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

--aHc6/oq18GMk/W3p
Content-Type: text/plain; charset=utf-8
Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable

Hi Dominique,

Dominique Dumont, on 2026-06-22:
> On Sunday, 21 June 2026 22:38:20 Central European Summer Time =C3=89tienn=
e Mollier=20
> wrote:
> > After further investigations, this:
> > >        t/Ontology/OntologyEngine.t .. 1/31 Undefined subroutine
> > >        &main::throws_ok called at t/Ontology/OntologyEngine.t line 11=
7.
> > and friends looks to stem from Bio::Root::Test not reexporting
> > Test::Most submodules anymore.  I'm not entirely sure whether
> > the bug is in bioperl or Test::Most, but fixing the issue from
> > bioperl is manageable, by patching lib/Bio/Root/Test.pm
>=20
> I don't recommend reexporting functions route as this makes harder to kno=
w=20
> where the test functions come from.

Thanks for chiming in!  I have not liaised with upstream yet.  I
have to agree that I'm feeling uncomfortable with this hiding of
namespaces.  I think this is even why addressing the issue was
somewhat difficult in the first place.

In it's initial implementation, Bio::Root::Test provides those
test functions in such a way that they are expected to be this
way by the test suite and downstream consumers.  Please note I'm
not considering myself as a Perl specialist: it is very likely
that I misunderstood you or missed better corrections.  Per
chance, do you think of a more appropriate course of action to
resolve the issue at play?

Have a nice day,  :)
--=20
  .''`.  =C3=89tienne Mollier <[email protected]>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/1, please excuse my verbosity
   `-

--aHc6/oq18GMk/W3p
Content-Type: application/pgp-signature; name=signature.asc

-----BEGIN PGP SIGNATURE-----
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=X8Bs
-----END PGP SIGNATURE-----

--aHc6/oq18GMk/W3p--