[Debian-med-packaging] Samtools fails to build on several architectures [noreply at buildd.debian.org: failed i386 build of samtools 1.0-1]

[Andreas Tille]

Hi folks on debian-mentors,

Charles Plessy uncovered a very strange difference when building
samtools either using pbuilder or sbuild and it remains totally unclear
to us how this might happen.  Please see his mail[1] linked below.

I also noticed that while the autobuild on i386 shows a very different
number of failed tests than if you run pdebuild on a local i386
machine[2].  The specific error on i386 sounds so untypical for an
architecture difference:

      did not have Usage:
      usage did not mention samtools stats

that it smells like something would went really wrong here.  Any hint
would be welcome.

Kind regards

       Andreas.

On Tue, Sep 23, 2014 at 07:17:47PM +0900, Charles Plessy wrote:
> Le Tue, Sep 23, 2014 at 11:52:05AM +0200, Andreas Tille a écrit :
> > 
> > However, after looking into the build-log (I copied it to
> > /var/tmp/samtools blends.debian.net) the failures are:
> > 
> > $ grep -B 5 '^\.\. failed' *.build
> > 
> > test_usage_subcommand:
> >         samtools stats
> > 
> >         did not have Usage:
> > .. failed ...
> > 
> > 
> >         usage did not mention samtools stats
> > .. failed ...
> > 
> > 
> > which sounds pretty basic to me.  I wonder if such things might be
> > hidden by the autopkgtest approach since I have no idea whether
> > autopkgtest will be runned on all architectures.
> 
> Well, last Monday I spent more than 3 hours trying to understand the problem by
> adding debug messages in the test script, and found no explanation for the
> failure.  When I added something like “print `samtools stats`”, it showed that
> in the sbuild chroot only, the samtools stats command behaves as if it were
> invoked with a file in the argument, except that it analysed no data.  See the
> following email for details.

[1] http://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-September/029476.html
[2] http://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-September/029750.html

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