Hi Andreas,
I've created another binary called gasic-examples and moved all examples
there.
I ran the tests again, and they all pass in my chroot. I also rebuilt the
chroot in case there was something wrong there, and turns out they still
pass. I also tried adding:
bowtie-build dwv.fasta dwv.fasta
to the autopkgtests for the bowtie package, and all of those pass too.
For the purpose of completing autopkgtests for gasic, I have tried to
circumvent this issue by changing the mapper for gasic from bowtie to bwa,
so bowtie will no longer be required for testing gasic.
I've also fixed a patch and added some more tests.
Please take a look - specially at the new binary (in case I've misplaced
some file) - and if these tests work now, please sponsor.
Regarding bowtie, I'm unable to reproduce the issue, so if you have any
ideas that I can try, please let me know.
Regards,
Pranav
On Sun, May 10, 2020 at 10:53 AM Andreas Tille <[email protected]> wrote:
> Hi Pranav,
>
> On Sun, May 10, 2020 at 02:58:32AM +0530, Pranav Ballaney wrote:
> > I've added autopkgtests to gasic. Please review and sponsor.
> > https://salsa.debian.org/med-team/gasic/
>
> thank you for adding this test. There is one cosmetic issue and a
> problematic issue. The cosmetic thing is that the additional data are
> blowing up this quite small package a lot. I do not think that we
> should bloat user machines too much. Thus it would be better to ship
> the data in an extra binary package gasic-examples.
>
> But here comes the harder part: I get
>
> autopkgtest [05:12:46]: test run-unit-test: [-----------------------
> /tmp/autopkgtest.qJbg1v/tree/debian/tests/run-unit-test: line 23: 903
> Segmentation fault bowtie-build dwv.fasta dwv.fasta
> autopkgtest [05:12:47]: test run-unit-test: -----------------------]
>
> in my pbuilder chroot. I remember I once had a similar issue with
> bowtie before. Its a bit hard to seek in BTS and I have no idea
> whether it makes sense to seek at all. But it would be great if you
> could reproduce this somehow and we could debug that issue - which
> is probably an issue in bowtie - it just should not segfault.
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>
> ᐧ
