hi gregor,
cross-posted to debian-med, as maybe someone with more adequate
background than myself on libchado-perl might be of help on its
test suite.
gregor herrmann, on 2021-04-22 18:53:37 +0200:
> On Wed, 21 Apr 2021 22:42:10 +0200, Étienne Mollier wrote:
> > The only problem I caught is libchado-perl autopkgtest. The
> > package does not declare any Testsuite, and the d/rules test
> > target is skipped, due to needing a database access. But if I
> > trigger an autopkgtest, then the autodep8 starts, and chokes on
> > a couple of issues. I'm not too sure whether this is blocking,
> > but if so, will need to ping Debian Med.
>
> Hm … Good question. And it raises some questions :)
>
> - Do the problems happen with the libgraph-perl version in stable and
> testing/unstable as well?
Yes, problems do happen with unmodified libgraph-perl from
stable, testing and sid. That is why I think they are most
likely unrelated to the security fix you cherry picked.
> - What did you do to run which tests? (I stared at the package bit
> but it's not really obvious to me).
I mostly stuck to running the entire autopkgtest, with bells and
whistles:
autopkgtest libchado-perl -- schroot sid-amd64-sbuild
autopkgtest libchado-perl -- schroot testing-amd64-sbuild
autopkgtest libchado-perl -- schroot buster-amd64-schroot
Variations around --no-auto-control do behave though, since
there are no tests in the package:
autopkgtest --no-auto-control libchado-perl -- schroot sid-amd64-sbuild
that is why I am not too sure how much of a blocker it would be
for the libgraph-perl upgrade. Maybe it will be recognized as
"Not a regression".
> - Which tests fail how? (I only see ./t/01_okay.t which triest to
> load Bio::Chado::LoadDBI which doesn't exist anywhere in Debian ?!)
By order of appearance in an autodep8 run against the Testing
distribution, i.e. without the patched libgraph-perl:
- test autodep8-perl-build-deps t/01_okay.t catches the use
Bio::Chado::LoadDBI you mention, the nearest file I find in
Debian is the following Perl5 module source:
libchado-perl: /usr/share/gmod/chado/load/tt2/LoadDBI.tt2
which by the way contains the following:
<!-- Not creating LoadDBI.pm at make time anymore (now it depends on Bio::GMOD::DB::Config)
- test autodep8-perl-recommends returns a bunch of various
issues:
- a series of syntax.t issues like:
# Failed test '/usr/bin/perl -wc /usr/share/perl5/Bio/FeatureIO/chado.pm exited successfully'
# at /usr/share/pkg-perl-autopkgtest/runtime-deps-and-recommends.d/syntax.t line 124.
- Can't locate Bio/Chado/LoadDBI.pm in @INC [...] at /usr/share/perl5/Bio/FeatureIO/chado.pm line 7
- a couple of the following in various files:
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/share/perl5/Bio/GMOD/DB/Adapter.pm line 498.
- Can't locate Chado/AutoDBI.pm in @INC [...] at /usr/share/perl5/Bio/GMOD/Load/GFF.pm line 5
- Can't locate GMOD/Chado/LoadDBI.pm in @INC [...] at /usr/share/perl5/Bio/GMOD/SeqUtils.pm line 41
> - Does this package actually use modules from libgraph-perl?
> (Grepping show some Bio::Graphics stuff but libbio-graphics-perl
> doesn't depend on libgraph-perl.)
It does not appear so on grepping libgraph-perl source code, or
binary packages content, on my end neither. Removing dependency
on libgraph-perl does not visibly affect buildability of the
package, and does not seem to make differences in the test
suite. It happens that the libgraph-perl is pulled as a
transitive recommends of the binary packages though.
> - Do you have any output or any other details?
I added an sbuild with autopkgtest output of the libchado-perl
against sid in attachment, without dependency to libgraph-perl.
The output is a bit trimmed down for readability, and reduce the
weight on mailboxes.
As far as I can see, although it is a Perl package, it looks
like provided elements are mostly supposed to be used like a
regular application. Maybe all these issues are just not caught
in regular package usage?
> Cheers,
> gregor, cc'ing the bug report
I'm sorry, I hope it is not too much at once.
Kind Regards, keeping the bug report around,
--
Étienne Mollier <etienne.mollier@mailoo.org>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/2, please excuse my verbosity.
Attachment:
signature.asc
Description: PGP signature