[Debian-med-packaging] Bug#820621: python-biom-format: FTBFS when built with dpkg-buildpackage -A (build-indep fails)

[Santiago Vila]

Package: src:python-biom-format
Version: 2.1.5+dfsg-1
User: sanvila at debian.org
Usertags: binary-indep
Severity: important

Dear maintainer:

I tried to build this package with "dpkg-buildpackage -A"
(i.e. only architecture-independent packages), and it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep --with python2,python3,bash-completion --buildsystem=pybuild
   dh_testdir -i -O--buildsystem=pybuild
   dh_update_autotools_config -i -O--buildsystem=pybuild
   dh_auto_configure -i -O--buildsystem=pybuild
	pybuild --configure --test-nose -i python{version} -p 2.7 --dir .
I: pybuild base:184: python2.7 setup.py config 
running config
	pybuild --configure --test-nose -i python{version} -p 3.5 --dir .
I: pybuild base:184: python3.5 setup.py config 
running config
   debian/rules override_dh_auto_build-indep

[... snipped ...]


======================================================================
ERROR: Failure: ImportError (No module named biom.parse)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build/tests/test_parse.py", line 19, in <module>
    from biom.parse import generatedby, MetadataMap, parse_biom_table, parse_uc
ImportError: No module named biom.parse

======================================================================
ERROR: Failure: ImportError (No module named biom)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build/tests/test_table.py", line 23, in <module>
    from biom import example_table
ImportError: No module named biom

======================================================================
ERROR: Failure: ImportError (No module named biom.table)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build/tests/test_util.py", line 20, in <module>
    from biom.table import Table
ImportError: No module named biom.table

----------------------------------------------------------------------
Ran 11 tests in 0.002s

FAILED (errors=11)
E: pybuild pybuild:274: test: plugin distutils failed with: exit code=1: cd /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose tests
dh_auto_test: pybuild --test --test-nose -i python{version} -p 2.7 --dir . returned exit code 13
debian/rules:14: recipe for target 'build-indep' failed
make: *** [build-indep] Error 25
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2
--------------------------------------------------------------------------------

To reproduce, please build the package with "dpkg-buildpackage -A".

That should create python-biom-format-doc_2.1.5+dfsg-1_all.deb
and only such package.

Thanks.