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Bowtie2 segfault error (Re: Autopkgtest for SOAPdenovo)



Hi Andreas,

Sorry for the delay in continuing with tests! I remembered that I was required to create a blog to document my internship every two weeks. But three weeks passed, and I had not even started to create it... So I spent my time on it yesterday. The most time-consuming part is done already. Since there is only introductory post now, I will share my blog with you when I finish with the next post about the intermediate results of my work!

On Sat, 9 Jun 2018 at 13:37 Andreas Tille <andreas@an3as.eu> wrote:

For the next test I have another issue.  Bowtie2 has tests and it is
passing these tests.  However, recently I was working on a package that
hat bowtie2 as a Build-Depends.  Due to some error unrelated to bowtie2
the build failed and I was in a shell of the pbuilder chroot.  By chance
I simply called bowtie2 to see whether it was in the PATH.  If I called
it without any argument it was SEGFAULTing.  I can not reproduce this
in a usual installation - just in the minimized pbuilder chroot.

I tried to reproduce this segfault error in sbuild chroot and pbuilder chroot, but have not succeeded. For this I installed bowtie2 in chroot environment and tried to call it without any arguments: it prints help message and exits with non-zero code.
 
  Since
no command should segfault if simply called I wonder whether you could
add another test to bowtie2 and just call

    bowtie2

in it (which should respond with the help screen).
If it fails we have
something to do ...

Should I add the test anyway? Do I understand correctly that this test has to detect help message and then exit with zero?

With regards,
Liubov

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