Your message dated Wed, 14 Sep 2016 16:29:41 +0000
with message-id <e1bkd49-00013c...@franck.debian.org>
and subject line Bug#835213: fixed in python-cogent 1.9-1
has caused the Debian Bug report #835213,
regarding python-cogent: FTBFS in testing (AssertionError)
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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misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
835213: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=835213
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:python-cogent
Version: 1.5.3-10
Severity: serious
Dear maintainer:
I tried to build this package in stretch with "dpkg-buildpackage -A"
(which is what the "Arch: all" autobuilder would do to build it)
but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-indep
dh build-indep --with python2 --buildsystem=pybuild
dh_testdir -i -O--buildsystem=pybuild
dh_update_autotools_config -i -O--buildsystem=pybuild
dh_auto_configure -i -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py config
running config
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
I: pybuild base:184: /usr/bin/python setup.py build
running build
running build_py
[... snipped ...]
File "/<<PKGBUILDDIR>>/cogent/util/unit_test.py", line 316, in failUnlessEqual
(msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got [['cdhit_test_seqs_0'], ['cdhit_test_seqs_1'],
['cdhit_test_seqs_2'], ['cdhit_test_seqs_3'], ['cdhit_test_seqs_4'],
['cdhit_test_seqs_5'], ['cdhit_test_seqs_6'], ['cdhit_test_seqs_7'],
['cdhit_test_seqs_8'], ['cdhit_test_seqs_9']], but expected
[['cdhit_test_seqs_0'], ['cdhit_test_seqs_1'], ['cdhit_test_seqs_2'],
['cdhit_test_seqs_3'], ['cdhit_test_seqs_4'], ['cdhit_test_seqs_5'],
['cdhit_test_seqs_6', 'cdhit_test_seqs_8'], ['cdhit_test_seqs_7'],
['cdhit_test_seqs_9']]
======================================================================
FAIL: test_base_command (test_app.test_cd_hit.CD_HIT_Tests)
CD_HIT BaseCommand should return the correct BaseCommand
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/tests/test_app/test_cd_hit.py", line 25, in
test_base_command
''.join(['cd "',getcwd(),'/"; ','cdhit']))
File "/<<PKGBUILDDIR>>/cogent/util/unit_test.py", line 316, in failUnlessEqual
(msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got 'cd "/<<PKGBUILDDIR>>/tests/"; cd-hit', but expected 'cd
"/<<PKGBUILDDIR>>/tests/"; cdhit'
======================================================================
FAIL: test_cdhit_from_seqs (test_app.test_cd_hit.CD_HIT_Tests)
CD_HIT should return expected seqs
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/tests/test_app/test_cd_hit.py", line 52, in
test_cdhit_from_seqs
self.assertEqual(res.toFasta(), protein_expected)
File "/<<PKGBUILDDIR>>/cogent/util/unit_test.py", line 316, in failUnlessEqual
(msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got
'>seq1\nMGNKWSKSWPQVRDRMRRAAPAPAADGVGAVSQDLAKHGAITSSNTAATNDDCAWLEAQTEEEVGFPVRPQVPLRPMTYK\n>seq2\nMGGKWSKSSIVGWSTVRERMRKTPPAADGVGAVSQDLDKHGAVTSSNTAFNNPDCAWLEAQEDEDVGFPVRPQVPLRPT\n>seq3\nMGGKWSKSSIVGWPAIRERMRRARPAADRVGTQPAADGVGAVSQDLARHGAVTSSNTSHNNPDCAWLEAQEEEEVGVR\n>seq4\nMGKIWSKSSIVGWPEIRERMRRQRPHEPAVEPAVGVGAASQDLANRGALTTSNTRTNNPTVAWVEAQEEEGEVVRPQ\n>seq6\nMGKIWSKSSLVGWPEIRERIRRQTPEPAVGVGAVSQDLANRGAITTSNTKDNNQTVAWLEAQEEPVRPQVPLRPM\n>seq7\nMGNALRKGKFEGWAAVRERMRRTRTFPESEPCAPGVGQISRELAARGGIPSSHTPQNNESHQEEEVGFPVAPQV\n>seq8\nMGNAWSKSKFAGWSEVRDRMRRSSSDPQQPCAPGVGAVSRELATRGGISSSALAFLDSHKDEDVGFPVRPQVP\n>seq9\nMGNVLGKDKFKGWAAVRERMRKTSSDPDPQPCAPGVGPVSRELSYTPQNNAALAFLESHEDEDVGFPVXPQV',
but expected
'>seq1\nMGNKWSKSWPQVRDRMRRAAPAPAADGVGAVSQDLAKHGAITSSNTAATNDDCAWLEAQTEEEVGFPVRPQVPLRPMTYK\n>seq2\nMGGKWSKSSIVGWSTVRERMRKTPPAADGVGAVSQDLDKHGAVTSSNTAFNNPDCAWLEAQEDEDVGFPVRPQVPLRPT\n>seq3\nMGGKWSKSSIVGWPAIRERMRRARPAADRVGTQPAADGVGAVSQDLARHGAVTSSNTSHNNPDCAWLEAQEEEEVGVR\n>seq4\nMGKIWSKSSIV
GWPEIRERMRRQRPHEPAVEPAVGVGAASQDLANRGALTTSNTRTNNPTVAWVEAQEEEGEVVRPQ\n>seq5\nMGKIWSKSSLVGWPEIRERMRRQTQEPAVEPAVGAGAASQDLANRGAITIRNTRDNNESIAWLEAQEEEFPVRPQV\n>seq7\nMGNALRKGKFEGWAAVRERMRRTRTFPESEPCAPGVGQISRELAARGGIPSSHTPQNNESHQEEEVGFPVAPQV\n>seq8\nMGNAWSKSKFAGWSEVRDRMRRSSSDPQQPCAPGVGAVSRELATRGGISSSALAFLDSHKDEDVGFPVRPQVP\n>seq9\nMGNVLGKDKFKGWAAVRERMRKTSSDPDPQPCAPGVGPVSRELSYTPQNNAALAFLESHEDEDVGFPVXPQV'
======================================================================
FAIL: test_changing_working_dir (test_app.test_cd_hit.CD_HIT_Tests)
CD_HIT BaseCommand should change according to WorkingDir
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/tests/test_app/test_cd_hit.py", line 38, in
test_changing_working_dir
''.join(['cd "','/tmp/cdhit_test','/"; ','cdhit']))
File "/<<PKGBUILDDIR>>/cogent/util/unit_test.py", line 316, in failUnlessEqual
(msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got 'cd "/tmp/cdhit_test/"; cd-hit', but expected 'cd
"/tmp/cdhit_test/"; cdhit'
----------------------------------------------------------------------
Ran 3518 tests in 60.189s
FAILED (failures=6)
debian/rules:71: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules:38: recipe for target 'build-indep' failed
make: *** [build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2
--------------------------------------------------------------------------------
The failure seems reproducible and it started to happen in stretch
at some point between 2016-08-17 and 2016-08-23.
The way it fails may be related to Bug #730515.
Once you manage to fix this, please consider uploading in source-only form,
so that we get pretty official build logs here:
https://buildd.debian.org/status/package.php?p=python-cogent
Thanks.
--- End Message ---
--- Begin Message ---
Source: python-cogent
Source-Version: 1.9-1
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 835...@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: Wed, 14 Sep 2016 17:06:59 +0200
Source: python-cogent
Binary: python-cogent python-cogent-doc
Architecture: source amd64 all
Version: 1.9-1
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: 835213
Changes:
python-cogent (1.9-1) unstable; urgency=medium
.
* New upstream version
* Fix watch file
* Fix homepage
* cme fix dpkg-control
* Build-Depends: python-setuptools
* revert cd-hit name change in Debian
Closes: #835213
* hardening=+bindnow
* Build-Depends: cdbfasta
Checksums-Sha1:
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c1f0e572491d2c5d9f4ac95bd587dcc5d92e43c8 10676
python-cogent_1.9-1.debian.tar.xz
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python-cogent-dbgsym_1.9-1_amd64.deb
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python-cogent-doc_1.9-1_all.deb
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Checksums-Sha256:
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python-cogent_1.9-1.dsc
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python-cogent_1.9.orig.tar.gz
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python-cogent_1.9-1.debian.tar.xz
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python-cogent-dbgsym_1.9-1_amd64.deb
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python-cogent-doc_1.9-1_all.deb
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Files:
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e5b3354a5fe72fbdd56e9141da1e774e 3744597 python optional
python-cogent_1.9.orig.tar.gz
037a7f4e39efa1e9c63e103304056656 10676 python optional
python-cogent_1.9-1.debian.tar.xz
0c1b14e719b38e6b8a8b90356409b945 937040 debug extra
python-cogent-dbgsym_1.9-1_amd64.deb
eb49a948d1a52e8a3d6eadd695491f0f 2930354 doc optional
python-cogent-doc_1.9-1_all.deb
9325d4331bf6cfc623633e094eb850db 1059182 python optional
python-cogent_1.9-1_amd64.deb
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