Bug#917143: t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: COREDUMP
Paul Gevers
elbrus at debian.org
Sun Dec 23 08:36:55 GMT 2018
Source: t-coffee, libbio-tools-run-alignment-tcoffee-perl
Control: found -1 t-coffee/12.00.7fb08c2-1
Control: found -1 libbio-tools-run-alignment-tcoffee-perl/1.7.4-1
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update
Dear maintainers,
With a recent upload of t-coffee the autopkgtest of
libbio-tools-run-alignment-tcoffee-perl fails in testing when that
autopkgtest is run with the binary packages of t-coffee from unstable.
It passes when run with only packages from testing. In tabular form:
pass fail
t-coffee from testing 12.00.7fb08c2-1
libbio-tools-run-alignment-tcoffee-perl from testing 1.7.4-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is contributing to the delay of the migration
of t-coffee 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? If needed, please
change the bug's severity.
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=t-coffee
https://ci.debian.net/data/autopkgtest/testing/amd64/libb/libbio-tools-run-alignment-tcoffee-perl/1569594/log.gz
autopkgtest [04:38:41]: test autodep8-perl-build-deps:
[-----------------------
t/TCoffee.t ..
ok 1 - An object of class 'Bio::Tools::Run::Alignment::TCoffee' isa
'Bio::Tools::Run::Alignment::TCoffee'
ok 2 - set factory parameter
ok 3 - get factory parameter
ok 4 - Code tested only on t_coffee versions > 1.22
ok 5
ok 6
ok 7
*************************************************************************************************
* FULL TRACE BACK PID: 14398
14420 -- ERROR: COREDUMP: T-COFFEE Version_12.00.7fb08c2 (2018-12-11
09:27:12 - Revision 7fb08c2 - Build 211)
*************************************************************************************************
******************************************************************
* Abnormal Termination
* Job NOT Completed:[T-COFFEE, Version_12.00.7fb08c2]
* Please CHECK:
* -1 The format of your Input Files
* -2 The parameters
* -3 The use of special characters in sequence names:
* (@, |, %...)
* -4 The Online Doc (http://www.tcoffee.org)
* -5 re-run your CL (see below) with the -debug option. This will
produce a debug file you can send us.
*
* NO
* to:
* cedric.notredame at gmail.com
* If you run T-Coffee over the WEB:
* Windows Cut and Paste is sometimes erratic and
* it can loose carriage returns. If you suspect this,
* try to cut and paste through an intermediate application
* (word pad) and inspect the results
* CONFIDENTIALITY:
* The File NO may contain your personal DATA
* Remove ALL confidential DATA from this file BEFORE sending it
******************************************************************
# Command Line: /usr/bin/t_coffee -profile KIQgXqyCHN -seq qjNOX7wp3O
-matrix blosum -method lalign_id_pair clustalw_pair -ktuple 3 -outfile
/tmp/notSa_tL8M/WVVAoNGLR6 -output clustalw -quiet [PROGRAM:T-COFFEE]
# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 14398 ppid 14316
#CL: /usr/bin/t_coffee -profile KIQgXqyCHN -seq qjNOX7wp3O -matrix
blosum -method lalign_id_pair clustalw_pair -ktuple 3 -outfile
/tmp/notSa_tL8M/WVVAoNGLR6 -output clustalw -quiet
ERROR: /var/tmp/tco/tco1xsm09w014398/3127314418402 FILE is NOT a
supported format [ERROR]
not ok 8
# Failed test at t/TCoffee.t line 74.
# died:
# ------------- EXCEPTION -------------
# MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee
-profile=KIQgXqyCHN -seq=qjNOX7wp3O -matrix=blosum
-method=lalign_id_pair,clustalw_pair -ktuple=3
-outfile=/tmp/notSa_tL8M/WVVAoNGLR6 -output=clustalw -quiet]
#
# STACK Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:150
# STACK Bio::Tools::Run::Alignment::TCoffee::_run
/usr/share/perl5/Bio/Tools/Run/Alignment/TCoffee.pm:272
# STACK Bio::Tools::Run::Alignment::TCoffee::profile_align
/usr/share/perl5/Bio/Tools/Run/Alignment/TCoffee.pm:198
# STACK Test::Exception::lives_ok t/TCoffee.t:74
# STACK toplevel t/TCoffee.t:74
# -------------------------------------
not ok 9 - no T-COFFEE errors
# Failed test 'no T-COFFEE errors'
# at t/TCoffee.t line 76.
ok 10
ok 11
ok 12
COULD NOT Append anything to /var/tmp/tco/tco1xsm09w014398//3127314417411
--COULD NOT READ
/tmp/autopkgtest-lxc.ysyqop3h/downtmp/autopkgtest_tmp//.t_coffee//cache//var/tmp/tco/tco1xsm09w014398//3127314417411
--ERROR: FORCED EXIT (NON INTERACTIVE MODE pid 14417)
COULD NOT Append anything to /var/tmp/tco/tco1xsm09w014398//3127314417410
ok 13
ok 14
ok 15
ok 16
ok 17 - expect 21 >= val >= 23
ok 18 - expect 47 or 48
ok 19 - simple generic run
ok 20
ok 21
ok 22 - no T-COFFEE errors
ok 23
ok 24 - expect 13 or 14
ok 25 - expect 41 or 42
1..25
rmdir /tmp/notSa_tL8M
# Looks like you failed 2 tests of 25.
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/25 subtests
Test Summary Report
-------------------
t/TCoffee.t (Wstat: 512 Tests: 25 Failed: 2)
Failed tests: 8-9
Non-zero exit status: 2
Files=1, Tests=25, 4 wallclock secs ( 0.03 usr 0.00 sys + 3.38 cusr
0.65 csys = 4.06 CPU)
Result: FAIL
autopkgtest [04:38:45]: test autodep8-perl-build-deps:
-----------------------]
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