gregor herrmann
2021-02-21 13:00:02 UTC
Reply
PermalinkVersion: 1.7.3-3
Severity: serious
Tags: ftbfs
Justification: fails to build from source
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Hash: SHA512
As seen on ci.debian.net:
https://ci.debian.net/data/autopkgtest/testing/amd64/libb/libbio-db-biofetch-perl/10589851/log.gz
the test suite can fail with:
t/BioFetch.t ..
ok 1
ok 2
ok 3 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::SeqI'
ok 4
ok 5
ok 6
- ------------- EXCEPTION -------------
MSG: BioFetch Error 12: No entries found.
STACK Bio::DB::BioFetch::postprocess_data /usr/share/perl5/Bio/DB/BioFetch.pm:450
STACK Bio::DB::WebDBSeqI::_stream_request /usr/share/perl5/Bio/DB/WebDBSeqI.pm:769
STACK Bio::DB::WebDBSeqI::get_seq_stream /usr/share/perl5/Bio/DB/WebDBSeqI.pm:476
STACK Bio::DB::BioFetch::get_Stream_by_acc /usr/share/perl5/Bio/DB/BioFetch.pm:525
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:194
STACK toplevel t/BioFetch.t:32
- -------------------------------------
- ------------- EXCEPTION -------------
MSG: acc J02231 does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:203
STACK toplevel t/BioFetch.t:32
- -------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 6.
Dubious, test returned 255 (wstat 65280, 0xff00)
All 6 subtests passed
Test Summary Report
- -------------------
t/BioFetch.t (Wstat: 65280 Tests: 6 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
Files=1, Tests=6, 2 wallclock secs ( 0.03 usr 0.00 sys + 0.21 cusr 0.03 csys = 0.27 CPU)
Result: FAIL
Trying locally, I get 1) no test failure during build, as my
cowbuilder doesn't allow internet access, which is gracefully caught:
t/BioFetch.t ............. skipped: no host: www.google.com
All tests successful.
2) The same test failure during autopkgtests:
t/BioFetch.t ..
ok 1
ok 2
ok 3 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::SeqI'
ok 4
ok 5
ok 6
- ------------- EXCEPTION -------------
MSG: BioFetch Error 12: No entries found.
STACK Bio::DB::BioFetch::postprocess_data /usr/share/perl5/Bio/DB/BioFetch.pm:450
STACK Bio::DB::WebDBSeqI::_stream_request /usr/share/perl5/Bio/DB/WebDBSeqI.pm:769
STACK Bio::DB::WebDBSeqI::get_seq_stream /usr/share/perl5/Bio/DB/WebDBSeqI.pm:476
STACK Bio::DB::BioFetch::get_Stream_by_acc /usr/share/perl5/Bio/DB/BioFetch.pm:525
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:194
STACK toplevel t/BioFetch.t:32
- -------------------------------------
- ------------- EXCEPTION -------------
MSG: acc J02231 does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:203
STACK toplevel t/BioFetch.t:32
- -------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 6.
Dubious, test returned 255 (wstat 65280, 0xff00)
Cheers,
gregor
- -- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (990, 'unstable'), (500, 'unstable-debug'), (500, 'oldoldstable'), (500, 'experimental'), (500, 'testing'), (500, 'stable'), (500, 'oldstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.10.0-3-amd64 (SMP w/4 CPU threads)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=C, LC_CTYPE=de_AT.utf8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /bin/bash
Init: sysvinit (via /sbin/init)
LSM: AppArmor: enabled