[Debian-med-packaging] Please check hmmer2 autopkgtest

[Andreas Tille]

Hi Pranav,

On Wed, Aug 12, 2020 at 10:17:29PM +0530, Pranav Ballaney wrote:
> The autopkgtest runs some binaries that are compiled as part of the build
> process. These binaries weren't being copied to the examples folder
> because of `make clean` in d/rules, and after removing that line, the
> autopkgtest suite passes.

Ahhh, that makes sense.
 
> However, even though the tests from these compiled binaries pass at build
> time, they fail during the autopkgtest. The return code is still 0 somehow,
> so the test suite as a whole passes. The test logs [1] indicate that the
> tests were passing in the previous version, so it seems to be an issue with
> the new version. Besides, the same tests pass during build time, so is it
> an issue with packaging / the chroot?

... or some missing dependency?  No idea. :-(
 
> Furthermore, is it okay to ship compiled binaries as examples in the
> hmmer2-doc package?

Not if doc package remains architecture: all.  Moreover I'd consider it
a perfect test to re-build those test binaries in the autopkgtest since
this would prove the development package libhmmer2-dev is working.

> If I try to recompile these binaries within the testing
> chroot instead of just copying them, it fails because it also needs files
> from the src/ directory (for example, src/config.h). So we will have to
> include those within hmmer2-doc too.

Shipping src/config.h (if really needed) as well as the sources for the
test scripts inside doc would be OK.
 
Thanks for checking the situation

      Andreas.

 
> [1]
> https://ci.debian.net/data/autopkgtest/testing/amd64/h/hmmer2/6605072/log.gz
> 
> 
> On Wed, Aug 12, 2020 at 3:27 PM Andreas Tille <andreas at an3as.eu> wrote:
> 
> > Hi,
> >
> > I checked the Debian Med packages that are using pvm but possibly should
> > not[1].  I spotted hmmer2.  Besides the fact that the effort to upgrade
> > it to some continued effort at Github (where I failed to find out the
> > status - Joshua could you possibly comment on this) was stalled I
> > decided to use this one since it seemed to have droped pvm anyway.
> >
> > The package now builds but the autopkgtest fails:
> >
> > autopkgtest [09:45:31]: test run-unit-test: [-----------------------
> > chmod: cannot access 'alignalign_test': No such file or directory
> > chmod: cannot access 'evd_test': No such file or directory
> > chmod: cannot access 'masks_test': No such file or directory
> > chmod: cannot access 'parsingviterbi_test': No such file or directory
> > chmod: cannot access 'tophits_test': No such file or directory
> > chmod: cannot access 'trace_test': No such file or directory
> > chmod: cannot access 'viterbi_exercise': No such file or directory
> > chmod: cannot access 'weeviterbi_test': No such file or directory
> > autopkgtest [09:45:31]: test run-unit-test: -----------------------]
> > run-unit-test        FAIL non-zero exit status 1
> >
> > It would be great if someone could have a look here.
> >
> > Kind regards
> >
> >        Andreas.
> >
> > [1] https://lists.debian.org/debian-mentors/2020/08/msg00066.html
> >
> > --
> > http://fam-tille.de
> >
> ᐧ

-- 
http://fam-tille.de