Kevin Bowling da3162c7c9 graphics/mesa-libs: Bump reverse deps for libglvnd ... Per discussion with bapt on helping pkg handle the changing of these deps and avoiding impossible upgrade senarios. PR: 246767 Reviewed by: manu, bapt Approved by: x11 Differential Revision: https://reviews.freebsd.org/D30824		2021-06-22 11:53:08 -07:00
..
abyss	biology/abyss: Update 2.3.0-3 -> 2.3.1	2021-04-22 10:18:02 -07:00
ad2vcf	biology/ad2vcf: Remove comment used to silence portlint	2021-06-11 10:39:02 -05:00
artemis	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
avida	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
babel	all: Remove all other $FreeBSD keywords.	2021-04-06 16:31:13 +02:00
bamtools	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
bbmap	biology/bbmap: BBMap short read aligner, and other bioinformatic tools	2021-04-18 11:21:29 -05:00
bcftools	math/gsl: update to 2.7	2021-06-16 21:31:27 +02:00
bedtools	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
bioawk	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
biococoa	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
biolibc	biology/biolibc: Remove comment used to silence portlint	2021-06-11 10:38:27 -05:00
bioparser	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
biosoup	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
biostar-tools	biostar-tools: Add sra-tools dependency to metaport	2021-06-22 13:00:23 -05:00
bolt-lmm	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
bowtie	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
bowtie2	biology/bowtie2: Update to 2.4.4	2021-05-24 11:35:43 -05:00
bwa	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
canu	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
cd-hit	biology/cd-hit: fix build on powerpc	2021-06-10 00:35:36 +00:00
cdbfasta	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
checkm	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
clustal-omega	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
clustalw	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
cufflinks	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
cytoscape	biology/cytoscape: mark unconditionally BROKEN	2021-05-12 14:55:52 +03:00
ddocent	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
diamond	biology/diamond: Update to 2.0.9	2021-04-12 21:55:49 -03:00
dsr-pdb	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
edlib	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
emboss	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
exonerate	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
fasta	Deorbit RESTRICTED && NO_CDROM, part two.	2021-05-06 13:47:48 +02:00
fasta3	Deorbit RESTRICTED && NO_CDROM, part one.	2021-05-06 13:47:41 +02:00
fastahack	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
fastdnaml	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
fastool	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
fastp	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
fastqc	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
fasttree	biology/fasttree: fix build on armv7	2021-06-15 08:41:19 +00:00
fastx-toolkit	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
figtree	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
fluctuate	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
freebayes	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
garlic	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
gatk	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
gcta	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
gemma	math/gsl: update to 2.7	2021-06-16 21:31:27 +02:00
generand	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
gff2ps	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
gmap	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
gperiodic	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
graphlan	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
groopm	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
haplohseq	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
hhsuite	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
hisat2	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
hmmer	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
htslib	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
hyphy	biology/hyphy: Update to 2.5.31	2021-06-05 20:00:24 -03:00
igv	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
infernal	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
iolib	biology/iolib: Drop maintainership	2021-05-19 20:56:24 +01:00
iqtree	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
jalview	biology/jalview: Broken on 11	2021-06-05 11:53:07 -07:00
jellyfish	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
kallisto	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
lamarc	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
libbigwig	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
libgtextutils	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
libsbml	biology/libsbml: Rename LIBXML option to LIBXML2	2021-05-12 05:46:56 +08:00
linux-foldingathome	Deorbit RESTRICTED && NO_CDROM, part one.	2021-05-06 13:47:41 +02:00
mafft	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
mapm3	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
migrate	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
minimap2	biology/minimap2: Update to 2.20	2021-05-29 16:06:34 -05:00
molden	graphics/mesa-libs: Bump reverse deps for libglvnd	2021-06-22 11:53:08 -07:00
mopac	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
mothur	biology/mothur: Update 1.45.2 -> 1.45.3	2021-05-09 09:11:11 -07:00
mrbayes	*: Remove unnecessary 'port' argument from USES=readline	2021-05-15 09:14:04 +02:00
mummer	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
muscle	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
ncbi-blast+	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
ncbi-cxx-toolkit	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
ncbi-entrez-direct	biology/ncbi-entrez-direct: Update to 14.9.20210423_1	2021-04-26 11:53:11 -05:00
ncbi-toolkit	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
ncbi-vdb	devel/libepoll-shim: update to 0.0.20210418	2021-04-26 14:17:32 +00:00
ngs-sdk	biology/ngs-sdk: Fix build on non-amd64 architectures that was broken by explicit 'amd64' instead of $ARCH	2021-04-15 10:01:31 -07:00
p5-AcePerl	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-ASN1-EntrezGene	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Cluster	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Coordinate	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Das	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Das-Lite	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-DB-EMBL	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-DB-NCBIHelper	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-FeatureIO	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-GFF3	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Glite	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Graphics	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-MAGETAB	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-NEXUS	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Phylo	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-SCF	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Variation	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-BioPerl	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-BioPerl-Run	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-transdecoder	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
p5-TrimGalore	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
paml	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
pbbam	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
pbseqan	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
peak-classifier	biology/peak-classifier: Classify peaks based on GFF features	2021-06-14 11:40:33 -05:00
pear-merger	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
phrap	Deorbit RESTRICTED && NO_CDROM, part two.	2021-05-06 13:47:48 +02:00
phred	Deorbit RESTRICTED && NO_CDROM, part two.	2021-05-06 13:47:48 +02:00
phyml	Clean up some things	2021-04-15 10:31:56 +02:00
picard-tools	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
plink	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
pooler	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
primer3	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
prodigal	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
prodigy-lig	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
protomol	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
psi88	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
py-bigwig	biology/py-bigwig: Fix packaging with Python 3.8+	2021-04-21 09:41:29 +02:00
py-biom-format	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-biopython	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
py-bx-python	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
py-crossmap	biology/py-crossmap: Update to 0.5.4	2021-04-21 08:31:13 -05:00
py-cutadapt	biology/py-cutadapt: Update strict py-dnaio dep version	2021-05-04 08:20:39 -05:00
py-dnaio	biology/py-dnaio: Update to 0.5.1	2021-05-04 08:19:25 -05:00
py-ete3	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-Genesis-PyAPI	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-gffutils	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-gtfparse	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-hits	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-loompy	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-macs2	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-multiqc	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
py-orange3-bioinformatics	biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1	2021-04-27 01:56:19 -07:00
py-orange3-single-cell	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-pandas-charm	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-pyfaidx	biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5	2021-04-23 14:57:50 -07:00
py-pysam	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-resdk	biology/py-resdk: Update 13.2.0 -> 13.3.0	2021-05-24 00:26:50 -07:00
py-scikit-bio	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-xenaPython	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
pyfasta	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
python-nexus	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
rainbow	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
rampler	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
readseq	biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint	2021-04-18 09:20:28 -05:00
recombine	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
ruby-bio	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
rubygem-bio	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
rubygem-bio-executables	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
rubygem-bio-old-biofetch-emulator	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
rubygem-bio-shell	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
samtools	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
scrm	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
seaview	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
seqan	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
seqan1	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
seqan3	biology/seqan3: Update 3.0.2-1195 -> 3.0.3	2021-05-29 22:38:08 -07:00
seqan-apps	biology/seqan-apps: fix packaging on armv7	2021-06-21 08:11:25 +00:00
seqio	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
seqkit	biology/seqkit: Update 0.16.0 -> 0.16.1	2021-05-19 23:02:26 -07:00
seqtk	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
sim4	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
slclust	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
smithwaterman	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
snpeff	biology/snpeff: Improvements to Makefile and patches	2021-04-19 11:41:58 -05:00
spoa	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
sra-tools	biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives	2021-06-22 12:55:15 -05:00
stacks	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
star	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
stringtie	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
subread	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
tabixpp	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
taxonkit	biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit	2021-05-26 15:25:22 -07:00
treekin	math/lapack: +math/blas et al., upgrade to 3.9.1	2021-06-13 19:48:12 +02:00
treepuzzle	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
trimadap	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
trimmomatic	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
tRNAscan-SE	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
ucsc-userapps	biology/ucsc-userapps: Update to v414	2021-05-15 10:23:08 -05:00
ugene	graphics/mesa-libs: Bump reverse deps for libglvnd	2021-06-22 11:53:08 -07:00
unikmer	biology/unikmer: New port: Toolkit for nucleic acid k-mer analysis, set operations on k-mers	2021-05-26 15:25:21 -07:00
vcf2hap	biology/vcf2hap: Remove comment used to silence portlint	2021-06-11 10:40:11 -05:00
vcf-split	biology/vcf-split: Update to 0.1.2	2021-06-11 10:05:19 -05:00
vcflib	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
vcftools	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
velvet	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
viennarna	math/gsl: update to 2.7	2021-06-16 21:31:27 +02:00
vsearch	biology/vsearch: Update to 2.17.1	2021-06-19 07:33:58 -05:00
vt	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
wise	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
Makefile	biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives	2021-06-22 12:55:15 -05:00