Your message dated Mon, 27 Jan 2025 22:06:55 +0000 with message-id <e1tcxfv-00gyt0...@fasolo.debian.org> and subject line Bug#1093338: fixed in libbio-eutilities-perl 1.77-3 has caused the Debian Bug report #1093338, regarding libbio-eutilities-perl: FTBFS: Failed 8/20 test programs. 0/174 subtests failed. 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.) -- 1093338: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1093338 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:libbio-eutilities-perl Version: 1.77-2 Severity: serious Tags: ftbfs trixie sid Dear maintainer: During a rebuild of all packages in unstable, your package failed to build: -------------------------------------------------------------------------------- [...] debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::EUtilities Writing MYMETA.yml and MYMETA.json dh_auto_build make -j2 make[1]: Entering directory '/<<PKGBUILDDIR>>' cp lib/Bio/Tools/EUtilities/EUtilDataI.pm blib/lib/Bio/Tools/EUtilities/EUtilDataI.pm cp lib/Bio/Tools/EUtilities/EUtilParameters.pm blib/lib/Bio/Tools/EUtilities/EUtilParameters.pm cp lib/Bio/Tools/EUtilities/Info.pm blib/lib/Bio/Tools/EUtilities/Info.pm cp lib/Bio/Tools/EUtilities.pm blib/lib/Bio/Tools/EUtilities.pm cp lib/Bio/Tools/EUtilities/Info/FieldInfo.pm blib/lib/Bio/Tools/EUtilities/Info/FieldInfo.pm cp lib/Bio/Tools/EUtilities/Summary.pm blib/lib/Bio/Tools/EUtilities/Summary.pm cp lib/Bio/Tools/EUtilities/HistoryI.pm blib/lib/Bio/Tools/EUtilities/HistoryI.pm cp lib/Bio/DB/EUtilities.pm blib/lib/Bio/DB/EUtilities.pm cp lib/Bio/Tools/EUtilities/Summary/ItemContainerI.pm blib/lib/Bio/Tools/EUtilities/Summary/ItemContainerI.pm cp lib/Bio/Tools/EUtilities/Query.pm blib/lib/Bio/Tools/EUtilities/Query.pm cp lib/Bio/EUtilities.pm blib/lib/Bio/EUtilities.pm cp lib/Bio/Tools/EUtilities/Info/LinkInfo.pm blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm cp lib/Bio/Tools/EUtilities/Summary/DocSum.pm blib/lib/Bio/Tools/EUtilities/Summary/DocSum.pm cp lib/Bio/Tools/EUtilities/Summary/Item.pm blib/lib/Bio/Tools/EUtilities/Summary/Item.pm cp lib/Bio/Tools/EUtilities/Link/LinkSet.pm blib/lib/Bio/Tools/EUtilities/Link/LinkSet.pm cp lib/Bio/Tools/EUtilities/Link/UrlLink.pm blib/lib/Bio/Tools/EUtilities/Link/UrlLink.pm cp lib/Bio/Tools/EUtilities/History.pm blib/lib/Bio/Tools/EUtilities/History.pm cp lib/Bio/Tools/EUtilities/Link.pm blib/lib/Bio/Tools/EUtilities/Link.pm cp lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm blib/lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm cp bin/bp_einfo blib/script/bp_einfo cp bin/bp_genbank_ref_extractor blib/script/bp_genbank_ref_extractor "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_einfo "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank_ref_extractor Manifying 2 pod documents Manifying 19 pod documents make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_test make -j2 test TEST_VERBOSE=1 make[1]: 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..21 ok 1 - Bio/DB/EUtilities.pm loaded ok ok 2 - Bio/EUtilities.pm loaded ok ok 3 - Bio/Tools/EUtilities.pm loaded ok ok 4 - Bio/Tools/EUtilities/EUtilDataI.pm loaded ok ok 5 - Bio/Tools/EUtilities/EUtilParameters.pm loaded ok ok 6 - Bio/Tools/EUtilities/History.pm loaded ok ok 7 - Bio/Tools/EUtilities/HistoryI.pm loaded ok ok 8 - Bio/Tools/EUtilities/Info.pm loaded ok ok 9 - Bio/Tools/EUtilities/Info/FieldInfo.pm loaded ok ok 10 - Bio/Tools/EUtilities/Info/LinkInfo.pm loaded ok ok 11 - Bio/Tools/EUtilities/Link.pm loaded ok ok 12 - Bio/Tools/EUtilities/Link/LinkSet.pm loaded ok ok 13 - Bio/Tools/EUtilities/Link/UrlLink.pm loaded ok ok 14 - Bio/Tools/EUtilities/Query.pm loaded ok ok 15 - Bio/Tools/EUtilities/Query/GlobalQuery.pm loaded ok ok 16 - Bio/Tools/EUtilities/Summary.pm loaded ok ok 17 - Bio/Tools/EUtilities/Summary/DocSum.pm loaded ok ok 18 - Bio/Tools/EUtilities/Summary/Item.pm loaded ok ok 19 - Bio/Tools/EUtilities/Summary/ItemContainerI.pm loaded ok ok 20 - bin/bp_einfo compiled ok ok 21 - bin/bp_genbank_ref_extractor compiled 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-syntax.t ....... skipped: these tests are for testing by the author t/egquery.t ................. 1..18 ok 1 - get_db ok 2 - get_database ok 3 - get_databases ok 4 - get_term ok 5 - get_count ok 6 - get_count ok 7 - get_count ok 8 - get_GlobalQueries ok 9 - get_term ok 10 - get_term ok 11 - get_term ok 12 - get_term ok 13 - get_term ok 14 - get_term ok 15 - get_term ok 16 - get_term ok 17 - get_term ok 18 - get_term ok t/einfo.t ................... 1..49 ok 1 - get_available_databases ok 2 - get_databases ok 3 - get_db ok 4 - get_record_count ok 5 - get_menu_name ok 6 - get_last_update ok 7 - get_description ok 8 - FieldInfo ok 9 - LinkInfo ok 10 - get_db ok 11 - get_dbs ok 12 - get_record_count ok 13 - get_menu_name ok 14 - get_last_update ok 15 - get_description ok 16 - FieldInfo ok 17 - get_term_count ok 18 - get_field_name ok 19 - get_field_code ok 20 - get_field_description ok 21 - is_date ok 22 - is_singletoken ok 23 - is_hierarchy ok 24 - is_hidden ok 25 - is_numerical ok 26 - get_term_count ok 27 - get_field_name ok 28 - get_field_code ok 29 - get_field_description ok 30 - is_date ok 31 - is_singletoken ok 32 - is_hierarchy ok 33 - is_hidden ok 34 - is_numerical ok 35 - LinkInfo ok 36 - get_dbto ok 37 - get_dbfrom ok 38 - get_link_name ok 39 - get_link_description ok 40 - get_priority ok 41 - get_html_tag ok 42 - get_url ok 43 - get_dbto ok 44 - get_dbfrom ok 45 - get_link_name ok 46 - get_link_description ok 47 - get_priority ok 48 - get_html_tag ok 49 - get_url ok choice/seq contains no opening bracket [Ln: 26, Col: 33] XML::Simple called at /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/EUtilities.pm line 144. # Looks like your test exited with 255 just after 1. t/elink_acheck.t ............ 1..128 ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link' Dubious, test returned 255 (wstat 65280, 0xff00) Failed 127/128 subtests choice/seq contains no opening bracket [Ln: 26, Col: 33] XML::Simple called at /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/EUtilities.pm line 144. # Looks like your test exited with 255 just after 1. t/elink_lcheck.t ............ 1..62 ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link' Dubious, test returned 255 (wstat 65280, 0xff00) Failed 61/62 subtests choice/seq contains no opening bracket [Ln: 26, Col: 33] XML::Simple called at /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/EUtilities.pm line 144. # Looks like your test exited with 255 just after 1. t/elink_llinks.t ............ 1..84 ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link' Dubious, test returned 255 (wstat 65280, 0xff00) Failed 83/84 subtests choice/seq contains no opening bracket [Ln: 26, Col: 33] XML::Simple called at /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/EUtilities.pm line 144. # Looks like your test exited with 255 just after 1. t/elink_ncheck.t ............ 1..58 ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link' Dubious, test returned 255 (wstat 65280, 0xff00) Failed 57/58 subtests choice/seq contains no opening bracket [Ln: 26, Col: 33] XML::Simple called at /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/EUtilities.pm line 144. # Looks like your test exited with 255 just after 1. t/elink_neighbor.t .......... 1..61 ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link' Dubious, test returned 255 (wstat 65280, 0xff00) Failed 60/61 subtests choice/seq contains no opening bracket [Ln: 26, Col: 33] XML::Simple called at /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/EUtilities.pm line 144. # Looks like your test exited with 255 just after 1. t/elink_neighbor_history.t .. 1..63 ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link' Dubious, test returned 255 (wstat 65280, 0xff00) Failed 62/63 subtests choice/seq contains no opening bracket [Ln: 26, Col: 33] XML::Simple called at /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/EUtilities.pm line 144. # Looks like your test exited with 255 just after 1. t/elink_scores.t ............ 1..56 ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link' Dubious, test returned 255 (wstat 65280, 0xff00) Failed 55/56 subtests t/epost.t ................... 1..15 ok 1 - An object of class 'Bio::Tools::EUtilities::Query' isa 'Bio::Tools::EUtilities::EUtilDataI' ok 2 - An object of class 'Bio::Tools::EUtilities::Query' isa 'Bio::Tools::EUtilities::Query' ok 3 - eutil ok 4 - datatype ok 5 - An object of class 'Bio::Tools::EUtilities::History' isa 'Bio::Tools::EUtilities::HistoryI' ok 6 - An object of class 'Bio::Tools::EUtilities::History' isa 'Bio::Tools::EUtilities::EUtilDataI' ok 7 - eutil ok 8 - eutil ok 9 - get_webenv ok 10 - get_query_key ok 11 - history ok 12 - get_database ok 13 - get_ids ok 14 - get_database ok 15 - get_ids ok t/esearch.t ................. 1..31 ok 1 - get_count ok 2 ok 3 - get_ids ok 4 - get_retstart ok 5 - get_retmax ok 6 - get_translation_from ok 7 - get_translation_to ok 8 - get_db ok 9 - get_database ok 10 - get_term ok 11 - get_db ok 12 - get_database ok 13 - get_term ok 14 - get_corrected_query ok 15 - get_replaced_terms ok 16 - get_count ok 17 - An object of class 'Bio::Tools::EUtilities::History' isa 'Bio::Tools::EUtilities::HistoryI' ok 18 - get_webenv ok 19 - get_query_key ok 20 - history ok 21 - get_ids ok 22 - get_retstart ok 23 - get_retmax ok 24 - get_translation_from ok 25 - get_translation_to ok 26 - get_db ok 27 - get_database ok 28 - get_term ok 29 - get_corrected_query ok 30 - get_replaced_terms ok 31 - get_GlobalQueries ok t/espell.t .................. 1..20 ok 1 - get_db ok 2 - get_dbs ok 3 - get_database ok 4 - get_databases ok 5 - get_term ok 6 - get_corrected_query ok 7 - get_replaced_terms ok 8 - get_replaced_terms ok 9 - get_count ok 10 ok 11 - get_ids ok 12 - get_retstart ok 13 - get_retmax ok 14 - get_translation_from ok 15 - get_translation_to ok 16 - get_db ok 17 - get_dbs ok 18 - get_database ok 19 - get_databases ok 20 - get_term ok choice/seq contains no opening bracket [Ln: 11, Col: 39] XML::Simple called at /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/EUtilities.pm line 144. # Looks like your test exited with 25 just after 1. t/esummary.t ................ 1..81 ok 1 - An object of class 'Bio::Tools::EUtilities::Summary' isa 'Bio::Tools::EUtilities::Summary' Dubious, test returned 25 (wstat 6400, 0x1900) Failed 80/81 subtests t/EUtilParameters.t ......... 1..12 ok 1 ok 2 - An object of class 'HTTP::Request' isa 'HTTP::Request' ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 - available_parameters ok 10 - available_parameters ok 11 - get_parameters ok 12 - get_parameters ok t/release-EUtilities.t ...... skipped: these tests are for release candidate testing Test Summary Report ------------------- t/elink_acheck.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 128 tests but ran 1. t/elink_lcheck.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 62 tests but ran 1. t/elink_llinks.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 84 tests but ran 1. t/elink_ncheck.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 58 tests but ran 1. t/elink_neighbor.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 61 tests but ran 1. t/elink_neighbor_history.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 63 tests but ran 1. t/elink_scores.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 56 tests but ran 1. t/esummary.t (Wstat: 6400 (exited 25) Tests: 1 Failed: 0) Non-zero exit status: 25 Parse errors: Bad plan. You planned 81 tests but ran 1. Files=20, Tests=174, 2 wallclock secs ( 0.04 usr 0.02 sys + 1.49 cusr 0.36 csys = 1.91 CPU) Result: FAIL Failed 8/20 test programs. 0/174 subtests failed. make[1]: *** [Makefile:983: test_dynamic] Error 255 make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_test: error: make -j2 test TEST_VERBOSE=1 returned exit code 2 make: *** [debian/rules:4: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- The above is just how the build ends and not necessarily the most relevant part. If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202501/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you could not reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:libbio-eutilities-perl, so that this is still visible in the BTS web page for this package. Thanks.
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--- Begin Message ---Source: libbio-eutilities-perl Source-Version: 1.77-3 Done: Étienne Mollier <emoll...@debian.org> We believe that the bug you reported is fixed in the latest version of libbio-eutilities-perl, 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 1093...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Étienne Mollier <emoll...@debian.org> (supplier of updated libbio-eutilities-perl 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: SHA512 Format: 1.8 Date: Mon, 27 Jan 2025 22:36:12 +0100 Source: libbio-eutilities-perl Architecture: source Version: 1.77-3 Distribution: unstable Urgency: medium Maintainer: Debian Perl Group <pkg-perl-maintain...@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll...@debian.org> Closes: 1093338 Changes: libbio-eutilities-perl (1.77-3) unstable; urgency=medium . * Team upload. * d/{control,rules}: ensure use of the XML::LibXML::SAX parser. (Closes: #1093338) * Declare compliance with Debian Policy 4.7.0. * inline-DTDs-on-testsuite: normalize dep3 header. The patch from originates upstream, hence the forwarding status. * typo.patch: fix a typo caught by lintian. Checksums-Sha1: 12dd699937661bae5f1289b9f06e29cc3b2f554d 2551 libbio-eutilities-perl_1.77-3.dsc 539e997fc3b11d045c0eedd7ba74b7d4b0aef1ae 5916 libbio-eutilities-perl_1.77-3.debian.tar.xz Checksums-Sha256: 55b6db244838dd01f360e5ebf5460edc16e8737ed8c0d8cf6efbced1de81b58d 2551 libbio-eutilities-perl_1.77-3.dsc eaedb2cd87f95475937aa42708482f4aac252d06972d6fecde8b9df5657f5b88 5916 libbio-eutilities-perl_1.77-3.debian.tar.xz Files: e7151cd15f7036cbdb1d3bdf86d4a0c9 2551 perl optional libbio-eutilities-perl_1.77-3.dsc fc3b3cd180026d0252188317ff2870ec 5916 perl optional libbio-eutilities-perl_1.77-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmeX/V0UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqeQRAAi8PvMcEqnvv8KTpuw6o4Yjv5EJ6T vl0M3tUitC9ytq40UwHeqqomeO2n+HOeOkfT59d5QC/5LC5/UEhdwLNZ8b/ayKf8 f0ufgFRNPES26ptgNtPcnHS2HSKVayzZdr4BezeCUqTHzBFYW0fVXmuG9hx/6+MY g3WwzmT8mY0ocJQJyc/jTF3ro3pMCxGvSmSEaqU+0/iJui9swsVpGvJy9S4yr83D lrGbGrdu/yvwbWxK7bU4fKfqBW5Wjig24OIC2RYSqYxTLYVMuHCNlR15u5YwLBN0 YFvyoQrWxDCQW+U7avQ+xolX2M8yzeoi4cnESu+vUngUex1iTZtaxMdozcyzgBUl YeCU+xncY3TcCLljdBTPGoxL7xSMO6MMuMYaWPW9sZE1vTKJwznI1NOXIx5kCAMh 7mii8eEOdxc/03zGPWhF/4HXt2+bhF66tTnjpx8gfZ+dryvGK0237vyM6e2XVt9u vYTto6noVtMUXD+MMJw2x/MQmwrTOfb6R1hvVIUZDJmmCWgU7O/HAmhAi5mEx0NY ykqX525u3fMMaUlN1d9Y43u9EKvIUH09wL1K/2xAxJn2y4FLxKIIQnMLPZh0Pdox /q1PR24lnOfMliXhRRIM36Ye8ybpzZxvml3F9s24zf7lBTbG0l4RKMo9NHY2xjOh 5KfECWdYm5qVjoU= =w4gO -----END PGP SIGNATURE-----
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