Discussion:
Bug#983238: libbio-db-biofetch-perl: test failure if internet available
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gregor herrmann
2021-02-21 13:00:02 UTC
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Source: libbio-db-biofetch-perl
Version: 1.7.3-3
Severity: serious
Tags: ftbfs
Justification: fails to build from source

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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
Debian Bug Tracking System
2021-02-22 22:30:02 UTC
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Your message dated Mon, 22 Feb 2021 22:18:46 +0000
with message-id <E1lEJXS-0003Ac-***@fasolo.debian.org>
and subject line Bug#983238: fixed in libbio-db-ncbihelper-perl 1.7.6-3
has caused the Debian Bug report #983238,
regarding libbio-db-biofetch-perl: test failure if internet available
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 ***@bugs.debian.org
immediately.)
--
983238: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=983238
Debian Bug Tracking System
Contact ***@bugs.debian.org with problems
Debian Bug Tracking System
2021-03-01 20:00:01 UTC
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Your message dated Mon, 01 Mar 2021 19:49:16 +0000
with message-id <E1lGoXc-000EIJ-***@fasolo.debian.org>
and subject line Bug#983238: fixed in libbio-db-biofetch-perl 1.7.3-4
has caused the Debian Bug report #983238,
regarding libbio-db-biofetch-perl: test failure if internet available
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 ***@bugs.debian.org
immediately.)
--
983238: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=983238
Debian Bug Tracking System
Contact ***@bugs.debian.org with problems
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