[Debian-med-packaging] r16437 - in trunk/packages/python-biopython/trunk/debian: . patches

[Andreas Tille]

Hi Philipp,

On Wed, Mar 12, 2014 at 06:09:16PM +0000, Philipp Benner wrote:
> Author: philipp
> Date: 2014-03-12 18:09:16 +0000 (Wed, 12 Mar 2014)
> New Revision: 16437
> 
> Added:
>    trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch
> Modified:
>    trunk/packages/python-biopython/trunk/debian/changelog
>    trunk/packages/python-biopython/trunk/debian/patches/series
>    trunk/packages/python-biopython/trunk/debian/rules
> Log:
> DSSP fix;

Strictly speaking this fix is not necessary any more since I recently
uploaded a dssp package containing a symlink /usr/bin/dssp but the patch
does not harm and might be helpful for biopython upstream if you would
report the problem.  Do you maintain some better connection than me
since I have the impression that my hints and patches are ignored.

> excluded BioSQL_MySQLdb BioSQL_psycopg2 which require internet access

The approach is probably correct (I had considered this as well) but the
documentation is wrong since the tests do actually not require internet
access but rather a running local database server which is not ready for
using in the build chroot.  So most probably skipping the tests is the
proper approach but I just commited a better documentation inside the
rules file as well as README.source to make sure we will understand what
we did also in future versions.

Unfortunately some failed test are remaining (and I noticed that you can
only fetch the full log about this via

   pdebuild 2>&1 | tee > ../my_build_log

and only this my_build_log contains things like


Ran 207 tests in 103.129 seconds

FAILED (failures = 3)


but not the default build log. :-(

Did you thought about adding autopkgtest control file?

Kind regards

       Andreas.


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