Source: libbio-tools-run-alignment-tcoffee-perl Version: 1.7.4-1 Severity: serious Justification: FTBFS on amd64 Tags: buster sid Usertags: ftbfs-20181229 ftbfs-buster
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[2]: Entering directory '/<<PKGBUILDDIR>>' > 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: 16494 > > 16518 -- 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.notred...@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 C3uHd27Vnl -seq rKVo1aRtb4 -matrix > blosum -method lalign_id_pair clustalw_pair -ktuple 3 -outfile > /tmp/D_LRrJQoYx/TbKy3eG8L7 -output clustalw -quiet [PROGRAM:T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 16494 ppid 16412 > #CL: /usr/bin/t_coffee -profile C3uHd27Vnl -seq rKVo1aRtb4 -matrix blosum > -method lalign_id_pair clustalw_pair -ktuple 3 -outfile > /tmp/D_LRrJQoYx/TbKy3eG8L7 -output clustalw -quiet > ERROR: /var/tmp/tco/tcouusjjsfj16494/9295616514392 FILE is NOT a supported > format [ERROR] > # Failed test at t/TCoffee.t line 74. > # died: > # ------------- EXCEPTION ------------- > # MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee > -profile=C3uHd27Vnl -seq=rKVo1aRtb4 -matrix=blosum > -method=lalign_id_pair,clustalw_pair -ktuple=3 > -outfile=/tmp/D_LRrJQoYx/TbKy3eG8L7 -output=clustalw -quiet] > # > # STACK Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:150 > # STACK Bio::Tools::Run::Alignment::TCoffee::_run > /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:272 > # STACK Bio::Tools::Run::Alignment::TCoffee::profile_align > /<<PKGBUILDDIR>>/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. > sh: 1: cannot create /var/tmp/tco/tcouusjjsfj16494/9295616494252: Directory > nonexistent > > --COULD NOT READ > /<<PKGBUILDDIR>>/debian/build//.t_coffee//cache//var/tmp/tco/tcouusjjsfj16494//9295616494252 > > --ERROR: FORCED EXIT (NON INTERACTIVE MODE pid 16516) > > COULD NOT Append anything to /var/tmp/tco/tcouusjjsfj16494//9295616513411 > > --COULD NOT READ > /<<PKGBUILDDIR>>/debian/build//.t_coffee//cache//var/tmp/tco/tcouusjjsfj16494//9295616513411 > > --ERROR: FORCED EXIT (NON INTERACTIVE MODE pid 16513) > > COULD NOT Append anything to /var/tmp/tco/tcouusjjsfj16494//9295616513410 > > > > > ************************************************************************************************* > * FULL TRACE BACK PID: 16724 > > 16742 -- 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.notred...@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 ZUWdpGE6Uy -seq L_aBwo2NbZ -matrix > blosum -method lalign_id_pair clustalw_pair -ktuple 3 -outfile > /tmp/D_LRrJQoYx/TbKy3eG8L7 -output clustalw -quiet [PROGRAM:T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 16724 ppid 16412 > #CL: /usr/bin/t_coffee -profile ZUWdpGE6Uy -seq L_aBwo2NbZ -matrix blosum > -method lalign_id_pair clustalw_pair -ktuple 3 -outfile > /tmp/D_LRrJQoYx/TbKy3eG8L7 -output clustalw -quiet > ERROR: /var/tmp/tco/tco5myvgsz416724/2288316740402 FILE is NOT a supported > format [ERROR] > # Failed test at t/TCoffee.t line 118. > # died: > # ------------- EXCEPTION ------------- > # MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee > -profile=ZUWdpGE6Uy -seq=L_aBwo2NbZ -matrix=blosum > -method=lalign_id_pair,clustalw_pair -ktuple=3 > -outfile=/tmp/D_LRrJQoYx/TbKy3eG8L7 -output=clustalw -quiet] > # > # STACK Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:150 > # STACK Bio::Tools::Run::Alignment::TCoffee::_run > /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:272 > # STACK Bio::Tools::Run::Alignment::TCoffee::profile_align > /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:198 > # STACK Bio::Tools::Run::Alignment::TCoffee::run > /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:148 > # STACK Test::Exception::lives_ok t/TCoffee.t:116 > # STACK toplevel t/TCoffee.t:118 > # ------------------------------------- > # Failed test 'no T-COFFEE errors' > # at t/TCoffee.t line 120. > # Failed test 'expect 13 or 14' > # at t/TCoffee.t line 128. > # Failed test 'expect 41 or 42' > # at t/TCoffee.t line 130. > # Looks like you failed 6 tests of 25. > > COULD NOT Append anything to /var/tmp/tco/tco5myvgsz416724//2288316739410 > > --COULD NOT READ > /<<PKGBUILDDIR>>/debian/build//.t_coffee//cache//var/tmp/tco/tco5myvgsz416724//2288316739410 > > --ERROR: FORCED EXIT (NON INTERACTIVE MODE pid 16739) > > COULD NOT Append anything to /var/tmp/tco/tco5myvgsz416724//2288316739411 > 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 > 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 > not ok 21 > not ok 22 - no T-COFFEE errors > ok 23 > not ok 24 - expect 13 or 14 > not ok 25 - expect 41 or 42 > 1..25 > rmdir /tmp/D_LRrJQoYx > Dubious, test returned 6 (wstat 1536, 0x600) > Failed 6/25 subtests > > Test Summary Report > ------------------- > t/TCoffee.t (Wstat: 1536 Tests: 25 Failed: 6) > Failed tests: 8-9, 21-22, 24-25 > Non-zero exit status: 6 > Files=7, Tests=26, 2 wallclock secs ( 0.03 usr 0.00 sys + 1.21 cusr 0.36 > csys = 1.60 CPU) > Result: FAIL > Failed 1/7 test programs. 6/26 subtests failed. > make[2]: *** [Makefile:865: test_dynamic] Error 6 > make[2]: Leaving directory '/<<PKGBUILDDIR>>' > dh_auto_test: make -j2 test TEST_VERBOSE=1 returned exit code 2 The full build log is available from: http://aws-logs.debian.net/2018/12/29/libbio-tools-run-alignment-tcoffee-perl_1.7.4-1_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
