Michael R. Crusoe

At the time of the last Lintian run, the following possible problems were found in packages maintained by Michael R. Crusoe <michael.crusoe@gmail.com>, listed by source package. See also the full report, including info, experimental and overridden tags. Also see their QA overview.

ctdconverter

• W manpage-has-errors-from-man
  • usr/share/man/man1/CTDConverter.1.gz 75: warning [p 2, 4.2i]: can't break line

• W ancient-python-version-field
  • x-python-version 2.6
  • x-python3-version 3.2

cwltool

• W executable-not-elf-or-script
  • usr/lib/python3/dist-packages/cwltool/tests/arg-empty-prefix-separate-false.cwl

libhts-dev

• W manpage-has-errors-from-man
  • usr/share/man/man5/faidx.5.gz file '<standard input>', around line 49:
  • usr/share/man/man5/vcf.5.gz file '<standard input>', around line 39:

• W inconsistent-appstream-metadata-license
  • debian/khmer.metainfo.xml (mit != bsd-3-clause)

• W dependency-is-not-multi-archified
  • libdeflate-dev depends on libdeflate0 (multi-arch: no)
  • libdeflate-dev depends on libdeflate0 (multi-arch: no)
  • libdeflate-dev depends on libdeflate0 (multi-arch: no)
  • libdeflate-dev depends on libdeflate0 (multi-arch: no)

libdeflate0

• W binary-without-manpage
  • usr/bin/libdeflate-gunzip [amd64, i386]
  • usr/bin/libdeflate-gzip [amd64, i386]

• W debian-rules-should-not-use-custom-compression-settings
  • dh_builddeb -- -Z xz (line 53)

• W missing-license-paragraph-in-dep5-copyright
  • gpl-2 (paragraph at line 23)

python3-gffutils

• W manpage-has-errors-from-man
  • usr/share/man/man1/gffutils-cli.1.gz 8: warning [p 1, 1.7i, div 'an-div', 0.0i]: cannot adjust line

python3-screed

• W binary-without-manpage
  • usr/bin/screed

r-cran-blockmodeling

• W spelling-error-in-description
  • algorithem algorithm [amd64, i386]

rsem

• W binary-without-manpage
  • usr/bin/extract-transcript-to-gene-map-from-trinity
  • usr/bin/rsem-bam2readdepth
  • usr/bin/rsem-build-read-index
  • usr/bin/rsem-calculate-credibility-intervals
  • usr/bin/rsem-extract-reference-transcripts
  • usr/bin/rsem-gen-transcript-plots
  • usr/bin/rsem-generate-data-matrix
  • usr/bin/rsem-get-unique
  • usr/bin/rsem-parse-alignments
  • usr/bin/rsem-plot-model
  • usr/bin/rsem-preref
  • usr/bin/rsem-refseq-extract-primary-assembly
  • usr/bin/rsem-run-em
  • usr/bin/rsem-run-gibbs
  • usr/bin/rsem-sam-validator
  • usr/bin/rsem-scan-for-paired-end-reads
  • usr/bin/rsem-synthesis-reference-transcripts
  • usr/bin/rsem-tbam2gbam
  • usr/bin/rsem_perl_utils.pm

• W ancient-standards-version
  • 3.9.8 (released 2016-04-06) (current is 4.4.1)
• W vcs-obsolete-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-colorize.git
  • vcs-git https://anonscm.debian.org/git/pkg-ruby-extras/ruby-colorize.git

libseqan2-dev

• W pkg-config-references-unknown-shared-library
  • usr/share/pkgconfig/seqan-2.pc -lbz2 (line 9)

sga

• 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)
  • 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)

libstaden-read-dev

• W binary-without-manpage
  • usr/bin/io_lib-config [amd64, i386]

staden-io-lib-examples

• W zero-byte-file-in-doc-directory
  • usr/share/doc/staden-io-lib/test/data/xx#blank.sam

staden-io-lib-utils

• W binary-without-manpage
  • usr/bin/convert_trace [amd64, i386]
  • usr/bin/cram_dump [amd64, i386]
  • usr/bin/cram_filter [amd64, i386]
  • usr/bin/cram_index [amd64, i386]
  • usr/bin/cram_size [amd64, i386]
  • usr/bin/extract_fastq [amd64, i386]
  • usr/bin/extract_qual [amd64, i386]
  • usr/bin/extract_seq [amd64, i386]
  • usr/bin/get_comment [amd64, i386]
  • usr/bin/hash_exp [amd64, i386]
  • usr/bin/hash_extract [amd64, i386]
  • usr/bin/hash_list [amd64, i386]
  • usr/bin/hash_sff [amd64, i386]
  • usr/bin/hash_tar [amd64, i386]
  • usr/bin/index_tar [amd64, i386]
  • usr/bin/makeSCF [amd64, i386]
  • usr/bin/scf_dump [amd64, i386]
  • usr/bin/scf_info [amd64, i386]
  • usr/bin/scf_update [amd64, i386]
  • usr/bin/scram_flagstat [amd64, i386]
  • usr/bin/scram_merge [amd64, i386]
  • usr/bin/scram_pileup [amd64, i386]
  • usr/bin/scram_test [amd64, i386]
  • usr/bin/srf_extract_hash [amd64, i386]
  • usr/bin/srf_extract_linear [amd64, i386]
  • usr/bin/trace_dump [amd64, i386]
  • usr/bin/ztr_dump [amd64, i386]

trinityrnaseq

• W bad-jar-name
  • usr/share/java/Butterfly-2.6.6.jar
• E python-script-but-no-python-dep
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/Compact_graph_partial.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/Compact_graph_whole.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/DP_matrix.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/GraphCycleException.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/Node_alignment.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/Node_path.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/Splice_model_refiner.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/TGraph.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/TNode.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/Topological_sort.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py #!python3
  • usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/Trinity_util.py #!python3
  • usr/lib/trinityrnaseq/util/misc/TPM_weighted_gene_length.py #!python3
  • usr/lib/trinityrnaseq/util/support_scripts/trinity_installer.py #!python3

trinityrnaseq-examples

• E depends-on-essential-package-without-using-version
  • depends: coreutils