[Debian-med-packaging] Bug#746624: python-biopython: FTBFS - t_coffee needs HOME or TMP

[Aaron M. Ucko]

Hi, Andreas.

This failure is due entirely to the autobuilders' configuration, which
supplies a nominal home directory path of /sbuild-nonexistent because
package builds should ignore users' actual home directories.  As such,
an automatic build on amd64 (for a binNMU, or to enforce a strict policy
of discarding uploaded binaries) would suffer the same fate.

I had hoped to reproduce the problem on my amd64 system by running

    svn-buildpackage --svn-builder=debuild -e HOME=/sbuild-nonexistent

but that proved insufficient, presumably because I still had a valid
home-directory entry in the passwd database.

-- Aaron

Andreas Tille <tille at debian.org> writes:

> Hi Aaron,
>
> thanks for your bug report.  I wonder whether you could test this at you
> site and add this variable to the line ind debian/rules starting with
>
>    env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss
>
> since the problem you reported does not occure on amd64 I can just wild
> guess and it would be great if you could test it on an architecture
> where this problem actually occures.
>
> It would be sufficient if you simply commit the change to SVN and I can
> upload your tested patch.
>
> Kind regards
>
>         Andreas.
>
> On Thu, May 01, 2014 at 11:09:52PM -0400, Aaron M. Ucko wrote:
>> Source: python-biopython
>> Version: 1.63+dfsg-1
>> Severity: serious
>> Justification: fails to build from source (but built successfully in the past)
>> 
>> Builds of python-biopython on the autobuilders, which decline to
>> provide home directories, have been failing:
>> 
>>   ApplicationError: Command 't_coffee -infile Fasta/fa01' returned non-zero exit status 135, '--ERROR:  : Could not set a HOME directory.Set any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:T-COFFEE]'
>> 
>> and likewise for the other two t_coffee tests.  Please arrange to
>> point one of those variables to a temporary directory in the build
>> tree.
>> 
>> Thanks!