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>
