Read the Docs build information
Build id: 1006927
Project: life-epigenetics-methylcheck
Version: latest
Commit: 04522bf0aefab7942eb1586b68d621f5ce9df6f2
Date: 2022-07-08T17:02:57.142880Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-07-08T17:02:59.151323Z, end-time: 2022-07-08T17:04:24.288766Z, duration: 85, 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: 2022-07-08T17:04:24.542065Z, end-time: 2022-07-08T17:04:25.153578Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to '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 switching back to a branch.

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

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 04522bf Feature/v0.8.5 - parquet support (#68)

[rtd-command-info] start-time: 2022-07-08T17:04:25.360612Z, end-time: 2022-07-08T17:04:25.422037Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-07-08T17:04:39.869925Z, end-time: 2022-07-08T17:04:44.760341Z, duration: 4, exit-code: 0
python3.8 -mvirtualenv --system-site-packages 
Using base prefix '/home/docs/.pyenv/versions/3.8.6'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python3.8
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: 2022-07-08T17:04:44.942495Z, end-time: 2022-07-08T17:04:46.770088Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (22.1.2)
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Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 63.1.0
    Uninstalling setuptools-63.1.0:
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[rtd-command-info] start-time: 2022-07-08T17:04:46.962173Z, end-time: 2022-07-08T17:05:13.769419Z, duration: 26, exit-code: 0
python -m pip install --upgrade --no-cache-dir -I 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 jinja2<3.1.0 setuptools<58.3.0
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Collecting MarkupSafe>=2.0
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Collecting urllib3<1.27,>=1.21.1
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Collecting charset-normalizer<3,>=2
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Collecting sphinxcontrib-serializinghtml
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Building wheels for collected packages: mock, pillow, 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=23773 sha256=911f8f1ac64e9cb1837fd78a2fafe8bdcb191a3cfcbd5b8d6fe9e390ee34b561
  Stored in directory: /tmp/pip-ephem-wheel-cache-63_rbjwq/wheels/41/7c/21/90057f91c6ead7c77a90c52d6e85ca48bf82d8b0d3f8dfbb65
  Building wheel for pillow (setup.py): started
  Building wheel for pillow (setup.py): finished with status 'done'
  Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1260058 sha256=ed79148cb8b7ae8b6c9101a2f6ad6472d3a6248e390bce3ae7f434a55592b6da
  Stored in directory: /tmp/pip-ephem-wheel-cache-63_rbjwq/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=42b20ae572920eeebc4257781743c96035a896023f404981fb54939d1c42034f
  Stored in directory: /tmp/pip-ephem-wheel-cache-63_rbjwq/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4
Successfully built mock pillow future
Installing collected packages: snowballstemmer, pytz, mock, alabaster, urllib3, sphinxcontrib-serializinghtml, six, setuptools, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, sphinxcontrib-websupport, requests, packaging, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible.
Successfully installed MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.6.15 charset-normalizer-2.1.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.8 recommonmark-0.5.0 requests-2.28.1 setuptools-58.2.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.10

[rtd-command-info] start-time: 2022-07-08T17:05:13.963490Z, end-time: 2022-07-08T17:05:33.471194Z, duration: 19, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
Requirement already satisfied: numpy in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from -r requirements.txt (line 1)) (1.19.2)
Collecting pandas>=1.3.0
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Building wheels for collected packages: m2r
  Building wheel for m2r (setup.py): started
  Building wheel for m2r (setup.py): finished with status 'done'
  Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10477 sha256=105f48fe9de9ebf313b4a6a0ea60a7c806bedfd3c06ca608f7291c94a5e3dbd6
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Successfully built m2r
Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, pickleshare, mistune, fastjsonschema, executing, backcall, zipp, xlsxwriter, traitlets, tqdm, tornado, tinycss2, soupsieve, scipy, pyzmq, python-dateutil, pyrsistent, psutil, prompt-toolkit, pillow, pexpect, pbr, parso, pandocfilters, nest-asyncio, m2r, jupyterlab-pygments, joblib, et-xmlfile, entrypoints, defusedxml, decorator, debugpy, bleach, attrs, asttokens, stack-data, pandas, openpyxl, matplotlib-inline, jupyter-core, jedi, importlib-resources, beautifulsoup4, sphinxcontrib-apidoc, seaborn, jupyter-client, jsonschema, ipython, nbformat, ipykernel, nbclient, nbconvert, nbsphinx
  Attempting uninstall: python-dateutil
    Found existing installation: python-dateutil 2.8.1
    Not uninstalling python-dateutil at /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest
    Can't uninstall 'python-dateutil'. No files were found to uninstall.
  Attempting uninstall: pillow
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    Uninstalling Pillow-5.4.1:
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  Attempting uninstall: pandas
    Found existing installation: pandas 1.1.3
    Not uninstalling pandas at /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest
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Successfully installed asttokens-2.0.5 attrs-21.4.0 backcall-0.2.0 beautifulsoup4-4.11.1 bleach-5.0.1 debugpy-1.6.2 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 et-xmlfile-1.1.0 executing-0.8.3 fastjsonschema-2.15.3 importlib-resources-5.8.0 ipykernel-6.15.1 ipython-8.4.0 jedi-0.18.1 joblib-1.1.0 jsonschema-4.6.2 jupyter-client-7.3.4 jupyter-core-4.11.1 jupyterlab-pygments-0.2.2 m2r-0.2.1 matplotlib-inline-0.1.3 mistune-0.8.4 nbclient-0.6.6 nbconvert-6.5.0 nbformat-5.4.0 nbsphinx-0.8.9 nest-asyncio-1.5.5 openpyxl-3.0.10 pandas-1.4.3 pandocfilters-1.5.0 parso-0.8.3 pbr-5.9.0 pexpect-4.8.0 pickleshare-0.7.5 pillow-9.2.0 prompt-toolkit-3.0.30 psutil-5.9.1 ptyprocess-0.7.0 pure-eval-0.2.2 pyrsistent-0.18.1 python-dateutil-2.8.2 pyzmq-23.2.0 scipy-1.8.1 seaborn-0.11.2 soupsieve-2.3.2.post1 sphinxcontrib-apidoc-0.3.0 stack-data-0.3.0 tinycss2-1.1.1 tornado-6.2 tqdm-4.64.0 traitlets-5.3.0 wcwidth-0.2.5 webencodings-0.5.1 xlsxwriter-3.0.3 zipp-3.8.0

[rtd-command-info] start-time: 2022-07-08T17:05:33.665457Z, end-time: 2022-07-08T17:05:34.793974Z, duration: 1, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Requirement already satisfied: docutils<0.18 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from -r docs/requirements.txt (line 1)) (0.17.1)

[rtd-command-info] start-time: 2022-07-08T17:05:36.361870Z, end-time: 2022-07-08T17:05:36.441956Z, 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 = '2022, FOXO Technologies, inc.'
author = 'FOXO Technologies, inc.'

# The short X.Y version
version = '0.8'
# The full version, including alpha/beta/rc tags
release = '0.8.4'


# -- 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'
]

autosummary_generate = True # new in sphinx 3.1 2020

# 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 = False

# 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',
     'FOXO Technologies, inc', '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', 'Methylation array quality control and filtering.',
     'Miscellaneous'),
]


# -- Extension configuration -------------------------------------------------

# numpydoc_show_class_members = False




###########################################################################
#          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/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

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",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("feature-v0.8.4", "/en/feature-v0.8.4/"),
    ],
    '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': '04522bf0',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





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")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/life-epigenetics-methylcheck/builds/1006927/'

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: 2022-07-08T17:05:36.628325Z, end-time: 2022-07-08T17:06:46.358261Z, duration: 69, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.6
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.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.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.reports.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.
[autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.ipynb, docs/poobah_filtering_tutorial.ipynb, docs/quality-control-example.ipynb, docs/release-history.md, docs/research_notebooks/postprocessQC_example.ipynb, docs/research_notebooks/pval.ipynb, docs/research_notebooks/rawQC_example.ipynb, docs/source/modules.rst, index.rst
Matplotlib is building the font cache; this may take a moment.
WARNING: [autosummary] failed to import 'methylcheck.assign': no module named methylcheck.assign
WARNING: [autosummary] failed to import 'methylcheck.beta_density_plot': no module named methylcheck.beta_density_plot
WARNING: [autosummary] failed to import 'methylcheck.beta_mds_plot': no module named methylcheck.beta_mds_plot
WARNING: [autosummary] failed to import 'methylcheck.cli': no module named methylcheck.cli
WARNING: [autosummary] failed to import 'methylcheck.combine_mds': no module named methylcheck.combine_mds
WARNING: [autosummary] failed to import 'methylcheck.cumulative_sum_beta_distribution': no module named methylcheck.cumulative_sum_beta_distribution
WARNING: [autosummary] failed to import 'methylcheck.drop_nan_probes': no module named methylcheck.drop_nan_probes
WARNING: [autosummary] failed to import 'methylcheck.exclude_probes': no module named methylcheck.exclude_probes
WARNING: [autosummary] failed to import 'methylcheck.exclude_sex_control_probes': no module named methylcheck.exclude_sex_control_probes
WARNING: [autosummary] failed to import 'methylcheck.get_sex': no module named methylcheck.get_sex
WARNING: [autosummary] failed to import 'methylcheck.list_problem_probes': no module named methylcheck.list_problem_probes
WARNING: [autosummary] failed to import 'methylcheck.load': no module named methylcheck.load
WARNING: [autosummary] failed to import 'methylcheck.load_both': no module named methylcheck.load_both
WARNING: [autosummary] failed to import 'methylcheck.mean_beta_compare': no module named methylcheck.mean_beta_compare
WARNING: [autosummary] failed to import 'methylcheck.mean_beta_plot': no module named methylcheck.mean_beta_plot
WARNING: [autosummary] failed to import 'methylcheck.plot_M_vs_U': no module named methylcheck.plot_M_vs_U
WARNING: [autosummary] failed to import 'methylcheck.plot_beta_by_type': no module named methylcheck.plot_beta_by_type
WARNING: [autosummary] failed to import 'methylcheck.plot_controls': no module named methylcheck.plot_controls
WARNING: [autosummary] failed to import 'methylcheck.predict': no module named methylcheck.predict
WARNING: [autosummary] failed to import 'methylcheck.probes': no module named methylcheck.probes
WARNING: [autosummary] failed to import 'methylcheck.qc_signal_intensity': no module named methylcheck.qc_signal_intensity
WARNING: [autosummary] failed to import 'methylcheck.read_geo': no module named methylcheck.read_geo
WARNING: [autosummary] failed to import 'methylcheck.run_pipeline': no module named methylcheck.run_pipeline
WARNING: [autosummary] failed to import 'methylcheck.run_qc': no module named methylcheck.run_qc
WARNING: [autosummary] failed to import 'methylcheck.sample_plot': no module named methylcheck.sample_plot
WARNING: [autosummary] failed to import 'methylcheck.samples': no module named methylcheck.samples
Failed to import 'methylcheck.load_processed': no module named methylcheck.load_processed
Failed to import 'methylcheck.read_geo_processed': no module named methylcheck.read_geo_processed
Failed to import 'methylcheck.reports.qc_report.run_pipeline': no module named methylcheck.reports.qc_report.run_pipeline
Failed to import 'methylcheck.probes': no module named methylcheck.probes
Failed to import 'methylcheck.samples': no module named methylcheck.samples
Failed to import 'methylcheck.qc_plot': no module named methylcheck.qc_plot
Failed to import 'methylcheck.predict': no module named methylcheck.predict
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 12 source files that are out of date
updating environment: 12 added, 0 changed, 0 removed
reading sources... [  8%] README
reading sources... [ 16%] docs/filtering-probes
reading sources... [ 25%] docs/loading-data
reading sources... [ 33%] docs/mds-example
reading sources... [ 41%] docs/poobah_filtering_tutorial
reading sources... [ 50%] docs/quality-control-example
reading sources... [ 58%] docs/release-history
reading sources... [ 66%] docs/research_notebooks/postprocessQC_example
reading sources... [ 75%] docs/research_notebooks/pval
reading sources... [ 83%] docs/research_notebooks/rawQC_example
reading sources... [ 91%] docs/source/modules
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/poobah_filtering_tutorial.ipynb:3394: WARNING: File not found: 'docs/quality-control-example.html#Predicting-Sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/poobah_filtering_tutorial.ipynb:3405: WARNING: File not found: 'docs/filtering-probes.html#Filtering-sex-linked-probes-and-control-probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.cli
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.run_pipeline
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.run_qc
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.read_geo
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.load
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.load_both
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.qc_signal_intensity
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_M_vs_U
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_controls
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_beta_by_type
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.list_problem_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.exclude_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.exclude_sex_control_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.drop_nan_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.samples
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.sample_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.beta_density_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.mean_beta_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.mean_beta_compare
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.beta_mds_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.combine_mds
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.cumulative_sum_beta_distribution
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.predict
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.get_sex
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.assign
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_qc'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.read_geo'
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WARNING: autodoc: failed to import module 'load_processed' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'read_geo_processed' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import class 'reports.qc_report.ReportPDF' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'reports.qc_report.run_pipeline' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'probes' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'samples' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'qc_plot' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'predict' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
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/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
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done
preparing documents... done
writing output... [  8%] README
writing output... [ 16%] docs/filtering-probes
writing output... [ 25%] docs/loading-data
writing output... [ 33%] docs/mds-example
writing output... [ 41%] docs/poobah_filtering_tutorial
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writing output... [ 58%] docs/release-history
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writing output... [ 83%] docs/research_notebooks/rawQC_example
writing output... [ 91%] docs/source/modules
writing output... [100%] index

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copying notebooks ... [ 12%] docs/filtering-probes.ipynb
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[rtd-command-info] start-time: 2022-07-08T17:06:46.784099Z, end-time: 2022-07-08T17:06:54.409489Z, duration: 7, exit-code: 0
python -m sphinx -T -E -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia
Running Sphinx v1.8.6
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.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.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.reports.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.
[autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.ipynb, docs/poobah_filtering_tutorial.ipynb, docs/quality-control-example.ipynb, docs/release-history.md, docs/research_notebooks/postprocessQC_example.ipynb, docs/research_notebooks/pval.ipynb, docs/research_notebooks/rawQC_example.ipynb, docs/source/modules.rst, index.rst
WARNING: [autosummary] failed to import 'methylcheck.assign': no module named methylcheck.assign
WARNING: [autosummary] failed to import 'methylcheck.beta_density_plot': no module named methylcheck.beta_density_plot
WARNING: [autosummary] failed to import 'methylcheck.beta_mds_plot': no module named methylcheck.beta_mds_plot
WARNING: [autosummary] failed to import 'methylcheck.cli': no module named methylcheck.cli
WARNING: [autosummary] failed to import 'methylcheck.combine_mds': no module named methylcheck.combine_mds
WARNING: [autosummary] failed to import 'methylcheck.cumulative_sum_beta_distribution': no module named methylcheck.cumulative_sum_beta_distribution
WARNING: [autosummary] failed to import 'methylcheck.drop_nan_probes': no module named methylcheck.drop_nan_probes
WARNING: [autosummary] failed to import 'methylcheck.exclude_probes': no module named methylcheck.exclude_probes
WARNING: [autosummary] failed to import 'methylcheck.exclude_sex_control_probes': no module named methylcheck.exclude_sex_control_probes
WARNING: [autosummary] failed to import 'methylcheck.get_sex': no module named methylcheck.get_sex
WARNING: [autosummary] failed to import 'methylcheck.list_problem_probes': no module named methylcheck.list_problem_probes
WARNING: [autosummary] failed to import 'methylcheck.load': no module named methylcheck.load
WARNING: [autosummary] failed to import 'methylcheck.load_both': no module named methylcheck.load_both
WARNING: [autosummary] failed to import 'methylcheck.mean_beta_compare': no module named methylcheck.mean_beta_compare
WARNING: [autosummary] failed to import 'methylcheck.mean_beta_plot': no module named methylcheck.mean_beta_plot
WARNING: [autosummary] failed to import 'methylcheck.plot_M_vs_U': no module named methylcheck.plot_M_vs_U
WARNING: [autosummary] failed to import 'methylcheck.plot_beta_by_type': no module named methylcheck.plot_beta_by_type
WARNING: [autosummary] failed to import 'methylcheck.plot_controls': no module named methylcheck.plot_controls
WARNING: [autosummary] failed to import 'methylcheck.predict': no module named methylcheck.predict
WARNING: [autosummary] failed to import 'methylcheck.probes': no module named methylcheck.probes
WARNING: [autosummary] failed to import 'methylcheck.qc_signal_intensity': no module named methylcheck.qc_signal_intensity
WARNING: [autosummary] failed to import 'methylcheck.read_geo': no module named methylcheck.read_geo
WARNING: [autosummary] failed to import 'methylcheck.run_pipeline': no module named methylcheck.run_pipeline
WARNING: [autosummary] failed to import 'methylcheck.run_qc': no module named methylcheck.run_qc
WARNING: [autosummary] failed to import 'methylcheck.sample_plot': no module named methylcheck.sample_plot
WARNING: [autosummary] failed to import 'methylcheck.samples': no module named methylcheck.samples
Failed to import 'methylcheck.load_processed': no module named methylcheck.load_processed
Failed to import 'methylcheck.read_geo_processed': no module named methylcheck.read_geo_processed
Failed to import 'methylcheck.reports.qc_report.run_pipeline': no module named methylcheck.reports.qc_report.run_pipeline
Failed to import 'methylcheck.probes': no module named methylcheck.probes
Failed to import 'methylcheck.samples': no module named methylcheck.samples
Failed to import 'methylcheck.qc_plot': no module named methylcheck.qc_plot
Failed to import 'methylcheck.predict': no module named methylcheck.predict
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 12 added, 0 changed, 0 removed
reading sources... [  8%] README
reading sources... [ 16%] docs/filtering-probes
reading sources... [ 25%] docs/loading-data
reading sources... [ 33%] docs/mds-example
reading sources... [ 41%] docs/poobah_filtering_tutorial
reading sources... [ 50%] docs/quality-control-example
reading sources... [ 58%] docs/release-history
reading sources... [ 66%] docs/research_notebooks/postprocessQC_example
reading sources... [ 75%] docs/research_notebooks/pval
reading sources... [ 83%] docs/research_notebooks/rawQC_example
reading sources... [ 91%] docs/source/modules
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/poobah_filtering_tutorial.ipynb:3394: WARNING: File not found: 'docs/quality-control-example.html#Predicting-Sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/poobah_filtering_tutorial.ipynb:3405: WARNING: File not found: 'docs/filtering-probes.html#Filtering-sex-linked-probes-and-control-probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.cli
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.run_pipeline
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.run_qc
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.read_geo
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.load
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.load_both
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.qc_signal_intensity
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_M_vs_U
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_controls
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_beta_by_type
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.list_problem_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.exclude_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.exclude_sex_control_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.drop_nan_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.samples
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.sample_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.beta_density_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.mean_beta_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.mean_beta_compare
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.beta_mds_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.combine_mds
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.cumulative_sum_beta_distribution
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.predict
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.get_sex
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.assign
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_qc'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.read_geo'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load_both'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.qc_signal_intensity'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_M_vs_U'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_controls'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_beta_by_type'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.list_problem_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.drop_nan_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.sample_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_density_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_compare'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_mds_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.combine_mds'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.predict'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign'
WARNING: autodoc: failed to import module 'load_processed' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'read_geo_processed' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import class 'reports.qc_report.ReportPDF' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'reports.qc_report.run_pipeline' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'probes' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'samples' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'qc_plot' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'predict' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
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/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... docs/loading-data docs/filtering-probes docs/quality-control-example docs/poobah_filtering_tutorial docs/mds-example docs/source/modules docs/source/_autosummary/methylcheck.cli /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.cli'
docs/source/_autosummary/methylcheck.run_pipeline /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_pipeline'
docs/source/_autosummary/methylcheck.run_qc /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_qc'
docs/source/_autosummary/methylcheck.read_geo /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.read_geo'
docs/source/_autosummary/methylcheck.load /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.load'
docs/source/_autosummary/methylcheck.load_both /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.load_both'
docs/source/_autosummary/methylcheck.qc_signal_intensity /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.qc_signal_intensity'
docs/source/_autosummary/methylcheck.plot_M_vs_U /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.plot_M_vs_U'
docs/source/_autosummary/methylcheck.plot_controls /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.plot_controls'
docs/source/_autosummary/methylcheck.plot_beta_by_type /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.plot_beta_by_type'
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docs/source/_autosummary/methylcheck.beta_density_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.beta_density_plot'
docs/source/_autosummary/methylcheck.mean_beta_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.mean_beta_plot'
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docs/source/_autosummary/methylcheck.beta_mds_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.beta_mds_plot'
docs/source/_autosummary/methylcheck.combine_mds /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.combine_mds'
docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution'
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[rtd-command-info] start-time: 2022-07-08T17:06:54.636983Z, end-time: 2022-07-08T17:07:00.711463Z, duration: 6, exit-code: 0
python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.8.6
loading translations [en]... done
making output directory...
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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.rst.
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Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.rst.
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Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.reports.rst.
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Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst.
[autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.ipynb, docs/poobah_filtering_tutorial.ipynb, docs/quality-control-example.ipynb, docs/release-history.md, docs/research_notebooks/postprocessQC_example.ipynb, docs/research_notebooks/pval.ipynb, docs/research_notebooks/rawQC_example.ipynb, docs/source/modules.rst, index.rst
WARNING: [autosummary] failed to import 'methylcheck.assign': no module named methylcheck.assign
WARNING: [autosummary] failed to import 'methylcheck.beta_density_plot': no module named methylcheck.beta_density_plot
WARNING: [autosummary] failed to import 'methylcheck.beta_mds_plot': no module named methylcheck.beta_mds_plot
WARNING: [autosummary] failed to import 'methylcheck.cli': no module named methylcheck.cli
WARNING: [autosummary] failed to import 'methylcheck.combine_mds': no module named methylcheck.combine_mds
WARNING: [autosummary] failed to import 'methylcheck.cumulative_sum_beta_distribution': no module named methylcheck.cumulative_sum_beta_distribution
WARNING: [autosummary] failed to import 'methylcheck.drop_nan_probes': no module named methylcheck.drop_nan_probes
WARNING: [autosummary] failed to import 'methylcheck.exclude_probes': no module named methylcheck.exclude_probes
WARNING: [autosummary] failed to import 'methylcheck.exclude_sex_control_probes': no module named methylcheck.exclude_sex_control_probes
WARNING: [autosummary] failed to import 'methylcheck.get_sex': no module named methylcheck.get_sex
WARNING: [autosummary] failed to import 'methylcheck.list_problem_probes': no module named methylcheck.list_problem_probes
WARNING: [autosummary] failed to import 'methylcheck.load': no module named methylcheck.load
WARNING: [autosummary] failed to import 'methylcheck.load_both': no module named methylcheck.load_both
WARNING: [autosummary] failed to import 'methylcheck.mean_beta_compare': no module named methylcheck.mean_beta_compare
WARNING: [autosummary] failed to import 'methylcheck.mean_beta_plot': no module named methylcheck.mean_beta_plot
WARNING: [autosummary] failed to import 'methylcheck.plot_M_vs_U': no module named methylcheck.plot_M_vs_U
WARNING: [autosummary] failed to import 'methylcheck.plot_beta_by_type': no module named methylcheck.plot_beta_by_type
WARNING: [autosummary] failed to import 'methylcheck.plot_controls': no module named methylcheck.plot_controls
WARNING: [autosummary] failed to import 'methylcheck.predict': no module named methylcheck.predict
WARNING: [autosummary] failed to import 'methylcheck.probes': no module named methylcheck.probes
WARNING: [autosummary] failed to import 'methylcheck.qc_signal_intensity': no module named methylcheck.qc_signal_intensity
WARNING: [autosummary] failed to import 'methylcheck.read_geo': no module named methylcheck.read_geo
WARNING: [autosummary] failed to import 'methylcheck.run_pipeline': no module named methylcheck.run_pipeline
WARNING: [autosummary] failed to import 'methylcheck.run_qc': no module named methylcheck.run_qc
WARNING: [autosummary] failed to import 'methylcheck.sample_plot': no module named methylcheck.sample_plot
WARNING: [autosummary] failed to import 'methylcheck.samples': no module named methylcheck.samples
Failed to import 'methylcheck.load_processed': no module named methylcheck.load_processed
Failed to import 'methylcheck.read_geo_processed': no module named methylcheck.read_geo_processed
Failed to import 'methylcheck.reports.qc_report.run_pipeline': no module named methylcheck.reports.qc_report.run_pipeline
Failed to import 'methylcheck.probes': no module named methylcheck.probes
Failed to import 'methylcheck.samples': no module named methylcheck.samples
Failed to import 'methylcheck.qc_plot': no module named methylcheck.qc_plot
Failed to import 'methylcheck.predict': no module named methylcheck.predict
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building [latex]: all documents
updating environment: [] 0 added, 1 changed, 0 removed
reading sources... [100%] docs/source/modules

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.cli
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.run_pipeline
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.run_qc
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.read_geo
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.load
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.load_both
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.qc_signal_intensity
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_M_vs_U
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_controls
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_beta_by_type
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.list_problem_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.exclude_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.exclude_sex_control_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.drop_nan_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.samples
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.sample_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.beta_density_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.mean_beta_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.mean_beta_compare
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.beta_mds_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.combine_mds
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.cumulative_sum_beta_distribution
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.predict
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.get_sex
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.assign
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_qc'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.read_geo'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load_both'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.qc_signal_intensity'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_M_vs_U'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_controls'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_beta_by_type'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.list_problem_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes'
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WARNING: autodoc: failed to import module 'load_processed' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'read_geo_processed' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import class 'reports.qc_report.ReportPDF' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'reports.qc_report.run_pipeline' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'probes' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'samples' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'qc_plot' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'predict' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
looking for now-outdated files... none found
pickling environment... done
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done
processing methylcheck.tex...index docs/loading-data docs/filtering-probes docs/quality-control-example docs/poobah_filtering_tutorial docs/mds-example docs/source/modules docs/source/_autosummary/methylcheck.cli /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages/sphinx/builders/latex/__init__.py:201: FutureWarning: 
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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).
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[rtd-command-info] start-time: 2022-07-08T17:07:05.684108Z, end-time: 2022-07-08T17:07:05.745018Z, 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: 2022-07-08T17:07:05.969946Z, end-time: 2022-07-08T17:07:29.744335Z, duration: 23, 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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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.
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<2008/02/07> (tvz)) (./footnotehyper-sphinx.sty)
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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
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Writing index file life-epigenetics-methylcheck.idx
(./life-epigenetics-methylcheck.aux)
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[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
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*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
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>><<oms.cmap>><<omx.cmap>>
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(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2]
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! LaTeX Error: Unknown graphics extension: .svg.

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                                                  ^^M

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                                                  ^^M

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                                                  ^^M

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                                                  ^^M

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                                                  ^^M

LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epi
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[1] [2 <./methylcheck_overview.png>]
Chapter 1.
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Chapter 3.
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[13]

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Overfull \vbox (13.12581pt too high) detected at line 829
[14]
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[]\T1/pcr/m/n/10 sdc[0]._SampleDataContainer__data_frame \T1/ptm/m/n/10 will gi
ve you a dataframe of the first

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[15]
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[16] [17 <./docs_loading-data_16_1.png>] [18 <./docs_loading-data_18_0.png>]
[19]

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[20]
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[23]
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[24 <./docs_filtering-probes_16_1.png>] [25 <./docs_filtering-probes_17_0.png>]


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[26]
Underfull \hbox (badness 10000) in paragraph at lines 1602--1603
[]\T1/ptm/m/n/10 The color-coded re-sults are con-tained in an ex-cel file that
 will be saved in the

Underfull \hbox (badness 10000) in paragraph at lines 1602--1603
\T1/ptm/m/n/10 same di-rec-tory that was spec-i-fied as an in-put. It will look
 sim-i-lar to this:

Overfull \hbox (283.13986pt too wide) in paragraph at lines 1602--1603
[]
[27 <./bead_array_report.png>]
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[28]
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! Package inputenc Error: Unicode char █ (U+2588)
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[]\T1/ptm/m/n/10 If you want a quick one-line ver-sion with no fur-ther re-port
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Chapter 5.
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[1] [2 <./methylcheck_overview.png>]
Chapter 1.
[3] [4]
Chapter 2.
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Chapter 3.
[7] [8]
Chapter 4.
[9] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd)

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[]\T1/pcr/m/n/10 sdc[0]._SampleDataContainer__data_frame \T1/ptm/m/n/10 will gi
ve you a dataframe of the first

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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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[15]
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[20]
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[26]
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[]\T1/ptm/m/n/10 The color-coded re-sults are con-tained in an ex-cel file that
 will be saved in the

Underfull \hbox (badness 10000) in paragraph at lines 1602--1603
\T1/ptm/m/n/10 same di-rec-tory that was spec-i-fied as an in-put. It will look
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[42 <./docs_quality-control-example_9_22.png>]
Underfull \hbox (badness 10000) in paragraph at lines 1989--1990
[]\T1/ptm/m/n/10 kwargs: \T1/pcr/m/n/10 filename, poobah_max_percent, pval_cuto
ff, title, author, subject,
[43 <./docs_quality-control-example_12_1.png>]
Underfull \hbox (badness 10000) in paragraph at lines 1993--1994
[]\T1/ptm/m/n/10 If you want a quick one-line ver-sion with no fur-ther re-port
 edit-ing, try \T1/pcr/m/n/10 methylcheck.
[44] [45]

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Chapter 5.
(./life-epigenetics-methylcheck.ind) [79] (./life-epigenetics-methylcheck.aux) 
)
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Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written
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See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.592 ...��██| 16/16 [00:00<00:00, 488.67it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.592 ...��██| 16/16 [00:00<00:00, 488.67it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.592 ...��██| 16/16 [00:00<00:00, 488.67it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.592 ...��██| 16/16 [00:00<00:00, 488.67it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.592 ...��██| 16/16 [00:00<00:00, 488.67it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.592 ...��██| 16/16 [00:00<00:00, 488.67it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.592 ...��██| 16/16 [00:00<00:00, 488.67it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s]
                                                  
[12]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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[13]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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Overfull \vbox (13.12581pt too high) detected at line 829
[14]
Underfull \hbox (badness 10000) in paragraph at lines 835--836
[]\T1/pcr/m/n/10 sdc[0]._SampleDataContainer__data_frame \T1/ptm/m/n/10 will gi
ve you a dataframe of the first

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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[15]
Underfull \vbox (badness 10000) detected at line 965

Overfull \vbox (2.68169pt too high) detected at line 965
[16] [17 <./docs_loading-data_16_1.png>] [18 <./docs_loading-data_18_0.png>]
[19]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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[20]
Underfull \vbox (badness 10000) detected at line 1295
[21 <./docs_filtering-probes_9_1.png>] [22 <./docs_filtering-probes_11_0.png>]
Underfull \vbox (badness 10000) detected at line 1420
[23]
Underfull \vbox (badness 10000) detected at line 1439
[24 <./docs_filtering-probes_16_1.png>] [25 <./docs_filtering-probes_17_0.png>]


! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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[]\T1/ptm/m/n/10 If you want a quick one-line ver-sion with no fur-ther re-port
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[]
[76] [77] [78]
Chapter 5.
(./life-epigenetics-methylcheck.ind) [79] (./life-epigenetics-methylcheck.aux) 
)
(see the transcript file for additional information){/usr/share/texlive/texmf-d
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.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/helvetic/uhvb8a.pfb></usr/share/texlive/texmf-dist/f
onts/type1/urw/helvetic/uhvbo8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
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share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on life-epigenetics-methylcheck.pdf (83 pages, 2141868 bytes).
Transcript written on life-epigenetics-methylcheck.log.
Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written
Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.pngheight=40">`' from line
  'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.png"height="40">`' not found on input line 24'
Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.pngheight=40">`' from line
  'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.png"height="40">`' not found on input line 240.'
Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf'
Latexmk: Errors, in force_mode: so I tried finishing targets
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 256

[rtd-command-info] start-time: 2022-07-08T17:07:29.965913Z, end-time: 2022-07-08T17:07:30.050958Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/latex/life-epigenetics-methylcheck.pdf /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/artifacts/latest/sphinx_pdf/life-epigenetics-methylcheck.pdf


[rtd-command-info] start-time: 2022-07-08T17:07:30.419067Z, end-time: 2022-07-08T17:07:47.212865Z, duration: 16, exit-code: 0
python -m sphinx -T -E -b epub -d _build/doctrees -D language=en . _build/epub
Running Sphinx v1.8.6
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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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.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.reports.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.
[autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.ipynb, docs/poobah_filtering_tutorial.ipynb, docs/quality-control-example.ipynb, docs/release-history.md, docs/research_notebooks/postprocessQC_example.ipynb, docs/research_notebooks/pval.ipynb, docs/research_notebooks/rawQC_example.ipynb, docs/source/modules.rst, index.rst
WARNING: [autosummary] failed to import 'methylcheck.assign': no module named methylcheck.assign
WARNING: [autosummary] failed to import 'methylcheck.beta_density_plot': no module named methylcheck.beta_density_plot
WARNING: [autosummary] failed to import 'methylcheck.beta_mds_plot': no module named methylcheck.beta_mds_plot
WARNING: [autosummary] failed to import 'methylcheck.cli': no module named methylcheck.cli
WARNING: [autosummary] failed to import 'methylcheck.combine_mds': no module named methylcheck.combine_mds
WARNING: [autosummary] failed to import 'methylcheck.cumulative_sum_beta_distribution': no module named methylcheck.cumulative_sum_beta_distribution
WARNING: [autosummary] failed to import 'methylcheck.drop_nan_probes': no module named methylcheck.drop_nan_probes
WARNING: [autosummary] failed to import 'methylcheck.exclude_probes': no module named methylcheck.exclude_probes
WARNING: [autosummary] failed to import 'methylcheck.exclude_sex_control_probes': no module named methylcheck.exclude_sex_control_probes
WARNING: [autosummary] failed to import 'methylcheck.get_sex': no module named methylcheck.get_sex
WARNING: [autosummary] failed to import 'methylcheck.list_problem_probes': no module named methylcheck.list_problem_probes
WARNING: [autosummary] failed to import 'methylcheck.load': no module named methylcheck.load
WARNING: [autosummary] failed to import 'methylcheck.load_both': no module named methylcheck.load_both
WARNING: [autosummary] failed to import 'methylcheck.mean_beta_compare': no module named methylcheck.mean_beta_compare
WARNING: [autosummary] failed to import 'methylcheck.mean_beta_plot': no module named methylcheck.mean_beta_plot
WARNING: [autosummary] failed to import 'methylcheck.plot_M_vs_U': no module named methylcheck.plot_M_vs_U
WARNING: [autosummary] failed to import 'methylcheck.plot_beta_by_type': no module named methylcheck.plot_beta_by_type
WARNING: [autosummary] failed to import 'methylcheck.plot_controls': no module named methylcheck.plot_controls
WARNING: [autosummary] failed to import 'methylcheck.predict': no module named methylcheck.predict
WARNING: [autosummary] failed to import 'methylcheck.probes': no module named methylcheck.probes
WARNING: [autosummary] failed to import 'methylcheck.qc_signal_intensity': no module named methylcheck.qc_signal_intensity
WARNING: [autosummary] failed to import 'methylcheck.read_geo': no module named methylcheck.read_geo
WARNING: [autosummary] failed to import 'methylcheck.run_pipeline': no module named methylcheck.run_pipeline
WARNING: [autosummary] failed to import 'methylcheck.run_qc': no module named methylcheck.run_qc
WARNING: [autosummary] failed to import 'methylcheck.sample_plot': no module named methylcheck.sample_plot
WARNING: [autosummary] failed to import 'methylcheck.samples': no module named methylcheck.samples
Failed to import 'methylcheck.load_processed': no module named methylcheck.load_processed
Failed to import 'methylcheck.read_geo_processed': no module named methylcheck.read_geo_processed
Failed to import 'methylcheck.reports.qc_report.run_pipeline': no module named methylcheck.reports.qc_report.run_pipeline
Failed to import 'methylcheck.probes': no module named methylcheck.probes
Failed to import 'methylcheck.samples': no module named methylcheck.samples
Failed to import 'methylcheck.qc_plot': no module named methylcheck.qc_plot
Failed to import 'methylcheck.predict': no module named methylcheck.predict
building [mo]: targets for 0 po files that are out of date
building [epub]: targets for 12 source files that are out of date
updating environment: 12 added, 0 changed, 0 removed
reading sources... [  8%] README
reading sources... [ 16%] docs/filtering-probes
reading sources... [ 25%] docs/loading-data
reading sources... [ 33%] docs/mds-example
reading sources... [ 41%] docs/poobah_filtering_tutorial
reading sources... [ 50%] docs/quality-control-example
reading sources... [ 58%] docs/release-history
reading sources... [ 66%] docs/research_notebooks/postprocessQC_example
reading sources... [ 75%] docs/research_notebooks/pval
reading sources... [ 83%] docs/research_notebooks/rawQC_example
reading sources... [ 91%] docs/source/modules
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/poobah_filtering_tutorial.ipynb:3394: WARNING: File not found: 'docs/quality-control-example.html#Predicting-Sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/poobah_filtering_tutorial.ipynb:3405: WARNING: File not found: 'docs/filtering-probes.html#Filtering-sex-linked-probes-and-control-probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.cli
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.run_pipeline
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.run_qc
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.read_geo
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.load
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.load_both
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.qc_signal_intensity
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_M_vs_U
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_controls
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.plot_beta_by_type
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.list_problem_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.exclude_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.exclude_sex_control_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.drop_nan_probes
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.samples
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.sample_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.beta_density_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.mean_beta_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.mean_beta_compare
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.beta_mds_plot
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.combine_mds
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.cumulative_sum_beta_distribution
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.predict
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.get_sex
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: failed to import methylcheck.assign
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_qc'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.read_geo'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load_both'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.qc_signal_intensity'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_M_vs_U'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_controls'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_beta_by_type'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.list_problem_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.drop_nan_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.sample_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_density_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_compare'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_mds_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.combine_mds'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.predict'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign'
WARNING: autodoc: failed to import module 'load_processed' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'read_geo_processed' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import class 'reports.qc_report.ReportPDF' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'reports.qc_report.run_pipeline' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'probes' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'samples' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'qc_plot' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
WARNING: autodoc: failed to import module 'predict' from module 'methylcheck'; the following exception was raised:
No module named 'methylprep'
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/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  8%] README
writing output... [ 16%] docs/filtering-probes
writing output... [ 25%] docs/loading-data
writing output... [ 33%] docs/mds-example
writing output... [ 41%] docs/poobah_filtering_tutorial
writing output... [ 50%] docs/quality-control-example
writing output... [ 58%] docs/release-history
writing output... [ 66%] docs/research_notebooks/postprocessQC_example
writing output... [ 75%] docs/research_notebooks/pval
writing output... [ 83%] docs/research_notebooks/rawQC_example
writing output... [ 91%] docs/source/modules
writing output... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot'
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