Your message dated Thu, 01 Aug 2019 08:47:13 +0000 with message-id <e1ht6jx-00049o...@fasolo.debian.org> and subject line Bug#933596: fixed in python-bx 0.8.4-2 has caused the Debian Bug report #933596, regarding python3-bx: missing Breaks: python3-bx-tools to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 933596: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=933596 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: python3-bx Version: 0.8.4-1 Severity: serious User: debian...@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
python3-bx-tools=0.8.2-1_python3-bx=0.8.4-1.log.gz
Description: application/gzip
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--- Begin Message ---Source: python-bx Source-Version: 0.8.4-2 We believe that the bug you reported is fixed in the latest version of python-bx, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 933...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated python-bx package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 01 Aug 2019 09:55:20 +0200 Source: python-bx Binary: python3-bx Architecture: source Version: 0.8.4-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: python3-bx - library to manage genomic data and its alignment Closes: 933596 Changes: python-bx (0.8.4-2) unstable; urgency=medium . * Team upload. * Breaks: python3-bx-tools Closes: #933596 * debhelper-compat 12 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.4.0 * Testsuite: autopkgtest-pkg-python * Secure URI in copyright format * Remove trailing whitespace in debian/copyright * Fix license name * hardening=+all Checksums-Sha1: ed3ab0c1621f27fc0d4a41bd6efd789ec1ba5b3d 2156 python-bx_0.8.4-2.dsc 6c88d987a05e5db0c7dc4ac5f996de450bcad608 8560 python-bx_0.8.4-2.debian.tar.xz Checksums-Sha256: c2b0a87dccc2f5442e55844f46a6cef028cafe94aff3c62287dfe43fd43a8a8d 2156 python-bx_0.8.4-2.dsc 636c05f243e7c3ab6d206b2a54cde58aca2fde7f2a472890c4df480f3527e0a3 8560 python-bx_0.8.4-2.debian.tar.xz Files: e797ec6936f318389e55487220098541 2156 python optional python-bx_0.8.4-2.dsc d239482ff2a565f8670e1fd10d79b771 8560 python optional python-bx_0.8.4-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl1CnFoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFzpg//QQOEs/LbY7Tis7Wz+xDJINqkHqRS5mFd FgfsBy7EsSpYYWgMsOiIaOwVUpUj1CxZ5yOuqR03ycV9akEpzPLXLyVMW+qosHuI QrVaUX8iwUpkm0kVVDb1FZrqJYi9GPgAukLGGzaen2MzTBo5S8RTrmSnmO7A2Ca8 5XOWneNm/4e4k60posvxYQxqU1agcHcEKX/LJLYMmVVEEGA7D5yo2x6Sm1ZICS26 UpV4Zkbj71mcxeULMC8P3tru6amONJhVg1trkp5crt2LbdKWheJc9SNHz2DChvwR Un885sPwc0RLf+ZUzfONZ+aHEtwJZRRzyP60gSYDTmgcjSFiJT4b9U3wUr3xOe8U c3thNLbjxMPEAOkfAWVDS+45Y0IHLFOXVFsonjNsoxLtk/DVs/JikjmrBx2A9eYe S0d++aKJC3ohvZv0HPLZeCK/EH9uvkgBp0ptfOgfX11/0ZOQW1YsbdQzTxKdt4Ln 5pZExvcRl80TsP+WFDTt1pBHlRASzeopkkG3T/e03xWgLbsZmF0w9WiziubFWuiS /+dskJcgAhYvVTNMM44JF5B2F4rHDWrz4QfGhUn9RUM3upK4+FIOgl5qsaoawJEe 1keUqb5dq9lFce2P1M0t1e8xrgPhUn77AK/PFMvRsGcTgZ8u2F1MwNNg3PBPLhkR 9KQMgCSXilA= =LBn6 -----END PGP SIGNATURE-----
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