[Debian-med-packaging] Bug#964677: cyvcf2: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 returned exit code 13

[Lucas Nussbaum]

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.