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

[Aaron M. Ucko]

Never mind, that command did reproduce the problem after all; I just
thought otherwise at first because t_coffee ran for a while before
reporting failure.

-- Aaron

"Aaron M. Ucko" <ucko at debian.org> writes:

> 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!