Your message dated Wed, 14 Sep 2016 16:29:41 +0000 with message-id <[email protected]> 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 message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 835213: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=835213 Debian Bug Tracking System Contact [email protected] 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.
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--- 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (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 [email protected]) -----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 <[email protected]> Changed-By: Andreas Tille <[email protected]> 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: dec932fa6c6f3b7fe4ae79ff1d32b4e2488254b6 2395 python-cogent_1.9-1.dsc 09f922195a2a3170fb29e52ee1a0d01f7c7edd12 3744597 python-cogent_1.9.orig.tar.gz c1f0e572491d2c5d9f4ac95bd587dcc5d92e43c8 10676 python-cogent_1.9-1.debian.tar.xz 0acb73532f753bb292f562ecfb7453583bf849c7 937040 python-cogent-dbgsym_1.9-1_amd64.deb 7a314ad63a7ad337ffb515666f8c6bad659ba402 2930354 python-cogent-doc_1.9-1_all.deb 2b967801649815b43fc7eae5969a46e867b9217c 1059182 python-cogent_1.9-1_amd64.deb Checksums-Sha256: 8d0cc2931271a5228a5f44d021978198c7d70127f4a63c6c0d66ac47584c6e33 2395 python-cogent_1.9-1.dsc c9f56d21d764aa62e3e8a9df5a300eb7fb59e502572bec41894d21df19aeceb5 3744597 python-cogent_1.9.orig.tar.gz d5a85879a3d7d220468737c5b19463f864c15d79bd2e8790d28c36c46c1cd48d 10676 python-cogent_1.9-1.debian.tar.xz 12fcd16c3d3caba294994021d33f124aa9a0d46188414baaa223b7aaddf0b617 937040 python-cogent-dbgsym_1.9-1_amd64.deb fd9b7e339860db50a6a3737bca05b78c0a549c81a16b3f05b04f1dde503f05a0 2930354 python-cogent-doc_1.9-1_all.deb e9aa30908d6fcbc263bc3d102d5ea998612273c14f5b285e2a198a93af266dca 1059182 python-cogent_1.9-1_amd64.deb Files: 1db91c75e51749eadd107cffcdcd8857 2395 python optional python-cogent_1.9-1.dsc 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJX2WkLAAoJEFeKBJTRxkbRRSMQAJrjLmAmc1Mi/nJLge8ehQpo FhIFOXMm1gKyQ7/bhjocbnDoMT4Xs7E+xQsDVRG39vS/L+r59MQABRO1BP9DtAwu snwuNxuRykQF1ROTzGNscp6l7h+quuYAfY02kG3BbkCtmWxqc+c72noZf10drVGv n1X912llgpRBtLw2oD9iRDSyi8mxObLX0BwVdaPejwvvNbvQyUM+cxkMz39Ha6rS rZISSb+Bq5uHfr/tssAKlO7aHSjsWlc+U0luE1uiIVXofpZnP8GGGEUvKZUNiTYT INQsVNFhVwajJpW4f4euxwJWEz1H6o5goGL10Xso1k8aXYsjCnIAEzH2TD48Prg8 DdNak1/KdGqHsxA96FSlEM3Z3i6nP58D66kV6v6kInKytEqs2yxgAKiIzih0LxXD b7eggFB+vBVu3u0AfaS6PFxWbKkil4rGb+nxFKrTVziRhoZDegKU4AqMulvubzbC ZNXAX/KMEWAmHIixdUtzICkiR/wH2lethRUYgvBhlTlbG9+90D/noqXok9fYnIFw z1gVnPLJXb1N8o3hdLLTRFUNfXhq1JunJTLimdzZL0RmvKbDlQ5fF0cgahjq3XOS W+Di3bN7+OtutV443cpzOAhcGkntEwK0EOjgoNgq1abVG0/3vlhU+7hepWcNyRfq HWc5Iz6yHT8vma/0pDwi =wAwQ -----END PGP SIGNATURE-----
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