Your message dated Mon, 05 Dec 2016 15:23:21 +0000
with message-id <e1cdv6v-00062q...@fasolo.debian.org>
and subject line Bug#847082: fixed in python-cogent 1.9-7
has caused the Debian Bug report #847082,
regarding python-cogent: FTBFS: Fails to build from source with
ncbi-data>=6.1.20160908-1
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
847082: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=847082
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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>
--- End Message ---
--- Begin Message ---
Source: python-cogent
Source-Version: 1.9-7
We believe that the bug you reported is fixed in the latest version of
python-cogent, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 847...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated python-cogent package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 05 Dec 2016 11:32:17 +0100
Source: python-cogent
Binary: python-cogent python-cogent-doc
Architecture: source amd64 all
Version: 1.9-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
python-cogent - framework for genomic biology
python-cogent-doc - docs for python-cogent
Closes: 847082
Changes:
python-cogent (1.9-7) unstable; urgency=medium
.
* Skip more tests to enable build on mips & mips64el
* Skip tests that are not working any more since ncbi-tools6 >=6.1.20160908-1
Closes: #847082
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