Read the Docs build information
Build id: 299411
Project: life-epigenetics-methylcheck
Version: latest
Commit: 71b4515fbec1b3f31cac23141c3df6f0bebc9a52
Date: 2020-03-09T21:47:22.424253Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-03-09T21:47:25.126420Z, end-time: 2020-03-09T21:47:34.294445Z, duration: 9, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/LifeEGX/methylcheck.git .
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[rtd-command-info] start-time: 2020-03-09T21:47:34.664669Z, end-time: 2020-03-09T21:47:35.376041Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 71b4515 v0.4.0 (#27)

[rtd-command-info] start-time: 2020-03-09T21:47:35.532319Z, end-time: 2020-03-09T21:47:35.858469Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-03-09T21:47:38.608591Z, end-time: 2020-03-09T21:47:43.746489Z, duration: 5, exit-code: 0
python3.7 -mvirtualenv --no-site-packages 
Using base prefix '/home/docs/.pyenv/versions/3.7.3'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-03-09T21:47:43.908530Z, end-time: 2020-03-09T21:47:44.874797Z, duration: 0, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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 (20.0.2)

[rtd-command-info] start-time: 2020-03-09T21:47:45.179755Z, end-time: 2020-03-09T21:47:56.722511Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=67d9e5431c276189bda3b32d910bdbe039af87d33f1fdbd350f114e72bfac994
  Stored in directory: /tmp/pip-ephem-wheel-cache-i9_et7yd/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b
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Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, idna, urllib3, chardet, certifi, requests, MarkupSafe, Jinja2, snowballstemmer, six, pyparsing, packaging, pytz, babel, imagesize, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
    Found existing installation: setuptools 46.0.0
    Uninstalling setuptools-46.0.0:
      Successfully uninstalled setuptools-46.0.0
Successfully installed Jinja2-2.11.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.3 pillow-5.4.1 pyparsing-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.0 urllib3-1.25.8

[rtd-command-info] start-time: 2020-03-09T21:47:56.888231Z, end-time: 2020-03-09T21:48:27.290751Z, duration: 30, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 9)) (2.3.1)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 9)) (41.0.1)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 9)) (0.7.12)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 9)) (2.11.1)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 9)) (2.0.0)
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Building wheels for collected packages: m2r, tornado, backcall, pandocfilters, pyrsistent
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  Building wheel for tornado (setup.py): finished with status 'done'
  Created wheel for tornado: filename=tornado-6.0.4-cp37-cp37m-linux_x86_64.whl size=428563 sha256=92fe0599fb5eaa2c0ad0c8106f1ebb05b6fd0f888366f05f9bcde3a373c80a5c
  Stored in directory: /tmp/pip-ephem-wheel-cache-13g6s808/wheels/7d/14/fa/d88fb5da77d813ea0ffca38a2ab2a052874e9e1142bad0b348
  Building wheel for backcall (setup.py): started
  Building wheel for backcall (setup.py): finished with status 'done'
  Created wheel for backcall: filename=backcall-0.1.0-py3-none-any.whl size=10413 sha256=4212fbb871af0aff68870694777ce400a1e591451a5e1f0ec85776da132c918d
  Stored in directory: /tmp/pip-ephem-wheel-cache-13g6s808/wheels/9e/56/4f/da13e448a8a5b8671b2954600d5355cf36e557c7aa5020139b
  Building wheel for pandocfilters (setup.py): started
  Building wheel for pandocfilters (setup.py): finished with status 'done'
  Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7856 sha256=c157c22737b28564191d8b55b5a3bf27883e48342651126ee0e914c18946555d
  Stored in directory: /tmp/pip-ephem-wheel-cache-13g6s808/wheels/63/99/01/9fe785b86d1e091a6b2a61e06ddb3d8eb1bc9acae5933d4740
  Building wheel for pyrsistent (setup.py): started
  Building wheel for pyrsistent (setup.py): finished with status 'done'
  Created wheel for pyrsistent: filename=pyrsistent-0.15.7-cp37-cp37m-linux_x86_64.whl size=115957 sha256=c651c3ecfe7d20ce4380fad36ba9bce77e95b4921816e0e8e87941fecb45e6a4
  Stored in directory: /tmp/pip-ephem-wheel-cache-13g6s808/wheels/57/74/e3/61db397ec89f304e49711ec9f68490f15814b80c1c0ee9b8c0
Successfully built m2r tornado backcall pandocfilters pyrsistent
Installing collected packages: numpy, python-dateutil, pandas, scipy, cycler, kiwisolver, matplotlib, seaborn, xlrd, zipp, importlib-metadata, pluggy, wcwidth, py, more-itertools, attrs, pytest, coverage, pbr, sphinxcontrib-apidoc, mistune, m2r, tqdm, decorator, ipython-genutils, traitlets, jupyter-core, pyzmq, tornado, jupyter-client, parso, jedi, prompt-toolkit, backcall, pickleshare, ptyprocess, pexpect, ipython, ipykernel, pyrsistent, jsonschema, nbformat, entrypoints, pandocfilters, webencodings, bleach, defusedxml, testpath, nbconvert, nbsphinx
Successfully installed attrs-19.3.0 backcall-0.1.0 bleach-3.1.1 coverage-5.0.3 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-1.5.0 ipykernel-5.1.4 ipython-7.13.0 ipython-genutils-0.2.0 jedi-0.16.0 jsonschema-3.2.0 jupyter-client-6.0.0 jupyter-core-4.6.3 kiwisolver-1.1.0 m2r-0.2.1 matplotlib-3.2.0 mistune-0.8.4 more-itertools-8.2.0 nbconvert-5.6.1 nbformat-5.0.4 nbsphinx-0.5.1 numpy-1.18.1 pandas-1.0.1 pandocfilters-1.4.2 parso-0.6.2 pbr-5.4.4 pexpect-4.8.0 pickleshare-0.7.5 pluggy-0.13.1 prompt-toolkit-3.0.4 ptyprocess-0.6.0 py-1.8.1 pyrsistent-0.15.7 pytest-5.3.5 python-dateutil-2.8.1 pyzmq-19.0.0 scipy-1.4.1 seaborn-0.10.0 sphinxcontrib-apidoc-0.3.0 testpath-0.4.4 tornado-6.0.4 tqdm-4.43.0 traitlets-4.3.3 wcwidth-0.1.8 webencodings-0.5.1 xlrd-1.2.0 zipp-3.1.0

[rtd-command-info] start-time: 2020-03-09T21:48:27.448435Z, end-time: 2020-03-09T21:48:30.805339Z, duration: 3, 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
creating methylcheck.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
writing manifest file 'methylcheck.egg-info/SOURCES.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
creating build/lib
creating build/lib/methylcheck
copying methylcheck/qc_report.py -> build/lib/methylcheck
copying methylcheck/progress_bar.py -> build/lib/methylcheck
copying methylcheck/__init__.py -> build/lib/methylcheck
copying methylcheck/read_geo_processed.py -> build/lib/methylcheck
copying methylcheck/qc_plot.py -> build/lib/methylcheck
copying methylcheck/cli.py -> build/lib/methylcheck
copying methylcheck/__main__.py -> build/lib/methylcheck
copying methylcheck/p_value_probe_detection.py -> build/lib/methylcheck
copying methylcheck/load_processed.py -> build/lib/methylcheck
creating build/lib/methylcheck/data_files
copying methylcheck/data_files/__init__.py -> build/lib/methylcheck/data_files
creating build/lib/methylcheck/predict
copying methylcheck/predict/__init__.py -> build/lib/methylcheck/predict
copying methylcheck/predict/sex.py -> build/lib/methylcheck/predict
copying methylcheck/data_files/450k_control.npy -> build/lib/methylcheck/data_files
copying methylcheck/data_files/450k_polymorphic_crossRxtve_probes.csv.gz -> build/lib/methylcheck/data_files
copying methylcheck/data_files/450k_sex.npy -> build/lib/methylcheck/data_files
copying methylcheck/data_files/EPIC+_control.npy -> build/lib/methylcheck/data_files
copying methylcheck/data_files/EPIC+_sex.npy -> build/lib/methylcheck/data_files
copying methylcheck/data_files/EPIC_control.npy -> build/lib/methylcheck/data_files
copying methylcheck/data_files/EPIC_polymorphic_crossRxtve_probes.csv.gz -> build/lib/methylcheck/data_files
copying methylcheck/data_files/EPIC_sex.npy -> build/lib/methylcheck/data_files
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/qc_report.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_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_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/__init__.py -> 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+_control.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/data_files/450k_polymorphic_crossRxtve_probes.csv.gz -> build/bdist.linux-x86_64/egg/methylcheck/data_files
copying build/lib/methylcheck/progress_bar.py -> build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/read_geo_processed.py -> build/bdist.linux-x86_64/egg/methylcheck
creating build/bdist.linux-x86_64/egg/methylcheck/predict
copying build/lib/methylcheck/predict/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck/predict
copying build/lib/methylcheck/predict/sex.py -> build/bdist.linux-x86_64/egg/methylcheck/predict
copying build/lib/methylcheck/qc_plot.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/__main__.py -> build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/p_value_probe_detection.py -> build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/load_processed.py -> build/bdist.linux-x86_64/egg/methylcheck
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/qc_report.py to qc_report.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/data_files/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/progress_bar.py to progress_bar.cpython-37.pyc
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/read_geo_processed.py to read_geo_processed.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/predict/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/predict/sex.py to sex.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/qc_plot.py to qc_plot.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/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/p_value_probe_detection.py to p_value_probe_detection.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/load_processed.py to load_processed.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
creating 'dist/methylcheck-0.4.0-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-0.4.0-py3.7.egg
Copying methylcheck-0.4.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Adding methylcheck 0.4.0 to easy-install.pth file
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-0.4.0-py3.7.egg
Processing dependencies for methylcheck==0.4.0
Searching for scikit-learn
Reading https://pypi.org/simple/scikit-learn/
Downloading https://files.pythonhosted.org/packages/41/b6/126263db075fbcc79107749f906ec1c7639f69d2d017807c6574792e517e/scikit_learn-0.22.2.post1-cp37-cp37m-manylinux1_x86_64.whl#sha256=84e759a766c315deb5c85139ff879edbb0aabcddb9358acf499564ed1c21e337
Best match: scikit-learn 0.22.2.post1
Processing scikit_learn-0.22.2.post1-cp37-cp37m-manylinux1_x86_64.whl
Installing scikit_learn-0.22.2.post1-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/scikit_learn-0.22.2.post1-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt
Adding scikit-learn 0.22.2.post1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/scikit_learn-0.22.2.post1-py3.7-linux-x86_64.egg
Searching for joblib>=0.11
Reading https://pypi.org/simple/joblib/
Downloading https://files.pythonhosted.org/packages/28/5c/cf6a2b65a321c4a209efcdf64c2689efae2cb62661f8f6f4bb28547cf1bf/joblib-0.14.1-py2.py3-none-any.whl#sha256=bdb4fd9b72915ffb49fde2229ce482dd7ae79d842ed8c2b4c932441495af1403
Best match: joblib 0.14.1
Processing joblib-0.14.1-py2.py3-none-any.whl
Installing joblib-0.14.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Adding joblib 0.14.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/joblib-0.14.1-py3.7.egg
Searching for tqdm==4.43.0
Best match: tqdm 4.43.0
Adding tqdm 4.43.0 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==3.2.0
Best match: matplotlib 3.2.0
Adding matplotlib 3.2.0 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 seaborn==0.10.0
Best match: seaborn 0.10.0
Adding seaborn 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 pandas==1.0.1
Best match: pandas 1.0.1
Adding pandas 1.0.1 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==1.18.1
Best match: numpy 1.18.1
Adding numpy 1.18.1 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==1.4.1
Best match: scipy 1.4.1
Adding scipy 1.4.1 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 pyparsing==2.4.6
Best match: pyparsing 2.4.6
Adding pyparsing 2.4.6 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==2.8.1
Best match: python-dateutil 2.8.1
Adding python-dateutil 2.8.1 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 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 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 pytz==2019.3
Best match: pytz 2019.3
Adding pytz 2019.3 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==1.14.0
Best match: six 1.14.0
Adding six 1.14.0 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==0.4.0

[rtd-command-info] start-time: 2020-03-09T21:48:32.079106Z, end-time: 2020-03-09T21:48:32.387027Z, 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", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/pdf/"),
    ("html", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"),
    ("epub", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/epub/"),
    ],
    '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',
    'proxied_api_host': '/_',
    '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': '71b4515f',
}




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: 2020-03-09T21:48:32.547186Z, end-time: 2020-03-09T21:48:46.887624Z, duration: 14, 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.cli.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.load_processed.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.p_value_probe_detection.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.progress_bar.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.qc_plot.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.qc_report.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.read_geo_processed.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/methylcheck.data_files.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.sex.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.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 13 source files that are out of date
updating environment: 13 added, 0 changed, 0 removed
reading sources... [  7%] README
reading sources... [ 15%] docs/another-methylcheck-qc-example
reading sources... [ 23%] docs/demo-methylprep-to-methylcheck-example
reading sources... [ 30%] docs/demo_qc_functions
reading sources... [ 38%] docs/demo_read_geo_processed
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reading sources... [ 53%] docs/filtering_probes
reading sources... [ 61%] docs/methylprep_methylcheck_example
reading sources... [ 69%] docs/postprocessQC_example
reading sources... [ 76%] docs/pval
reading sources... [ 84%] docs/rawQC_example
reading sources... [ 92%] docs/source/methylcheck
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:98: 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:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARNING: autodoc: failed to import module 'filters' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.filters'
WARNING: autodoc: failed to import module 'postprocessQC' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.postprocessQC'
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/pval.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
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writing output... [ 76%] docs/pval
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writing output... [ 92%] docs/source/methylcheck
writing output... [100%] index

generating indices... genindex py-modindex
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writing additional pages... search
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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, 9 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2020-03-09T21:48:47.097737Z, end-time: 2020-03-09T21:49:01.872333Z, duration: 14, 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.cli.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.load_processed.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.p_value_probe_detection.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.progress_bar.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.qc_plot.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.qc_report.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.read_geo_processed.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/methylcheck.data_files.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.sex.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.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: 33 added, 0 changed, 0 removed
reading sources... [  3%] README
reading sources... [  6%] _build/doctrees-readthedocs/nbsphinx/docs/another-methylcheck-qc-example
reading sources... [  9%] _build/doctrees-readthedocs/nbsphinx/docs/demo-methylprep-to-methylcheck-example
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/html/docs/filtering_probes.ipynb:98: 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/_build/html/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:98: 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:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARNING: autodoc: failed to import module 'filters' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.filters'
WARNING: autodoc: failed to import module 'postprocessQC' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.postprocessQC'
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[rtd-command-info] start-time: 2020-03-09T21:49:02.106837Z, end-time: 2020-03-09T21:49:27.403894Z, duration: 25, 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...
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/filtering_probes.ipynb:98: 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/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/html/docs/filtering_probes.ipynb:98: 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/_build/html/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:98: 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:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARNING: autodoc: failed to import module 'filters' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.filters'
WARNING: autodoc: failed to import module 'postprocessQC' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.postprocessQC'
looking for now-outdated files... none found
pickling environment... done
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done
processing methylcheck.tex...index docs/demo-methylprep-to-methylcheck-example docs/demo_read_geo_processed docs/filtering_probes docs/methylprep_methylcheck_example docs/demo_qc_functions docs/another-methylcheck-qc-example docs/demo_using_matched_meta_data docs/source/methylcheck 
resolving references...
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copying TeX support files...
done
build succeeded, 74 warnings.

The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
(use `make latexpdf' here to do that automatically).

[rtd-command-info] start-time: 2020-03-09T21:49:47.100389Z, end-time: 2020-03-09T21:49:47.413151Z, duration: 0, exit-code: 0
cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %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: 2020-03-09T21:49:47.584171Z, end-time: 2020-03-09T21:50:06.495239Z, duration: 18, 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, <GEN1> chunk 1.
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Subroutine makeglo redefined at (eval 11) line 7, <GEN2> chunk 1.
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Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
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Chapter 7.
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Writing index file life-epigenetics-methylcheck.idx
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(./life-epigenetics-methylcheck.out) (./life-epigenetics-methylcheck.out)
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>><<oms.cmap>><<omx.cmap>>
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nts/map/pdftex/updmap/pdftex.map}] [2] (./life-epigenetics-methylcheck.toc)
[1] [2]

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Chapter 1.
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Chapter 2.
[5] [6]
Chapter 3.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8]
Chapter 4.
[9] [10]
Chapter 5.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [11] [12]
Chapter 6.
[13]

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Chapter 7.
[85] [86] [87] (./life-epigenetics-methylcheck.ind [88] [89])
(./life-epigenetics-methylcheck.aux) )
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Output written on life-epigenetics-methylcheck.pdf (93 pages, 3871544 bytes).
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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: 2020-03-09T21:50:06.684885Z, end-time: 2020-03-09T21:50:06.998795Z, duration: 0, exit-code: 0
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[rtd-command-info] start-time: 2020-03-09T21:50:07.157089Z, end-time: 2020-03-09T21:51:10.702232Z, duration: 63, 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
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
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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/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/filtering_probes.ipynb:98: 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/_build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/nbsphinx/_build/html/docs/filtering_probes.ipynb:98: 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/_build/doctrees/nbsphinx/_build/html/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/nbsphinx/docs/filtering_probes.ipynb:98: 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/_build/doctrees/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/html/docs/filtering_probes.ipynb:98: 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/_build/html/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:98: 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:362: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARNING: autodoc: failed to import module 'filters' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.filters'
WARNING: autodoc: failed to import module 'postprocessQC' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.postprocessQC'
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/_build/doctrees-readthedocs/nbsphinx/docs/another-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree
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build succeeded, 261 warnings.

The ePub file is in _build/epub.

[rtd-command-info] start-time: 2020-03-09T21:51:10.940987Z, end-time: 2020-03-09T21:51:11.264382Z, duration: 0, exit-code: 0
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