[Debian-med-packaging] Bug#1042247: nitime: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13
Lucas Nussbaum
lucas at debian.org
Wed Jul 26 21:06:43 BST 2023
Source: nitime
Version: 0.9-5
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20230726 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules binary
> dh binary --with python3 --buildsystem pybuild
> dh_update_autotools_config -O--buildsystem=pybuild
> dh_autoreconf -O--buildsystem=pybuild
> dh_auto_configure -O--buildsystem=pybuild
> I: pybuild base:240: python3.11 setup.py config
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:240: /usr/bin/python3 setup.py build
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest
> ============================= test session starts ==============================
> platform linux -- Python 3.11.4, pytest-7.4.0, pluggy-1.2.0
> rootdir: /<<PKGBUILDDIR>>
> collected 123 items
>
> nitime/algorithms/tests/test_autoregressive.py ..... [ 4%]
> nitime/algorithms/tests/test_coherence.py ..........s.... [ 16%]
> nitime/algorithms/tests/test_correlation.py . [ 17%]
> nitime/algorithms/tests/test_entropy.py ..... [ 21%]
> nitime/algorithms/tests/test_event_related.py . [ 21%]
> nitime/algorithms/tests/test_spectral.py ................ [ 34%]
> nitime/analysis/tests/test_base.py . [ 35%]
> nitime/analysis/tests/test_coherence.py ...... [ 40%]
> nitime/analysis/tests/test_correlation.py . [ 41%]
> nitime/analysis/tests/test_granger.py .. [ 43%]
> nitime/analysis/tests/test_snr.py . [ 43%]
> nitime/fmri/tests/test_io.py F [ 44%]
> nitime/tests/test_algorithms.py ........ [ 51%]
> nitime/tests/test_analysis.py ....... [ 56%]
> nitime/tests/test_descriptors.py . [ 57%]
> nitime/tests/test_lazy.py .. [ 59%]
> nitime/tests/test_timeseries.py .................................... [ 88%]
> nitime/tests/test_utils.py ........... [ 97%]
> nitime/tests/test_viz.py ... [100%]
>
> =================================== FAILURES ===================================
> __________________________ test_time_series_from_file __________________________
>
> @pytest.mark.skipif(no_nibabel, reason=no_nibabel_msg)
> def test_time_series_from_file():
>
> """Testing reading of data from nifti files, using nibabel"""
>
> TR = 1.35
> ts_ff = io.time_series_from_file
>
> #File names:
> fmri_file1 = os.path.join(data_path,'fmri1.nii.gz')
> fmri_file2 = os.path.join(data_path,'fmri2.nii.gz')
>
> #Spatial coordinates into the volumes:
> coords1 = np.array([[5,5,5,5],[5,5,5,5],[1,2,3,4]])
> coords2 = np.array([[6,6,6,6],[6,6,6,6],[3,4,5,6]])
>
> #No averaging, no normalization:
> > t1 = ts_ff([fmri_file1,fmri_file2],[coords1,coords2],TR)
>
> nitime/fmri/tests/test_io.py:43:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> nitime/fmri/io.py:121: in time_series_from_file
> data = im.get_data()
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> args = (<nibabel.nifti1.Nifti1Image object at 0x7fa5373b5950>,), kwargs = {}
>
> @functools.wraps(func)
> def deprecated_func(*args: P.args, **kwargs: P.kwargs) -> T:
> if until and self.is_bad_version(until):
> > raise exception(message)
> E nibabel.deprecator.ExpiredDeprecationError: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
> E
> E * deprecated from version: 3.0
> E * Raises <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
>
> /usr/lib/python3/dist-packages/nibabel/deprecator.py:208: ExpiredDeprecationError
> =============================== warnings summary ===============================
> nitime/algorithms/event_related.py:13
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/event_related.py:13: DeprecationWarning: invalid escape sequence '\h'
> """
>
> nitime/algorithms/tests/test_coherence.py:206
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_coherence.py:206: DeprecationWarning: invalid escape sequence '\c'
> """
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py:73: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig1 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_get_spectra_complex
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py:78: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig2 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_periodogram
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py:121: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_periodogram_csd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py:146: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig1 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py::test_periodogram_csd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/tests/test_spectral.py:150: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
> arsig2 = r + c * scipy.sqrt(-1)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SparseCoherenceAnalyzer
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:200: RuntimeWarning: invalid value encountered in divide
> delay[i, j] = this_phase / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:200: RuntimeWarning: divide by zero encountered in divide
> delay[i, j] = this_phase / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/cohere.py:699: RuntimeWarning: divide by zero encountered in divide
> return (((np.abs(Rxy - Rxr * Rry)) ** 2) /
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_CoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/cohere.py:699: RuntimeWarning: invalid value encountered in divide
> return (((np.abs(Rxy - Rxr * Rry)) ** 2) /
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SparseCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:523: RuntimeWarning: invalid value encountered in divide
> return self.relative_phases / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:730: RuntimeWarning: invalid value encountered in divide
> return self.relative_phases / (2 * np.pi * self.frequencies)
>
> .pybuild/cpython3_3.11/build/nitime/analysis/tests/test_coherence.py::test_SeedCoherenceAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/analysis/coherence.py:94: RuntimeWarning: In nitime.analysis, the provided input time-series is shorter than the requested NFFT + n_overlap. All coherence values will be set to 1.
> warnings.warn(e_s, RuntimeWarning)
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py::test_scipy_resample
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py:27: DeprecationWarning: Please use `resample` from the `scipy.signal` namespace, the `scipy.signal.signaltools` namespace is deprecated.
> t_up = signaltools.resample(tst, 128)
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py::test_scipy_resample
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py:30: DeprecationWarning: Please use `resample` from the `scipy.signal` namespace, the `scipy.signal.signaltools` namespace is deprecated.
> t_dn = signaltools.resample(tst, 32)
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py::test_scipy_resample
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/tests/test_algorithms.py:36: DeprecationWarning: Please use `resample` from the `scipy.signal` namespace, the `scipy.signal.signaltools` namespace is deprecated.
> t_dn2 = signaltools.resample(tst, 48)
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_analysis.py::test_MorletWaveletAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/wavelet.py:77: RuntimeWarning: divide by zero encountered in log
> wf = (2 * np.exp(-(np.log(f) - np.log(f0)) ** 2 / (2 * sfl ** 2)) *
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_analysis.py::test_MorletWaveletAnalyzer
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/algorithms/wavelet.py:77: RuntimeWarning: invalid value encountered in log
> wf = (2 * np.exp(-(np.log(f) - np.log(f0)) ** 2 / (2 * sfl ** 2)) *
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_lazy.py::test_lazy_noreload
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/tests/test_lazy.py:40: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses
> import imp
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_viz.py::test_drawgraph_channels
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/nitime/viz.py:681: DeprecationWarning: adj_matrix is deprecated and will be removed in version 3.0.
> Use `adjacency_matrix` instead
>
> amat = nx.adj_matrix(G).A # get a normal array out of it
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_viz.py::test_drawgraph_channels
> /usr/lib/python3/dist-packages/networkx/linalg/graphmatrix.py:187: FutureWarning: adjacency_matrix will return a scipy.sparse array instead of a matrix in Networkx 3.0.
> return adjacency_matrix(G, nodelist, dtype, weight)
>
> .pybuild/cpython3_3.11/build/nitime/tests/test_viz.py::test_drawgraph_channels
> /usr/lib/python3/dist-packages/networkx/linalg/graphmatrix.py:173: DeprecationWarning:
>
> The scipy.sparse array containers will be used instead of matrices
> in Networkx 3.0. Use `to_scipy_sparse_array` instead.
> return nx.to_scipy_sparse_matrix(G, nodelist=nodelist, dtype=dtype, weight=weight)
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED nitime/fmri/tests/test_io.py::test_time_series_from_file - nibabel.dep...
> ============ 1 failed, 121 passed, 1 skipped, 29 warnings in 31.50s ============
> E: pybuild pybuild:388: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2023/07/26/nitime_0.9-5_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230726;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230726&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
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!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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