Your message dated Fri, 10 Jul 2020 08:33:45 +0000 with message-id <[email protected]> and subject line Bug#964677: fixed in cyvcf2 0.20.1-1 has caused the Debian Bug report #964677, regarding cyvcf2: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 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.) -- 964677: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=964677 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Source: cyvcf2 Version: 0.11.6-2 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20200709 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_3.8_cyvcf2/build; > python3.8 -m nose -v > cyvcf2.tests.test_cli.test_version ... ok > 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_3.8_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.) > ERROR > 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.) > 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.) > 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.) > ERROR > 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.) > 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: cyvcf2.tests.test_reader.test_set_format_float > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/case.py", line 197, in runTest > self.test(*self.arg) > File > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cyvcf2/build/cyvcf2/tests/test_reader.py", > line 592, in test_set_format_float > v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) > File "cyvcf2/cyvcf2.pyx", line 1390, in cyvcf2.cyvcf2.Variant.set_format > raise Exception("format: currently only float and int numpy arrays are > supported. got %s", data.dtype) > Exception: ('format: currently only float and int numpy arrays are supported. > got %s', dtype('float32')) > > ====================================================================== > ERROR: cyvcf2.tests.test_reader.test_set_format_int_c > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/case.py", line 197, in runTest > self.test(*self.arg) > File > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cyvcf2/build/cyvcf2/tests/test_reader.py", > line 616, in test_set_format_int_c > v.set_format("PI", np.array([9998, 99911], dtype=np.int32)) > File "cyvcf2/cyvcf2.pyx", line 1390, in cyvcf2.cyvcf2.Variant.set_format > raise Exception("format: currently only float and int numpy arrays are > supported. got %s", data.dtype) > Exception: ('format: currently only float and int numpy arrays are supported. > got %s', dtype('int32')) > > ---------------------------------------------------------------------- > Ran 73 tests in 0.727s > > FAILED (errors=2) > E: pybuild pybuild:352: test: plugin distutils failed with: exit code=1: cd > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cyvcf2/build; python3.8 -m nose -v > dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 > returned exit code 13 The full build log is available from: http://qa-logs.debian.net/2020/07/09/cyvcf2_0.11.6-2_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: 0.20.1-1 Done: Nilesh Patra <[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. Nilesh Patra <[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: SHA512 Format: 1.8 Date: Thu, 09 Jul 2020 23:17:28 +0530 Source: cyvcf2 Architecture: source Version: 0.20.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Nilesh Patra <[email protected]> Closes: 964677 Changes: cyvcf2 (0.20.1-1) unstable; urgency=medium . * Team Upload. * New upstream version 0.20.1 (Closes: #964677) * Refresh patch and cythonize modules * Do not import numpy during clean * compat version: 13 Checksums-Sha1: 0bb46eac449f50a9715cb63c274c52bcd2cb081b 2253 cyvcf2_0.20.1-1.dsc 382867dfe9bae1e9860845b0cd0cb9e974f28959 400592 cyvcf2_0.20.1.orig.tar.gz 9873795d804c1edee15f708e6f541be8408604d0 5272 cyvcf2_0.20.1-1.debian.tar.xz 2381149938882a434c7e230d237a0415b4073a3b 7822 cyvcf2_0.20.1-1_amd64.buildinfo Checksums-Sha256: 81ce9c6e7a7ec66f89fceaaead31b7887e18309cb709d770a3afc9b1180a29a0 2253 cyvcf2_0.20.1-1.dsc 4df81df2181cf4e51cf5347604e0ec66d10c135dd2bcb77f757c96b4f75128f5 400592 cyvcf2_0.20.1.orig.tar.gz 35f710c9828a8fb3a22bd13c6a3877281d247df07f278a0e59920af975b88dd9 5272 cyvcf2_0.20.1-1.debian.tar.xz bec89a2a0468c2b46407d00a17daf4df558fc1441f439c8c2a5a51e4d8d31e10 7822 cyvcf2_0.20.1-1_amd64.buildinfo Files: 87a577e4d5bb90c96d125edc0a46dd84 2253 science optional cyvcf2_0.20.1-1.dsc 2836cf47a1acfff79aa81b54a2c31984 400592 science optional cyvcf2_0.20.1.orig.tar.gz 43caab6256e9c0a8fb022f85d9e18225 5272 science optional cyvcf2_0.20.1-1.debian.tar.xz 5bba871c2fb510eb73e65cbe7270b769 7822 science optional cyvcf2_0.20.1-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAl8IIIQUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafG9rQ/6Asc+15qdxCyZKzsTAXbaE4215kY4 eCorpGxT04hExMXqJ5ApXjNZth2dJR9OcQZQGbt6Y0h0u/5hDP1PoBYwF89HfPGP fErXYk4Y3miD+HPxn2jOxQi9RVJULOEqQ79iCZeoRUASX3tYQxGb0+khvrD0r2LJ nLZ2lrcxmRLnwEmRKMBlMmEI7wBz8k0LDrfqeE40Hd3hBBWmctPvR8zyYdzPXPyH 4F00Ud+JBQIGBQYup5FV9DE9iaBrkMlUs4J59DK0xeHZ09tLsbtdPukPGyYi/IYm RdTCFrNU4BdrWfJDwUUzP1/njm0TFAsj2iBVWvofgO7p6syFjDWOf5OnFGoSt4Fe +uerot4dlpMi4TJNRja/ZOEH/Pb1GfxBokl+JeSBBYERZjTKoMz+cy95bqXjatb5 CyOJBJIU3wsNMnFB3NQvacGVi+r3quygYSgUnPjbIDPUaSWfNlJUv5EhRuqTDBTi sloZ4Fiyn+Cm29WIIEcmRaCrYSI+yPcb7mpU9WBSkHrUojuUOKWJ6Wdm2s4QrzSn 3n//0HJP1p1zD1m3vZ7o72fMEB4npbvSUaRo1ScLV3bSHjHCjS0RCiDc3z6HVzYl +QCr9LXYHBOERQH8t+lj0931awZDnhHvbecu4tK7Flp8/9diJccrOXqfSdwRINmD XC+AJ2AX0OHAYvQ= =N2Qv -----END PGP SIGNATURE-----
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