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.

• W spelling-error-in-patch-description
  • debian/patches/controldir Forwaded Forwarded

cnvkit (0.9.6-1+b1; main)

• W binary-without-manpage
  • usr/bin/cnvkit-cnv_annotate
  • usr/bin/cnvkit-cnv_expression_correlate
  • usr/bin/cnvkit-cnv_updater
  • usr/bin/cnvkit-cnv_ztest
  • usr/bin/cnvkit-guess_baits
  • usr/bin/cnvkit-skg_convert
  • usr/bin/snpfilter.sh
• W manpage-has-errors-from-man
  • usr/share/man/man1/cnvkit.1.gz 8: warning [p 1, 1.7i]: cannot adjust line
• W package-contains-timestamped-gzip
  • usr/share/doc/cnvkit/examples/test/formats/GRCh37_BRAF.gff.gz
• W script-with-language-extension
  • usr/bin/snpfilter.sh

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)

libbio-db-gff-perl

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

libbio-db-seqfeature-perl

• W binary-without-manpage
  • usr/bin/bp_seqfeature_delete
  • usr/bin/bp_seqfeature_gff3

libbio-searchio-hmmer-perl

• W manpage-has-bad-whatis-entry
  • usr/share/man/man3/Bio::SearchIO::hmmer3.3pm.gz

• 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)

mypy

• W manpage-has-errors-from-man
  • usr/share/man/man1/dmypy.1.gz 8: warning [p 1, 1.7i]: cannot adjust line

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

python3-bx

• W binary-without-manpage
  • usr/bin/aggregate_scores_in_intervals.py
  • usr/bin/align_print_template.py
  • usr/bin/axt_extract_ranges.py
  • usr/bin/axt_to_fasta.py
  • usr/bin/axt_to_lav.py
  • usr/bin/axt_to_maf.py
  • usr/bin/bed_bigwig_profile.py
  • usr/bin/bed_build_windows.py
  • usr/bin/bed_complement.py
  • usr/bin/bed_count_by_interval.py
  • usr/bin/bed_count_overlapping.py
  • usr/bin/bed_coverage.py
  • usr/bin/bed_coverage_by_interval.py
  • usr/bin/bed_diff_basewise_summary.py
  • usr/bin/bed_extend_to.py
  • usr/bin/bed_intersect.py
  • usr/bin/bed_intersect_basewise.py
  • usr/bin/bed_merge_overlapping.py
  • usr/bin/bed_rand_intersect.py
  • usr/bin/bed_subtract_basewise.py
  • usr/bin/bnMapper.py
  • usr/bin/div_snp_table_chr.py
  • usr/bin/find_in_sorted_file.py
  • usr/bin/gene_fourfold_sites.py
  • usr/bin/get_scores_in_intervals.py
  • usr/bin/int_seqs_to_char_strings.py
  • usr/bin/interval_count_intersections.py
  • usr/bin/interval_join.py
  • usr/bin/lav_to_axt.py
  • usr/bin/lav_to_maf.py
  • usr/bin/line_select.py
  • usr/bin/lzop_build_offset_table.py
  • usr/bin/mMK_bitset.py
  • usr/bin/maf_build_index.py
  • usr/bin/maf_chop.py
  • usr/bin/maf_chunk.py
  • usr/bin/maf_col_counts.py
  • usr/bin/maf_col_counts_all.py
  • usr/bin/maf_count.py
  • usr/bin/maf_covered_ranges.py
  • usr/bin/maf_covered_regions.py
  • usr/bin/maf_div_sites.py
  • usr/bin/maf_drop_overlapping.py
  • usr/bin/maf_extract_chrom_ranges.py
  • usr/bin/maf_extract_ranges.py
  • usr/bin/maf_extract_ranges_indexed.py
  • usr/bin/maf_filter.py
  • usr/bin/maf_filter_max_wc.py
  • usr/bin/maf_gap_frequency.py
  • usr/bin/maf_gc_content.py
  • usr/bin/maf_interval_alignibility.py
  • usr/bin/maf_limit_to_species.py
  • usr/bin/maf_mapping_word_frequency.py
  • usr/bin/maf_mask_cpg.py
  • usr/bin/maf_mean_length_ungapped_piece.py
  • usr/bin/maf_percent_columns_matching.py
  • usr/bin/maf_percent_identity.py
  • usr/bin/maf_print_chroms.py
  • usr/bin/maf_print_scores.py
  • usr/bin/maf_randomize.py
  • usr/bin/maf_region_coverage_by_src.py
  • usr/bin/maf_select.py
  • usr/bin/maf_shuffle_columns.py
  • usr/bin/maf_species_in_all_files.py
  • usr/bin/maf_split_by_src.py
  • usr/bin/maf_thread_for_species.py
  • usr/bin/maf_tile.py
  • usr/bin/maf_tile_2.py
  • usr/bin/maf_tile_2bit.py
  • usr/bin/maf_to_axt.py
  • usr/bin/maf_to_concat_fasta.py
  • usr/bin/maf_to_fasta.py
  • usr/bin/maf_to_int_seqs.py
  • usr/bin/maf_translate_chars.py
  • usr/bin/maf_truncate.py
  • usr/bin/maf_word_frequency.py
  • usr/bin/mask_quality.py
  • usr/bin/nib_chrom_intervals_to_fasta.py
  • usr/bin/nib_intervals_to_fasta.py
  • usr/bin/nib_length.py
  • usr/bin/one_field_per_line.py
  • usr/bin/out_to_chain.py
  • usr/bin/prefix_lines.py
  • usr/bin/pretty_table.py
  • usr/bin/qv_to_bqv.py
  • usr/bin/random_lines.py
  • usr/bin/table_add_column.py
  • usr/bin/table_filter.py
  • usr/bin/tfloc_summary.py
  • usr/bin/ucsc_gene_table_to_intervals.py
  • usr/bin/wiggle_to_array_tree.py
  • usr/bin/wiggle_to_binned_array.py
  • usr/bin/wiggle_to_chr_binned_array.py
  • usr/bin/wiggle_to_simple.py

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

pybedtools-bin

• W binary-without-manpage
  • usr/bin/annotate.py
  • usr/bin/intersection_matrix.py
  • usr/bin/intron_exon_reads.py
  • usr/bin/pbt_plotting_example.py
  • usr/bin/peak_pie.py
  • usr/bin/pybedtools
  • usr/bin/venn_gchart.py
  • usr/bin/venn_mpl.py
• W executable-not-elf-or-script
  • usr/bin/annotate.py
  • usr/bin/pbt_plotting_example.py

python3-pybedtools

• W script-not-executable
  • usr/lib/python3/dist-packages/pybedtools/scripts/pybedtools

python3-screed

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

r-cran-blockmodeling

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

• E missing-python-build-dependency

rapmap

• W binary-without-manpage
  • usr/bin/RunRapMap.sh

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

• W ancient-standards-version
  • 3.9.8 (released 2016-04-06) (current is 4.4.0)
• W vcs-obsolete-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-yell.git
  • vcs-git https://anonscm.debian.org/git/pkg-ruby-extras/ruby-yell.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]

• W timewarp-standards-version
  • (2019-03-21 < 2019-07-07)

toil

• W binary-without-manpage
  • usr/bin/toil-cwl-runner
  • usr/bin/toil-wdl-runner

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