Console Output

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