Your message dated Mon, 04 Feb 2019 10:50:33 +0000 with message-id <e1gqbph-0007ww...@fasolo.debian.org> and subject line Bug#917143: fixed in t-coffee 12.00.7fb08c2-2 has caused the Debian Bug report #917143, regarding libbio-tools-run-alignment-tcoffee-perl: FTBFS: dh_auto_test: make -j2 test TEST_VERBOSE=1 returned exit code 2 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 ow...@bugs.debian.org immediately.) -- 917143: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=917143 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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.
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--- Begin Message ---Source: t-coffee Source-Version: 12.00.7fb08c2-2 We believe that the bug you reported is fixed in the latest version of t-coffee, 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 917...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Liubov Chuprikova <chuprikov...@gmail.com> (supplier of updated t-coffee 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: SHA256 Format: 1.8 Date: Mon, 04 Feb 2019 10:37:01 +0100 Source: t-coffee Binary: t-coffee t-coffee-examples Architecture: source Version: 12.00.7fb08c2-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Liubov Chuprikova <chuprikov...@gmail.com> Description: t-coffee - Multiple Sequence Alignment t-coffee-examples - annotated examples for the use of T-Coffee Closes: 917143 Changes: t-coffee (12.00.7fb08c2-2) unstable; urgency=medium . * Team upload. * Fix "t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: COREDUMP" fix_tempfile_name_sharing.patch (Closes: #917143) * Standards-Version: 4.3.0 Checksums-Sha1: 8f54bd07d1fe83616c91102fb60c843b4577ae70 2153 t-coffee_12.00.7fb08c2-2.dsc 451bfbb0b169cd6971f23627914b8f9d0818d0ca 14672 t-coffee_12.00.7fb08c2-2.debian.tar.xz Checksums-Sha256: cd31f813ecd8863513a93fa0172487ffe1ee3e488f015ccbda0c90c4bd3308b2 2153 t-coffee_12.00.7fb08c2-2.dsc a64b0e203d4cad4ac58d175033e85433242e60904778ed1a7de6c258b6266d70 14672 t-coffee_12.00.7fb08c2-2.debian.tar.xz Files: c0c3cc820ec200194403dc72e972c4a8 2153 science optional t-coffee_12.00.7fb08c2-2.dsc b3c868079e959ae3f3d6f04d724ee3ea 14672 science optional t-coffee_12.00.7fb08c2-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJCBAEBCAAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxYFAEOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtHL8Q//TAQ8lwbHW7lyVGMF92dVJpQhwt8mO2m3dkDX Xbd4OrMN3M3VHHaIo40JuaIYUXkR7/tdzb/0doEUaYsHpuyyCdUXMFHAxMJ/zIsm lWosltLfKqklykPAOfgZ+EJ+wyPIrgBYbL6RYqt91at+WyMPICrEaVgIioM2kQ2z Hcvi+wTh+IrGIUnr68XrOMSqo7OzzfCndxGPv9Gk2V+Nx+4Zxw98wHp7LHicw76J Ocjq8Ml1yL2p3JXO6gbRARtv8JY7qkw10ShVGqtDNbe7A6VVuBplvcfdtggjFD7Y WIAY0qShvKXPuUR8tRnxejaOVKAKTDVrL0j1hCionR73BKinoDMX9yfmB7kr1hwy 1TdUHeWrysEFyRPWf0gvhaskjMuDNCuGZumMr+atgYixD5985ak2h10XZ4thCqwE 6szF+vS8ROzXLPM1bJIEvIQgxRy21MIdXfMF0r11XbnbX4uHnsOr87zbfbJ7e7W1 1CP/GRm4ihctkzPd6Q+l4b9ommEUCt7VCSnwbAokhEDqfe6GCLY/rtDJCSuAl5LW EBfrfR0JbIy3nbVPnOXGrAIb6fpbvxX7DZxF1UrPLA/Zt867A7ccTQrdySNBfNse zBsi6ULpD3mL539H+IVnhDFJ6VRek4GxPNceye2lmYGo1Lqijil2vLdQxsIg0nCU uCU3EY4= =b8lE -----END PGP SIGNATURE-----
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