Bug#1093338: libbio-eutilities-perl: FTBFS: Failed 8/20 test programs. 0/174 subtests failed.

Fri Jan 17 18:53:32 GMT 2025

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.