[Debian-med-packaging] Bug#947463: bio-tradis: autopkgtest regression: Use of uninitialized value $total_uis (and lots of mv: cannot stat '/tmp/aut.....)

[Paul Gevers]

Source: bio-tradis
Version: 1.4.5+dfsg-1
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression
Control: affects -1 src:samtools

Dear maintainers,

With a recent upload of bio-tradis the autopkgtest of bio-tradis fails
in testing when that autopkgtest is run with the binary packages of
bio-tradis from unstable. It passes when run with only packages from
testing. In tabular form:
                       pass            fail
bio-tradis             from testing    1.4.5+dfsg-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?

Additionally, looking at the failure mode in unstable, it seems some
package (samtools?) made your (test?) dependencies non-installable in
unstable. You probably need to fix that as well, or raise the issue with
the samtools maintainer.

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=bio-tradis

https://ci.debian.net/data/autopkgtest/testing/amd64/b/bio-tradis/3765198/log.gz

t/Bio/Tradis/CommandLine/TradisAnalysis.t ..
ok 1 - use Bio::Tradis::CommandLine::TradisAnalysis;
ok 2 - creating object
Use of uninitialized value $total_uis in concatenation (.) or string at
/usr/share/perl5/Bio/Tradis/RunTradis.pm line 468.
Use of uninitialized value $total_uis in numeric gt (>) at
/usr/share/perl5/Bio/Tradis/RunTradis.pm line 470.
mv: cannot stat
'/tmp/autopkgtest-lxc.sfremfei/downtmp/autopkgtest_tmp/smokezkXJAM/tmp_TradisAnalysis_tests_lTLCo/tmp_run_tradis_MG155/test_1.out*':
No such file or directory
Use of uninitialized value $total_uis in concatenation (.) or string at
/usr/share/perl5/Bio/Tradis/RunTradis.pm line 468.
Use of uninitialized value $total_uis in numeric gt (>) at
/usr/share/perl5/Bio/Tradis/RunTradis.pm line 470.
mv: cannot stat
'/tmp/autopkgtest-lxc.sfremfei/downtmp/autopkgtest_tmp/smokezkXJAM/tmp_TradisAnalysis_tests_lTLCo/tmp_run_tradis_xXbiS/test_2.out*':
No such file or directory
ok 3 - testing run
ok 4 - both files have reads with tag
mv: cannot stat
'/tmp/autopkgtest-lxc.sfremfei/downtmp/autopkgtest_tmp/smokezkXJAM/tmp_TradisAnalysis_tests_K2kqu/tmp_run_tradis_AFhbT/test_2.out*':
No such file or directory
ok 5 - testing run with tag only found in one fastq
not ok 6 - one warning raised

#   Failed test 'one warning raised'
#   at t/Bio/Tradis/CommandLine/TradisAnalysis.t line 58.
#          got: '3'
#     expected: '1'

[...]

Test Summary Report
-------------------
t/Bio/Tradis/CommandLine/TradisAnalysis.t (Wstat: 256 Tests: 10 Failed: 1)
  Failed test:  6
  Non-zero exit status: 1
t/Bio/Tradis/Map.t                       (Wstat: 1536 Tests: 21 Failed: 6)
  Failed tests:  11-15, 18
  Non-zero exit status: 6
t/Bio/Tradis/RunTradisBWA.t              (Wstat: 2304 Tests: 45 Failed: 9)
  Failed tests:  18, 27-28, 30-31, 34-35, 38, 41
  Non-zero exit status: 9
t/Bio/Tradis/RunTradisTaglessBwa.t       (Wstat: 1280 Tests: 22 Failed: 5)
  Failed tests:  5, 14-15, 17-18
  Non-zero exit status: 5
Files=16, Tests=310, 14 wallclock secs ( 1.33 usr  0.03 sys +  6.97 cusr
 1.19 csys =  9.52 CPU)
Result: FAIL

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