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freebsd-ports/biology
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Dmitry Marakasov b28e6ccdb9 biology/gatk: mark BROKEN 
FAILURE: Build failed with an exception.

* Where:
Build file '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.2.6.1/build.gradle' line: 15

* What went wrong:
Plugin [id: 'de.undercouch.download', version: '4.1.2'] was not found in any of the following sources:

- Gradle Core Plugins (plugin is not in 'org.gradle' namespace)
- Plugin Repositories (could not resolve plugin artifact 'de.undercouch.download:de.undercouch.download.gradle.plugin:4.1.2')
  Searched in the following repositories:
    Gradle Central Plugin Repository

Reported by:	pkg-fallout
Approved by:	portmgr blanket
2022-08-11 21:33:41 +03:00
..
abyss biology/abyss: Add test target 2022-07-30 00:34:34 -07:00
ad2vcf biology/ad2vcf: Update to 0.1.6 2022-06-11 09:26:57 -05:00
artemis biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
avida biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
babel biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
bamtools
bamutil
bbmap
bcftools biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
bedtools
bfc
bio-mocha
bioawk
biococoa
biolibc biology/biolibc: Update to 0.2.3 2022-06-11 09:26:56 -05:00
biolibc-tools biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
bioparser
biosig biology/biosig: Update 2.4.1 -> 2.4.2 2022-06-19 09:53:42 -07:00
biosoup
biostar-tools
bolt-lmm devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
bowtie
bowtie2 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
bwa
canu devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
cd-hit
cdbfasta biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
checkm
clustal-omega
clustalw biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
cufflinks biology/cufflinks: Unbreak 2022-07-27 20:43:06 -07:00
cytoscape
ddocent
diamond
dsr-pdb devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
edlib
emboss biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
erminej
exonerate biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
fasta biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
fasta3 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
fastahack
fastdnaml biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
fastool
fastp
fastq-trim
fastqc
fasttree
fastx-toolkit
figtree
flash
fluctuate biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
freebayes
garlic biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
gatk biology/gatk: mark BROKEN 2022-08-11 21:33:41 +03:00
gcta biology/gcta: Use bundled version of eigen3 2022-07-06 13:40:04 -07:00
gemma
generand
gff2ps biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
gffread
gmap biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
gperiodic cleanup: remove '$MCom' tag 2022-07-20 21:44:12 +02:00
graphlan
groopm
haplohseq devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
hhsuite biology/hhsuite: Fix build on some architectures 2022-08-04 09:21:45 -07:00
hisat2
hmmer biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
htslib biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
hyphy biology/hyphy: Update 2.5.40 -> 2.5.41 2022-08-06 15:23:11 -07:00
igv
infernal
iolib biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
iqtree devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
jalview biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
jellyfish
kallisto science/hdf5: bump PORTREVISION of consumers 2022-07-20 16:35:24 +02:00
kmcp biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale genome searching 2022-08-07 13:30:47 -07:00
lamarc biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
libbigwig
libgff
libgtextutils
libneurosim
libnuml
libsbml biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
libsedml biology/{,py-}libsedml: Update 2.0.31 -> 2.0.32 2022-06-08 22:53:28 -07:00
linux-foldingathome biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
mafft biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
mapm3 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
migrate biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
minimap2
mmseqs2 biology/mmseqs2: Not require OpenMP on systems where OpenMP isn't enabled 2022-07-23 09:40:43 -07:00
molden biology/molden: Update 6.7 -> 7.1 2022-07-23 13:00:53 -07:00
mothur biology/mothur: Update 1.47.0 -> 1.48.0 2022-05-19 19:10:18 -07:00
mrbayes biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
mummer biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
muscle biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
ncbi-blast+ devel/grpc: Update to 1.48.0 2022-07-30 13:57:09 +08:00
ncbi-cxx-toolkit biology/ncbi-cxx-toolkit: Broken on armv6 2022-08-06 16:28:43 -07:00
ncbi-entrez-direct all: Bump PORTREVISION after Go update 2022-08-03 16:35:13 -05:00
ncbi-toolkit biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
ncbi-vdb science/hdf5: bump PORTREVISION of consumers 2022-07-20 16:35:24 +02:00
ngs-sdk biology/ngs-sdk: Broken on armv6, armv7 2022-07-22 15:34:07 -07:00
p5-AcePerl biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-ASN1-EntrezGene biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Cluster biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Coordinate biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Das biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Das-Lite biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-DB-EMBL biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-DB-NCBIHelper biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-FeatureIO biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-GFF3 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Glite biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Graphics biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-MAGETAB biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-NEXUS biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Phylo biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-SCF biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Variation biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-BioPerl biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-BioPerl-Run biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-transdecoder
p5-TrimGalore
paml biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
pbbam devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
pbseqan
peak-classifier biology/peak-classifier: Update to 0.1.4 2022-06-11 09:26:57 -05:00
pear-merger
phrap
phred biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
phyml biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
picard-tools
plink
pooler biology/pooler: Update to 1.85 2022-07-12 07:47:45 -05:00
primer3 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
prodigal
prodigy-lig
protomol biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
psi88 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
py-bcbio-gff
py-biom-format
py-biopython biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
py-bx-python biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
py-crossmap
py-cutadapt
py-deeptools
py-deeptoolsintervals
py-dna-features-viewer
py-dnaio
py-ete3 biology/py-ete3: Add tests 2022-08-06 15:23:11 -07:00
py-Genesis-PyAPI
py-gffutils biology/py-gffutils: Update 0.10.1 -> 0.11.0 2022-06-06 17:38:48 -07:00
py-goatools
py-gtfparse
py-hits
py-libnuml
py-libsedml biology/{,py-}libsedml: Update 2.0.31 -> 2.0.32 2022-06-08 22:53:28 -07:00
py-loompy
py-macs2
py-mrcfile biology/py-mrcfile: Update 1.4.0 -> 1.4.2 2022-07-29 01:46:46 -07:00
py-multiqc
py-ont-fast5-api
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-py2bit
py-pybigwig
py-pyfaidx
py-pysam biology/py-pysam: Remove BROKEN lines 2022-07-19 08:51:56 -07:00
py-PySCeS biology/py-PySCeS: Update 1.0.1 -> 1.0.2 2022-05-20 15:02:59 -07:00
py-python-libsbml
py-pywgsim
py-resdk biology/py-resdk: Update 14.1.0 -> 15.0.0 2022-06-06 17:38:49 -07:00
py-scikit-bio biology/py-scikit-bio: Broken on aarch64 2022-06-03 15:56:03 -07:00
py-xenaPython
pyfasta biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
python-nexus biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
rainbow
rampler
readseq
recombine biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
ruby-bio biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
rubygem-bio biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
rubygem-bio-executables biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
rubygem-bio-old-biofetch-emulator biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
rubygem-bio-shell biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
sam2pairwise
samtools biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
scrm
seaview biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
seqan biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
seqan1 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
seqan3 biology/seqan3: Update 3.1.0 -> 3.2.0 2022-06-24 00:20:46 -07:00
seqan-apps biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
seqio biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
seqkit all: Bump PORTREVISION after Go update 2022-08-03 16:35:13 -05:00
seqtk
sigviewer
sim4 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
slclust
smithwaterman
snpeff cleanup: remove expired versions of OpenJDK (12 through 16) 2022-05-24 22:09:35 +02:00
spoa
sra-tools science/hdf5: bump PORTREVISION of consumers 2022-07-20 16:35:24 +02:00
stacks
star biology/star: Broken on systems where OpenMP isn't enabled 2022-07-23 18:24:10 -07:00
stringtie
subread
tabixpp
taxonkit all: Bump PORTREVISION after Go update 2022-08-03 16:35:13 -05:00
treekin
treepuzzle biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
trimadap
trimmomatic biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
tRNAscan-SE biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
ucsc-userapps biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
ugene biology/ugene: Correct BROKEN message 2022-08-04 09:35:24 -07:00
unikmer all: Bump PORTREVISION after Go update 2022-08-03 16:35:13 -05:00
vcf2hap biology/vcf2hap: Update to 0.1.6 2022-06-11 09:26:57 -05:00
vcf-split biology/vcf-split: Update to 0.1.5 2022-06-11 09:26:56 -05:00
vcflib Fix CONFLICTS_INSTALL in benchmarks and biology 2022-06-29 16:53:54 +02:00
vcftools
velvet biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
viennarna biology/viennarna: Update 2.5.0 -> 2.5.1 2022-07-31 01:12:49 -07:00
vsearch
vt
wise biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
Makefile biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale genome searching 2022-08-07 13:30:47 -07:00