Your message dated Wed, 12 Dec 2018 17:11:20 +0000 with message-id <capors_2-pv5adn5br-mhjarusxkth3qg9axfuzu2jq8udlw...@mail.gmail.com> and subject line not our bug has caused the Debian Bug report #909502, regarding libbio-tools-run-alignment-tcoffee-perl: FTBFS (test failures) with t-coffee 11.00.8cbe486-7 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. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 909502: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=909502 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Source: libbio-tools-run-alignment-tcoffee-perl Version: 1.7.4-1 Severity: serious Tags: sid buster Justification: fails to build from source -----BEGIN PGP SIGNED MESSAGE----- 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 -----BEGIN PGP SIGNATURE----- iQKTBAEBCgB9FiEE0eExbpOnYKgQTYX6uzpoAYZJqgYFAlupBApfFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldEQx RTEzMTZFOTNBNzYwQTgxMDREODVGQUJCM0E2ODAxODY0OUFBMDYACgkQuzpoAYZJ qgaoyhAAxkZGYVcmaJsSSPUW2wy4aSDxuKXzGIm5PPyK54qhj4TXK3h9MTz3Lib/ tE3hzWNsSTvGFb8ASTJuuXfpK6CEggEKW4wVp8RC8gxjGTpy1Mk7NzR2i04Dn+1p Zdd+IeDRzhM3qC0jXSYOTMhSJMA8MmkBY6dnwYHgq+PZPnRaZMyZzfxy3qAJbdiv aHr3/Ghr2rFBd4iHsx2IDOczBAfaKkykacyM46QcSZGabAxUXrh2SsiCCZ9n2rGI 6KsNXOnoftZCHzRzY2RGMQuYBSTbkJcT3d665pl+axafwRcfmwkKnvWu/YoQkVPS R184s59u31nM9EJFg9RHqobtNeiQp5cGVVVGHBVS8y4ZPn7Q5n4dLf6kTtUjmT/2 BCvGt+6hoehg4fkN+reKlBx0rooXnxt8HabhXBSL4eElXd+wqxfnf43EY/Py24mW rFu6x3bD4M8RDx3P2fsQqxJPdA/xZffLo4GTEhSHXVQwz+/ZrC5SqJFOc9AsGVKE dbdlYiPxHXhN3vjyK2exdBATNh+of3mwWCAZAitNg+K44Qe92qM/k5JZKUi10sDL qMw4AbdEb7mbfBiR/h8x1zyCeEsqgBsX8dz0sLmrMULME4yVgZ6xxg0MP053ucKg 0MT+E5UaeOqi5KYL4RzzhT4Mqw/Xr+ZHQuyC595zqIvf3Hllwgo= =Fo5q -----END PGP SIGNATURE-----
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--- Begin Message ---This was never our bug. The issue is actually bug #909530 (a dependency that fails to build from source). The dependency t-coffee version 11.00.8cbe486-7 had a change that made it fail. The issue is unique to the version the debian -7 version which never made it past sid and is pretty much useless. There is nothing to do here. We could add a Build-Depends and Depends for earlier and later than -7 version but that is a bit silly. Having to list every single dependency version that has an issue does not scale. This is specially true for this case because the dependency is completely useless in the problematic version and that version was never distributed outside sid.
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