[Debian-med-packaging] Please check hmmer2 autopkgtest

[Pranav Ballaney]

Hi,
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.

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?

Furthermore, is it okay to ship compiled binaries as examples in the
hmmer2-doc package? 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.

Regards,
Pranav

[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
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