Your message dated Mon, 30 Mar 2020 09:03:56 +0000 with message-id <[email protected]> and subject line Bug#954603: fixed in cyvcf2 0.11.6-2 has caused the Debian Bug report #954603, regarding cyvcf2: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.7 3.8" returned exit code 13 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.) -- 954603: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=954603 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Source: cyvcf2 Version: 0.11.6-1 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20200321 ftbfs-bullseye Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>' > dh_auto_test > I: pybuild base:217: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build; > python3.7 -m nose -v > Failure: ModuleNotFoundError (No module named 'humanfriendly.terminal') ... > ERROR > make sure that we are getting the correct gt_types ... ok > cyvcf2.tests.test_reader.test_init ... ok > cyvcf2.tests.test_reader.test_type ... ok > cyvcf2.tests.test_reader.test_format_str ... [W::vcf_parse] Contig '7' is not > defined in the header. (Quick workaround: index the file with tabix.) > ok > cyvcf2.tests.test_reader.test_missing_samples ... ok > cyvcf2.tests.test_reader.test_ibd ... ok > cyvcf2.tests.test_reader.test_relatedness ... tested: 44 variants out of 115 > ok > cyvcf2.tests.test_reader.test_pls ... ok > cyvcf2.tests.test_reader.test_gt_alt_freqs ... ok > cyvcf2.tests.test_reader.test_str ... ok > cyvcf2.tests.test_reader.test_region ... ok > cyvcf2.tests.test_reader.test_empty_info ... ok > cyvcf2.tests.test_reader.test_phases ... ok > cyvcf2.tests.test_reader.test_bad_init ... [E::hts_open_format] Failed to > open file "XXXXX" : No such file or directory > ok > cyvcf2.tests.test_reader.test_samples ... ok > cyvcf2.tests.test_reader.test_next ... ok > cyvcf2.tests.test_reader.test_variant ... ok > cyvcf2.tests.test_reader.test_info_dict ... ok > cyvcf2.tests.test_reader.test_attrs ... ok > cyvcf2.tests.test_reader.test_empty ... ok > cyvcf2.tests.test_reader.test_format_field ... ok > cyvcf2.tests.test_reader.test_writer_from_string ... [W::vcf_parse] Contig > 'chr1' is not defined in the header. (Quick workaround: index the file with > tabix.) > ok > cyvcf2.tests.test_reader.test_writer ... ok > cyvcf2.tests.test_reader.test_add_info_to_header ... ok > cyvcf2.tests.test_reader.test_read_flag ... ok > cyvcf2.tests.test_reader.test_add_flag ... ok > cyvcf2.tests.test_reader.test_constants ... ok > cyvcf2.tests.test_reader.test_add_filter_to_header ... ok > cyvcf2.tests.test_reader.test_seqnames ... ok > cyvcf2.tests.test_reader.test_different_index ... ok > cyvcf2.tests.test_reader.test_var_type ... ok > cyvcf2.tests.test_reader.test_header_info ... ok > cyvcf2.tests.test_reader.test_snpeff_header ... ok > cyvcf2.tests.test_reader.test_gt_types ... ok > cyvcf2.tests.test_reader.test_raw_header ... ok > cyvcf2.tests.test_reader.test_iterate ... ok > cyvcf2.tests.test_reader.test_empty_call ... ok > cyvcf2.tests.test_reader.test_haploid ... ok > cyvcf2.tests.test_reader.test_diploid ... ok > cyvcf2.tests.test_reader.test_format ... ok > cyvcf2.tests.test_reader.test_header_stuff ... ok > cyvcf2.tests.test_reader.test_bcf ... > OK > no intervals found for > b'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf' > at 1:69260-69438 > ok > cyvcf2.tests.test_reader.test_issue12 ... [W::vcf_parse] Contig '7' is not > defined in the header. (Quick workaround: index the file with tabix.) > ok > Ensure gt_bases works with more complex base representations. ... ok > cyvcf2.tests.test_reader.test_set_format_float ... [W::vcf_parse] Contig '7' > is not defined in the header. (Quick workaround: index the file with tabix.) > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:586: > FutureWarning: Conversion of the second argument of issubdtype from `int` to > `np.signedinteger` is deprecated. In future, it will be treated as `np.int64 > == np.dtype(int).type`. > v.set_format("PS", np.array([0.555, 1.111], dtype=np.float)) > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:586: > FutureWarning: Conversion of the second argument of issubdtype from `float` > to `np.floating` is deprecated. In future, it will be treated as `np.float64 > == np.dtype(float).type`. > v.set_format("PS", np.array([0.555, 1.111], dtype=np.float)) > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:589: > FutureWarning: Conversion of the second argument of issubdtype from `int` to > `np.signedinteger` is deprecated. In future, it will be treated as `np.int64 > == np.dtype(int).type`. > v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:589: > FutureWarning: Conversion of the second argument of issubdtype from `float` > to `np.floating` is deprecated. In future, it will be treated as `np.float64 > == np.dtype(float).type`. > v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:592: > FutureWarning: Conversion of the second argument of issubdtype from `int` to > `np.signedinteger` is deprecated. In future, it will be treated as `np.int64 > == np.dtype(int).type`. > v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:592: > FutureWarning: Conversion of the second argument of issubdtype from `float` > to `np.floating` is deprecated. In future, it will be treated as `np.float64 > == np.dtype(float).type`. > v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) > ok > cyvcf2.tests.test_reader.test_set_format_int_a ... [W::vcf_parse] Contig '7' > is not defined in the header. (Quick workaround: index the file with tabix.) > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:600: > FutureWarning: Conversion of the second argument of issubdtype from `int` to > `np.signedinteger` is deprecated. In future, it will be treated as `np.int64 > == np.dtype(int).type`. > v.set_format("PI", np.array([5, 1], dtype=np.int)) > ok > cyvcf2.tests.test_reader.test_set_format_int_b ... [W::vcf_parse] Contig '7' > is not defined in the header. (Quick workaround: index the file with tabix.) > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:608: > FutureWarning: Conversion of the second argument of issubdtype from `int` to > `np.signedinteger` is deprecated. In future, it will be treated as `np.int64 > == np.dtype(int).type`. > v.set_format("PI", np.array([855, 11], dtype=np.int64)) > ok > cyvcf2.tests.test_reader.test_set_format_int_c ... [W::vcf_parse] Contig '7' > is not defined in the header. (Quick workaround: index the file with tabix.) > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:616: > FutureWarning: Conversion of the second argument of issubdtype from `int` to > `np.signedinteger` is deprecated. In future, it will be treated as `np.int64 > == np.dtype(int).type`. > v.set_format("PI", np.array([9998, 99911], dtype=np.int32)) > ok > test that we can handle multiple (in this case 3) values per sample ... > [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: > index the file with tabix.) > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:626: > FutureWarning: Conversion of the second argument of issubdtype from `int` to > `np.signedinteger` is deprecated. In future, it will be treated as `np.int64 > == np.dtype(int).type`. > v.set_format("P3", exp) > ok > cyvcf2.tests.test_reader.test_set_gts ... [W::vcf_parse] Contig '7' is not > defined in the header. (Quick workaround: index the file with tabix.) > ok > cyvcf2.tests.test_reader.test_info_del ... ok > cyvcf2.tests.test_reader.test_filter_id ... ok > cyvcf2.tests.test_reader.test_access_gts ... [W::vcf_parse] Contig '7' is not > defined in the header. (Quick workaround: index the file with tabix.) > ok > cyvcf2.tests.test_reader.test_access_genotype ... [W::vcf_parse] Contig '7' > is not defined in the header. (Quick workaround: index the file with tabix.) > ok > cyvcf2.tests.test_reader.test_alt_homozygous_gt ... ok > cyvcf2.tests.test_reader.test_write_missing_contig ... [W::vcf_parse] Contig > '1' is not defined in the header. (Quick workaround: index the file with > tabix.) > ok > cyvcf2.tests.test_reader.test_set_samples ... ok > cyvcf2.tests.test_reader.test_hrec ... ok > cyvcf2.tests.test_reader.test_issue44 ... ok > cyvcf2.tests.test_reader.test_id_field_updates ... ok > cyvcf2.tests.test_reader.test_set_pos ... ok > cyvcf2.tests.test_reader.test_set_qual ... ok > cyvcf2.tests.test_reader.test_strict_gt_option_flag ... ok > cyvcf2.tests.test_reader.test_alt_repr ... ok > cyvcf2.tests.test_reader.test_closed_iter ... ok > cyvcf2.tests.test_reader.test_issue72 ... ok > cyvcf2.tests.test_reader.test_is_transition ... ok > cyvcf2.tests.test_reader.test_decomposed ... ok > cyvcf2.tests.test_reader.test_fd ... ok > cyvcf2.tests.test_reader.test_set_reference ... ok > cyvcf2.tests.test_reader.test_set_alternates ... ok > cyvcf2.tests.test_reader.test_no_seqlen ... ok > > ====================================================================== > ERROR: Failure: ModuleNotFoundError (No module named 'humanfriendly.terminal') > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest > raise self.exc_val.with_traceback(self.tb) > File "/usr/lib/python3/dist-packages/nose/loader.py", line 417, in > loadTestsFromName > addr.filename, addr.module) > File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in > importFromPath > return self.importFromDir(dir_path, fqname) > File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in > importFromDir > mod = load_module(part_fqname, fh, filename, desc) > File "/usr/lib/python3.7/imp.py", line 234, in load_module > return load_source(name, filename, file) > File "/usr/lib/python3.7/imp.py", line 171, in load_source > module = _load(spec) > File "<frozen importlib._bootstrap>", line 696, in _load > File "<frozen importlib._bootstrap>", line 677, in _load_unlocked > File "<frozen importlib._bootstrap_external>", line 728, in exec_module > File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed > File > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_cli.py", > line 6, in <module> > from cyvcf2.cli import cyvcf2 > File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cli.py", > line 4, in <module> > import coloredlogs > File "/usr/lib/python3/dist-packages/coloredlogs/__init__.py", line 192, in > <module> > from humanfriendly.terminal import ANSI_COLOR_CODES, ansi_wrap, > terminal_supports_colors > ModuleNotFoundError: No module named 'humanfriendly.terminal' > > ---------------------------------------------------------------------- > Ran 73 tests in 0.723s > > FAILED (errors=1) > E: pybuild pybuild:352: test: plugin distutils failed with: exit code=1: cd > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cyvcf2/build; python3.7 -m nose -v > dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.7 > 3.8" returned exit code 13 The full build log is available from: http://qa-logs.debian.net/2020/03/21/cyvcf2_0.11.6-1_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
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--- Begin Message ---Source: cyvcf2 Source-Version: 0.11.6-2 Done: Andreas Tille <[email protected]> We believe that the bug you reported is fixed in the latest version of cyvcf2, 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 cyvcf2 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, 30 Mar 2020 10:00:07 +0200 Source: cyvcf2 Architecture: source Version: 0.11.6-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Closes: 954603 Changes: cyvcf2 (0.11.6-2) unstable; urgency=medium . * Team upload. * Bug #954640 of python3-humanfriendly was fixed Closes: #954603 * Add salsa-ci file (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. Checksums-Sha1: e49c544e7c6cd5f930c69cfe675df7ade9a6105d 2249 cyvcf2_0.11.6-2.dsc a40732e17e7084fa1d1f8c3594198f05741ce629 4544 cyvcf2_0.11.6-2.debian.tar.xz ee4bd66770b44776b36715abb8b41c443cbd5a27 8022 cyvcf2_0.11.6-2_amd64.buildinfo Checksums-Sha256: fef2da065a0f016ac415faace3f1244b315f63a61fb75c77d2c8d2177b52eda8 2249 cyvcf2_0.11.6-2.dsc 7a3f9a26dc19628b790979551448f25a10ca4c29f282d57bb83d97fe986b4c29 4544 cyvcf2_0.11.6-2.debian.tar.xz 4ce36c97b8c5dfff455e88f0b7774b11615045fc0aa6a59f77f3708bf0a88cf1 8022 cyvcf2_0.11.6-2_amd64.buildinfo Files: d0ab30f74a9f95754e9cf6a58c205897 2249 science optional cyvcf2_0.11.6-2.dsc 3a1f86c9c49db5975fa87a978f58caff 4544 science optional cyvcf2_0.11.6-2.debian.tar.xz 57a7427b57f3c958d804f0684e10cf2d 8022 science optional cyvcf2_0.11.6-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl6BsmYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGwLw//afPxwJ+YY+PN7c14kTExG7amNekazTSb 2LQ2iJZAdx+QZ0TuamrgT4+hNxMBo7Kd2pmT3xPKDSE0EKeYiPxMIdedegZ0Rigs 2GfCAH3zqxi34XYjn4ZGTSSoBDSpYZPTItEhj6uVIUhEFOcDoOCKTMIeUMsX0T4j ViO4+LnTKGGMX8FZaPYCYS+jzizln+4cFfzKPxmtACysfndkWuTVmky11dOJJGPh hkiETT2lLp0touC9N2C+YOoiEqZVke10G3hgDNCHeYHVuYIt8TMKYCDJ7BlSQ7tL 0NKPXmfQv7K+PcbJMwvaq+0fp+JQtIjWzx5HkPXE1H2/fjU3/YraKZ9G6BnSc4Mp ff7xSd7OF45gnkzDpKqKbpi2XOVx3t54k+ZMJ7cnei20EZK4rVyJRUueMDKw5es4 V7q4Qfq73aUPnJ6OywtdgpOFOJz+NNNzsVGKfeSI+n/yyRZM0WODaKaAfWMuDA3n MA6T2fpj7zdWxW7SpPIwjpUyoze666chW3MRH/0hmCbNsjFH9VV3JOVmVBifEQ24 kNKnhjqIeaII33q3K1/hH0wdnTF6hdPx6H+NAK1O3joPUI0AUcTRDQOjZd2ioMOI byQmm3M2+XOYYOAWr2h7KzsJ6JOzZKvtNystodlK1YuASmnAenhOmtHydct9Xzqz MXPSI7JlmpQ= =ayjO -----END PGP SIGNATURE-----
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