Source: libbio-tools-run-alignment-tcoffee-perl
Version: 1.7.4-1
Severity: serious
Tags: sid buster
Justification: fails to build from source
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Hash: SHA512
As first seen on ci.debian.net, the upgrade of t-coffee from
11.00.8cbe486-6 to 11.00.8cbe486-7 breaks
libbio-tools-run-alignment-tcoffee-perl's test suite:
debian/rules override_dh_auto_test
make[1]: Entering directory
'/build/libbio-tools-run-alignment-tcoffee-perl-1.7.4'
mkdir -p /build/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/build
HOME=/build/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/build
dh_auto_test
make -j4 test TEST_VERBOSE=1
make[2]: Entering directory
'/build/libbio-tools-run-alignment-tcoffee-perl-1.7.4'
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness"
"-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')"
t/*.t
t/00-compile.t ...........
1..1
ok 1 - Bio/Tools/Run/Alignment/TCoffee.pm loaded ok
ok
t/author-eol.t ........... skipped: these tests are for testing by the author
t/author-mojibake.t ...... skipped: these tests are for testing by the author
t/author-no-tabs.t ....... skipped: these tests are for testing by the author
t/author-pod-coverage.t .. skipped: these tests are for testing by the author
t/author-pod-syntax.t .... skipped: these tests are for testing by the author
*************************************************************************************************
* FULL TRACE BACK PID: 2227
2243 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 -
Revision 8cbe486 - Build 477)
*************************************************************************************************
******************************************************************
* Abnormal Termination
* Job NOT Completed:[T-COFFEE, Version_11.00.8cbe486]
* 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 tze -debug option. This will
produce a debug file you can send us.
*
* NO
* to:
* [email protected]
* 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 otOrqlTVt8 -seq g5USs5RIgV -matrix
blosum -method lalign_id_pair clustalw_pair -ktuple 3 -outfile
/tmp/McVdzikYRh/smBiz31aXb -output clustalw -quiet [PROGRAM:T-COFFEE]
# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 2227 ppid 2133
#CL: /usr/bin/t_coffee -profile otOrqlTVt8 -seq g5USs5RIgV -matrix blosum
-method lalign_id_pair clustalw_pair -ktuple 3 -outfile
/tmp/McVdzikYRh/smBiz31aXb -output clustalw -quiet
# Failed test at t/TCoffee.t line 74.
# died:
# ------------- EXCEPTION -------------
# MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee
-profile=otOrqlTVt8 -seq=g5USs5RIgV -matrix=blosum
-method=lalign_id_pair,clustalw_pair -ktuple=3
-outfile=/tmp/McVdzikYRh/smBiz31aXb -output=clustalw -quiet]
#
# STACK Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:150
# STACK Bio::Tools::Run::Alignment::TCoffee::_run
/build/libbio-tools-run-alignment-tcoffee-perl-1.7.4/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:272
# STACK Bio::Tools::Run::Alignment::TCoffee::profile_align
/build/libbio-tools-run-alignment-tcoffee-perl-1.7.4/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:198
# STACK Test::Exception::lives_ok t/TCoffee.t:74
# STACK toplevel t/TCoffee.t:74
# -------------------------------------
# Failed test 'no T-COFFEE errors'
# at t/TCoffee.t line 76.
*************************************************************************************************
* FULL TRACE BACK PID: 2285
2300 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 -
Revision 8cbe486 - Build 477)
*************************************************************************************************
******************************************************************
* Abnormal Termination
* Job NOT Completed:[T-COFFEE, Version_11.00.8cbe486]
* 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 tze -debug option. This will
produce a debug file you can send us.
*
* NO
* to:
* [email protected]
* 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 oZLh5DP3lo nCCBUSzQsD -matrix blosum
-method lalign_id_pair clustalw_pair -ktuple 3 -outfile
/tmp/McVdzikYRh/smBiz31aXb -output clustalw -quiet [PROGRAM:T-COFFEE]
# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 2285 ppid 2133
#CL: /usr/bin/t_coffee -profile oZLh5DP3lo nCCBUSzQsD -matrix blosum -method
lalign_id_pair clustalw_pair -ktuple 3 -outfile /tmp/McVdzikYRh/smBiz31aXb
-output clustalw -quiet
- ------------- EXCEPTION -------------
MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee
-profile=oZLh5DP3lo,nCCBUSzQsD -matrix=blosum
-method=lalign_id_pair,clustalw_pair -ktuple=3
-outfile=/tmp/McVdzikYRh/smBiz31aXb -output=clustalw -quiet]
STACK Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:150
STACK Bio::Tools::Run::Alignment::TCoffee::_run
/build/libbio-tools-run-alignment-tcoffee-perl-1.7.4/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:272
STACK Bio::Tools::Run::Alignment::TCoffee::profile_align
/build/libbio-tools-run-alignment-tcoffee-perl-1.7.4/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:198
STACK toplevel t/TCoffee.t:87
- -------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 12.
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
not ok 8
not ok 9 - no T-COFFEE errors
ok 10
ok 11
ok 12
rmdir /tmp/McVdzikYRh
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/12 subtests
Test Summary Report
- -------------------
t/TCoffee.t (Wstat: 512 Tests: 12 Failed: 2)
Failed tests: 8-9
Non-zero exit status: 2
Parse errors: No plan found in TAP output
Files=7, Tests=13, 1 wallclock secs ( 0.05 usr 0.01 sys + 0.76 cusr 0.32
csys = 1.14 CPU)
Result: FAIL
Cheers,
gregor
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