Your message dated Mon, 30 Mar 2020 09:03:56 +0000
with message-id <e1jiqkq-0006gp...@fasolo.debian.org>
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 ow...@bugs.debian.org
immediately.)
--
954603: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=954603
Debian Bug Tracking System
Contact ow...@bugs.debian.org 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.
--- End Message ---
--- Begin Message ---
Source: cyvcf2
Source-Version: 0.11.6-2
Done: Andreas Tille <ti...@debian.org>
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 954...@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 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 ftpmas...@ftp-master.debian.org)
-----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
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
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
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--- End Message ---
