Your message dated Sat, 11 Jan 2020 16:19:14 +0000
with message-id <e1iqjtm-000j5s...@fasolo.debian.org>
and subject line Bug#947463: fixed in bio-tradis 1.4.5+dfsg2-1
has caused the Debian Bug report #947463,
regarding bio-tradis: autopkgtest regression: Use of uninitialized value
$total_uis (and lots of mv: cannot stat '/tmp/aut.....)
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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--
947463: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=947463
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: bio-tradis
Version: 1.4.5+dfsg-1
X-Debbugs-CC: debian...@lists.debian.org
Severity: serious
User: debian...@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
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: bio-tradis
Source-Version: 1.4.5+dfsg2-1
We believe that the bug you reported is fixed in the latest version of
bio-tradis, 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 947...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <michael.cru...@gmail.com> (supplier of updated bio-tradis
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: Sat, 11 Jan 2020 16:41:24 +0100
Source: bio-tradis
Architecture: source
Version: 1.4.5+dfsg2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <michael.cru...@gmail.com>
Closes: 947463
Changes:
bio-tradis (1.4.5+dfsg2-1) unstable; urgency=medium
.
* Team upload.
* debian/patches/samtools1.10: remove version parsing code that can't handle
samtools version 1.10 (Closes: #947463)
* Switch to cpan for the source
* autopkgtests: ignore the tests that are not yet updated for
samtools 1.10.x
* Set fields Upstream-Contact in debian/copyright.
* Remove obsolete fields Contact from debian/upstream/metadata.
Checksums-Sha1:
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bio-tradis_1.4.5+dfsg2.orig.tar.xz
78b636d9f67178b906189b693bf9821a2d980cde 5980
bio-tradis_1.4.5+dfsg2-1.debian.tar.xz
ef1362f65f548de1aa052969a802355edc976527 6838
bio-tradis_1.4.5+dfsg2-1_source.buildinfo
Checksums-Sha256:
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bio-tradis_1.4.5+dfsg2-1.dsc
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bio-tradis_1.4.5+dfsg2.orig.tar.xz
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bio-tradis_1.4.5+dfsg2-1.debian.tar.xz
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bio-tradis_1.4.5+dfsg2-1_source.buildinfo
Files:
9773a3174daa6a419c5dc6e3bfd8c6c5 2238 perl optional
bio-tradis_1.4.5+dfsg2-1.dsc
c31ec74b7db82cd7bf39386caf70859f 7876340 perl optional
bio-tradis_1.4.5+dfsg2.orig.tar.xz
e6f4dc91f849275edbca4da5646abe28 5980 perl optional
bio-tradis_1.4.5+dfsg2-1.debian.tar.xz
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bio-tradis_1.4.5+dfsg2-1_source.buildinfo
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