Read the Docs build information Build id: 240058 Project: life-epigenetics-methylcheck Version: latest Commit: 73d073bc1f636cb4f48cbeb116544691a3a116ff Date: 2019-09-09T16:45:49.635461Z State: finished Success: True [rtd-command-info] start-time: 2019-09-09T16:45:50.098135Z, end-time: 2019-09-09T16:45:50.115025Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/LifeEGX/methylcheck.git [rtd-command-info] start-time: 2019-09-09T16:45:50.196746Z, end-time: 2019-09-09T16:45:50.479615Z, duration: 0, exit-code: 0 git fetch origin --tags --prune --prune-tags --depth 50 From https://github.com/LifeEGX/methylcheck db9db35..73d073b master -> origin/master [rtd-command-info] start-time: 2019-09-09T16:45:50.694225Z, end-time: 2019-09-09T16:45:50.713913Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was db9db35 Update modules.rst HEAD is now at 73d073b Delete modules.rst [rtd-command-info] start-time: 2019-09-09T16:45:50.795218Z, end-time: 2019-09-09T16:45:50.829026Z, duration: 0, exit-code: 0 git clean -d -f -f Removing _build/doctrees-epub/ Removing _build/doctrees-readthedocs/ Removing _build/doctrees-readthedocssinglehtmllocalmedia/ Removing _build/doctrees/ Removing _build/epub/ Removing _build/html/ Removing _build/json/ Removing _build/latex/LICRcyr2utf8.xdy Removing _build/latex/LICRlatin2utf8.xdy Removing _build/latex/LatinRules.xdy Removing _build/latex/Makefile Removing _build/latex/docs_demo-methylprep-to-methylcheck-example_7_1.png Removing _build/latex/docs_demo-methylprep-to-methylcheck-example_7_1.xbb Removing _build/latex/docs_demo-methylprep-to-methylcheck-example_8_0.png Removing _build/latex/docs_demo-methylprep-to-methylcheck-example_8_0.xbb Removing _build/latex/docs_demo-methylprep-to-methylcheck-example_9_3.png Removing _build/latex/docs_demo-methylprep-to-methylcheck-example_9_3.xbb Removing _build/latex/docs_filtering_probes_10_1.png Removing _build/latex/docs_filtering_probes_10_1.xbb 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_build/latex/sphinxmulticell.sty Removing _build/localmedia/ Removing _sphinx_build/conf.rst Removing _sphinx_build/methylcheck.QCreport.rst Removing _sphinx_build/methylcheck.cli.rst Removing _sphinx_build/methylcheck.filters.rst Removing _sphinx_build/methylcheck.postprocessQC.rst Removing _sphinx_build/methylcheck.rawQC.rst Removing _sphinx_build/methylcheck.rst Removing _sphinx_build/modules.rst Removing _sphinx_build/setup.rst [rtd-command-info] start-time: 2019-09-09T16:45:51.968063Z, end-time: 2019-09-09T16:45:55.929722Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.7.1' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python3.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python3.7) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-09-09T16:45:56.023240Z, end-time: 2019-09-09T16:45:57.372641Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (19.2.3) [rtd-command-info] start-time: 2019-09-09T16:45:57.445268Z, end-time: 2019-09-09T16:46:00.514943Z, duration: 3, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (2.3.1) Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (41.0.1) Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (0.14) Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (1.0.1) Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (5.4.1) Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (0.7.12) Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (0.8.1) Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (0.5.0) Requirement already up-to-date: sphinx<2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (1.8.5) Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (0.4.3) Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (1.0.0) Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from commonmark==0.8.1) (0.17.1) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.10.1) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.12.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.7.0) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx<2) (19.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.9.1) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2019.6.16) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (1.25.3) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2.8) Requirement already satisfied, skipping upgrade: attrs in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from packaging->sphinx<2) (19.1.0) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from packaging->sphinx<2) (2.4.2) [rtd-command-info] start-time: 2019-09-09T16:46:00.592770Z, end-time: 2019-09-09T16:46:02.026357Z, duration: 1, exit-code: 0 python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/.cache/pip -r requirements.txt Requirement already satisfied: numpy in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (1.17.2) Requirement already satisfied: pandas in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 2)) (0.25.1) Requirement already satisfied: scipy in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 3)) (1.3.1) Requirement already satisfied: matplotlib in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 4)) (3.1.1) Requirement already satisfied: seaborn in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 5)) (0.9.0) Requirement already satisfied: pytest in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 6)) (5.1.2) Requirement already satisfied: coverage in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 7)) (4.5.4) Requirement already satisfied: coveralls-python in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 8)) (0.0.1) Requirement already satisfied: sphinx>=1.4 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 9)) (1.8.5) Requirement already satisfied: sphinxcontrib-apidoc in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 10)) (0.3.0) Requirement already satisfied: m2r in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 11)) (0.2.1) Requirement already satisfied: tqdm in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 12)) (4.35.0) Requirement already satisfied: ipykernel in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 13)) (5.1.2) Requirement already satisfied: nbsphinx in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages 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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-apidoc->-r requirements.txt (line 10)) (5.4.3) Requirement already satisfied: mistune in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from m2r->-r requirements.txt (line 11)) (0.8.4) Requirement already satisfied: jupyter-client in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipykernel->-r requirements.txt (line 13)) (5.3.1) Requirement already satisfied: ipython>=5.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipykernel->-r requirements.txt (line 13)) (7.8.0) Requirement already satisfied: tornado>=4.2 in 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(from importlib-metadata>=0.12; python_version < "3.8"->pytest->-r requirements.txt (line 6)) (0.6.0) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.4->-r requirements.txt (line 9)) (1.1.1) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 9)) (1.25.3) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 9)) (2019.6.16) Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 9)) (2.8) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 9)) (3.0.4) Requirement already satisfied: pyzmq>=13 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from jupyter-client->ipykernel->-r requirements.txt (line 13)) (18.1.0) Requirement already satisfied: jupyter-core in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from jupyter-client->ipykernel->-r requirements.txt (line 13)) (4.5.0) Requirement already satisfied: decorator in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 13)) (4.4.0) Requirement already satisfied: jedi>=0.10 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 13)) (0.15.1) Requirement already satisfied: backcall in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 13)) (0.1.0) Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 13)) (2.0.9) Requirement already satisfied: pickleshare in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 13)) (0.7.5) Requirement already satisfied: pexpect; sys_platform != "win32" in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 13)) (4.7.0) Requirement already satisfied: ipython-genutils in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from traitlets>=4.1.0->ipykernel->-r requirements.txt (line 13)) (0.2.0) Requirement already satisfied: bleach in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 14)) (3.1.0) Requirement already satisfied: entrypoints>=0.2.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 14)) (0.3) Requirement already satisfied: testpath in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 14)) (0.4.2) Requirement already satisfied: pandocfilters>=1.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 14)) (1.4.2) Requirement already satisfied: defusedxml in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 14)) (0.6.0) Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from nbformat->nbsphinx->-r requirements.txt (line 14)) (3.0.2) Requirement already satisfied: parso>=0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from jedi>=0.10->ipython>=5.0.0->ipykernel->-r requirements.txt (line 13)) (0.5.1) Requirement already satisfied: ptyprocess>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from pexpect; sys_platform != "win32"->ipython>=5.0.0->ipykernel->-r requirements.txt (line 13)) (0.6.0) Requirement already satisfied: webencodings in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from bleach->nbconvert!=5.4->nbsphinx->-r requirements.txt (line 14)) (0.5.1) Requirement already satisfied: pyrsistent>=0.14.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat->nbsphinx->-r requirements.txt (line 14)) (0.15.4) [rtd-command-info] start-time: 2019-09-09T16:46:02.127722Z, end-time: 2019-09-09T16:46:03.773122Z, duration: 1, exit-code: 0 python /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/setup.py install --force running install running bdist_egg running egg_info writing methylcheck.egg-info/PKG-INFO writing dependency_links to methylcheck.egg-info/dependency_links.txt writing entry points to methylcheck.egg-info/entry_points.txt writing requirements to methylcheck.egg-info/requires.txt writing top-level names to methylcheck.egg-info/top_level.txt reading manifest file 'methylcheck.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'README.rst' writing manifest file 'methylcheck.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/cli.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/postprocessQC.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/__main__.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/QCreport.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/filters.py -> build/bdist.linux-x86_64/egg/methylcheck creating build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/450k_polymorphic_crossRxtve_probes.csv.gz -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/EPIC_control.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/450k_sex.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/EPIC+_sex.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/EPIC+_control.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/450k_control.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/EPIC_sex.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/EPIC_polymorphic_crossRxtve_probes.csv.gz -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/rawQC.py -> build/bdist.linux-x86_64/egg/methylcheck byte-compiling build/bdist.linux-x86_64/egg/methylcheck/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/cli.py to cli.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/postprocessQC.py to postprocessQC.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/QCreport.py to QCreport.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/filters.py to filters.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/rawQC.py to rawQC.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... creating 'dist/methylcheck-0.2.4-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing methylcheck-0.2.4-py3.7.egg Removing /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/methylcheck-0.2.4-py3.7.egg Copying methylcheck-0.2.4-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages methylcheck 0.2.4 is already the active version in easy-install.pth Installing methylcheck-cli script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/methylcheck-0.2.4-py3.7.egg Processing dependencies for methylcheck==0.2.4 Searching for scikit-learn==0.21.3 Best match: scikit-learn 0.21.3 Processing scikit_learn-0.21.3-py3.7-linux-x86_64.egg scikit-learn 0.21.3 is already the active version in easy-install.pth Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/scikit_learn-0.21.3-py3.7-linux-x86_64.egg Searching for tqdm==4.35.0 Best match: tqdm 4.35.0 Adding tqdm 4.35.0 to easy-install.pth file Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for matplotlib==3.1.1 Best match: matplotlib 3.1.1 Adding matplotlib 3.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for seaborn==0.9.0 Best match: seaborn 0.9.0 Adding seaborn 0.9.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for pandas==0.25.1 Best match: pandas 0.25.1 Adding pandas 0.25.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for numpy==1.17.2 Best match: numpy 1.17.2 Adding numpy 1.17.2 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for scipy==1.3.1 Best match: scipy 1.3.1 Adding scipy 1.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for joblib==0.13.2 Best match: joblib 0.13.2 Processing joblib-0.13.2-py3.7.egg joblib 0.13.2 is already the active version in easy-install.pth Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/joblib-0.13.2-py3.7.egg Searching for cycler==0.10.0 Best match: cycler 0.10.0 Adding cycler 0.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for python-dateutil==2.8.0 Best match: python-dateutil 2.8.0 Adding python-dateutil 2.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for kiwisolver==1.1.0 Best match: kiwisolver 1.1.0 Adding kiwisolver 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for pyparsing==2.4.2 Best match: pyparsing 2.4.2 Adding pyparsing 2.4.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for pytz==2019.2 Best match: pytz 2019.2 Adding pytz 2019.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for six==1.12.0 Best match: six 1.12.0 Adding six 1.12.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for setuptools==41.0.1 Best match: setuptools 41.0.1 Adding setuptools 41.0.1 to easy-install.pth file Installing easy_install script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Installing easy_install-3.6 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Finished processing dependencies for methylcheck==0.2.4 [rtd-command-info] start-time: 2019-09-09T16:46:04.520863Z, end-time: 2019-09-09T16:46:04.865355Z, duration: 0, exit-code: 0 cat conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. # # This file does only contain a selection of the most common options. For a # full list see the documentation: # http://www.sphinx-doc.org/en/master/config # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import sys sys.path.insert(0, os.path.abspath('.')) # -- Project information ----------------------------------------------------- project = 'methylcheck' copyright = '2019, Life Epigenetics' author = 'Life Epigenetics' # The short X.Y version version = '0.2' # The full version, including alpha/beta/rc tags release = '0.2' # -- General configuration --------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', 'sphinxcontrib.apidoc', 'm2r', 'nbsphinx' ] # instead of CLI "sphinx-autodoc . _build/html" you write this apidoc_module_dir = '.' apidoc_output_dir = '_sphinx_build' apidoc_excluded_paths = ['tests'] apidoc_separate_modules = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_sphinx_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] # source_suffix = '.rst' # The master toctree document. master_doc = 'index' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path . exclude_patterns = ['_sphinx_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' #'alabaster' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_sphinx_static'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # The default sidebars (for documents that don't match any pattern) are # defined by theme itself. Builtin themes are using these templates by # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', # 'searchbox.html']``. # # html_sidebars = {} # -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = 'methylcheckdoc' # -- Options for LaTeX output ------------------------------------------------ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'methylcheck.tex', 'methylcheck Documentation', 'Life Epigenetics', 'manual'), ] # -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'methylcheck', 'methylcheck Documentation', [author], 1) ] # -- Options for Texinfo output ---------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'methylcheck', 'methylcheck Documentation', author, 'methylcheck', 'One line description of project.', 'Miscellaneous'), ] # -- Extension configuration ------------------------------------------------- ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//readthedocs.com/projects/life-epigenetics-methylcheck/downloads/pdf/latest/"), ("html", "//readthedocs.com/projects/life-epigenetics-methylcheck/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/life-epigenetics-methylcheck/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylcheck', 'name': u'methylcheck', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://life-epigenetics-methylcheck.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'LifeEGX', 'github_repo': 'methylcheck', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '73d073bc', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' [rtd-command-info] start-time: 2019-09-09T16:46:04.973192Z, end-time: 2019-09-09T16:46:16.269806Z, duration: 11, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.QCreport.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.cli.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.filters.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.postprocessQC.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rawQC.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst. building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 8 source files that are out of date updating environment: 8 added, 0 changed, 0 removed reading sources... [ 12%] README reading sources... [ 25%] docs/demo-methylprep-to-methylcheck-example reading sources... [ 37%] docs/filtering_probes reading sources... [ 50%] docs/methylprep_methylcheck_example reading sources... [ 62%] docs/postprocessQC_example reading sources... [ 75%] docs/rawQC_example reading sources... [ 87%] docs/source/methylcheck reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:100: WARNING: Title level inconsistent: Filter either by the publication source, or by the type of effect (e.g. Polymorphism) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methylprep_methylcheck_example.ipynb:370: WARNING: Title level inconsistent: (These return a filtered data set) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_probes:8: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:26: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:31: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:34: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:43: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:47: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:57: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:36: WARNING: Unexpected section title. returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:41: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:2: WARNING: Unexpected section title. combine (or segment) datasets how it works ------------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:15: WARNING: Unexpected section title. inputs ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:16: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:18: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:21: WARNING: Unexpected section title. optional keyword arguments -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:32: WARNING: Unexpected section title. analysis parameters ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:34: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Title underline too short. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Unexpected section title. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:39: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/modules' looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 12%] README writing output... [ 25%] docs/demo-methylprep-to-methylcheck-example writing output... [ 37%] docs/filtering_probes writing output... [ 50%] docs/methylprep_methylcheck_example writing output... [ 62%] docs/postprocessQC_example writing output... [ 75%] docs/rawQC_example writing output... [ 87%] docs/source/methylcheck writing output... [100%] index generating indices... genindex py-modindex writing additional pages... search copying images... [ 5%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_demo-methylprep-to-methylcheck-example_7_1.png copying images... [ 11%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_demo-methylprep-to-methylcheck-example_8_0.png copying images... [ 17%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_demo-methylprep-to-methylcheck-example_9_3.png copying images... [ 23%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_filtering_probes_6_1.png copying images... 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[ 82%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_postprocessQC_example_7_0.png copying images... [ 88%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_postprocessQC_example_8_0.png copying images... [ 94%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_postprocessQC_example_13_0.png copying images... [100%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_postprocessQC_example_15_0.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_static' does not exist done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 35 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2019-09-09T16:46:16.410696Z, end-time: 2019-09-09T16:46:22.735191Z, duration: 6, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.QCreport.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.cli.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.filters.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.postprocessQC.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rawQC.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst. building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 8 added, 0 changed, 0 removed reading sources... [ 12%] README reading sources... [ 25%] docs/demo-methylprep-to-methylcheck-example reading sources... [ 37%] docs/filtering_probes reading sources... [ 50%] docs/methylprep_methylcheck_example reading sources... [ 62%] docs/postprocessQC_example reading sources... [ 75%] docs/rawQC_example reading sources... [ 87%] docs/source/methylcheck reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:100: WARNING: Title level inconsistent: Filter either by the publication source, or by the type of effect (e.g. Polymorphism) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methylprep_methylcheck_example.ipynb:370: WARNING: Title level inconsistent: (These return a filtered data set) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_probes:8: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:26: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:31: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:34: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:43: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:47: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:57: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:36: WARNING: Unexpected section title. returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:41: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:2: WARNING: Unexpected section title. combine (or segment) datasets how it works ------------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:15: WARNING: Unexpected section title. inputs ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:16: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:18: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:21: WARNING: Unexpected section title. optional keyword arguments -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:32: WARNING: Unexpected section title. analysis parameters ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:34: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Title underline too short. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Unexpected section title. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:39: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/modules' looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... docs/demo-methylprep-to-methylcheck-example docs/filtering_probes docs/methylprep_methylcheck_example docs/source/methylcheck writing... done writing additional files... copying images... 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WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 35 warnings. The HTML page is in _build/localmedia. [rtd-command-info] start-time: 2019-09-09T16:46:22.881008Z, end-time: 2019-09-09T16:46:30.832665Z, duration: 7, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.QCreport.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.cli.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.filters.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.postprocessQC.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rawQC.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst. 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Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:26: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:31: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:34: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:43: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:47: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:57: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:36: WARNING: Unexpected section title. returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:41: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:2: WARNING: Unexpected section title. combine (or segment) datasets how it works ------------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:15: WARNING: Unexpected section title. inputs ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:16: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:18: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:21: WARNING: Unexpected section title. optional keyword arguments -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:32: WARNING: Unexpected section title. analysis parameters ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:34: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Title underline too short. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Unexpected section title. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:39: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/modules' looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree done processing methylcheck.tex...index docs/demo-methylprep-to-methylcheck-example docs/filtering_probes docs/methylprep_methylcheck_example docs/source/methylcheck resolving references... README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://readthedocs.com/projects/life-epigenetics-methylcheck/badge/?version=latest) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/badge/License-MIT-yellow.svg) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://circleci.com/gh/LifeEGX/methylcheck.svg?style=shield&circle-token=58a514d3924fcfe0287c109d2323b7f697956ec9) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://ci.appveyor.com/api/projects/status/j15lpvjg1q9u2y17?svg=true) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://api.codacy.com/project/badge/Grade/aedf5c223e39415180ff35153b2bad89) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://coveralls.io/repos/github/LifeEGX/methylcheck/badge.svg?t=OVL45Q) writing... done copying images... 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' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2019-09-09T16:46:37.281720Z, end-time: 2019-09-09T16:46:43.425510Z, duration: 6, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=life-epigenetics-methylcheck -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylcheck" "methylcheck.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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[33] [34] LaTeX Warning: Reference `docs/source/methylcheck:module-methylcheck.cli' on pa ge 35 undefined on input line 1836. LaTeX Warning: Reference `docs/source/methylcheck:module-methylcheck.filters' o n page 35 undefined on input line 1837. LaTeX Warning: Reference `docs/source/methylcheck:module-methylcheck.postproces sQC' on page 35 undefined on input line 1838. [35] No file life-epigenetics-methylcheck.ind. (./life-epigenetics-methylcheck.aux) Package rerunfilecheck Warning: File `life-epigenetics-methylcheck.out' has cha nged. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on life-epigenetics-methylcheck.pdf (39 pages, 834197 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written Latexmk: Missing input file: 'life-epigenetics-methylcheck.ind' from line 'No file life-epigenetics-methylcheck.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Latexmk: List of undefined refs and citations: Reference `docs/source/methylcheck:module-methylcheck.cli' on page 35 undefined on input line 1836 Reference `docs/source/methylcheck:module-methylcheck.filters' on page 35 undefined on input line 1837 Reference `docs/source/methylcheck:module-methylcheck.postprocessQC' on page 35 undefined on input line 1838 Latexmk: Summary of warnings: Latex failed to resolve 3 reference(s) Rule 'makeindex life-epigenetics-methylcheck.idx': File changes, etc: Non-existent destination files: 'life-epigenetics-methylcheck.ind' ------------ Run number 1 of rule 'makeindex life-epigenetics-methylcheck.idx' ------------ ------------ Running 'makeindex -s python.ist -o "life-epigenetics-methylcheck.ind" "life-epigenetics-methylcheck.idx"' ------------ Latexmk: applying rule 'makeindex life-epigenetics-methylcheck.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file life-epigenetics-methylcheck.idx....done (17 entries accepted, 0 rejected). Sorting entries....done (78 comparisons). Generating output file life-epigenetics-methylcheck.ind....done (46 lines written, 0 warnings). Output written in life-epigenetics-methylcheck.ind. Transcript written in life-epigenetics-methylcheck.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylcheck.aux' 'life-epigenetics-methylcheck.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylcheck" "methylcheck.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./methylcheck.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on life-epigenetics-methylcheck.pdf (41 pages, 840687 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylcheck.aux' 'life-epigenetics-methylcheck.out' 'life-epigenetics-methylcheck.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylcheck" "methylcheck.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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Underfull \hbox (badness 10000) in paragraph at lines 1461--1464 \T1/ptm/m/n/10 `ch.9.98957343R_II_R_O_rep1_EPIC', `ch.9.98959675F_II_F_O_rep1_E PIC', Underfull \hbox (badness 10000) in paragraph at lines 1477--1477 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray\T1/ptm/m/n/10 , \T1 /ptm/m/it/10 no_sex=True\T1/ptm/m/n/10 , Overfull \hbox (135.51994pt too wide) in paragraph at lines 1484--1485 []\T1/ptm/m/n/10 {`27k', `450k', `EPIC'} or {`Il-lu-mi-naHu-man-Methy-la-tion27 k','IlluminaHumanMethylation450k','IlluminaHumanMethylationEPIC',} (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [28] Underfull \hbox (badness 10000) in paragraph at lines 1598--1598 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 save=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1625--1629 [] Overfull \hbox (182.34753pt too wide) in paragraph at lines 1625--1629 \T1/ptm/m/n/10 manifest_file = pd.read_csv(`/Users/nrigby/GitHub/stp-prelim-ana lysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[[`IlmnID', Underfull \hbox (badness 10000) in paragraph at lines 1625--1629 \T1/ptm/m/n/10 `CHR']] probe_names_no_sex_probes = man-i-fest_file.loc[manifest _file[`CHR'].apply(lambda Underfull \hbox (badness 10000) in paragraph at lines 1625--1629 \T1/ptm/m/n/10 x: x not in [`X', `Y', np.nan]), `Ilm-nID'].values probe_names_s ex_probes = man-i- [29] Underfull \hbox (badness 10000) in paragraph at lines 1758--1758 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cut-off=0.7\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1758--1758 \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1758--1758 \T1/ptm/m/it/10 save=False\T1/ptm/m/n/10 , [30] Underfull \hbox (badness 10000) in paragraph at lines 1788--1788 []\T1/ptm/m/it/10 df1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 df2\T1/ptm/m/n/10 , \T1/p tm/m/it/10 save=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n /10 , [31] [32] Chapter 5. [33] [34] [35] (./life-epigenetics-methylcheck.ind [36] Underfull \hbox (badness 10000) in paragraph at lines 8--10 []\T1/pcr/m/n/10 beta_density_plot() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 10--11 []\T1/pcr/m/n/10 beta_mds_plot() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 15--16 []\T1/pcr/m/n/10 combine_mds() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/pcr/m/n/10 cumulative_sum_beta_distribution() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/pcr/m/n/10 drop_nan_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/pcr/m/n/10 exclude_sex_control_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 35--36 []\T1/pcr/m/n/10 list_problem_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 39--41 []\T1/pcr/m/n/10 mean_beta_compare() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 41--42 []\T1/pcr/m/n/10 mean_beta_plot() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule [37]) (./life-epigenetics-methylcheck.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on life-epigenetics-methylcheck.pdf (41 pages, 840746 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2019-09-09T16:46:43.529316Z, end-time: 2019-09-09T16:46:43.884898Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/./_build/latex/life-epigenetics-methylcheck.pdf /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/artifacts/latest/sphinx_pdf/life-epigenetics-methylcheck.pdf [rtd-command-info] start-time: 2019-09-09T16:46:43.974529Z, end-time: 2019-09-09T16:47:00.637598Z, duration: 16, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.QCreport.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.cli.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.filters.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.postprocessQC.rst. 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:100: WARNING: Title level inconsistent: Filter either by the publication source, or by the type of effect (e.g. Polymorphism) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methylprep_methylcheck_example.ipynb:370: WARNING: Title level inconsistent: (These return a filtered data set) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_probes:8: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title. 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Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title. 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