[Debian-med-packaging] Bug#1077454: bioperl-run: t/SABlastPlus.t failure

[Étienne Mollier]

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 <emollier at debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/2, please excuse my verbosity
   `-    on air: Grand Tour - Back In The Zone
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