[Debian-med-packaging] Bug#906980: kmer: autopkgtest fails with segfault in testing/unstable while it passes in stable

[Liubov Chuprikova]

Hi Andreas,

On Thu, 23 Aug 2018 at 08:58 Andreas Tille <andreas at fam-tille.de> wrote:

>
> On Wed, Aug 22, 2018 at 09:42:13PM +0200, Liubov Chuprikova wrote:
> > An autopkgtest fails with segfault in testing and unstable [1].
> >
> > ```
> > /usr/bin/../lib/atac/bin/statsGenerator -a
> /tmp/autopkgtest-lxc.epng5fx9/downtmp/autopkgtest_tmp/results/EcolivsSent.atac
> > -p
> /tmp/autopkgtest-lxc.epng5fx9/downtmp/autopkgtest_tmp/results/stats/EcolivsSent
> > -g A >
> /tmp/autopkgtest-lxc.epng5fx9/downtmp/autopkgtest_tmp/results/stats/EcolivsSent.stats
> >
> > Segmentation fault
> > Failed to ganerate statistics.
> > ```
> >
> > Notably, that building and testing in stable were successful (I tested
> > it in clean chroot). JFI, I tried installing an older version of gcc on
> > testing, the one that is used in stable (4:6.3.0-4), and this eliminated
> > the segfault.
>
> Thanks for this good catch which proves how important your Outreachy
> project is for providing stable and working packages in Debian Med.
>

Now I see!


> Thanks also for verifying that older compilers seem to produce working
> code while newer don't.
>

This seemed just something to go on.

I wonder whether you feel able to do some debugging what position of
> code causes the issue.

My first shout would be to grep for
>    "Failed to ganerate statistics"
> which is probably in a wrapper around some code and than use some
> debugging techniques (either you are comfortable with gdb / want to
> become comfortable with gdb or simply use some
>     printf("DEBUG %s(%i): ...", __FILE__, __LINE__, ...);
> statements in the code to watch what's happening.



> It might be helpful to lower / switch off optimisation options to see
> whether some optimisation feature of some later gcc will deal
> differently with some not properly specified code part.
>

Thanks a lot for your advise! I tried debugging with grep when I had just
caught the error for the first time, but it was without result at that
moment. Turning off optimization flags, as you recommended, also did not
help. After that I made one more attemp to debug with grep and printing
some statements and finally found what it is called classical non-bug in
gcc [1].

I have just uploaded a patch. Could you please sponsor an upload?

With regards,
Liubov

[1] https://gcc.gnu.org/bugs/#nonbugs_c
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