Your message dated Mon, 05 Dec 2016 15:23:21 +0000 with message-id <[email protected]> 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 message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 847082: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=847082 Debian Bug Tracking System Contact [email protected] 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>
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--- 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 [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: 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 <[email protected]> Changed-By: Andreas Tille <[email protected]> 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 Checksums-Sha1: d77cd935345c7a9e6f4258c2a52f730187323237 2431 python-cogent_1.9-7.dsc 83595e4fdc0f9d1b088d9cb05ccf75fbdcb93538 16612 python-cogent_1.9-7.debian.tar.xz 781298aae100cd92fca36be34af752e353cd11c9 955358 python-cogent-dbgsym_1.9-7_amd64.deb 39bd0bdd2daef479e22eea070183804360da763d 2929484 python-cogent-doc_1.9-7_all.deb 78530b719d7f817b10449eeae776043fe2832b84 11976 python-cogent_1.9-7_amd64.buildinfo e9a37f0df3a3bb5a9fccc138db589cffcbb164c6 1063138 python-cogent_1.9-7_amd64.deb Checksums-Sha256: 7a60d1864ea2cf150f4842e43cbff78dd942f67b4eb3462fbc19090c8e86d034 2431 python-cogent_1.9-7.dsc 0a9124b410ac6e08bd48fd39215b732614432224c7331c2240eb73ac4a45d49b 16612 python-cogent_1.9-7.debian.tar.xz c43abcafd11ff4b8d015d5d93312bdb4ef06dfd4412d43394e069e451e4c0e8d 955358 python-cogent-dbgsym_1.9-7_amd64.deb 9d50593cc898b76c8fb67c465edb91114b5e239d36c31623619e9cd447953ee9 2929484 python-cogent-doc_1.9-7_all.deb 0f279446ab5af7f5437f66c91cfb0ca956b80e9c2715d32a0a694aae5ce3449a 11976 python-cogent_1.9-7_amd64.buildinfo 827528a1d76d1feb8ef389277e8017d70262fbe5a01f34b1a61910c508561aff 1063138 python-cogent_1.9-7_amd64.deb Files: fc3c5bf9e7faa9c773a20a0adc8f9826 2431 python optional python-cogent_1.9-7.dsc b69a85cb442782e437d7239db90b6ce9 16612 python optional python-cogent_1.9-7.debian.tar.xz dc61918e654fd6c6ce05d1f4ba1040cb 955358 debug extra python-cogent-dbgsym_1.9-7_amd64.deb 76d9c85b7ba4aa194d1dbd90f421ca62 2929484 doc optional python-cogent-doc_1.9-7_all.deb e4114fc6ebb16036bf1678eeddb49df6 11976 python optional python-cogent_1.9-7_amd64.buildinfo 7b8873b8135dedad0d1d0e4d69a607d2 1063138 python optional python-cogent_1.9-7_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJYRXTMAAoJEFeKBJTRxkbRfnIQAIbaLTMnVWPbwpMNDhk3IsyT QhHi7eLknC1cDFEDCg0O75Uem2I5E2+Cp2ffIcKkv6aWuc9s9TNzhGeTad9oIniU ex8YeDIzH72CPXnAsuD1j7sj52N7lEhcrDKeAWLwgqSfiBjf+28oUfPFTVVzi8fu 1e5yrhNn8JrTngLW826kifscVZ5G+PqDoKqPInZrNghpvYOUE3ZOo8KK0zxIIJQp 0lL3eZO6h1ti2IrASfX11uFswwasQhOXpKMNgW5UDX27XWfGxfRve2Os2CJe2jRP bG+ufkk0Vf7b1glI1C4kLqVL3aXWum6/K1MfX/yXFL/zaGyEvGoyshd3CFTqYsqG w1Iac4RuVR0qW0d4PsdJisrYq213MX6FuPKO/a28PrpT3qXsnoPhBZK2gnX7jFps KAiLJRvdr9Ls/fZ5PYRcE+bsO8qvXYZogjqTqxMzQV+njIdGMvOZ19aIJvw4ZbNv R5QiV1/o2AJOaq1CUZtqed0HFfGfmK0R9m3ozfc+j9yq4Ow9Y/2V2SuYQtFR9Ao4 JR5+ciIr/uKodwDkTfivo6JXH600CJmhdH+yC/iz3qr6xFaiyoiOASM3D03E1kcl d1ooWd4CfOhEYOS9se9DhGem98jZ7jVMguM9vUipfHPS+5hcSN+sluECxEm9ihtv y76DJFsA7b+WAwnNFrme =4PmT -----END PGP SIGNATURE-----
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