[Debian-med-packaging] Bug#994259: resfinder: autopkgtest regression on armhf and i386: db_resfinder --kmaPath /usr/bin/kma' returned non-zero exit status 1

[Paul Gevers]

Source: resfinder
Version: 4.1.5-1
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression

Dear maintainer(s),

With a recent upload of resfinder the autopkgtest of resfinder fails in
testing on armhf and i386 when that autopkgtest is run with the binary
packages of resfinder from unstable. It passes when run with only
packages from testing. In tabular form:

                       pass            fail
resfinder              from testing    4.1.5-1
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 to testing [1]. Can
you please investigate the situation and fix it?

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=resfinder

https://ci.debian.net/data/autopkgtest/testing/armhf/r/resfinder/15226272/log.gz

Indexing files as needed
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['INSTALL.py']
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Done
['INSTALL.py']
Running tests
.E.E
======================================================================
ERROR: test_on_data_with_just_acquired_resgene_using_kma
(__main__.ResFinderRunTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/tmp/autopkgtest-lxc.3mj3v4rg/downtmp/autopkgtest_tmp/functional_tests.py",
line 151, in test_on_data_with_just_acquired_resgene_using_kma
    procs = run(cmd_acquired, shell=True, stdout=PIPE, stderr=PIPE,
  File "/usr/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'run_resfinder.py -ifq
data/test_isolate_01_1.fq data/test_isolate_01_2.fq -o
running_test/test2 -s 'Escherichia coli' --min_cov 0.6 -t 0.8 --acquired
--db_path_res
/tmp/autopkgtest-lxc.3mj3v4rg/downtmp/autopkgtest_tmp/db_resfinder
--kmaPath /usr/bin/kma' returned non-zero exit status 1.

======================================================================
ERROR: test_on_data_with_just_point_mut_using_kma
(__main__.ResFinderRunTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/tmp/autopkgtest-lxc.3mj3v4rg/downtmp/autopkgtest_tmp/functional_tests.py",
line 253, in test_on_data_with_just_point_mut_using_kma
    procs = run(cmd_acquired, shell=True, stdout=PIPE, stderr=PIPE,
  File "/usr/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'run_resfinder.py -ifq
data/test_isolate_05_1.fq data/test_isolate_05_2.fq -o
running_test/test4 -s 'Escherichia coli' --min_cov 0.6 --threshold 0.8
--point --db_path_point
/tmp/autopkgtest-lxc.3mj3v4rg/downtmp/autopkgtest_tmp/db_pointfinder
--db_path_res
/tmp/autopkgtest-lxc.3mj3v4rg/downtmp/autopkgtest_tmp/db_resfinder
--kmaPath /usr/bin/kma' returned non-zero exit status 1.

----------------------------------------------------------------------
Ran 4 tests in 16.971s

FAILED (errors=2)

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