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 <email@example.com> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity.
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