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Re: RFS: gasic

Hi Pranav,

On Wed, May 13, 2020 at 02:47:11AM +0530, Pranav Ballaney wrote:
> Hi Andreas,
> I've created another binary called gasic-examples and moved all examples
> there.

I've checked this and did some slight changes.  Please note that all the
dependencies you copied from gasic package are not needed to the examples.
You can simply install the data files without any dependencies.

I've also moved the data files to /usr/share/doc/gasic/examples.
Finally the user wants to have examples for gasic and chances are better
that they will be found 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.

I confirm that I injected that call into the build of the bowtie package
where it succeeded.  Strangely enough the whole autopkgtest of bowtie
failed in my pbuilder chroot which I'm using as a hook in my build
environment.  So may be this environment has some issues since bowtie at
ci.debian.org is fine.
> 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.

Hmmm, I admit I've read this to late.  May be you forgot to push?  But
don't mind about this.  The package needs to go to the new queue due to
the new binary package and needs another source only upload afterwards.
We can add your changes than.

> 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.

I've uploaded now - please check whether you have uncommitted changes and
merge these for the future upload.
> Regarding bowtie, I'm unable to reproduce the issue, so if you have any
> ideas that I can try, please let me know.

If you are using cowbuilder you might like to copy




This will run the autopkgtest right inside the pbuilder chroot.  This is
what I'm using in all my builds with less than 1% of false positives
like in the bowtie case.  Probably having another hook in analogy to
C99_failed_build to stay in the autopkgtest root and fire up gdb would
uncover some issues.
Thank you for your work on this



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