Read the Docs build information
Build id: 473120
Project: life-epigenetics-methylcheck
Version: latest
Commit: fd7d1fadcef5153edaea319eef668a81d31d3629
Date: 2020-11-06T19:57:13.249527Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-11-06T19:57:14.866661Z, end-time: 2020-11-06T19:57:27.220331Z, duration: 12, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylcheck.git .
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[rtd-command-info] start-time: 2020-11-06T19:57:27.584515Z, end-time: 2020-11-06T19:57:27.933540Z, 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 fd7d1fa v0.6.4 (#36)

[rtd-command-info] start-time: 2020-11-06T19:57:28.050224Z, end-time: 2020-11-06T19:57:28.102607Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-11-06T19:57:34.820876Z, end-time: 2020-11-06T19:57:38.726259Z, duration: 3, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
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: 2020-11-06T19:57:38.911285Z, end-time: 2020-11-06T19:57:39.596032Z, 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 (20.2.4)

[rtd-command-info] start-time: 2020-11-06T19:57:39.706770Z, end-time: 2020-11-06T19:57:47.862467Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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<2.2
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=f619e60cdb78a68e168f78d193a566aba58ff9e543227e575a699c718a7f2c38
  Stored in directory: /tmp/pip-ephem-wheel-cache-k3srxy0a/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b
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Successfully built mock future
Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, snowballstemmer, MarkupSafe, Jinja2, pytz, babel, Pygments, six, imagesize, certifi, urllib3, chardet, idna, requests, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, pyparsing, packaging, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
    Found existing installation: setuptools 50.3.2
    Uninstalling setuptools-50.3.2:
      Successfully uninstalled setuptools-50.3.2
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.2 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.11

[rtd-command-info] start-time: 2020-11-06T19:57:48.004413Z, end-time: 2020-11-06T19:58:07.002399Z, duration: 18, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.15.0)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (41.0.1)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (20.4)
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->-r requirements.txt (line 11)) (0.7.12)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.2.4)
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->-r requirements.txt (line 11)) (2.0.0)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (2.24.0)
Requirement already satisfied: 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->-r requirements.txt (line 11)) (2.8.0)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.2.0)
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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->-r requirements.txt (line 11)) (2020.6.20)
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Building wheels for collected packages: m2r, pandocfilters, pyrsistent
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  Stored in directory: /tmp/pip-ephem-wheel-cache-d11gc67b/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f
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  Building wheel for pandocfilters (setup.py): finished with status 'done'
  Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=7991 sha256=32222bdc33ceda44a672f059ac889e3310ff368b71af9b4889ecccdab5e15ed0
  Stored in directory: /tmp/pip-ephem-wheel-cache-d11gc67b/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000
  Building wheel for pyrsistent (setup.py): started
  Building wheel for pyrsistent (setup.py): finished with status 'done'
  Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp37-cp37m-linux_x86_64.whl size=115299 sha256=848d77f1eb01fc3852eeccf818c350a610ebb4aa7f644c316da1160205598d90
  Stored in directory: /tmp/pip-ephem-wheel-cache-d11gc67b/wheels/a5/52/bf/71258a1d7b3c8cbe1ee53f9314c6f65f20385481eaee573cc5
Successfully built m2r pandocfilters pyrsistent
Installing collected packages: numpy, python-dateutil, pandas, scipy, kiwisolver, cycler, matplotlib, seaborn, xlrd, tqdm, pbr, sphinxcontrib-apidoc, mistune, m2r, ipython-genutils, traitlets, defusedxml, webencodings, bleach, jupyter-core, attrs, zipp, importlib-metadata, pyrsistent, jsonschema, nbformat, async-generator, nest-asyncio, pyzmq, tornado, jupyter-client, nbclient, jupyterlab-pygments, entrypoints, pandocfilters, testpath, nbconvert, nbsphinx, wcwidth, prompt-toolkit, backcall, decorator, ptyprocess, pexpect, parso, jedi, pickleshare, ipython, ipykernel
Successfully installed async-generator-1.10 attrs-20.3.0 backcall-0.2.0 bleach-3.2.1 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-2.0.0 ipykernel-5.3.4 ipython-7.19.0 ipython-genutils-0.2.0 jedi-0.17.2 jsonschema-3.2.0 jupyter-client-6.1.7 jupyter-core-4.6.3 jupyterlab-pygments-0.1.2 kiwisolver-1.3.1 m2r-0.2.1 matplotlib-3.1.2 mistune-0.8.4 nbclient-0.5.1 nbconvert-6.0.7 nbformat-5.0.8 nbsphinx-0.8.0 nest-asyncio-1.4.2 numpy-1.19.4 pandas-1.1.4 pandocfilters-1.4.3 parso-0.7.1 pbr-5.5.1 pexpect-4.8.0 pickleshare-0.7.5 prompt-toolkit-3.0.8 ptyprocess-0.6.0 pyrsistent-0.17.3 python-dateutil-2.8.1 pyzmq-19.0.2 scipy-1.5.4 seaborn-0.11.0 sphinxcontrib-apidoc-0.3.0 testpath-0.4.4 tornado-6.1 tqdm-4.51.0 traitlets-5.0.5 wcwidth-0.2.5 webencodings-0.5.1 xlrd-1.2.0 zipp-3.4.0

[rtd-command-info] start-time: 2020-11-06T19:58:07.158590Z, end-time: 2020-11-06T19:58:09.685562Z, duration: 2, 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/version.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/samples
copying methylcheck/samples/sklearn_mds.py -> build/lib/methylcheck/samples
copying methylcheck/samples/assign_groups.py -> build/lib/methylcheck/samples
copying methylcheck/samples/__init__.py -> build/lib/methylcheck/samples
copying methylcheck/samples/postprocessQC.py -> build/lib/methylcheck/samples
creating build/lib/methylcheck/predict
copying methylcheck/predict/__init__.py -> build/lib/methylcheck/predict
copying methylcheck/predict/sex.py -> build/lib/methylcheck/predict
creating build/lib/methylcheck/probes
copying methylcheck/probes/__init__.py -> build/lib/methylcheck/probes
copying methylcheck/probes/filters.py -> build/lib/methylcheck/probes
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
copying methylcheck/data_files/illumina_sketchy_probes_996.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/illumina_sketchy_probes_996.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_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
creating build/bdist.linux-x86_64/egg/methylcheck/samples
copying build/lib/methylcheck/samples/sklearn_mds.py -> build/bdist.linux-x86_64/egg/methylcheck/samples
copying build/lib/methylcheck/samples/assign_groups.py -> build/bdist.linux-x86_64/egg/methylcheck/samples
copying build/lib/methylcheck/samples/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck/samples
copying build/lib/methylcheck/samples/postprocessQC.py -> build/bdist.linux-x86_64/egg/methylcheck/samples
copying build/lib/methylcheck/read_geo_processed.py -> build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/version.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
creating build/bdist.linux-x86_64/egg/methylcheck/probes
copying build/lib/methylcheck/probes/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck/probes
copying build/lib/methylcheck/probes/filters.py -> build/bdist.linux-x86_64/egg/methylcheck/probes
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/samples/sklearn_mds.py to sklearn_mds.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/samples/assign_groups.py to assign_groups.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/samples/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/samples/postprocessQC.py to postprocessQC.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/version.py to version.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/probes/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/probes/filters.py to filters.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-0.6.4-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-0.6.4-py3.7.egg
Copying methylcheck-0.6.4-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Adding methylcheck 0.6.4 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-0.6.4-py3.7.egg
Processing dependencies for methylcheck==0.6.4
Searching for statsmodels
Reading https://pypi.org/simple/statsmodels/
Downloading https://files.pythonhosted.org/packages/93/97/67bf20df36a88ce8dd84828f83453b91177e1ff0abd8c92f2e0a47782689/statsmodels-0.12.1-cp37-cp37m-manylinux1_x86_64.whl#sha256=588c0f7e29403161ca952dcdad3d67970583742e9f11f66c7c5b08ac97a0408c
Best match: statsmodels 0.12.1
Processing statsmodels-0.12.1-cp37-cp37m-manylinux1_x86_64.whl
Installing statsmodels-0.12.1-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/statsmodels-0.12.1-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt
Adding statsmodels 0.12.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/statsmodels-0.12.1-py3.7-linux-x86_64.egg
Searching for patsy>=0.5
Reading https://pypi.org/simple/patsy/
Downloading https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl#sha256=5465be1c0e670c3a965355ec09e9a502bf2c4cbe4875e8528b0221190a8a5d40
Best match: patsy 0.5.1
Processing patsy-0.5.1-py2.py3-none-any.whl
Installing patsy-0.5.1-py2.py3-none-any.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/patsy-0.5.1-py3.7.egg/EGG-INFO/requires.txt
Adding patsy 0.5.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/patsy-0.5.1-py3.7.egg
Searching for tqdm==4.51.0
Best match: tqdm 4.51.0
Adding tqdm 4.51.0 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 seaborn==0.11.0
Best match: seaborn 0.11.0
Adding seaborn 0.11.0 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 matplotlib==3.1.2
Best match: matplotlib 3.1.2
Adding matplotlib 3.1.2 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 pandas==1.1.4
Best match: pandas 1.1.4
Adding pandas 1.1.4 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==1.19.4
Best match: numpy 1.19.4
Adding numpy 1.19.4 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==1.5.4
Best match: scipy 1.5.4
Adding scipy 1.5.4 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==1.3.1
Best match: kiwisolver 1.3.1
Adding kiwisolver 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 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 pyparsing==2.4.7
Best match: pyparsing 2.4.7
Adding pyparsing 2.4.7 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 pytz==2020.4
Best match: pytz 2020.4
Adding pytz 2020.4 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==1.15.0
Best match: six 1.15.0
Adding six 1.15.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Finished processing dependencies for methylcheck==0.6.4

[rtd-command-info] start-time: 2020-11-06T19:58:10.830827Z, end-time: 2020-11-06T19:58:10.900212Z, 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',
    'sphinx.ext.autosummary'
]

# 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://assets.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://assets.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',
    'github_user': 'FOXOBioScience',
    'proxied_api_host': '/_',
    '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,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'fd7d1fad',
}




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'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2020-11-06T19:58:11.018399Z, end-time: 2020-11-06T19:58:20.646545Z, duration: 9, 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.version.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/methylcheck.probes.filters.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.probes.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.assign_groups.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.postprocessQC.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.sklearn_mds.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.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 15 source files that are out of date
updating environment: 15 added, 0 changed, 0 removed
reading sources... [  6%] README
reading sources... [ 13%] docs/another-methylcheck-qc-example
reading sources... [ 20%] docs/demo-methylprep-to-methylcheck-example
reading sources... [ 26%] docs/demo_qc_functions
reading sources... [ 33%] docs/demo_read_geo_processed
reading sources... [ 40%] docs/demo_using_matched_meta_data
reading sources... [ 46%] docs/filtering_probes
reading sources... [ 53%] docs/methylprep_methylcheck_example
reading sources... [ 60%] docs/postprocessQC_example
reading sources... [ 66%] docs/pval
reading sources... [ 73%] docs/rawQC_example
reading sources... [ 80%] docs/release-history
reading sources... [ 86%] docs/source/methylcheck
reading sources... [ 93%] docs/testing_sns_upgrade_methylcheck_v0.6.2
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:106: 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:404: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.cli
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.run_pipeline
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.run_qc
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.read_geo
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.load
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.load_both
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.qc_signal_intensity
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_M_vs_U
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_controls
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_beta_by_type
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.list_problem_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.exclude_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.exclude_sex_control_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.drop_nan_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.samples
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.sample_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.beta_density_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.mean_beta_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.mean_beta_compare
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.beta_mds_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.combine_mds
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.cumulative_sum_beta_distribution
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.predict
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.get_sex
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.assign
WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
WARNING: autodoc: failed to import module 'probes' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
WARNING: autodoc: failed to import module 'samples' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
WARNING: autodoc: failed to import module 'predict' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/testing_sns_upgrade_methylcheck_v0.6.2.ipynb:6: WARNING: Each notebook should have at least one section title
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
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  6%] README
writing output... [ 13%] docs/another-methylcheck-qc-example
writing output... [ 20%] docs/demo-methylprep-to-methylcheck-example
writing output... [ 26%] docs/demo_qc_functions
writing output... [ 33%] docs/demo_read_geo_processed
writing output... [ 40%] docs/demo_using_matched_meta_data
writing output... [ 46%] docs/filtering_probes
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writing output... [ 60%] docs/postprocessQC_example
writing output... [ 66%] docs/pval
writing output... [ 73%] docs/rawQC_example
writing output... [ 80%] docs/release-history
writing output... [ 86%] docs/source/methylcheck
writing output... [ 93%] docs/testing_sns_upgrade_methylcheck_v0.6.2
writing output... [100%] index

generating indices... genindex
copying notebooks ... [  9%] docs/another-methylcheck-qc-example.ipynb
copying notebooks ... [ 18%] docs/demo-methylprep-to-methylcheck-example.ipynb
copying notebooks ... [ 27%] docs/demo_qc_functions.ipynb
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writing additional pages... search
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[rtd-command-info] start-time: 2020-11-06T19:58:20.929228Z, end-time: 2020-11-06T19:58:27.073820Z, 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.
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:106: 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:404: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.cli
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.run_pipeline
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.run_qc
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.read_geo
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.load
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.load_both
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.qc_signal_intensity
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_M_vs_U
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_controls
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_beta_by_type
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.list_problem_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.exclude_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.exclude_sex_control_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.drop_nan_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.samples
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.sample_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.beta_density_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.mean_beta_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.mean_beta_compare
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.beta_mds_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.combine_mds
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.cumulative_sum_beta_distribution
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.predict
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.get_sex
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.assign
WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
WARNING: autodoc: failed to import module 'probes' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
WARNING: autodoc: failed to import module 'samples' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
WARNING: autodoc: failed to import module 'predict' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/testing_sns_upgrade_methylcheck_v0.6.2.ipynb:6: WARNING: Each notebook should have at least one section title
looking for now-outdated files... none found
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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
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... docs/demo-methylprep-to-methylcheck-example docs/source/methylcheck 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/release-history 
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[rtd-command-info] start-time: 2020-11-06T19:58:27.265345Z, end-time: 2020-11-06T19:58:36.722385Z, duration: 9, 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.
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:106: 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:404: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.cli
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.run_pipeline
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.run_qc
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.read_geo
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.load
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.load_both
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.qc_signal_intensity
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_M_vs_U
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_controls
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_beta_by_type
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.list_problem_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.exclude_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.exclude_sex_control_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.drop_nan_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.samples
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.sample_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.beta_density_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.mean_beta_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.mean_beta_compare
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.beta_mds_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.combine_mds
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.cumulative_sum_beta_distribution
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.predict
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.get_sex
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.assign
WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
WARNING: autodoc: failed to import module 'probes' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
WARNING: autodoc: failed to import module 'samples' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
WARNING: autodoc: failed to import module 'predict' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/testing_sns_upgrade_methylcheck_v0.6.2.ipynb:6: WARNING: Each notebook should have at least one section title
looking for now-outdated files... none found
pickling environment... done
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/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
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree
done
processing methylcheck.tex...index docs/demo-methylprep-to-methylcheck-example docs/source/methylcheck 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/release-history 
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copying TeX support files...
done
build succeeded, 47 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).
WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/latex/_static/searchtools.js

[rtd-command-info] start-time: 2020-11-06T19:58:42.978598Z, end-time: 2020-11-06T19:58:43.034390Z, 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: 2020-11-06T19:58:43.176665Z, end-time: 2020-11-06T19:59:00.175284Z, duration: 16, 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.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, <GEN2> chunk 1.
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Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, <GEN2> 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'...
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>
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Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual)
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[]\T1/ptm/m/n/10 Exclude probes

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Chapter 7.
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 ...                                              
                                                  
l.228 ...3083485633693ce12e4792f1127c13dbb3}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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Type  H <return>  for immediate help.
 ...                                              
                                                  
l.230 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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Type  H <return>  for immediate help.
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l.230 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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Type  H <return>  for immediate help.
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l.232 ...3db41518e0f48edea52227/methylcheck}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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Type  H <return>  for immediate help.
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l.232 ...3db41518e0f48edea52227/methylcheck}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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Type  H <return>  for immediate help.
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l.234 ...2750c371f4f88911b/j15lpvjg1q9u2y17}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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Type  H <return>  for immediate help.
 ...                                              
                                                  
l.234 ...2750c371f4f88911b/j15lpvjg1q9u2y17}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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Type  H <return>  for immediate help.
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l.236 ...3/aedf5c223e39415180ff35153b2bad89}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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Type  H <return>  for immediate help.
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l.236 ...3/aedf5c223e39415180ff35153b2bad89}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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Type  H <return>  for immediate help.
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l.238 ...a5887c2be8734c7efa000abd8618/badge}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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Type  H <return>  for immediate help.
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l.238 ...a5887c2be8734c7efa000abd8618/badge}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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l.240 ...8a0a73393a0bbc7f192702/methylcheck}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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l.240 ...8a0a73393a0bbc7f192702/methylcheck}.svg}}
                                                  ^^M

Overfull \hbox (975.67087pt too wide) in paragraph at lines 2--243
[][][][][][] 
[1]
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[2 <./methylcheck_overview.png>] [3] [4]
Chapter 1.

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[5] [6 <./methylcheck_functions.png>]
Chapter 2.
[7] [8]
Chapter 3.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [9]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [10]
Chapter 4.
[11] [12]
Chapter 5.
[13] [14]
Chapter 6.
[15]

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Chapter 7.
(./life-epigenetics-methylcheck.ind) [89] (./life-epigenetics-methylcheck.aux) 
)
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Output written on life-epigenetics-methylcheck.pdf (93 pages, 3957478 bytes).
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Chapter 1.

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Chapter 2.
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Chapter 3.
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Chapter 6.
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[]\T1/ptm/m/n/10 Exclude probes

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[]

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[86] [87] [88]
Chapter 7.
(./life-epigenetics-methylcheck.ind) [89] (./life-epigenetics-methylcheck.aux) 
)
(see the transcript file for additional information){/usr/share/texlive/texmf-d
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Output written on life-epigenetics-methylcheck.pdf (93 pages, 3957478 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):
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Latexmk: Errors, in force_mode: so I tried finishing targets

[rtd-command-info] start-time: 2020-11-06T19:59:00.806592Z, end-time: 2020-11-06T19:59:00.866346Z, duration: 0, exit-code: 0
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[rtd-command-info] start-time: 2020-11-06T19:59:00.983288Z, end-time: 2020-11-06T19:59:20.710249Z, duration: 19, exit-code: 0
python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:106: WARNING: Title level inconsistent:

Filter either by the publication source, or by the type of effect (e.g. Polymorphism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised:
No module named 'joblib'
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No module named 'joblib'
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