Your message dated Thu, 24 Aug 2023 21:04:51 +0000
with message-id <e1qzhvb-007k4k...@fasolo.debian.org>
and subject line Bug#1042247: fixed in nitime 0.10.1-1
has caused the Debian Bug report #1042247,
regarding nitime: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i
python{version} -p 3.11 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.)
--
1042247: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1042247
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: nitime
Version: 0.9-5
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@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=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230726&fusertaguser=lu...@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.
--- End Message ---
--- Begin Message ---
Source: nitime
Source-Version: 0.10.1-1
Done: Nilesh Patra <nil...@debian.org>
We believe that the bug you reported is fixed in the latest version of
nitime, 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 1042...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <nil...@debian.org> (supplier of updated nitime 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: Fri, 25 Aug 2023 01:55:48 +0530
Source: nitime
Architecture: source
Version: 0.10.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nil...@debian.org>
Closes: 1042247
Changes:
nitime (0.10.1-1) unstable; urgency=medium
.
[ Andreas Tille ]
* Drop debian/blends which is unused
.
[ Étienne Mollier ]
* New upstream version 0.10.1 (Closes: #1042247)
* do-not-set-lowerbound-zero-in-iir.patch: delete: fixed upstream.
* fix-psd-test.patch: delete: fixed upstream.
* numpy_1.24.patch: remove: applied upstream.
.
[ Nilesh Patra ]
* Use deprecated networkx function for now, as the drop-in replacement
upstream used is causing a regression.
Proper Fix suggested upstream already.
* Add patch to fix doc FTBFS with new matplotlib
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53ff0e1909ca942ec4717f31086f6b3e2fa80427 9000 nitime_0.10.1-1.debian.tar.xz
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Files:
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--- End Message ---
