Hints

Michael R. Crusoe

We have the following e-mail addresses on file:

• crusoe@debian.org
• michael.crusoe@gmail.com
• mcrusoe@msu.edu
• crusoe@ucdavis.edu

Found 528 issues in 58 maintained sources. To see all packaging hints, please click on the source.

• abyss 2.2.5+dfsg-1
• abyss_2.2.5+dfsg-1_amd64.deb (main)
  • W privacy-breach-generic usr/share/doc/abyss/README.html [<img src="https://img.shields.io/conda/dn/bioconda/abyss?label=conda" alt="conda" />] (https://img.shields.io/conda/dn/bioconda/abyss?label=conda)
  • W privacy-breach-generic usr/share/doc/abyss/README.html [<img src="https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github" alt="downloads" />] (https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github)
  • W privacy-breach-generic usr/share/doc/abyss/README.html [<img src="https://img.shields.io/github/issues/bcgsc/abyss.svg" alt="issues" />] (https://img.shields.io/github/issues/bcgsc/abyss.svg)
  • W privacy-breach-generic usr/share/doc/abyss/README.html [<img src="https://img.shields.io/github/release/bcgsc/abyss.svg" alt="release" />] (https://img.shields.io/github/release/bcgsc/abyss.svg)
• ataqv 1.2.1+ds-1
• ataqv_1.2.1+ds-1+b1_amd64.deb (main)
  • W no-manual-page usr/bin/make_ataqv_pipeline
  • W no-manual-page usr/bin/run_ataqv_example
  • W package-contains-timestamped-gzip usr/share/doc/ataqv/examples/testdata/exclude.dac.bed.gz 2020-12-12T13:00:51
  • W package-contains-timestamped-gzip usr/share/doc/ataqv/examples/testdata/exclude.duke.bed.gz 2020-12-12T13:00:51
  • W package-contains-timestamped-gzip usr/share/doc/ataqv/examples/testdata/hg19.tss.refseq.bed.gz 2020-12-12T13:00:51
  • W package-contains-timestamped-gzip usr/share/doc/ataqv/examples/testdata/SRR891275.peaks.gz 2020-12-12T13:00:51
  • W package-contains-timestamped-gzip usr/share/doc/ataqv/examples/testdata/SRR891278.peaks.gz 2020-12-12T13:00:51
  • W package-contains-timestamped-gzip usr/share/doc/ataqv/examples/testdata/test.peaks.gz 2020-12-12T13:00:51
• bamtools 2.5.1+dfsg-9
• bamtools_2.5.1+dfsg-9_amd64.deb (main)
  • E malformed-override Unknown tag description-contains-duplicated-word in line 2
• bcftools 1.13-1
• bcftools_1.13-1_amd64.deb (main)
  • W no-manual-page usr/bin/gff2gff.py
  • W no-manual-page usr/bin/guess-ploidy.py
  • W no-manual-page usr/bin/plot-roh.py
  • W no-manual-page usr/bin/run-roh.pl
  • W script-with-language-extension usr/bin/color-chrs.pl
  • W script-with-language-extension usr/bin/gff2gff.py
  • W script-with-language-extension usr/bin/guess-ploidy.py
  • W script-with-language-extension usr/bin/plot-roh.py
  • W script-with-language-extension usr/bin/run-roh.pl
  • W script-with-language-extension usr/bin/vcfutils.pl
• benchmark 1.5.2-2
• libbenchmark-tools_1.5.2-2_all.deb (main)
  • W unusual-interpreter usr/share/benchmark/compare.py python
  • W unusual-interpreter usr/share/benchmark/strip_asm.py python
• berkeley-express 1.5.3+dfsg-1
• berkeley-express_1.5.3+dfsg-1.dsc (main)
  • W tab-in-license-text debian/copyright (starting at line 18)
• cnvkit 0.9.8-1
• cnvkit_0.9.8-1_amd64.deb (main)
  • W breakout-link usr/lib/debian-med/bin/cnvkit.py -> usr/bin/cnvkit
  • W groff-message usr/share/man/man1/cnvkit.1.gz (line 1) 8: warning [p 1, 1.7i]: cannot adjust line
  • W groff-message usr/share/man/man1/cnvkit.1.gz (line 2) 8: warning [p 1, 1.8i]: cannot adjust line
  • W groff-message usr/share/man/man1/cnvkit.1.gz (line 3) 14: warning [p 1, 2.8i, div 'an-div', 0.0i]: cannot adjust line
  • W groff-message usr/share/man/man1/cnvkit.1.gz (line 4) 14: warning [p 1, 2.8i, div 'an-div', 0.2i]: cannot adjust line
  • W no-manual-page usr/bin/cnvkit-cnv_annotate
  • W no-manual-page usr/bin/cnvkit-cnv_expression_correlate
  • W no-manual-page usr/bin/cnvkit-cnv_updater
  • W no-manual-page usr/bin/cnvkit-guess_baits
  • W no-manual-page usr/bin/cnvkit-skg_convert
  • W no-manual-page usr/bin/snpfilter.sh
  • W script-with-language-extension usr/bin/snpfilter.sh
• ctdconverter 2.1-3
• ctdconverter_2.1-3.dsc (main)
  • W superficial-tests
• ctdconverter_2.1-3_all.deb (main)
  • W groff-message usr/share/man/man1/CTDConverter.1.gz (line 1) 75: warning [p 2, 1.8i]: can't break line
  • W groff-message usr/share/man/man1/CTDConverter.1.gz (line 2) 126: warning [p 2, 9.3i]: can't break line
• cwltool 3.0.20210124104916-3
• cwltool_3.0.20210124104916-3_all.deb (main)
  • W mismatched-override unusual-interpreter usr/lib/python3/dist-packages/cwltool/hello.simg #!run-singularity
  • W unusual-interpreter usr/lib/python3/dist-packages/cwltool/hello.simg run-singularity
• golang-github-abeconnelly-autoio 0.0~git20150803.989b7b0-3
• golang-github-abeconnelly-autoio_0.0~git20150803.989b7b0-3.dsc (main)
  • W no-nmu-in-changelog
  • W source-nmu-has-incorrect-version-number 0.0~git20150803.989b7b0-3
• guzzle-sphinx-theme 0.7.11-5
• guzzle-sphinx-theme_0.7.11-5.dsc (main)
  • E old-dpmt-vcs Browser
  • E old-dpmt-vcs Git
  • E python-teams-merged Debian Python Modules Team <python-modules-team@lists.alioth.debian.org>
  • W pypi-homepage https://pypi.python.org/pypi/guzzle_sphinx_theme
• python3-guzzle-sphinx-theme_0.7.11-5_all.deb (main)
  • E malformed-override Unknown tag package-contains-broken-symlink in line 10
  • E malformed-override Unknown tag package-contains-broken-symlink in line 4
  • E malformed-override Unknown tag package-contains-broken-symlink in line 5
  • E malformed-override Unknown tag package-contains-broken-symlink in line 6
  • E malformed-override Unknown tag package-contains-broken-symlink in line 7
  • E malformed-override Unknown tag package-contains-broken-symlink in line 8
  • E malformed-override Unknown tag package-contains-broken-symlink in line 9
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/css/bootstrap.min.css -> usr/share/javascript/bootstrap/css/bootstrap.min.css
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/css/bootstrap-theme.min.css -> usr/share/javascript/bootstrap/css/bootstrap-theme.min.css
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.eot -> usr/share/javascript/bootstrap/fonts/glyphicons-halflings-regular.eot
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.svg -> usr/share/javascript/bootstrap/fonts/glyphicons-halflings-regular.svg
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.ttf -> usr/share/javascript/bootstrap/fonts/glyphicons-halflings-regular.ttf
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.woff2 -> usr/share/javascript/bootstrap/fonts/glyphicons-halflings-regular.woff2
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.woff -> usr/share/javascript/bootstrap/fonts/glyphicons-halflings-regular.woff
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/LiberationSans-Italic.ttf -> usr/share/fonts/truetype/liberation/LiberationSans-Italic.ttf
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/LiberationSans-Regular.ttf -> usr/share/fonts/truetype/liberation/LiberationSans-Regular.ttf
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/LiberationSerif-Regular.ttf -> usr/share/fonts/truetype/liberation/LiberationSerif-Regular.ttf
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/jquery.js -> usr/share/javascript/jquery/jquery.js
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/jquery.min.js -> usr/share/javascript/jquery/jquery.min.js
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/js/bootstrap.js -> usr/share/javascript/bootstrap/js/bootstrap.js
  • W breakout-link usr/lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/js/bootstrap.min.js -> usr/share/javascript/bootstrap/js/bootstrap.min.js
• hisat2 2.2.1-2
• python3-hisat2_2.2.1-2_all.deb (main)
  • W no-manual-page usr/bin/hisat2_extract_exons.py
  • W no-manual-page usr/bin/hisat2_extract_snps_haplotypes_UCSC.py
  • W no-manual-page usr/bin/hisat2_extract_snps_haplotypes_VCF.py
  • W no-manual-page usr/bin/hisat2_extract_splice_sites.py
• htscodecs 1.1.1-2
• htscodecs_1.1.1-2.dsc (main)
  • W patch-file-present-but-not-mentioned-in-series big-endian
  • W patch-file-present-but-not-mentioned-in-series ship_varint_h
• htslib 1.13+ds-2
• libhts3_1.13+ds-2_amd64.deb (main)
  • W bad-whatis-entry usr/share/man/man7/htslib-s3-plugin.7.gz
• jellyfish 2.3.0-12
• jellyfish-examples_2.3.0-12_all.deb (main)
  • W breakout-link usr/lib/jellyfish/bin/jellyfish -> usr/bin/jellyfish
• libjellyfish-2.0-dev_2.3.0-12_amd64.deb (main)
  • W package-name-defined-in-config-h usr/include/jellyfish/config.h
• khmer 2.1.2+dfsg-8
• khmer_2.1.2+dfsg-8.dsc (main)
  • W inconsistent-appstream-metadata-license debian/copyright debian/khmer.metainfo.xml (mit != bsd-3-clause)
• khmer_2.1.2+dfsg-8_amd64.deb (main)
  • W broken-bz2 usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.bz2
  • W broken-bz2 usr/lib/python3/dist-packages/khmer/tests/test-data/test-empty.fa.bz2
  • W broken-gz usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz
• libbio-db-ace-perl 1.7.3-2
• libbio-db-ace-perl_1.7.3-2.dsc (main)
  • W upstream-metadata-field-unknown Homepage
• libbio-db-biofetch-perl 1.7.3-4
• libbio-db-biofetch-perl_1.7.3-4.dsc (main)
  • W obsolete-runtime-tests-restriction needs-recommends in line 18
  • W superficial-tests
• libbio-db-embl-perl 1.7.4-4
• libbio-db-embl-perl_1.7.4-4.dsc (main)
  • W obsolete-runtime-tests-restriction needs-recommends in line 18
  • W superficial-tests
• libbio-db-gff-perl 1.7.4-1
• libbio-db-gff-perl_1.7.4-1.dsc (main)
  • W upstream-metadata-field-unknown Homepage
• libbio-db-gff-perl_1.7.4-1_all.deb (main)
  • W no-manual-page usr/bin/bp_das_server
• libbio-db-ncbihelper-perl 1.7.6-4
• libbio-db-ncbihelper-perl_1.7.6-4.dsc (main)
  • W obsolete-runtime-tests-restriction needs-recommends in line 18
  • W superficial-tests
• libbio-db-seqfeature-perl 1.7.4-1
• libbio-db-seqfeature-perl_1.7.4-1.dsc (main)
  • W upstream-metadata-field-unknown Homepage
• libbio-db-seqfeature-perl_1.7.4-1_all.deb (main)
  • W no-manual-page usr/bin/bp_seqfeature_delete
  • W no-manual-page usr/bin/bp_seqfeature_gff3
• libbio-searchio-hmmer-perl 1.7.3-2
• libbio-searchio-hmmer-perl_1.7.3-2.dsc (main)
  • W upstream-metadata-field-unknown Homepage
• libbio-searchio-hmmer-perl_1.7.3-2_all.deb (main)
  • W bad-whatis-entry usr/share/man/man3/Bio::SearchIO::hmmer3.3pm.gz
• libbio-variation-perl 1.7.5-2
• libbio-variation-perl_1.7.5-2_all.deb (main)
  • W bad-whatis-entry usr/share/man/man3/Bio::Variation.3pm.gz
• libcereal 1.3.0+dfsg-1
• libcereal_1.3.0+dfsg-1.dsc (main)
  • W unnecessary-team-upload
• libdeflate 1.7-2
• libdeflate-tools_1.7-2_amd64.deb (main)
  • W no-manual-page usr/bin/libdeflate-gunzip
  • W no-manual-page usr/bin/libdeflate-gzip
• libjung-free-java 2.0.1+dfsg-1.1
• libjung-free-java_2.0.1+dfsg-1.1.dsc (main)
  • W no-nmu-in-changelog
  • W package-uses-deprecated-debhelper-compat-version 9
  • W patch-file-present-but-not-mentioned-in-series use-apache-commons-collections
  • W vcs-obsolete-in-debian-infrastructure Browser https://anonscm.debian.org/cgit/debian-med/libjung-java.git
  • W vcs-obsolete-in-debian-infrastructure Git git://anonscm.debian.org/debian-med/libjung-java.git
• libjung-free-java-doc_2.0.1+dfsg-1.1_all.deb (main)
  • E doc-base-file-references-wrong-path libjung-free-java-doc:8 //usr/share/doc/libjung-free-java/api
  • E doc-base-file-references-wrong-path libjung-free-java-doc:9 //usr/share/doc/libjung-free-java/api/*.html
  • W embedded-javascript-library usr/share/doc/libjung-free-java/api/jquery/external/jquery/jquery.js please use libjs-jquery
  • W embedded-javascript-library usr/share/doc/libjung-free-java/api/jquery/jquery-3.5.1.js please use libjs-jquery
  • W embedded-javascript-library usr/share/doc/libjung-free-java/api/jquery/jquery-ui.css please use libjs-jquery-ui
  • W embedded-javascript-library usr/share/doc/libjung-free-java/api/jquery/jquery-ui.js please use libjs-jquery-ui
  • W embedded-javascript-library usr/share/doc/libjung-free-java/api/jquery/jquery-ui.min.css please use libjs-jquery-ui
  • W embedded-javascript-library usr/share/doc/libjung-free-java/api/jquery/jquery-ui.min.js please use libjs-jquery-ui
• macs 2.2.7.1-3
• macs_2.2.7.1-3+b2_amd64.deb (main)
  • W groff-message usr/share/man/man1/macs2.1.gz (line 1) 8: warning [p 1, 1.7i]: cannot adjust line
  • W groff-message usr/share/man/man1/macs2.1.gz (line 2) 14: warning [p 1, 2.7i]: cannot adjust line
  • W mismatched-override manpage-has-errors-from-man usr/share/man/man1/macs2.1.gz 8: warning [p 1, 1.7i]: cannot adjust line
  • W package-contains-timestamped-gzip usr/share/doc/macs/examples/aluY.chr1.bed.gz 2020-12-07T14:56:13
  • W package-contains-timestamped-gzip usr/share/doc/macs/examples/gerp.chr1.bed.gz 2020-12-07T14:56:13
• mypy 0.812-1
• mypy_0.812-1_all.deb (main)
  • W no-manual-page usr/bin/mypyc
  • W no-manual-page usr/bin/stubtest
• python3-mypy_0.812-1_amd64.deb (main)
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/api.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/applytype.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/argmap.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/binder.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/build.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/analysis/dataflow.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/analysis/__init__.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/build.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/codegen/cstring.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/codegen/emitclass.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/codegen/emit.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/codegen/emitfunc.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/codegen/emitmodule.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/codegen/emitwrapper.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/codegen/__init__.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/common.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/crash.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/errors.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/checker.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/checkexpr.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/checkmember.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/checkstrformat.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/__init__.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/builder.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/callable_class.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/classdef.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/context.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/env_class.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/expression.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/for_helpers.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/function.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/generator.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/__init__.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/ll_builder.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/main.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/mapper.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/nonlocalcontrol.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/prebuildvisitor.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/prepare.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/specialize.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/statement.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/targets.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/util.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/visitor.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/irbuild/vtable.cpython-39-x86_64-linux-gnu.so
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  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/primitives/dict_ops.cpython-39-x86_64-linux-gnu.so
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  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypyc/transform/exceptions.cpython-39-x86_64-linux-gnu.so
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  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/strconv.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/stubdoc.cpython-39-x86_64-linux-gnu.so
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  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/subtypes.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/suggestions.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/test/visitors.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/traverser.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/treetransform.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/tvar_scope.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/typeanal.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/typeops.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/types.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/typestate.cpython-39-x86_64-linux-gnu.so
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  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/typevars.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/type_visitor.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/util.cpython-39-x86_64-linux-gnu.so
  • W shared-library-lacks-prerequisites usr/lib/python3/dist-packages/mypy/visitor.cpython-39-x86_64-linux-gnu.so
• prokka 1.14.6+dfsg-4
• prokka_1.14.6+dfsg-4_amd64.deb (main)
  • W package-contains-vcs-control-file usr/share/prokka/db/cm/__build/.gitignore
  • W script-not-executable usr/share/prokka/db/cm/__build/update.sh
• python3-antlr4 4.9.1-1
• python3-antlr4_4.9.1-1_all.deb (main)
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• python-bx 0.8.9-1
• python3-bx_0.8.9-1_amd64.deb (main)
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  • W no-manual-page usr/bin/axt_to_fasta.py
  • W no-manual-page usr/bin/axt_to_lav.py
  • W no-manual-page usr/bin/axt_to_maf.py
  • W no-manual-page usr/bin/bed_bigwig_profile.py
  • W no-manual-page usr/bin/bed_build_windows.py
  • W no-manual-page usr/bin/bed_complement.py
  • W no-manual-page usr/bin/bed_count_by_interval.py
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  • W no-manual-page usr/bin/bed_coverage_by_interval.py
  • W no-manual-page usr/bin/bed_coverage.py
  • W no-manual-page usr/bin/bed_diff_basewise_summary.py
  • W no-manual-page usr/bin/bed_extend_to.py
  • W no-manual-page usr/bin/bed_intersect_basewise.py
  • W no-manual-page usr/bin/bed_intersect.py
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  • W no-manual-page usr/bin/bed_rand_intersect.py
  • W no-manual-page usr/bin/bed_subtract_basewise.py
  • W no-manual-page usr/bin/bnMapper.py
  • W no-manual-page usr/bin/div_snp_table_chr.py
  • W no-manual-page usr/bin/find_in_sorted_file.py
  • W no-manual-page usr/bin/gene_fourfold_sites.py
  • W no-manual-page usr/bin/get_scores_in_intervals.py
  • W no-manual-page usr/bin/interval_count_intersections.py
  • W no-manual-page usr/bin/interval_join.py
  • W no-manual-page usr/bin/int_seqs_to_char_strings.py
  • W no-manual-page usr/bin/lav_to_axt.py
  • W no-manual-page usr/bin/lav_to_maf.py
  • W no-manual-page usr/bin/line_select.py
  • W no-manual-page usr/bin/lzop_build_offset_table.py
  • W no-manual-page usr/bin/maf_build_index.py
  • W no-manual-page usr/bin/maf_chop.py
  • W no-manual-page usr/bin/maf_chunk.py
  • W no-manual-page usr/bin/maf_col_counts_all.py
  • W no-manual-page usr/bin/maf_col_counts.py
  • W no-manual-page usr/bin/maf_count.py
  • W no-manual-page usr/bin/maf_covered_ranges.py
  • W no-manual-page usr/bin/maf_covered_regions.py
  • W no-manual-page usr/bin/maf_div_sites.py
  • W no-manual-page usr/bin/maf_drop_overlapping.py
  • W no-manual-page usr/bin/maf_extract_chrom_ranges.py
  • W no-manual-page usr/bin/maf_extract_ranges_indexed.py
  • W no-manual-page usr/bin/maf_extract_ranges.py
  • W no-manual-page usr/bin/maf_filter_max_wc.py
  • W no-manual-page usr/bin/maf_filter.py
  • W no-manual-page usr/bin/maf_gap_frequency.py
  • W no-manual-page usr/bin/maf_gc_content.py
  • W no-manual-page usr/bin/maf_interval_alignibility.py
  • W no-manual-page usr/bin/maf_limit_to_species.py
  • W no-manual-page usr/bin/maf_mapping_word_frequency.py
  • W no-manual-page usr/bin/maf_mask_cpg.py
  • W no-manual-page usr/bin/maf_mean_length_ungapped_piece.py
  • W no-manual-page usr/bin/maf_percent_columns_matching.py
  • W no-manual-page usr/bin/maf_percent_identity.py
  • W no-manual-page usr/bin/maf_print_chroms.py
  • W no-manual-page usr/bin/maf_print_scores.py
  • W no-manual-page usr/bin/maf_randomize.py
  • W no-manual-page usr/bin/maf_region_coverage_by_src.py
  • W no-manual-page usr/bin/maf_select.py
  • W no-manual-page usr/bin/maf_shuffle_columns.py
  • W no-manual-page usr/bin/maf_species_in_all_files.py
  • W no-manual-page usr/bin/maf_split_by_src.py
  • W no-manual-page usr/bin/maf_thread_for_species.py
  • W no-manual-page usr/bin/maf_tile_2bit.py
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  • W no-manual-page usr/bin/nib_chrom_intervals_to_fasta.py
  • W no-manual-page usr/bin/nib_intervals_to_fasta.py
  • W no-manual-page usr/bin/nib_length.py
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  • W no-manual-page usr/bin/tfloc_summary.py
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  • W no-manual-page usr/bin/wiggle_to_array_tree.py
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  • W no-manual-page usr/bin/wiggle_to_chr_binned_array.py
  • W no-manual-page usr/bin/wiggle_to_simple.py
  • W unusual-interpreter usr/lib/python3/dist-packages/bx/pwm/bed_score_aligned_pwm.py python2.4
  • W unusual-interpreter usr/lib/python3/dist-packages/bx/pwm/bed_score_aligned_string.py python2.4
  • W unusual-interpreter usr/lib/python3/dist-packages/bx/pwm/maf_select_motifs.py python2.4
  • W unusual-interpreter usr/lib/python3/dist-packages/bx/pwm/pwm_score_maf.py /usr/bin/python2.4
  • W unusual-interpreter usr/lib/python3/dist-packages/bx/pwm/pwm_score_motifs.py python2.4
  • W unusual-interpreter usr/lib/python3/dist-packages/bx/pwm/pwm_score_positions.py python2.4
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  • E debian-watch-file-pubkey-file-is-missing
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  • W source-nmu-has-incorrect-version-number 0.8.0-5
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  • W no-manual-page usr/bin/annotate.py
  • W no-manual-page usr/bin/intersection_matrix.py
  • W no-manual-page usr/bin/intron_exon_reads.py
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  • W embedded-javascript-library usr/share/doc/python-pybedtools-doc/html/_static/language_data.js please use sphinx
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  • W package-contains-timestamped-gzip usr/lib/python3/dist-packages/pybedtools/test/data/dm3-chr2L-5M.gff.gz 2020-12-07T11:30:43
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  • W executable-not-elf-or-script usr/lib/python3/dist-packages/schema_salad/tests/formattest2.cwl
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  • W no-manual-page usr/bin/screed
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  • W executable-not-elf-or-script usr/lib/python3/dist-packages/stubserver-1.1.egg-info/PKG-INFO
  • W executable-not-elf-or-script usr/lib/python3/dist-packages/stubserver-1.1.egg-info/top_level.txt
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  • W pypi-homepage https://pypi.python.org/pypi/typing-extensions/
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  • W mismatched-override spelling-error-in-binary usr/bin/rapmap YelD Yield
  • W no-manual-page usr/bin/RunRapMap.sh
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  • W tab-in-license-text debian/copyright (starting at line 14)
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  • W national-encoding usr/lib/R/site-library/PSCBS/NEWS
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  • E library-not-linked-against-libc usr/lib/R/site-library/Rook/libs/Rook.so
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  • W breakout-link usr/lib/R/site-library/Rook/exampleApps/Hmisc/javascript/prototype.js -> usr/share/javascript/prototype/prototype.js
• r-cran-sna 2.6-1
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  • W no-nmu-in-changelog
  • W source-nmu-has-incorrect-version-number 2.6-1
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  • W no-manual-page usr/bin/extract-transcript-to-gene-map-from-trinity
  • W no-manual-page usr/bin/rsem-bam2readdepth
  • W no-manual-page usr/bin/rsem-build-read-index
  • W no-manual-page usr/bin/rsem-calculate-credibility-intervals
  • W no-manual-page usr/bin/rsem-extract-reference-transcripts
  • W no-manual-page usr/bin/rsem-generate-data-matrix
  • W no-manual-page usr/bin/rsem-gen-transcript-plots
  • W no-manual-page usr/bin/rsem-get-unique
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  • W no-manual-page usr/bin/rsem-preref
  • W no-manual-page usr/bin/rsem-refseq-extract-primary-assembly
  • W no-manual-page usr/bin/rsem-run-em
  • W no-manual-page usr/bin/rsem-run-gibbs
  • W no-manual-page usr/bin/rsem-sam-validator
  • W no-manual-page usr/bin/rsem-scan-for-paired-end-reads
  • W no-manual-page usr/bin/rsem-synthesis-reference-transcripts
  • W no-manual-page usr/bin/rsem-tbam2gbam
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  • W package-uses-deprecated-debhelper-compat-version 9
  • W vcs-obsolete-in-debian-infrastructure Browser https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-colorize.git
  • W vcs-obsolete-in-debian-infrastructure Git https://anonscm.debian.org/git/pkg-ruby-extras/ruby-colorize.git
• ruby-colorize_0.8.1-1_all.deb (main)
  • W ruby-interpreter-is-deprecated ruby | ruby-interpreter
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  • E ruby-script-but-no-ruby-dep usr/bin/crb-blast /usr/bin/ruby
  • W ruby-interpreter-is-deprecated ruby | ruby-interpreter
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  • W description-synopsis-starts-with-article
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  • W rubygem-homepage http://rubygems.org/gems/fix-trinity-output
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  • E ruby-script-but-no-ruby-dep usr/bin/fix-trinity-output /usr/bin/ruby
  • W ruby-interpreter-is-deprecated ruby | ruby-interpreter
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  • W ruby-interpreter-is-deprecated ruby | ruby-interpreter
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  • W ruby-interpreter-is-deprecated ruby | ruby-interpreter
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  • W ruby-interpreter-is-deprecated ruby | ruby-interpreter
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  • W privacy-breach-generic usr/share/doc/sga/index.html [<img border="0" width="90" src="http://github.com/images/modules/download/tar.png">] (http://github.com/images/modules/download/tar.png)
  • W privacy-breach-generic usr/share/doc/sga/index.html [<img border="0" width="90" src="http://github.com/images/modules/download/zip.png">] (http://github.com/images/modules/download/zip.png)
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  • W globbing-patterns-out-of-order debian/copyright assembler/ext/src/samtools/bcftools/kmin.* assembler/ext/src/samtools/* assembler/ext/src/samtools/bcftools/kmin.c
  • W globbing-patterns-out-of-order debian/copyright assembler/ext/src/samtools/bcftools/kmin.* assembler/ext/src/samtools/* assembler/ext/src/samtools/bcftools/kmin.h
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  • W breakout-link usr/lib/spades/bin/spades-bwa -> usr/bin/bwa
  • W breakout-link usr/lib/spades/bin/VERSION -> usr/share/spades/VERSION
  • W package-contains-timestamped-gzip usr/share/spades/test_dataset/ecoli_1K_1.fq.gz 2020-11-19T01:35:41
  • W package-contains-timestamped-gzip usr/share/spades/test_dataset/ecoli_1K_2.fq.gz 2020-11-19T01:35:41
  • W package-contains-timestamped-gzip usr/share/spades/test_dataset_plasmid/pl1.fq.gz 2020-11-19T01:35:41
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  • W package-contains-timestamped-gzip usr/share/spades/test_dataset/reference_1K.fa.gz 2020-11-19T01:35:41
  • W package-contains-timestamped-gzip usr/share/spades/test_dataset_truspades/A_R1.fastq.gz 2020-11-19T01:35:41
  • W package-contains-timestamped-gzip usr/share/spades/test_dataset_truspades/A_R2.fastq.gz 2020-11-19T01:35:41
  • W package-contains-timestamped-gzip usr/share/spades/test_dataset_truspades/B_R1.fastq.gz 2020-11-19T01:35:41
  • W package-contains-timestamped-gzip usr/share/spades/test_dataset_truspades/B_R2.fastq.gz 2020-11-19T01:35:41
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  • W no-manual-page usr/bin/io_lib-config
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  • W zero-byte-file-in-doc-directory usr/share/doc/staden-io-lib/test/data/xx#blank.sam
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  • W no-manual-page usr/bin/convert_trace
  • W no-manual-page usr/bin/cram_dump
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  • W no-manual-page usr/bin/cram_index
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  • W no-manual-page usr/bin/extract_fastq
  • W no-manual-page usr/bin/extract_qual
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  • W no-manual-page usr/bin/srf_extract_hash
  • W no-manual-page usr/bin/srf_extract_linear
  • W no-manual-page usr/bin/trace_dump
  • W no-manual-page usr/bin/ztr_dump
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  • E python-traceback-in-manpage usr/share/man/man1/toil.1.gz
  • W no-manual-page usr/bin/toil-cwl-runner
  • W no-manual-page usr/bin/_toil_kubernetes_executor
  • W no-manual-page usr/bin/toil-wdl-runner
  • W script-not-executable usr/lib/python3/dist-packages/toil/test/cwl/alwaysfails.cwl
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  • W executable-not-elf-or-script usr/lib/trinityrnaseq/util/misc/SAM_to_bed.pl
  • W no-manual-page usr/bin/BubbleUpClustering
  • W no-manual-page usr/bin/Chrysalis
  • W no-manual-page usr/bin/CreateIwormFastaBundle
  • W no-manual-page usr/bin/FastaToDeBruijn
  • W no-manual-page usr/bin/fastaToKmerCoverageStats
  • W no-manual-page usr/bin/GraphFromFasta
  • W no-manual-page usr/bin/inchworm
  • W no-manual-page usr/bin/QuantifyGraph
  • W no-manual-page usr/bin/ReadsToTranscripts
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  • W breakout-link usr/lib/trinityrnaseq/sample_data -> usr/share/trinityrnaseq/sample_data
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  • W no-manual-page usr/bin/uncalled
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  • E malformed-override Expected a colon in line 5