Your message dated Mon, 19 Dec 2022 21:31:47 +0000
with message-id <e1p7njf-000vmh...@fasolo.debian.org>
and subject line Bug#1024835: fixed in python-pauvre 0.2.3-2
has caused the Debian Bug report #1024835,
regarding python-pauvre: ftbfs with biopython 1.80
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.
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--
1024835: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024835
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: python-pauvre
Version: 0.2.3-1
Severity: important
Tags: ftbfs
Dear Maintainer,
python-pauvre fails its build time test suite when built against
biopython 1.80 in experimental but builds successfully against
biopython 1.79. The relevant part of the log in case of failure
shows:
I: pybuild base:240: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build; python3.10 -m unittest
discover -v
test_normal_plotting_scenario
(pauvre.tests.test_synplot.libSeq_test_case)
This verifies that the LibSeq class is constructed with all of the ...
+ export PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build
+ PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build
+ exec python3
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/pauvre_main.py
synplot --aln_dir
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/tests/testdata/alignments/
--fileform pdf --gff_paths
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/tests/testdata/gff_files/Bf201706.gff
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/tests/testdata/gff_files/JN392469.gff
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/tests/testdata/gff_files/NC016117.gff
--center_on COX1 --gff_labels 'B. forskalii' 'P. bachei' 'M. leidyi'
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/pauvre_main.py",
line 636, in <module>
main()
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/pauvre_main.py",
line 630, in main
args.func(parser, args)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/pauvre_main.py",
line 62, in run_subtool
import pauvre.synplot as submodule
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/synplot.py", line
46, in <module>
import Bio.SubsMat.MatrixInfo as MI
ModuleNotFoundError: No module named 'Bio.SubsMat'
Have a nice day, :)
Étienne.
-- System Information:
Debian Release: bookworm/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.0.0-4-amd64 (SMP w/12 CPU threads; PREEMPT)
Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: python-pauvre
Source-Version: 0.2.3-2
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
python-pauvre, 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 1024...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated python-pauvre
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: SHA512
Format: 1.8
Date: Sun, 18 Dec 2022 15:56:49 +0100
Source: python-pauvre
Architecture: source
Version: 0.2.3-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1024835
Changes:
python-pauvre (0.2.3-2) unstable; urgency=medium
.
* biopython-1.80.patch: add; migrate away from Bio.SubsMat.
This patch fixes build time test failures with Biopython 1.80 caused
by removal of Bio.SubsMat in favor of Bio.Align.substitution_matrices.
(Closes: 1024835)
* d/control: declare compliance to standards version 4.6.2.
* d/copyright: update debian/ authors and year.
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