Your message dated Sun, 07 Nov 2021 18:48:59 +0000
with message-id <[email protected]>
and subject line Bug#998015: fixed in minimap2 2.22+dfsg-3
has caused the Debian Bug report #998015,
regarding minimap2 breaks nanolyse autopkgtest on i386: undefined symbol:
ksw_extz2_sse
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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--
998015: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=998015
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: minimap2, nanolyse
Control: found -1 minimap2/2.22+dfsg-1
Control: found -1 nanolyse/1.2.0-2
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: [email protected]
User: [email protected]
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of minimap2 the autopkgtest of nanolyse fails in
testing when that autopkgtest is run with the binary packages of
minimap2 from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
minimap2 from testing 2.22+dfsg-1
nanolyse from testing 1.2.0-2
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of minimap2 to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=minimap2
https://ci.debian.net/data/autopkgtest/testing/i386/n/nanolyse/16256284/log.gz
cat: paired_reads.fastq: No such file or directory
Traceback (most recent call last):
File "/usr/bin/NanoLyse", line 33, in <module>
sys.exit(load_entry_point('NanoLyse==1.2.0', 'console_scripts',
'NanoLyse')())
File "/usr/bin/NanoLyse", line 25, in importlib_load_entry_point
return next(matches).load()
File "/usr/lib/python3.9/importlib/metadata.py", line 77, in load
module = import_module(match.group('module'))
File "/usr/lib/python3.9/importlib/__init__.py", line 127, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in
_call_with_frames_removed
File "/usr/lib/python3/dist-packages/nanolyse/NanoLyse.py", line 4, in
<module>
import mappy as mp
ImportError:
/usr/lib/python3/dist-packages/mappy.cpython-39-i386-linux-gnu.so:
undefined symbol: ksw_extz2_sse
autopkgtest [13:09:50]: test run-unit-test
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: minimap2
Source-Version: 2.22+dfsg-3
Done: Michael R. Crusoe <[email protected]>
We believe that the bug you reported is fixed in the latest version of
minimap2, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <[email protected]> (supplier of updated minimap2 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 07 Nov 2021 19:23:30 +0100
Source: minimap2
Architecture: source
Version: 2.22+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 998015
Changes:
minimap2 (2.22+dfsg-3) unstable; urgency=medium
.
* Team upload
* Add SIMDe bits to python-sse4-arch.patch ; adjust SIMDe patch.
Closes: #998015
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