Control: tags -1 confirmed upstream Control: forwarded -1 https://github.com/bioperl/bioperl-run/issues/62
Hi,
I think I pinpointed the test failure in bioperl-run stems from
ongoing ncbi-blast+ upgrade to version 2.16.0. bioperl-run is
still building properly on testing, but if I bump ncbi-blast+
version, then I reproduce the error.
Relevant part of the error to reduce scroll back and forth is:
# DB and mask make tests
# Failed test 'right type'
# at t/SABlastPlus.t line 37.
# got: undef
# expected: 'nucl'
# Failed test 'correct type'
# at t/SABlastPlus.t line 53.
# got: undef
# expected: 'nucl'
------------- EXCEPTION -------------
MSG: Masker 'windowmasker' can't use a blastdb as primary input
STACK Bio::Tools::Run::StandAloneBlastPlus::make_mask
/<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm:818
STACK toplevel t/SABlastPlus.t:55
-------------------------------------
# Looks like your test exited with 29 just after 14.
t/SABlastPlus.t ...............
1..71
ok 1 - use Bio::Tools::Run::StandAloneBlastPlus;
ok 2 - use Bio::Tools::Run::WrapperBase;
ok 3 - use Bio::Tools::Run::WrapperBase::CommandExts;
ok 4 - BlastPlus factory
ok 5 - make factory
ok 6 - test db made with fasta
ok 7 - temp db
not ok 8 - right type
ok 9
ok 10 - named db made
ok 11 - check_db
ok 12 - correct name
ok 13 - dbinfo hash returned
not ok 14 - correct type
Dubious, test returned 29 (wstat 7424, 0x1d00)
Failed 59/71 subtests
The test includes several calls to the makeblastdb command,
through various "factories" (in the sense of design patterns).
My impression is that the test suite may have to adjust its
makeblastdb invocation, at least the one spanning lines 55-58,
as it seems to include the faulty windowmasker invocation. As
it very much feels like the test may need update, I informed
upstream of the issue.
Have a nice day, :)
--
.''`. Étienne Mollier <emoll...@debian.org>
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