[Debian-med-packaging] Bug#847082: python-cogent: FTBFS: Fails to build from source with ncbi-data>=6.1.20160908-1

[Andreas Tille]

Package: python-cogent
Severity: serious
Tags: patch
Justification: Policy 1.2.3

Hi,

after ncbi-tools6 version 6.1.20160908-1 was in unstable python-cogent
does not build any more since some tests are failing.  In two cases the
build process needed to be interupted and other test cases and up in
failures:

======================================================================
FAIL: test_blast_against_new_db (test_app.test_formatdb.FormatDbTests)
Formatdb: blastall against a newly created DB functions as expected
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/python-cogent-1.9/tests/test_app/test_formatdb.py", line 89, in test_blast_against_new_db
    "Not getting any blast results.")
AssertionError: Not getting any blast results.

======================================================================
FAIL: test_build_blast_db_from_fasta_file (test_app.test_formatdb.FormatDbTests)
build_blast_db_from_fasta_file works with open files as input
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/python-cogent-1.9/tests/test_app/test_formatdb.py", line 180, in test_build_blast_db_from_fasta_file
    len(blastn(self.test_seq,blast_db=blast_db,e_value=0.0)),1)
  File "/build/python-cogent-1.9/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got 0, but expected 1

======================================================================
FAIL: test_build_blast_db_from_fasta_path (test_app.test_formatdb.FormatDbTests)
build_blast_db_from_fasta_path convenience function works as expected
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/python-cogent-1.9/tests/test_app/test_formatdb.py", line 132, in test_build_blast_db_from_fasta_path
    len(blastn(self.test_seq,blast_db=blast_db)),1)
  File "/build/python-cogent-1.9/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got 0, but expected 1

======================================================================
FAIL: test_build_blast_db_from_fasta_path_aln (test_app.test_formatdb.FormatDbTests)
build_blast_db_from_fasta_path works with alignment as input
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/python-cogent-1.9/tests/test_app/test_formatdb.py", line 155, in test_build_blast_db_from_fasta_path_aln
    len(blastn(self.test_seq,blast_db=blast_db,e_value=0.0)),1)
  File "/build/python-cogent-1.9/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got 0, but expected 1

======================================================================
FAIL: test_build_blast_db_from_seqs (test_app.test_formatdb.FormatDbTests)
build_blast_db_from_seqs convenience function works as expected
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/python-cogent-1.9/tests/test_app/test_formatdb.py", line 107, in test_build_blast_db_from_seqs
    len(blastn(self.test_seq,blast_db=blast_db)),1)
  File "/build/python-cogent-1.9/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got 0, but expected 1

----------------------------------------------------------------------
Ran 3587 tests in 85.818s


The issue is dealt with in packaging SVN currently but this bug is just
opened to document the issue.

Kind regards

      Andreas.

-- System Information:
Debian Release: 8.6
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages python-cogent depends on:
ii  libc6              2.19-18+deb8u6
ii  python             2.7.9-1
pn  python-numpy       <none>
pn  python-numpy-abi9  <none>

python-cogent recommends no packages.

Versions of packages python-cogent suggests:
pn  python-cogent-doc  <none>