-exporter) depending on py-lxml5 since they limit upper
version to less than 6.

PR:		289491
Approved by:	Michiel van Baak Jansen <michiel@vanbaak.eu>, arrowd,
		crees, madpilot, delphij, marcus, nivit, kai,
		skreuzer, fluffy, bofh, thierry, stephen, sunpoet,
		0mp, Eric Camachat <eric@camachat.org>
 		2025-09-15 22:55:40 +09:00
..
R-cran-Biobase biology/R-cran-Biobase: Update to 2.66.0 2025-04-11 14:28:35 +00:00
R-cran-BiocGenerics biology/R-cran-BiocGenerics: Update to 0.52.0 2025-04-11 14:28:35 +00:00
R-cran-BiocManager biology/R-cran-BiocManager: Update to 1.30.26 2025-07-15 07:27:51 +02:00
abyss Mk/bsd.commands.mk: Use absolute path to define GMAKE 2024-12-29 12:34:56 +01:00
ad2vcf
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andi
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artemis Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
atac-seq all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
augustus */*: chase the upgrade to SuiteSparse 2025-08-01 23:08:37 +02:00
avida
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babel
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bamtools biology/bamtools: Update to 2.5.3 2025-05-19 16:21:57 -05:00
bamutil
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barrnap
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bbmap biology/bbmap: Update to 39.34 2025-08-21 15:31:40 -05:00
bcf-score */*: chase the upgrade to SuiteSparse 2025-08-01 23:08:37 +02:00
bcftools biology/bcftools: Update to 1.22 2025-06-04 08:26:12 -05:00
bedtools
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bfc
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bifrost biology/bifrost: Remove USE_GCC, fix build with clang19 2025-05-27 09:08:27 -05:00
bio-mocha biology/bio-mocha: Use latest versions of htslib and bcftools 2025-06-21 17:08:50 -05:00
bioawk
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biococoa GNUstep: Bump dependent PORTREVISION 2025-08-12 08:03:53 -03:00
biolibc biology/biolibc: Update to 0.2.7 2025-04-26 15:35:36 -05:00
biolibc-tools biology/biolibc-tools: Update to 0.1.5 2025-04-26 15:40:24 -05:00
bioparser
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biosig */*: chase the upgrade to SuiteSparse 2025-08-01 23:08:37 +02:00
biosoup
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biostar-tools all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
bolt-lmm devel/boost: bump consumers after Boost update 2025-06-02 03:40:43 +03:00
bowtie
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bowtie2
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btllib biology/btllib: update 1.7.3 → 1.7.5 2024-12-05 10:11:11 -08:00
bwa */*: Älven's ports to use FreeBSD.org email 2025-07-29 01:38:52 +04:00
canu devel/boost: bump consumers after Boost update 2025-06-02 03:40:43 +03:00
cd-hit
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cdbfasta
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chip-seq all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
clustal-omega
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clustalw
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coverm lang/rust: Bump revisions after 1.89.0 2025-09-01 10:25:04 +02:00
cufflinks devel/boost: bump consumers after Boost update 2025-06-02 03:40:43 +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 2.1.14 2025-09-10 23:03:41 -03:00
dsr-pdb devel/boost: bump consumers after Boost update 2025-06-02 03:40:43 +03:00
edlib
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emboss
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erminej Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
exonerate
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fasda biology/fasda: Update to 0.2.0.1 2025-05-25 09:26:46 -05:00
fasda-utils all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
fasta
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fasta3
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fastahack
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fastani biology/fastani: Broken where OpenMP isn't available; Update WWW 2024-11-02 23:47:52 -07:00
fastdnaml
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fastool
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fastp biology/fastp: Update to 0.26.0 2025-06-07 07:28:25 -05:00
fastq-trim biology/fastq-trim: Update to 0.1.4 2025-04-30 06:11:14 -05:00
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
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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
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fluctuate
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freebayes biology/freebayes: Update to 1.3.9 2025-02-18 14:45:11 -06:00
garlic
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gatk biology/gatk: update 4.6.1.0 → 4.6.2.0 2025-08-27 10:24:54 -07:00
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
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gff2ps
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gffread
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gkl biology/gkl: update 0.8.11-9 → 0.9.1 2025-08-23 11:26:47 -07:00
gmap
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gperiodic gnome.mk: rename gdkpixbuf2 to gdkpixbuf to prepare for port move 2025-03-17 00:02:08 -04:00
graphlan
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groopm all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
haplohseq devel/boost: bump consumers after Boost update 2025-06-02 03:40:43 +03:00
hhsuite
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hisat2
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hmmer
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htslib biology/*: remove useless USES=pathfix 2025-07-23 17:07:20 +02:00
hyphy biology/hyphy: Fix build on i386 2025-08-22 16:45:17 -03:00
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
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iqtree devel/boost: bump consumers after Boost update 2025-06-02 03:40:43 +03:00
jalview Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
jellyfish
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kallisto biology/kallisto: Remove USE_GCC, fix build with clang19 2025-05-27 09:19:38 -05:00
kmcp many: Bump go ports for go-1.24.7 2025-09-04 13:53:24 -04:00
lamarc biology/lamarc: New maintainer hayzam@alchemilla.io 2025-05-20 18:16:25 -05:00
libbigwig biology/libbigwig: update 0.4.7 → 0.4.8 2025-01-18 01:52:23 -08:00
libcombine libxml2: chase libxml soversion bump 2025-06-30 11:04:22 +02:00
libgff
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libgtextutils biology/*: remove useless USES=pathfix 2025-07-23 17:07:20 +02:00
libneurosim
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libnuml libxml2: chase libxml soversion bump 2025-06-30 11:04:22 +02:00
libsbml biology/*: remove useless USES=pathfix 2025-07-23 17:07:20 +02:00
libsedml libxml2: chase libxml soversion bump 2025-06-30 11:04:22 +02:00
linux-foldingathome biology/linux-foldingathome: Fix WRKSRC paths 2025-09-03 14:30:55 +02:00
locarna
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mafft
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mapm3
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mashmap
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mca-calling
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megahit biology/megahit: Update to 1.2.9.20 2025-05-23 07:33:33 -05:00
metaeuk biology/metaeuk: builds now fine on powerpc64le 2025-01-29 17:56:26 +01:00
migrate
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minimap2 biology/minimap2: Remove extraneous file that snuck in the last commit 2025-06-21 16:47:09 -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
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mummer biology/mummer: update 4.0.0 → 4.0.1 2025-02-08 00:07:06 -08:00
muscle
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ncbi-blast+ biology/ncbi-blast+: Update to 2.17.0 2025-07-24 16:05:11 -05:00
ncbi-cxx-toolkit biology/ncbi-cxx-toolkit: Broken on i386 2025-03-10 01:13:13 -07:00
ncbi-entrez-direct many: Bump go ports for go-1.24.7 2025-09-04 13:53:24 -04:00
ncbi-toolkit
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ngs-sdk
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Cluster
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p5-Bio-Coordinate
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p5-Bio-DB-EMBL
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p5-Bio-DB-NCBIHelper
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p5-Bio-Das
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p5-Bio-Das-Lite
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p5-Bio-FeatureIO
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p5-Bio-GFF3
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p5-Bio-Glite
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p5-Bio-Graphics
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p5-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
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p5-Bio-SCF
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p5-Bio-Variation
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p5-BioPerl
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p5-BioPerl-Run
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p5-TrimGalore perl@: adopt a few ports 2025-05-28 10:28:10 +02:00
p5-transdecoder
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paml biology/paml: Update to 4.10.9 2025-05-14 12:59:29 -03:00
pbbam devel/boost: bump consumers after Boost update 2025-06-02 03:40:43 +03:00
peak-classifier all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
pear-merger
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phrap
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phred
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phyml
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picard-tools Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
plink biology/plink: enable on powerpc64le by using SSE translation 2025-08-13 17:33:19 +02:00
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
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prodigal
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prodigy-lig all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
protomol
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psi88
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py-Genesis-PyAPI python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-PySCeS all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
py-bcbio-gff python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-biom-format python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-biopython all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
py-biosig python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 2025-06-19 16:28:47 -04:00
py-bx-python biology/py-bx-python: update 0.13.0 → 0.14.0 2025-08-24 20:30:53 -07:00
py-crossmap python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-cutadapt biology/py-cutadapt: update to 5.1 2025-06-06 12:37:20 +02:00
py-deeptools all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
py-deeptoolsintervals python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-dna-features-viewer all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
py-dnaio Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test} 2025-04-09 22:55:11 +08:00
py-ete3 */*: switch dependency from devel/py-lxml5 to devel/py-lxml 2025-09-15 22:55:40 +09:00
py-gffutils python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-goatools python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-gtfparse all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
py-hits python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-htseq all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
py-libnuml biology/{,py-}libnuml: update 1.1.6 → 1.1.7 2025-03-28 02:54:11 -07:00
py-libsedml biology/{,py-}libsedml: update 2.0.32 → 2.0.33 2025-04-24 00:33:39 -07:00
py-loompy python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-macs2 python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-macs3 Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test} 2025-04-09 22:55:11 +08:00
py-mrcfile python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-multiqc all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
py-newick biology/py-newick: Update to 1.10.0 2025-03-22 13:41:03 +00:00
py-ont-fast5-api python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-pandas-charm python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-py2bit python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-pybigwig python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-pydeseq2 all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
py-pyfaidx python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-pyrodigal python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 2025-06-19 16:28:47 -04:00
py-pysam python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 2025-06-19 16:28:47 -04:00
py-python-libsbml python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 2025-06-19 16:28:47 -04:00
py-pywgsim python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-resdk biology/py-resdk: update 21.2.1 → 22.0.0 2025-04-02 02:10:43 -07:00
py-scikit-bio all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
py-valerius python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
py-xenaPython python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
pyfasta python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
python-nexus python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 2025-03-07 23:05:21 -05:00
rainbow
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rampler
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readseq Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
rna-seq all: bump PORTREVISION after updating graphics/libyuv 2025-08-31 12:30:51 +02:00
ruby-bio
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rubygem-bio biology/rubygem-bio: Update to 2.0.6 2025-03-19 11:46:26 +08:00
rubygem-bio-executables
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rubygem-bio-old-biofetch-emulator
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rubygem-bio-shell
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salmon biology/salmon: Update to tag 1.10.3 2025-07-27 16:04:26 -05:00
sam2pairwise
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samtools biology/samtools: Update to 1.22 2025-06-04 08:26:12 -05:00
scrm
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seaview biology/seaview: Update version 5.0.5=>5.1 2025-03-26 08:36:45 +01:00
seqan
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seqan-apps
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seqan1
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seqan3 biology/seqan3: update 3.3.0 → 3.4.0 2025-08-28 12:28:16 -07:00
seqkit many: Bump go ports for go-1.24.7 2025-09-04 13:53:24 -04:00
seqtk biology/seqtk: Update to 1.5 2025-06-04 09:20:45 -05:00
seqwish biology/seqwish: Set OPENMP=OFF and broken where OpenMP isn't available 2025-02-23 11:42:19 -08:00
sigviewer
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slclust
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smithwaterman
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snpeff Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
spoa
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sra-tools biology/sra-tools: Update to 3.2.1 2025-03-21 06:27:22 -05:00
stacks biology/stacks: fix build without libomp 2025-01-22 12:27:04 +01:00
star
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stringtie
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subread biology/subread: Update to 2.1.0 2025-03-27 17:05:26 -05:00
tRNAscan-SE
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tabixpp biology/tabixpp: Undeprecate and update to 1.1.2 2025-02-18 09:39:35 -06:00
taxonkit many: Bump go ports for go-1.24.7 2025-09-04 13:53:24 -04:00
treekin */*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS 2025-01-24 13:18:28 +01:00
treepuzzle
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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
ucsc-userapps biology/ucsc-userapps: Update to v474 2024-11-28 09:59:20 -06:00
ugene
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unikmer many: Bump go ports for go-1.24.7 2025-09-04 13:53:24 -04:00
vcf-split
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vcf2hap
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vcflib python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 2025-06-19 16:28:47 -04:00
vcftools biology/vcftools: Update to 0.1.17 2025-05-15 07:26:46 -05:00
velvet
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viennarna biology/viennarna: Broken on 13 2025-07-22 15:03:45 -07:00
vsearch biology/vsearch: Update to 2.30.0 2025-03-02 06:37:09 -06:00
vt
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wfa2-lib
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wise
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Makefile biology/py-orange3-bioinformatics: Remove expired port 2025-06-23 21:01:46 +02:00