[Debian-med-packaging] Bug#933596: python3-bx: missing Breaks: python3-bx-tools

[Andreas Beckmann]

Package: python3-bx
Version: 0.8.4-1
Severity: serious
User: debian-qa at lists.debian.org
Usertags: piuparts replaces-without-breaks

Hi,

during a test with piuparts and DOSE tools I noticed your package causes
removal of files that also belong to another package.
This is caused by using Replaces without corresponding Breaks.

The installation sequence to reproduce this problem is

  apt-get install python3-bx-tools
  # (1)
  apt-get install python3-bx
  apt-get remove python3-bx
  # (2)

The list of installed files at points (1) and (2) should be identical,
but the following files have disappeared:

  /usr/bin/aggregate_scores_in_intervals.py
  /usr/bin/align_print_template.py
  /usr/bin/axt_extract_ranges.py
  ...
  /usr/bin/wiggle_to_binned_array.py
  /usr/bin/wiggle_to_chr_binned_array.py
  /usr/bin/wiggle_to_simple.py
  

This is a serious bug violating policy 7.6, see
https://www.debian.org/doc/debian-policy/ch-relationships.html#overwriting-files-and-replacing-packages-replaces
and also see the footnote that describes this incorrect behavior:
https://www.debian.org/doc/debian-policy/ch-relationships.html#id13

The python3-bx package has the following relationships with python3-bx-tools:

  Conflicts: n/a
  Breaks:    n/a
  Replaces:  python3-bx-tools
  Provides:  python3-bx-tools

>From the attached log (scroll to the bottom...):

1m38.9s DEBUG: Modified(user, group, mode, size, target): /var/lib/dpkg/info/python3-bx-tools.list expected(root, root, - 100644, 3087, None) != found(root, root, - 100644, 263, None)
1m38.9s ERROR: FAIL: After purging files have disappeared:
  /usr/bin/aggregate_scores_in_intervals.py      owned by: python3-bx
  /usr/bin/align_print_template.py       owned by: python3-bx
  /usr/bin/axt_extract_ranges.py         owned by: python3-bx
  /usr/bin/axt_to_fasta.py       owned by: python3-bx
  /usr/bin/axt_to_lav.py         owned by: python3-bx
  /usr/bin/axt_to_maf.py         owned by: python3-bx
  /usr/bin/bed_bigwig_profile.py         owned by: python3-bx
  /usr/bin/bed_build_windows.py  owned by: python3-bx
  /usr/bin/bed_complement.py     owned by: python3-bx
  /usr/bin/bed_count_by_interval.py      owned by: python3-bx
  /usr/bin/bed_count_overlapping.py      owned by: python3-bx
...
  /usr/bin/pretty_table.py       owned by: python3-bx
  /usr/bin/qv_to_bqv.py  owned by: python3-bx
  /usr/bin/random_lines.py       owned by: python3-bx
  /usr/bin/table_add_column.py   owned by: python3-bx
  /usr/bin/table_filter.py       owned by: python3-bx
  /usr/bin/tfloc_summary.py      owned by: python3-bx
  /usr/bin/ucsc_gene_table_to_intervals.py       owned by: python3-bx
  /usr/bin/wiggle_to_array_tree.py       owned by: python3-bx
  /usr/bin/wiggle_to_binned_array.py     owned by: python3-bx
  /usr/bin/wiggle_to_chr_binned_array.py         owned by: python3-bx
  /usr/bin/wiggle_to_simple.py   owned by: python3-bx

1m38.9s ERROR: FAIL: After purging files have been modified:
  /var/lib/dpkg/info/python3-bx-tools.list       not owned


cheers,

Andreas
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