Started by GitHub push by thvitt Running as SYSTEM Building remotely on build3 (digibib) in workspace /mnt/data/jenkins/workspace/pydelta-next The recommended git tool is: NONE using credential Github > /usr/bin/git rev-parse --resolve-git-dir /mnt/data/jenkins/workspace/pydelta-next/.git # timeout=10 Fetching changes from the remote Git repository > /usr/bin/git config remote.origin.url https://github.com/cophi-wue/pydelta # timeout=10 Fetching upstream changes from https://github.com/cophi-wue/pydelta > /usr/bin/git --version # timeout=10 > git --version # 'git version 2.20.1' using GIT_ASKPASS to set credentials > /usr/bin/git fetch --tags --force --progress -- https://github.com/cophi-wue/pydelta +refs/heads/*:refs/remotes/origin/* # timeout=10 > /usr/bin/git rev-parse refs/remotes/origin/next^{commit} # timeout=10 Checking out Revision 3eed8fc410bbd27ef44eb7b802d431c11db0b866 (refs/remotes/origin/next) > /usr/bin/git config core.sparsecheckout # timeout=10 > /usr/bin/git checkout -f 3eed8fc410bbd27ef44eb7b802d431c11db0b866 # timeout=10 Commit message: "Updated version no" > /usr/bin/git rev-list --no-walk 01d6c5dfb18ba1f6598f57194bd667ef0fb472ef # timeout=10 No emails were triggered. $ bash -c "[ -d \$HOME/.pyenv ]" $ bash -c "cd /mnt/data/jenkins/workspace/pydelta-next && env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.7.9 \$HOME/.pyenv/bin/pyenv local 2>/dev/null || true" $ bash -c "mkdir \$HOME/.pyenv.lock" $ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.7.9 \$HOME/.pyenv/bin/pyenv versions --bare" $ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.7.9 \$HOME/.pyenv/bin/pyenv rehash" $ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.7.9 \$HOME/.pyenv/bin/pyenv exec pip list" $ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.7.9 \$HOME/.pyenv/bin/pyenv rehash" $ bash -c "rm -rf \$HOME/.pyenv.lock" [pydelta-next] $ /bin/sh -xe /tmp/jenkins8048694282131908129.sh + poetry install Installing dependencies from lock file Package operations: 97 installs, 0 updates, 0 removals • Installing ipython-genutils (0.2.0) • Installing zipp (3.4.1) • Installing attrs (20.3.0) • Installing importlib-metadata (1.7.0) • Installing pyparsing (2.4.7) • Installing pyrsistent (0.17.3) • Installing six (1.16.0) • Installing traitlets (5.0.5) • Installing certifi (2021.5.30) • Installing chardet (4.0.0) • Installing idna (2.10) • Installing jsonschema (3.2.0) • Installing jupyter-core (4.7.1) • Installing markupsafe (2.0.1) • Installing packaging (20.9) • Installing pycparser (2.20) • Installing urllib3 (1.26.6) • Installing webencodings (0.5.1) • Installing bleach (3.3.0) • Installing cffi (1.14.5) • Installing defusedxml (0.7.1) • Installing entrypoints (0.3) • Installing jinja2 (3.0.1) • Installing mistune (0.8.4) • Installing nbformat (5.1.3) • Installing pandocfilters (1.4.3) • Installing ptyprocess (0.7.0) • Installing pygments (2.9.0) • Installing python-dateutil (2.8.1) • Installing pyzmq (22.1.0) • Installing requests (2.25.1) • Installing sniffio (1.2.0) • Installing testpath (0.5.0) • Installing tornado (6.1) • Installing typing-extensions (3.10.0.0) • Installing anyio (3.2.1) • Installing argon2-cffi (20.1.0) • Installing jupyter-client (6.1.12) • Installing nbconvert (5.6.1) • Installing prometheus-client (0.11.0) • Installing requests-unixsocket (0.2.0) • Installing send2trash (1.7.1) • Installing smmap (4.0.0) • Installing terminado (0.10.1) • Installing websocket-client (1.1.0) • Installing gitdb (4.0.7) • Installing jupyter-server (1.9.0) • Installing numpy (1.21.0) • Installing parso (0.8.2) • Installing pytz (2021.1) • Installing wcwidth (0.2.5) • Installing alabaster (0.7.12) • Installing babel (2.9.1) • Installing backcall (0.2.0) • Installing colorama (0.4.4) • Installing decorator (5.0.9) • Installing docutils (0.17.1) • Installing gitpython (3.1.18) • Installing imagesize (1.2.0) • Installing iniconfig (1.1.1) • Installing jedi (0.18.0) • Installing joblib (1.0.1) • Installing jupyter-server-mathjax (0.2.3) • Installing matplotlib-inline (0.1.2) • Installing pexpect (4.8.0) • Installing pickleshare (0.7.5) • Installing pluggy (0.13.1) • Installing prompt-toolkit (3.0.19) • Installing py (1.10.0) • Installing scipy (1.7.0) • Installing snowballstemmer (2.1.0) • Installing sphinxcontrib-applehelp (1.0.2) • Installing sphinxcontrib-devhelp (1.0.2) • Installing sphinxcontrib-htmlhelp (2.0.0) • Installing sphinxcontrib-jsmath (1.0.1) • Installing sphinxcontrib-qthelp (1.0.3) • Installing sphinxcontrib-serializinghtml (1.1.5) • Installing threadpoolctl (2.1.0) • Installing toml (0.10.2) • Installing coverage (5.5) • Installing cycler (0.10.0) • Installing importlib-resources (5.2.0) • Installing kiwisolver (1.3.1) • Installing nbdime (3.1.0) • Installing pillow (8.2.0) • Installing pytest (6.2.4) • Installing ipython (7.25.0) • Installing scikit-learn (0.24.2) • Installing sphinx (4.0.2) • Installing ipykernel (5.5.5) • Installing matplotlib (3.4.2) • Installing nbsphinx (0.8.6) • Installing pandas (1.2.5) • Installing pytest-cov (2.12.1) • Installing pytest-notebook (0.6.1) • Installing regex (2021.4.4) • Installing scikit-learn-extra (0.2.0) Installing the current project: delta (2.2.0.dev0) + poetry run pytest ============================= test session starts ============================== platform linux -- Python 3.7.9, pytest-6.2.4, py-1.10.0, pluggy-0.13.1 rootdir: /mnt/data/jenkins/workspace/pydelta-next, configfile: pyproject.toml plugins: notebook-0.6.1, cov-2.12.1, anyio-3.2.1 collected 29 items delta/graphics.py . [ 3%] delta/util.py .... [ 17%] test/corpus_test.py ........... [ 55%] test/deltas_test.py ......... [ 86%] test/test_issue6.py .... [100%] --- generated xml file: /mnt/data/jenkins/workspace/pydelta-next/pytest.xml ---- ============================== 29 passed in 5.40s ============================== + poetry run sh -c cd docs && make clean html rm -rf _build/* sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v4.0.2 making output directory... done WARNING: html_static_path entry '_static' does not exist loading intersphinx inventory from http://docs.python.org/objects.inv... loading intersphinx inventory from http://pandas.pydata.org/pandas-docs/stable/objects.inv... intersphinx inventory has moved: http://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv intersphinx inventory has moved: http://pandas.pydata.org/pandas-docs/stable/objects.inv -> https://pandas.pydata.org/pandas-docs/stable/objects.inv building [mo]: targets for 0 po files that are out of date building [html]: targets for 9 source files that are out of date updating environment: [new config] 9 added, 0 changed, 0 removed reading sources... [ 11%] CustomizingPipeline reading sources... [ 22%] GettingStarted reading sources... [ 33%] README reading sources... [ 44%] README-branch reading sources... [ 55%] concept reading sources... [ 66%] delta reading sources... [ 77%] index reading sources... [ 88%] modules reading sources... [100%] refactoring-notes /mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:37: WARNING: File not found: 'delta.html#delta.corpus.Corpus' /mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:320: WARNING: File not found: 'delta.html#corpus.Corpus.relative_frequencies' /mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:320: WARNING: File not found: 'delta.html#corpus.Corpus.get_mfw_table' /mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:353: WARNING: File not found: 'delta.html#deltas.DistanceMatrix' /mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:645: WARNING: File not found: 'delta.html#graph.Dendrogram' /mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:645: WARNING: File not found: 'delta.html#corpus.DocumentDescriber' /mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:67: WARNING: Unknown interpreted text role "function". /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.tokenize:3: WARNING: Unknown interpreted text role "param". /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.metadata:3: WARNING: Unexpected indentation. /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.DeltaFunction.distance:11: WARNING: Inline strong start-string without end-string. /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.DeltaFunction.iterate_distance:13: WARNING: Inline strong start-string without end-string. /mnt/data/jenkins/workspace/pydelta-next/delta/graphics.py:docstring of delta.graphics.Dendrogram:33: WARNING: Unknown interpreted text role "module". /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.tokenize:3: WARNING: Unknown interpreted text role "param". /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.FeatureGenerator.metadata:3: WARNING: Unexpected indentation. /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.DeltaFunction.distance:11: WARNING: Inline strong start-string without end-string. /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.DeltaFunction.iterate_distance:13: WARNING: Inline strong start-string without end-string. /mnt/data/jenkins/workspace/pydelta-next/delta/graphics.py:docstring of delta.graphics.Dendrogram:33: WARNING: Unknown interpreted text role "module". /mnt/data/jenkins/workspace/pydelta-next/delta/experiments.py:docstring of delta.experiments:13: WARNING: Unknown target name: "facet". /mnt/data/jenkins/workspace/pydelta-next/delta/experiments.py:docstring of delta.experiments:18: WARNING: Unknown target name: "facet". /mnt/data/jenkins/workspace/pydelta-next/delta/experiments.py:docstring of delta.experiments:23: WARNING: Unknown target name: "facet". /mnt/data/jenkins/workspace/pydelta-next/docs/refactoring-notes.rst:9: WARNING: Unexpected indentation. /mnt/data/jenkins/workspace/pydelta-next/docs/refactoring-notes.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /mnt/data/jenkins/workspace/pydelta-next/docs/README-branch.rst: WARNING: document isn't included in any toctree /mnt/data/jenkins/workspace/pydelta-next/docs/modules.rst: WARNING: document isn't included in any toctree /mnt/data/jenkins/workspace/pydelta-next/docs/refactoring-notes.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 11%] CustomizingPipeline writing output... [ 22%] GettingStarted writing output... [ 33%] README writing output... [ 44%] README-branch writing output... [ 55%] concept writing output... [ 66%] delta writing output... [ 77%] index writing output... [ 88%] modules writing output... [100%] refactoring-notes /mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:624: WARNING: undefined label: /delta.rst#cluster.clustering /mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:794: WARNING: undefined label: /delta.rst#cluster.flatclustering /mnt/data/jenkins/workspace/pydelta-next/docs/README.rst:54: WARNING: 'any' reference target not found: pytest /mnt/data/jenkins/workspace/pydelta-next/docs/README.rst:54: WARNING: 'any' reference target not found: cd docs && make html /mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:31: WARNING: 'any' reference target not found: sort /mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:32: WARNING: 'any' reference target not found: reparse_column /mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:33: WARNING: 'any' reference target not found: relativize /mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:34: WARNING: more than one target found for 'any' cross-reference 'top_n': could be :py:meth:`delta.corpus.Corpus.top_n` or :py:meth:`delta.Corpus.top_n` /mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:35: WARNING: more than one target found for 'any' cross-reference 'cull': could be :py:meth:`delta.corpus.Corpus.cull` or :py:meth:`delta.Corpus.cull` /mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:36: WARNING: 'any' reference target not found: normalize /mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:50: WARNING: more than one target found for 'any' cross-reference 'normalization': could be :py:func:`delta.deltas.normalization` or :py:func:`delta.normalization` /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator:1: WARNING: 'any' reference target not found: subdir /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.postprocess_tokens:4: WARNING: 'any' reference target not found: lower_case /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.count_tokens:1: WARNING: 'any' reference target not found: lines /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.process_file:3: WARNING: 'any' reference target not found: filename /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus:29: WARNING: 'any' reference target not found: subdir /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus:29: WARNING: 'any' reference target not found: subdir /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus.new_data:1: WARNING: 'any' reference target not found: DataFrame /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus.get_mfw_table:11: WARNING: 'any' reference target not found: mfwords /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus.top_n:6: WARNING: 'any' reference target not found: mfwords /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.DeltaFunction:16: WARNING: 'any' reference target not found: f /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.DeltaFunction.iterate_distance:: WARNING: more than one target found for cross-reference 'Corpus': delta.corpus.Corpus, delta.Corpus /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.DeltaFunction.create_result:: WARNING: more than one target found for cross-reference 'Corpus': delta.corpus.Corpus, delta.Corpus /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.PreprocessingDeltaFunction:7: WARNING: 'any' reference target not found: f /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.MetricDeltaFunction:18: WARNING: 'any' reference target not found: fix_symmetry /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.DistanceMatrix.compare_with:5: WARNING: more than one target found for 'any' cross-reference 'compare_pairwise': could be :py:func:`delta.util.compare_pairwise` or :py:func:`delta.compare_pairwise` /mnt/data/jenkins/workspace/pydelta-next/delta/graphics.py:docstring of delta.graphics.Dendrogram:: WARNING: more than one target found for cross-reference 'Clustering': delta.cluster.Clustering, delta.Clustering /mnt/data/jenkins/workspace/pydelta-next/delta/util.py:docstring of delta.util.compare_pairwise:3: WARNING: 'any' reference target not found: :func:ssd.squareform /mnt/data/jenkins/workspace/pydelta-next/delta/util.py:docstring of delta.util.compare_pairwise:19: WARNING: 'any' reference target not found: :class:np.ufunc /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus:29: WARNING: 'any' reference target not found: subdir /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus:29: WARNING: 'any' reference target not found: subdir /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus.new_data:1: WARNING: 'any' reference target not found: DataFrame /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus.get_mfw_table:11: WARNING: 'any' reference target not found: mfwords /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus.top_n:6: WARNING: 'any' reference target not found: mfwords /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator:1: WARNING: 'any' reference target not found: subdir /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.postprocess_tokens:4: WARNING: 'any' reference target not found: lower_case /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.count_tokens:1: WARNING: 'any' reference target not found: lines /mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.process_file:3: WARNING: 'any' reference target not found: filename /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.DeltaFunction:16: WARNING: 'any' reference target not found: f /mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.MetricDeltaFunction:18: WARNING: 'any' reference target not found: fix_symmetry /mnt/data/jenkins/workspace/pydelta-next/delta/__init__.py:docstring of delta.util.compare_pairwise:3: WARNING: 'any' reference target not found: :func:ssd.squareform /mnt/data/jenkins/workspace/pydelta-next/delta/__init__.py:docstring of delta.util.compare_pairwise:19: WARNING: 'any' reference target not found: :class:np.ufunc generating indices... genindex py-modindex done copying notebooks ... [ 50%] CustomizingPipeline.ipynb copying notebooks ... [100%] GettingStarted.ipynb highlighting module code... [ 16%] delta.cluster highlighting module code... [ 33%] delta.corpus highlighting module code... [ 50%] delta.deltas highlighting module code... [ 66%] delta.features highlighting module code... [ 83%] delta.graphics highlighting module code... [100%] delta.util writing additional pages... search done copying images... [ 33%] _build/doctrees/nbsphinx/CustomizingPipeline_11_1.png copying images... [ 66%] _build/doctrees/nbsphinx/CustomizingPipeline_22_1.png copying images... [100%] _build/doctrees/nbsphinx/GettingStarted_23_1.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 68 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. [htmlpublisher] Archiving HTML reports... [htmlpublisher] Archiving at PROJECT level /mnt/data/jenkins/workspace/pydelta-next/build/sphinx/html to /mnt/data/jenkins/jobs/pydelta-next/htmlreports/Documentation ERROR: Specified HTML directory '/mnt/data/jenkins/workspace/pydelta-next/build/sphinx/html' does not exist. Build step 'Publish HTML reports' changed build result to FAILURE Recording test results [Checks API] No suitable checks publisher found. [Cobertura] Publishing Cobertura coverage report... [Set GitHub commit status (universal)] ERROR on repos [GHRepository@4759465a[nodeId=MDEwOlJlcG9zaXRvcnk4NDYzMzk3MQ==,description=an experimental implementation of Burrow's delta in Python 3,homepage=http://dev.digital-humanities.de/ci/job/pydelta-next/Documentation/index.html,name=pydelta,fork=true,archived=false,size=3496,milestones={},language=Jupyter Notebook,commits={},isTemplate=<null>,url=https://api.github.com/repos/cophi-wue/pydelta,id=84633971,nodeId=<null>,createdAt=2017-03-11T08:03:36Z,updatedAt=2021-06-28T15:36:45Z]] (sha:3eed8fc) with context:pydelta-next Setting commit status on GitHub for https://github.com/cophi-wue/pydelta/commit/3eed8fc410bbd27ef44eb7b802d431c11db0b866 Started calculate disk usage of build Finished Calculation of disk usage of build in 0 seconds Started calculate disk usage of workspace Finished Calculation of disk usage of workspace in 0 seconds Notifying upstream projects of job completion Email was triggered for: Failure - Any Sending email for trigger: Failure - Any Sending email to: thorsten.vitt@uni-wuerzburg.de Finished: FAILURE