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 <[email protected]>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/4, please excuse my verbosity
`-
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