Your message dated Sun, 22 Dec 2019 07:19:13 +0000
with message-id <e1iivwd-0004u1...@fasolo.debian.org>
and subject line Bug#943622: fixed in python-biom-format 2.1.7+dfsg-5
has caused the Debian Bug report #943622,
regarding some python-biom-format tests fail with python3.8
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.
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--
943622: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=943622
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:python-biom-format
Version: 2.1.7+dfsg-3
Severity: important
Tags: sid bullseye
User: debian-pyt...@lists.debian.org
Usertags: python3.8
======================================================================
ERROR: Test an invalid HDF5 table
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/numpy/testing/_private/decorators.py",
line 155, in skipper_func
return f(*args, **kwargs)
File
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_validate_table.py",
line 88, in test_invalid_hdf5
copy(self.hdf5_file_valid, 'invalid.hdf5')
File "/usr/lib/python3.8/shutil.py", line 409, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/usr/lib/python3.8/shutil.py", line 259, in copyfile
with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory:
'/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/examples/min_sparse_otu_table_hdf5.biom'
======================================================================
ERROR: Test a valid HDF5 table
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/numpy/testing/_private/decorators.py",
line 155, in skipper_func
return f(*args, **kwargs)
File
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_validate_table.py",
line 79, in test_valid_hdf5
obs = self.cmd(table=self.hdf5_file_valid)
File
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py",
line 112, in __call__
return self.run(table=table, format_version=format_version,
File
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py",
line 78, in run
is_json = not is_hdf5_file(kwargs['table'])
File
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/util.py",
line 518, in is_hdf5_file
with open(fp, 'rb') as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/examples/min_sparse_otu_table_hdf5.biom'
======================================================================
ERROR: test_valid_hdf5_metadata_v210
(biom.tests.test_cli.test_validate_table.TableValidatorTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/numpy/testing/_private/decorators.py",
line 155, in skipper_func
return f(*args, **kwargs)
File
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_validate_table.py",
line 62, in test_valid_hdf5_metadata_v210
obs = self.cmd(table=self.hdf5_file_valid,
File
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py",
line 112, in __call__
return self.run(table=table, format_version=format_version,
File
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py",
line 78, in run
is_json = not is_hdf5_file(kwargs['table'])
File
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/util.py",
line 518, in is_hdf5_file
with open(fp, 'rb') as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/examples/min_sparse_otu_table_hdf5.biom'
----------------------------------------------------------------------
Ran 336 tests in 4.624s
FAILED (SKIP=1, errors=3)
E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd
/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build;
python3.8 -m nose -v
dh_auto_test: pybuild --test --test-nose -i python{version} -p "3.8 3.7"
returned exit code 13
--- End Message ---
--- Begin Message ---
Source: python-biom-format
Source-Version: 2.1.7+dfsg-5
We believe that the bug you reported is fixed in the latest version of
python-biom-format, 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 943...@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 python-biom-format
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: Sun, 22 Dec 2019 07:51:11 +0100
Source: python-biom-format
Architecture: source
Version: 2.1.7+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 943622
Changes:
python-biom-format (2.1.7+dfsg-5) unstable; urgency=medium
.
* Set upstream metadata fields: Bug-Database, Repository, Repository-
Browse.
* Fix Build time test
Closes: #943622
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