Control: tags -1 help Hi,
I upgraded q2-quality-filter to the latest upstream version in Git. The build time tests were disabled as for other QIIME modules that need registering in QIIME which is not possible at build time. However, also the autopkgtest fails with: autopkgtest [13:08:01]: test run-unit-test: [----------------------- /usr/lib/python3/dist-packages/skbio/util/_testing.py:15: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead. import pandas.util.testing as pdt EFEEE..... ====================================================================== ERROR: test_q_score (q2_quality_filter.test.test_filter.FilterTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/autopkgtest.Oa4qOC/autopkgtest_tmp/q2_quality_filter/test/test_filter.py", line 108, in test_q_score with redirected_stdio(stdout=os.devnull): File "/usr/lib/python3.9/contextlib.py", line 117, in __enter__ return next(self.gen) File "/usr/lib/python3/dist-packages/qiime2/util.py", line 24, in redirected_stdio with _redirected_fd(to=stdout, stdio=sys.stdout): File "/usr/lib/python3.9/contextlib.py", line 117, in __enter__ return next(self.gen) File "/usr/lib/python3/dist-packages/qiime2/util.py", line 43, in _redirected_fd stdio_fd = _get_fileno(stdio) File "/usr/lib/python3/dist-packages/qiime2/util.py", line 64, in _get_fileno fd = getattr(file_or_fd, 'fileno', lambda: file_or_fd)() io.UnsupportedOperation: fileno -------------------- >> begin captured logging << -------------------- bibtexparser.bparser: DEBUG: Found Entry: ['Article', 'Bolyen2019', {'url': 'https://doi.org/10.1038/s41587-019-0209-9', 'doi': '10.1038/s41587-019-0209-9', 'issn': '1546-1696', 'pages': '852 Traceback (most recent call last): File "/tmp/autopkgtest.Oa4qOC/autopkgtest_tmp/q2_quality_filter/test/test_filter.py", line 108, in test_q_score with redirected_stdio(stdout=os.devnull): File "/usr/lib/python3.9/contextlib.py", line 117, in __enter__ return next(self.gen) File "/usr/lib/python3/dist-packages/qiime2/util.py", line 24, in redirected_stdio with _redirected_fd(to=stdout, stdio=sys.stdout): File "/usr/lib/python3.9/contextlib.py", line 117, in __enter__ return next(self.gen) File "/usr/lib/python3/dist-packages/qiime2/util.py", line 43, in _redirected_fd stdio_fd = _get_fileno(stdio) File "/usr/lib/python3/dist-packages/qiime2/util.py", line 64, in _get_fileno fd = getattr(file_or_fd, 'fileno', lambda: file_or_fd)() io.UnsupportedOperation: fileno -------------------- >> begin captured logging << -------------------- bibtexparser.bparser: DEBUG: Found Entry: ['Article', 'Bolyen2019', {'url': 'https://doi.org/10.1038/s41587-019-0209-9', 'doi': '10.1038/s41587-019-0209-9', 'issn': '1546-1696', 'pages': '852 ====================================================================== ERROR: test_q_score_numeric_ids (q2_quality_filter.test.test_filter.FilterTests) ---------------------------------------------------------------------- ... Kind regards Andreas. -- http://fam-tille.de