[Debian-med-packaging] Bug#1136915: [help] bioperl: FTBFS: Failed 26/211 test programs. 1/11707 subtests failed.

[Étienne Mollier]

Hi,

Andreas Tille, on 2026-05-27:
> bioperl was building nicely two months ago but since two weeks ago some
> change seems to have broken some tests.  I tried my luck with a bit of
> quilt patching in Git but I have the strong feeling I'm just fiddling
> around with some symptoms rather than fixing the root problem.

I see two remaining issues here, which do not appear in the bug
tracker, but are part of the build log uploaded to people.d.o.
The first issue is reproducible with:

	$ prove t/LocalDB/Fasta.t
	t/LocalDB/Fasta.t .. 1/109 Subroutine new redefined at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1121.
	Subroutine next_seq redefined at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1130.
	Subroutine TIEHANDLE redefined at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1139.
	Subroutine READLINE redefined at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1144.
	
	------------- EXCEPTION: Bio::Root::Exception -------------
	MSG: FASTA header doesn't match '>(\S+)': > foo
	
	STACK: Error::throw
	STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
	STACK: Bio::DB::Fasta::_calculate_offsets /usr/share/perl5/Bio/DB/Fasta.pm:195
	STACK: Bio::DB::IndexedBase::_index_files /usr/share/perl5/Bio/DB/IndexedBase.pm:660
	STACK: Bio::DB::IndexedBase::index_dir /usr/share/perl5/Bio/DB/IndexedBase.pm:447
	STACK: Bio::DB::IndexedBase::new /usr/share/perl5/Bio/DB/IndexedBase.pm:362
	STACK: t/LocalDB/Fasta.t:330
	-----------------------------------------------------------
	# Looks like your test exited with 25 just after 102.
	t/LocalDB/Fasta.t .. Dubious, test returned 25 (wstat 6400, 0x1900)
	Failed 7/109 subtests 
	
	Test Summary Report
	-------------------
	t/LocalDB/Fasta.t (Wstat: 6400 (exited 25) Tests: 102 Failed: 0)
	  Non-zero exit status: 25
	  Parse errors: Bad plan.  You planned 109 tests but ran 102.
	Files=1, Tests=102,  0 wallclock secs ( 0.04 usr  0.01 sys +  0.18 cusr  0.05 csys =  0.28 CPU)
	Result: FAIL

The second issue is:

	$ prove t/Ontology/OntologyEngine.t
	t/Ontology/OntologyEngine.t .. 1/31 Undefined subroutine &main::throws_ok called at t/Ontology/OntologyEngine.t line 117.
	# Looks like your test exited with 255 just after 7.
	t/Ontology/OntologyEngine.t .. Dubious, test returned 255 (wstat 65280, 0xff00)
	Failed 24/31 subtests 
	
	Test Summary Report
	-------------------
	t/Ontology/OntologyEngine.t (Wstat: 65280 (exited 255) Tests: 7 Failed: 0)
	  Non-zero exit status: 255
	  Parse errors: Bad plan.  You planned 31 tests but ran 7.
	Files=1, Tests=7,  0 wallclock secs ( 0.01 usr  0.01 sys +  0.10 cusr  0.03 csys =  0.15 CPU)
	Result: FAIL

Other items look to be resolved.  Let's see if I can make heads
or tails of those…

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/4, please excuse my verbosity
   `-
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