[Debian-med-packaging] Bug#775621: python-biopython: FTBFS in jessie: Tests failures

[Lucas Nussbaum]

Source: python-biopython
Version: 1.64+dfsg-5
Severity: serious
Tags: jessie sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20150117 qa-ftbfs
Justification: FTBFS in jessie on amd64

Hi,

During a rebuild of all packages in jessie (in a jessie chroot, not a
sid chroot), your package failed to build on amd64.

Relevant part (hopefully):
> E: pybuild pybuild:256: test: plugin custom failed with: exit code=1: set -e; \
>                              mkdir -p /«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/home; \
>                              mkdir -p /«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
>                              cp -a Doc/Tutorial.tex /«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
>                              cp -a Tests /«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build; \
>                              cd /«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests; \
>                              env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/home python2.7 run_tests.py --offline
> dh_auto_test: pybuild --test -i python{version} -p 2.7 --test --system=custom --test-args=set -e; \
>                              mkdir -p {build_dir}/home; \
>                              mkdir -p {build_dir}/Doc; \
>                              cp -a Doc/Tutorial.tex {build_dir}/Doc; \
>                              cp -a Tests {build_dir}; \
>                              cd {build_dir}/Tests; \
>                              env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline --dir . returned exit code 13
> make[1]: *** [override_dh_auto_test] Error 13
> debian/rules:71: recipe for target 'override_dh_auto_test' failed

The full build log is available from:
   http://aws-logs.debian.net/ftbfs-logs/2015/01/17/python-biopython_1.64+dfsg-5_jessie.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.