[Debian-med-packaging] Bug#998015: minimap2 breaks nanolyse autopkgtest on i386: undefined symbol: ksw_extz2_sse

[Paul Gevers]

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: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
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


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