On Tue, 21 Jul 2020 15:52:22 +0200 Andreas Tille <ti...@debian.org> wrote: > Control: tags -1 - upstream > Control: tags -1 pending > > The build time test issue was solved thanks to upstream (switched from > nose to pytest). Unfortunately there are now issues with sphinx to > build the docs. My dirty workaroung did not worked so I simply added > ' || true ' behind the sphinx call. This needs to be sorted out before > uploading. > > Moreover autopkgtest should be switched from nose to pytest. > > Any help is welcome
I don't see such an error in the build log on my system. Pasting the relevant part below: PYTHONPATH=/<<PKGBUILDDIR>> /usr/bin/make -C doc html SPHINXBUILD=/usr/share/sphinx/scripts/python3/sphinx-build PYTHON=python3 make[2]: Entering directory '/<<PKGBUILDDIR>>/doc' mkdir -p ../build/html ../build/doctrees python3 tools/build_modref_templates.py nibabel source/reference False /usr/share/sphinx/scripts/python3/sphinx-build -b html -d ../build/doctrees source ../build/html /<<PKGBUILDDIR>>/doc/tools/apigen.py:210: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment Please use with caution. We would be grateful for your help in improving them mod = __import__(uri, fromlist=[uri.split('.')[-1]]) *** 3.1.1 Generating docs for nibabel: -> nibabel Generating docs for nibabel._h5py_compat: -> nibabel._h5py_compat WARNING: Empty - nibabel._h5py_compat Generating docs for nibabel._version: -> nibabel._version Generating docs for nibabel.affines: -> nibabel.affines Generating docs for nibabel.analyze: -> nibabel.analyze Generating docs for nibabel.arrayproxy: -> nibabel.arrayproxy Generating docs for nibabel.arraywriters: -> nibabel.arraywriters Generating docs for nibabel.batteryrunners: -> nibabel.batteryrunners Generating docs for nibabel.benchmarks: -> nibabel.benchmarks WARNING: Empty - nibabel.benchmarks -> nibabel.benchmarks.bench_array_to_file -> nibabel.benchmarks.bench_arrayproxy_slicing -> nibabel.benchmarks.bench_fileslice -> nibabel.benchmarks.bench_finite_range -> nibabel.benchmarks.bench_load_save -> nibabel.benchmarks.bench_streamlines -> nibabel.benchmarks.butils Generating docs for nibabel.brikhead: -> nibabel.brikhead Generating docs for nibabel.casting: -> nibabel.casting Generating docs for nibabel.cifti2: -> nibabel.cifti2 WARNING: Empty - nibabel.cifti2 -> nibabel.cifti2.cifti2 -> nibabel.cifti2.cifti2_axes -> nibabel.cifti2.parse_cifti2 Generating docs for nibabel.cmdline: -> nibabel.cmdline WARNING: Empty - nibabel.cmdline -> nibabel.cmdline.conform -> nibabel.cmdline.dicomfs -> nibabel.cmdline.diff -> nibabel.cmdline.ls -> nibabel.cmdline.nifti_dx -> nibabel.cmdline.parrec2nii -> nibabel.cmdline.tck2trk -> nibabel.cmdline.trk2tck -> nibabel.cmdline.utils Generating docs for nibabel.data: -> nibabel.data Generating docs for nibabel.dataobj_images: -> nibabel.dataobj_images Generating docs for nibabel.deprecated: -> nibabel.deprecated Generating docs for nibabel.deprecator: -> nibabel.deprecator Generating docs for nibabel.dft: -> nibabel.dft Generating docs for nibabel.ecat: -> nibabel.ecat Generating docs for nibabel.environment: -> nibabel.environment Generating docs for nibabel.eulerangles: -> nibabel.eulerangles Generating docs for nibabel.filebasedimages: -> nibabel.filebasedimages Generating docs for nibabel.fileholders: -> nibabel.fileholders Generating docs for nibabel.filename_parser: -> nibabel.filename_parser Generating docs for nibabel.fileslice: -> nibabel.fileslice Generating docs for nibabel.fileutils: -> nibabel.fileutils Generating docs for nibabel.freesurfer: -> nibabel.freesurfer WARNING: Empty - nibabel.freesurfer -> nibabel.freesurfer.io -> nibabel.freesurfer.mghformat Generating docs for nibabel.funcs: -> nibabel.funcs Generating docs for nibabel.gifti: -> nibabel.gifti WARNING: Empty - nibabel.gifti -> nibabel.gifti.gifti -> nibabel.gifti.giftiio -> nibabel.gifti.parse_gifti_fast -> nibabel.gifti.util WARNING: Empty - nibabel.gifti.util Generating docs for nibabel.imageclasses: -> nibabel.imageclasses Generating docs for nibabel.imageglobals: -> nibabel.imageglobals Generating docs for nibabel.keywordonly: -> nibabel.keywordonly Generating docs for nibabel.loadsave: -> nibabel.loadsave Generating docs for nibabel.minc1: -> nibabel.minc1 Generating docs for nibabel.minc2: -> nibabel.minc2 Generating docs for nibabel.mriutils: -> nibabel.mriutils Generating docs for nibabel.nicom: -> nibabel.nicom WARNING: Empty - nibabel.nicom -> nibabel.nicom.csareader -> nibabel.nicom.dicomreaders -> nibabel.nicom.dicomwrappers -> nibabel.nicom.dwiparams -> nibabel.nicom.structreader -> nibabel.nicom.utils Generating docs for nibabel.nifti1: -> nibabel.nifti1 Generating docs for nibabel.nifti2: -> nibabel.nifti2 Generating docs for nibabel.onetime: -> nibabel.onetime Generating docs for nibabel.openers: -> nibabel.openers Generating docs for nibabel.optpkg: -> nibabel.optpkg Generating docs for nibabel.orientations: -> nibabel.orientations Generating docs for nibabel.parrec: -> nibabel.parrec Generating docs for nibabel.processing: -> nibabel.processing Generating docs for nibabel.pydicom_compat: -> nibabel.pydicom_compat Generating docs for nibabel.quaternions: -> nibabel.quaternions Generating docs for nibabel.rstutils: -> nibabel.rstutils Generating docs for nibabel.spaces: -> nibabel.spaces Generating docs for nibabel.spatialimages: -> nibabel.spatialimages Generating docs for nibabel.spm2analyze: -> nibabel.spm2analyze Generating docs for nibabel.spm99analyze: -> nibabel.spm99analyze Generating docs for nibabel.streamlines: -> nibabel.streamlines -> nibabel.streamlines.array_sequence -> nibabel.streamlines.header -> nibabel.streamlines.tck -> nibabel.streamlines.tractogram -> nibabel.streamlines.tractogram_file -> nibabel.streamlines.trk -> nibabel.streamlines.utils Generating docs for nibabel.tmpdirs: -> nibabel.tmpdirs Generating docs for nibabel.trackvis: -> nibabel.trackvis Generating docs for nibabel.tripwire: -> nibabel.tripwire Generating docs for nibabel.viewers: -> nibabel.viewers Generating docs for nibabel.volumeutils: -> nibabel.volumeutils Generating docs for nibabel.wrapstruct: -> nibabel.wrapstruct Generating docs for nibabel.xmlutils: -> nibabel.xmlutils 60 files written Running Sphinx v2.4.3 Build API docs...done. building [mo]: targets for 0 po files that are out of date building [html]: targets for 115 source files that are out of date updating environment: [new config] 115 added, 0 changed, 0 removed reading sources... [ 0%] api reading sources... [ 1%] changelog reading sources... [ 2%] coordinate_systems reading sources... [ 3%] devel/add_image_format reading sources... [ 4%] devel/add_test_data reading sources... [ 5%] devel/advanced_testing reading sources... [ 6%] devel/bv_formats reading sources... [ 6%] devel/data_pkg_design reading sources... [ 7%] devel/data_pkg_discuss reading sources... [ 8%] devel/data_pkg_uses reading sources... [ 9%] devel/devdiscuss reading sources... [ 10%] devel/devguide reading sources... [ 11%] devel/image_design reading sources... [ 12%] devel/index reading sources... [ 13%] devel/make_release reading sources... [ 13%] devel/modified_images reading sources... [ 14%] devel/scaling reading sources... [ 15%] devel/spm_use reading sources... [ 16%] dicom/dcm2nii_algorithms reading sources... [ 17%] dicom/dicom reading sources... [ 18%] dicom/dicom_fields reading sources... [ 19%] dicom/dicom_info reading sources... [ 20%] dicom/dicom_intro reading sources... [ 20%] dicom/dicom_mosaic reading sources... [ 21%] dicom/dicom_niftiheader reading sources... [ 22%] dicom/dicom_orientation reading sources... [ 23%] dicom/siemens_csa reading sources... [ 24%] dicom/spm_dicom reading sources... [ 25%] gettingstarted reading sources... [ 26%] gitwash/configure_git reading sources... [ 26%] gitwash/development_workflow reading sources... [ 27%] gitwash/following_latest reading sources... [ 28%] gitwash/forking_hell reading sources... [ 29%] gitwash/git_development reading sources... [ 30%] gitwash/git_install reading sources... [ 31%] gitwash/git_intro reading sources... [ 32%] gitwash/git_resources reading sources... [ 33%] gitwash/index reading sources... [ 33%] gitwash/maintainer_workflow reading sources... [ 34%] gitwash/patching reading sources... [ 35%] gitwash/set_up_fork reading sources... [ 36%] image_orientation reading sources... [ 37%] images_and_memory reading sources... [ 38%] index reading sources... [ 39%] installation reading sources... [ 40%] installing_data reading sources... [ 40%] legal reading sources... [ 41%] manual reading sources... [ 42%] neuro_radio_conventions reading sources... [ 43%] nibabel_images reading sources... [ 44%] nifti_images reading sources... [ 45%] notebooks/index reading sources... [ 46%] old/ioimplementation reading sources... [ 46%] reference/index reading sources... [ 47%] reference/nibabel reading sources... [ 48%] reference/nibabel._h5py_compat reading sources... [ 49%] reference/nibabel._version reading sources... [ 50%] reference/nibabel.affines reading sources... [ 51%] reference/nibabel.analyze reading sources... [ 52%] reference/nibabel.arrayproxy reading sources... [ 53%] reference/nibabel.arraywriters reading sources... [ 53%] reference/nibabel.batteryrunners reading sources... [ 54%] reference/nibabel.benchmarks reading sources... [ 55%] reference/nibabel.brikhead reading sources... [ 56%] reference/nibabel.casting reading sources... [ 57%] reference/nibabel.cifti2 reading sources... [ 58%] reference/nibabel.cmdline reading sources... [ 59%] reference/nibabel.data reading sources... [ 60%] reference/nibabel.dataobj_images reading sources... [ 60%] reference/nibabel.deprecated reading sources... [ 61%] reference/nibabel.deprecator reading sources... [ 62%] reference/nibabel.dft reading sources... [ 63%] reference/nibabel.ecat reading sources... [ 64%] reference/nibabel.environment reading sources... [ 65%] reference/nibabel.eulerangles reading sources... [ 66%] reference/nibabel.filebasedimages reading sources... [ 66%] reference/nibabel.fileholders reading sources... [ 67%] reference/nibabel.filename_parser reading sources... [ 68%] reference/nibabel.fileslice reading sources... [ 69%] reference/nibabel.fileutils reading sources... [ 70%] reference/nibabel.freesurfer reading sources... [ 71%] reference/nibabel.funcs reading sources... [ 72%] reference/nibabel.gifti reading sources... [ 73%] reference/nibabel.imageclasses reading sources... [ 73%] reference/nibabel.imageglobals reading sources... [ 74%] reference/nibabel.keywordonly reading sources... [ 75%] reference/nibabel.loadsave reading sources... [ 76%] reference/nibabel.minc1 reading sources... [ 77%] reference/nibabel.minc2 reading sources... [ 78%] reference/nibabel.mriutils reading sources... [ 79%] reference/nibabel.nicom reading sources... [ 80%] reference/nibabel.nifti1 reading sources... [ 80%] reference/nibabel.nifti2 reading sources... [ 81%] reference/nibabel.onetime reading sources... [ 82%] reference/nibabel.openers reading sources... [ 83%] reference/nibabel.optpkg reading sources... [ 84%] reference/nibabel.orientations reading sources... [ 85%] reference/nibabel.parrec reading sources... [ 86%] reference/nibabel.processing reading sources... [ 86%] reference/nibabel.pydicom_compat reading sources... [ 87%] reference/nibabel.quaternions reading sources... [ 88%] reference/nibabel.rstutils reading sources... [ 89%] reference/nibabel.spaces reading sources... [ 90%] reference/nibabel.spatialimages reading sources... [ 91%] reference/nibabel.spm2analyze reading sources... [ 92%] reference/nibabel.spm99analyze reading sources... [ 93%] reference/nibabel.streamlines reading sources... [ 93%] reference/nibabel.tmpdirs reading sources... [ 94%] reference/nibabel.trackvis reading sources... [ 95%] reference/nibabel.tripwire reading sources... [ 96%] reference/nibabel.viewers reading sources... [ 97%] reference/nibabel.volumeutils reading sources... [ 98%] reference/nibabel.wrapstruct reading sources... [ 99%] reference/nibabel.xmlutils reading sources... [100%] tutorials /usr/lib/python3.8/importlib/__init__.py:127: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment Please use with caution. We would be grateful for your help in improving them return _bootstrap._gcd_import(name[level:], package, level) /<<PKGBUILDDIR>>/nibabel/cifti2/__init__.py:docstring of nibabel.cifti2.rst:5: WARNING: autosummary: stub file not found 'nibabel.cifti2.cifti2'. Check your autosummary_generate setting. /<<PKGBUILDDIR>>/nibabel/cifti2/__init__.py:docstring of nibabel.cifti2.rst:5: WARNING: autosummary: stub file not found 'nibabel.cifti2.cifti2_axes'. Check your autosummary_generate setting. /<<PKGBUILDDIR>>/nibabel/gifti/__init__.py:docstring of nibabel.gifti.rst:5: WARNING: autosummary: stub file not found 'nibabel.gifti.giftiio'. Check your autosummary_generate setting. /<<PKGBUILDDIR>>/nibabel/gifti/__init__.py:docstring of nibabel.gifti.rst:5: WARNING: autosummary: stub file not found 'nibabel.gifti.gifti'. Check your autosummary_generate setting. /<<PKGBUILDDIR>>/nibabel/nicom/__init__.py:docstring of nibabel.nicom.rst:5: WARNING: autosummary: stub file not found 'nibabel.nicom.csareader'. Check your autosummary_generate setting. /<<PKGBUILDDIR>>/nibabel/nicom/__init__.py:docstring of nibabel.nicom.rst:5: WARNING: autosummary: stub file not found 'nibabel.nicom.dicomreaders'. Check your autosummary_generate setting. /<<PKGBUILDDIR>>/nibabel/nicom/__init__.py:docstring of nibabel.nicom.rst:5: WARNING: autosummary: stub file not found 'nibabel.nicom.dicomwrappers'. Check your autosummary_generate setting. /<<PKGBUILDDIR>>/nibabel/nicom/__init__.py:docstring of nibabel.nicom.rst:5: WARNING: autosummary: stub file not found 'nibabel.nicom.dwiparams'. Check your autosummary_generate setting. /<<PKGBUILDDIR>>/nibabel/nicom/__init__.py:docstring of nibabel.nicom.rst:5: WARNING: autosummary: stub file not found 'nibabel.nicom.structreader'. Check your autosummary_generate setting. /<<PKGBUILDDIR>>/nibabel/processing.py:docstring of nibabel.processing.conform:7: WARNING: Unexpected indentation. looking for now-outdated files... none found pickling environment... done checking consistency... /<<PKGBUILDDIR>>/doc/source/devel/bv_formats.rst: WARNING: document isn't included in any toctree /<<PKGBUILDDIR>>/doc/source/devel/data_pkg_discuss.rst: WARNING: document isn't included in any toctree /<<PKGBUILDDIR>>/doc/source/devel/data_pkg_uses.rst: WARNING: document isn't included in any toctree /<<PKGBUILDDIR>>/doc/source/devel/image_design.rst: WARNING: document isn't included in any toctree /<<PKGBUILDDIR>>/doc/source/devel/scaling.rst: WARNING: document isn't included in any toctree /<<PKGBUILDDIR>>/doc/source/installing_data.rst: WARNING: document isn't included in any toctree /<<PKGBUILDDIR>>/doc/source/notebooks/index.rst: WARNING: document isn't included in any toctree /<<PKGBUILDDIR>>/doc/source/old/ioimplementation.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] api writing output... [ 1%] changelog writing output... [ 2%] coordinate_systems writing output... [ 3%] devel/add_image_format writing output... [ 4%] devel/add_test_data writing output... [ 5%] devel/advanced_testing writing output... [ 6%] devel/bv_formats writing output... [ 6%] devel/data_pkg_design writing output... [ 7%] devel/data_pkg_discuss writing output... [ 8%] devel/data_pkg_uses writing output... [ 9%] devel/devdiscuss writing output... [ 10%] devel/devguide writing output... [ 11%] devel/image_design writing output... [ 12%] devel/index writing output... [ 13%] devel/make_release writing output... [ 13%] devel/modified_images writing output... [ 14%] devel/scaling writing output... [ 15%] devel/spm_use writing output... [ 16%] dicom/dcm2nii_algorithms writing output... [ 17%] dicom/dicom writing output... [ 18%] dicom/dicom_fields writing output... [ 19%] dicom/dicom_info writing output... [ 20%] dicom/dicom_intro writing output... [ 20%] dicom/dicom_mosaic writing output... [ 21%] dicom/dicom_niftiheader writing output... [ 22%] dicom/dicom_orientation writing output... [ 23%] dicom/siemens_csa writing output... [ 24%] dicom/spm_dicom writing output... [ 25%] gettingstarted writing output... [ 26%] gitwash/configure_git writing output... [ 26%] gitwash/development_workflow writing output... [ 27%] gitwash/following_latest writing output... [ 28%] gitwash/forking_hell writing output... [ 29%] gitwash/git_development writing output... [ 30%] gitwash/git_install writing output... [ 31%] gitwash/git_intro writing output... [ 32%] gitwash/git_resources writing output... [ 33%] gitwash/index writing output... [ 33%] gitwash/maintainer_workflow writing output... [ 34%] gitwash/patching writing output... [ 35%] gitwash/set_up_fork writing output... [ 36%] image_orientation writing output... [ 37%] images_and_memory writing output... [ 38%] index writing output... [ 39%] installation writing output... [ 40%] installing_data writing output... [ 40%] legal writing output... [ 41%] manual writing output... [ 42%] neuro_radio_conventions writing output... [ 43%] nibabel_images writing output... [ 44%] nifti_images writing output... [ 45%] notebooks/index writing output... [ 46%] old/ioimplementation writing output... [ 46%] reference/index writing output... [ 47%] reference/nibabel writing output... [ 48%] reference/nibabel._h5py_compat writing output... [ 49%] reference/nibabel._version writing output... [ 50%] reference/nibabel.affines writing output... [ 51%] reference/nibabel.analyze writing output... [ 52%] reference/nibabel.arrayproxy writing output... [ 53%] reference/nibabel.arraywriters writing output... [ 53%] reference/nibabel.batteryrunners writing output... [ 54%] reference/nibabel.benchmarks writing output... [ 55%] reference/nibabel.brikhead writing output... [ 56%] reference/nibabel.casting writing output... [ 57%] reference/nibabel.cifti2 writing output... [ 58%] reference/nibabel.cmdline writing output... [ 59%] reference/nibabel.data writing output... [ 60%] reference/nibabel.dataobj_images writing output... [ 60%] reference/nibabel.deprecated writing output... [ 61%] reference/nibabel.deprecator writing output... [ 62%] reference/nibabel.dft writing output... [ 63%] reference/nibabel.ecat writing output... [ 64%] reference/nibabel.environment writing output... [ 65%] reference/nibabel.eulerangles writing output... [ 66%] reference/nibabel.filebasedimages writing output... [ 66%] reference/nibabel.fileholders writing output... [ 67%] reference/nibabel.filename_parser writing output... [ 68%] reference/nibabel.fileslice writing output... [ 69%] reference/nibabel.fileutils writing output... [ 70%] reference/nibabel.freesurfer writing output... [ 71%] reference/nibabel.funcs writing output... [ 72%] reference/nibabel.gifti writing output... [ 73%] reference/nibabel.imageclasses writing output... [ 73%] reference/nibabel.imageglobals writing output... [ 74%] reference/nibabel.keywordonly writing output... [ 75%] reference/nibabel.loadsave writing output... [ 76%] reference/nibabel.minc1 writing output... [ 77%] reference/nibabel.minc2 writing output... [ 78%] reference/nibabel.mriutils writing output... [ 79%] reference/nibabel.nicom writing output... [ 80%] reference/nibabel.nifti1 writing output... [ 80%] reference/nibabel.nifti2 writing output... [ 81%] reference/nibabel.onetime writing output... [ 82%] reference/nibabel.openers writing output... [ 83%] reference/nibabel.optpkg writing output... [ 84%] reference/nibabel.orientations writing output... [ 85%] reference/nibabel.parrec writing output... [ 86%] reference/nibabel.processing writing output... [ 86%] reference/nibabel.pydicom_compat writing output... [ 87%] reference/nibabel.quaternions writing output... [ 88%] reference/nibabel.rstutils writing output... [ 89%] reference/nibabel.spaces writing output... [ 90%] reference/nibabel.spatialimages writing output... [ 91%] reference/nibabel.spm2analyze writing output... [ 92%] reference/nibabel.spm99analyze writing output... [ 93%] reference/nibabel.streamlines writing output... [ 93%] reference/nibabel.tmpdirs writing output... [ 94%] reference/nibabel.trackvis writing output... [ 95%] reference/nibabel.tripwire writing output... [ 96%] reference/nibabel.viewers writing output... [ 97%] reference/nibabel.volumeutils writing output... [ 98%] reference/nibabel.wrapstruct writing output... [ 99%] reference/nibabel.xmlutils writing output... [100%] tutorials generating indices... genindex py-modindexdone writing additional pages... searchdone copying images... [ 8%] ../../build/plot_directive/coordinate_systems-2.png copying images... [ 16%] ../../build/plot_directive/coordinate_systems-3_00.png copying images... [ 25%] ../../build/plot_directive/coordinate_systems-3_01.png copying images... [ 33%] images/localizer.png copying images... [ 41%] images/illustrating_affine.png copying images... [ 50%] dicom/mosaic_grid.png copying images... [ 58%] gitwash/branch_dropdown.png copying images... [ 66%] gitwash/pull_button.png copying images... [ 75%] gitwash/forking_button.png copying images... [ 83%] images/rorden_radio_neuro.jpg copying images... [ 91%] ../../build/plot_directive/neuro_radio_conventions-2_00.png copying images... [100%] ../../build/plot_directive/neuro_radio_conventions-2_01.png copying downloadable files... [ 16%] downloads/someones_epi.nii.gz copying downloadable files... [ 33%] downloads/someones_anatomy.nii.gz copying downloadable files... [ 50%] devel/register_me.py copying downloadable files... [ 66%] dicom/derivations/spm_dicom_orient.py copying downloadable files... [ 83%] notebooks/ata_error.ipynb copying downloadable files... [100%] notebooks/cross_product_error.ipynb copying static files... ... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 18 warnings. The HTML pages are in ../build/html. Build finished. The HTML pages are in ../build/html. make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc' # but remove jquery copy (later on link to Debian's version) rm build/html/_static/jquery.js # objects inventory is of no use for the package rm build/html/objects.inv # also doc source files only consume space rm -r build/html/_sources Is this a false postive for you (As happened a few times earlier)? Kind Regards, Nilesh
signature.asc
Description: OpenPGP digital signature