Read the Docs build information
Build id: 235004
Project: life-epigenetics-methylcheck
Version: latest
Commit: f65762576336e71f7ac2c121cd4b6f1e8ec8dae2
Date: 2019-08-22T19:38:11.947276Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-08-22T19:38:12.364409Z, end-time: 2019-08-22T19:38:16.348773Z, duration: 3, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/LifeEGX/methylcheck.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-08-22T19:38:16.558091Z, end-time: 2019-08-22T19:38:17.034426Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

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

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

  git checkout -b <new-branch-name>

HEAD is now at f657625 Renamed repo (#21)

[rtd-command-info] start-time: 2019-08-22T19:38:17.112451Z, end-time: 2019-08-22T19:38:17.119725Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-08-22T19:38:18.066766Z, end-time: 2019-08-22T19:38:22.283719Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.7.3'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-08-22T19:38:22.375695Z, end-time: 2019-08-22T19:38:24.842942Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/.cache/pip pip
Collecting pip
  Downloading https://files.pythonhosted.org/packages/8d/07/f7d7ced2f97ca3098c16565efbe6b15fafcba53e8d9bdb431e09140514b0/pip-19.2.2-py2.py3-none-any.whl (1.4MB)
Installing collected packages: pip
  Found existing installation: pip 19.1.1
    Uninstalling pip-19.1.1:
      Successfully uninstalled pip-19.1.1
Successfully installed pip-19.2.2

[rtd-command-info] start-time: 2019-08-22T19:38:24.925270Z, end-time: 2019-08-22T19:38:35.974426Z, duration: 11, exit-code: 0
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Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (41.0.1)
Collecting docutils==0.14
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Collecting commonmark==0.8.1
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Collecting recommonmark==0.5.0
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Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 (from requests>=2.0.0->sphinx<2)
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Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<2)
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Collecting attrs (from packaging->sphinx<2)
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Building wheels for collected packages: mock, future, snowballstemmer
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Successfully built mock future snowballstemmer
Installing collected packages: Pygments, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, six, urllib3, idna, chardet, certifi, requests, MarkupSafe, Jinja2, snowballstemmer, imagesize, attrs, pyparsing, packaging, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 attrs-19.1.0 babel-2.7.0 certifi-2019.6.16 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.17.1 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.1 pillow-5.4.1 pyparsing-2.4.2 pytz-2019.2 readthedocs-sphinx-ext-1.0.0 recommonmark-0.5.0 requests-2.22.0 six-1.12.0 snowballstemmer-1.9.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.3

[rtd-command-info] start-time: 2019-08-22T19:38:36.052891Z, end-time: 2019-08-22T19:39:03.489668Z, duration: 27, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/.cache/pip -r requirements.txt
Collecting numpy (from -r requirements.txt (line 1))
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Collecting pandas (from -r requirements.txt (line 2))
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Collecting matplotlib (from -r requirements.txt (line 4))
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Collecting pytest (from -r requirements.txt (line 6))
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Requirement already satisfied: sphinx>=1.4 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 9)) (1.8.5)
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Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from pandas->-r requirements.txt (line 2)) (2019.2)
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Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 4)) (2.4.2)
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Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 9)) (0.14)
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Installing collected packages: numpy, python-dateutil, pandas, scipy, cycler, kiwisolver, matplotlib, seaborn, atomicwrites, zipp, importlib-metadata, pluggy, more-itertools, py, wcwidth, pytest, coverage, coveralls-python, pbr, sphinxcontrib-apidoc, mistune, m2r, tqdm, decorator, ipython-genutils, traitlets, jupyter-core, pyzmq, tornado, jupyter-client, prompt-toolkit, backcall, parso, jedi, ptyprocess, pexpect, pickleshare, ipython, ipykernel, testpath, defusedxml, entrypoints, webencodings, bleach, pandocfilters, pyrsistent, jsonschema, nbformat, nbconvert, nbsphinx
Successfully installed atomicwrites-1.3.0 backcall-0.1.0 bleach-3.1.0 coverage-4.5.4 coveralls-python-0.0.1 cycler-0.10.0 decorator-4.4.0 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-0.19 ipykernel-5.1.2 ipython-7.7.0 ipython-genutils-0.2.0 jedi-0.15.1 jsonschema-3.0.2 jupyter-client-5.3.1 jupyter-core-4.5.0 kiwisolver-1.1.0 m2r-0.2.1 matplotlib-3.1.1 mistune-0.8.4 more-itertools-7.2.0 nbconvert-5.6.0 nbformat-4.4.0 nbsphinx-0.4.2 numpy-1.17.0 pandas-0.25.1 pandocfilters-1.4.2 parso-0.5.1 pbr-5.4.2 pexpect-4.7.0 pickleshare-0.7.5 pluggy-0.12.0 prompt-toolkit-2.0.9 ptyprocess-0.6.0 py-1.8.0 pyrsistent-0.15.4 pytest-5.1.1 python-dateutil-2.8.0 pyzmq-18.1.0 scipy-1.3.1 seaborn-0.9.0 sphinxcontrib-apidoc-0.3.0 testpath-0.4.2 tornado-6.0.3 tqdm-4.34.0 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1 zipp-0.5.2

[rtd-command-info] start-time: 2019-08-22T19:39:04.095928Z, end-time: 2019-08-22T19:39:04.400604Z, duration: 0, exit-code: 0
cat conf.py
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
sys.path.insert(0, os.path.abspath('.'))


# -- Project information -----------------------------------------------------

project = 'methylcheck'
copyright = '2019, Life Epigenetics'
author = 'Life Epigenetics'

# The short X.Y version
version = '0.2'
# The full version, including alpha/beta/rc tags
release = '0.2'


# -- General configuration ---------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.autodoc',
    'sphinxcontrib.apidoc',
    'm2r',
    'nbsphinx'
]

# instead of CLI "sphinx-autodoc . _build/html" you write this
apidoc_module_dir = '.'
apidoc_output_dir = '_sphinx_build'
apidoc_excluded_paths = ['tests']
apidoc_separate_modules = 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',
     'Life Epigenetics', 'manual'),
]


# -- Options for manual page output ------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'methylcheck', 'methylcheck Documentation',
     [author], 1)
]


# -- Options for Texinfo output ----------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'methylcheck', 'methylcheck Documentation',
     author, 'methylcheck', 'One line description of project.',
     'Miscellaneous'),
]


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




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#


import importlib
import sys
import os.path
from six import string_types

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
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    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    theme = importlib.import_module('sphinx_rtd_theme')
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://media.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://media.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("pdf", "//readthedocs.com/projects/life-epigenetics-methylcheck/downloads/pdf/latest/"),
    ("html", "//readthedocs.com/projects/life-epigenetics-methylcheck/downloads/htmlzip/latest/"),
    ("epub", "//readthedocs.com/projects/life-epigenetics-methylcheck/downloads/epub/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'life-epigenetics-methylcheck',
    'name': u'methylcheck',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://life-epigenetics-methylcheck.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'LifeEGX',
    'github_repo': 'methylcheck',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'f6576257',
}




if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
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    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

[rtd-command-info] start-time: 2019-08-22T19:39:04.496793Z, end-time: 2019-08-22T19:39:13.927076Z, duration: 9, exit-code: 0
python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst.
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 8 source files that are out of date
updating environment: 8 added, 0 changed, 0 removed
reading sources... [ 12%] README
reading sources... [ 25%] docs/demo-methpype-to-methQC-example
reading sources... [ 37%] docs/filtering_probes
reading sources... [ 50%] docs/methpype_methQC_example
reading sources... [ 62%] docs/postprocessQC_example
reading sources... [ 75%] docs/rawQC_example
reading sources... [ 87%] docs/source/methylcheck
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:100: WARNING: Title level inconsistent:

Filter either by the publication source, or by the type of effect (e.g. Polymorphism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methpype_methQC_example.ipynb:370: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:8: WARNING: Title underline too short.

methylcheck.QCreport module
----------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:8: WARNING: Title underline too short.

methylcheck.QCreport module
----------------------
WARNING: autodoc: failed to import module 'QCreport' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:16: WARNING: Title underline too short.

methylcheck.cli module
-----------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:16: WARNING: Title underline too short.

methylcheck.cli module
-----------------
WARNING: autodoc: failed to import module 'cli' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:24: WARNING: Title underline too short.

methylcheck.filters module
---------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:24: WARNING: Title underline too short.

methylcheck.filters module
---------------------
WARNING: autodoc: failed to import module 'filters' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:32: WARNING: Title underline too short.

methylcheck.postprocessQC module
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:32: WARNING: Title underline too short.

methylcheck.postprocessQC module
---------------------------
WARNING: autodoc: failed to import module 'postprocessQC' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
WARNING: autodoc: failed to import module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:10: WARNING: toctree contains reference to nonexisting document 'docs/demo-methylprep-to-methylcheck-example'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:10: WARNING: toctree contains reference to nonexisting document 'docs/methylprep_methylcheck_example'
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/demo-methpype-to-methQC-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methpype_methQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [ 12%] README
writing output... [ 25%] docs/demo-methpype-to-methQC-example
writing output... [ 37%] docs/filtering_probes
writing output... [ 50%] docs/methpype_methQC_example
writing output... [ 62%] docs/postprocessQC_example
writing output... [ 75%] docs/rawQC_example
writing output... [ 87%] docs/source/methylcheck
writing output... [100%] index

generating indices... genindex
writing additional pages... search
copying images... [  5%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_demo-methpype-to-methQC-example_7_1.png
copying images... [ 11%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_demo-methpype-to-methQC-example_8_0.png
copying images... [ 17%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_demo-methpype-to-methQC-example_9_3.png
copying images... [ 23%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_filtering_probes_6_1.png
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copying images... [ 47%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_methpype_methQC_example_10_1.png
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copying images... [ 82%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_postprocessQC_example_7_0.png
copying images... [ 88%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_postprocessQC_example_8_0.png
copying images... [ 94%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_postprocessQC_example_13_0.png
copying images... [100%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_postprocessQC_example_15_0.png

copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_static' does not exist
done
copying readthedocs static files... done
copying searchtools... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 23 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2019-08-22T19:39:14.051346Z, end-time: 2019-08-22T19:39:18.315827Z, duration: 4, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst.
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 8 added, 0 changed, 0 removed
reading sources... [ 12%] README
reading sources... [ 25%] docs/demo-methpype-to-methQC-example
reading sources... [ 37%] docs/filtering_probes
reading sources... [ 50%] docs/methpype_methQC_example
reading sources... [ 62%] docs/postprocessQC_example
reading sources... [ 75%] docs/rawQC_example
reading sources... [ 87%] docs/source/methylcheck
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:100: WARNING: Title level inconsistent:

Filter either by the publication source, or by the type of effect (e.g. Polymorphism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methpype_methQC_example.ipynb:370: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:8: WARNING: Title underline too short.

methylcheck.QCreport module
----------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:8: WARNING: Title underline too short.

methylcheck.QCreport module
----------------------
WARNING: autodoc: failed to import module 'QCreport' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:16: WARNING: Title underline too short.

methylcheck.cli module
-----------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:16: WARNING: Title underline too short.

methylcheck.cli module
-----------------
WARNING: autodoc: failed to import module 'cli' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:24: WARNING: Title underline too short.

methylcheck.filters module
---------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:24: WARNING: Title underline too short.

methylcheck.filters module
---------------------
WARNING: autodoc: failed to import module 'filters' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:32: WARNING: Title underline too short.

methylcheck.postprocessQC module
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:32: WARNING: Title underline too short.

methylcheck.postprocessQC module
---------------------------
WARNING: autodoc: failed to import module 'postprocessQC' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
WARNING: autodoc: failed to import module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:10: WARNING: toctree contains reference to nonexisting document 'docs/demo-methylprep-to-methylcheck-example'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:10: WARNING: toctree contains reference to nonexisting document 'docs/methylprep_methylcheck_example'
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/demo-methpype-to-methQC-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methpype_methQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... docs/filtering_probes docs/source/methylcheck 
writing... done
writing additional files...
copying images... [ 25%] docs/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs_filtering_probes_6_1.png
copying images... [ 50%] docs/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs_filtering_probes_8_1.png
copying images... [ 75%] docs/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs_filtering_probes_10_1.png
copying images... [100%] docs/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs_filtering_probes_11_1.png

copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_static' does not exist
done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded, 23 warnings.

The HTML page is in _build/localmedia.

[rtd-command-info] start-time: 2019-08-22T19:39:18.439355Z, end-time: 2019-08-22T19:39:24.590352Z, duration: 6, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst.
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 8 added, 0 changed, 0 removed
reading sources... [ 12%] README
reading sources... [ 25%] docs/demo-methpype-to-methQC-example
reading sources... [ 37%] docs/filtering_probes
reading sources... [ 50%] docs/methpype_methQC_example
reading sources... [ 62%] docs/postprocessQC_example
reading sources... [ 75%] docs/rawQC_example
reading sources... [ 87%] docs/source/methylcheck
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:100: WARNING: Title level inconsistent:

Filter either by the publication source, or by the type of effect (e.g. Polymorphism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methpype_methQC_example.ipynb:370: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:8: WARNING: Title underline too short.

methylcheck.QCreport module
----------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:8: WARNING: Title underline too short.

methylcheck.QCreport module
----------------------
WARNING: autodoc: failed to import module 'QCreport' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:16: WARNING: Title underline too short.

methylcheck.cli module
-----------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:16: WARNING: Title underline too short.

methylcheck.cli module
-----------------
WARNING: autodoc: failed to import module 'cli' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:24: WARNING: Title underline too short.

methylcheck.filters module
---------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:24: WARNING: Title underline too short.

methylcheck.filters module
---------------------
WARNING: autodoc: failed to import module 'filters' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:32: WARNING: Title underline too short.

methylcheck.postprocessQC module
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:32: WARNING: Title underline too short.

methylcheck.postprocessQC module
---------------------------
WARNING: autodoc: failed to import module 'postprocessQC' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:10: WARNING: toctree contains reference to nonexisting document 'docs/methylprep_methylcheck_example'
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done
processing methylcheck.tex...index docs/filtering_probes docs/source/methylcheck 
resolving references...
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done
build succeeded, 28 warnings.

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

[rtd-command-info] start-time: 2019-08-22T19:39:26.517198Z, end-time: 2019-08-22T19:39:26.834400Z, 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: 2019-08-22T19:39:27.100449Z, end-time: 2019-08-22T19:39:29.901747Z, duration: 2, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=life-epigenetics-methylcheck -interaction=nonstopmode
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Chapter 1.

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Chapter 2.
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[1] [2]
Chapter 1.

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[3]
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[8]
Chapter 2.
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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<<ot1.cmap>><<oml.cmap
>><<oms.cmap>><<omx.cmap>>
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[1] [2]
Chapter 1.

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[3]
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[8]
Chapter 2.
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Output written on life-epigenetics-methylcheck.pdf (13 pages, 293416 bytes).
Transcript written on life-epigenetics-methylcheck.log.
Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written
Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 256
Latexmk: Errors, in force_mode: so I tried finishing targets

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[rtd-command-info] start-time: 2019-08-22T19:39:30.387340Z, end-time: 2019-08-22T19:39:45.664822Z, duration: 15, exit-code: 0
python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:100: WARNING: Title level inconsistent:

Filter either by the publication source, or by the type of effect (e.g. Polymorphism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methpype_methQC_example.ipynb:370: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:8: WARNING: Title underline too short.

methylcheck.QCreport module
----------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:8: WARNING: Title underline too short.

methylcheck.QCreport module
----------------------
WARNING: autodoc: failed to import module 'QCreport' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:16: WARNING: Title underline too short.

methylcheck.cli module
-----------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:16: WARNING: Title underline too short.

methylcheck.cli module
-----------------
WARNING: autodoc: failed to import module 'cli' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:24: WARNING: Title underline too short.

methylcheck.filters module
---------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:24: WARNING: Title underline too short.

methylcheck.filters module
---------------------
WARNING: autodoc: failed to import module 'filters' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:32: WARNING: Title underline too short.

methylcheck.postprocessQC module
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:32: WARNING: Title underline too short.

methylcheck.postprocessQC module
---------------------------
WARNING: autodoc: failed to import module 'postprocessQC' from module 'methylcheck'; the following exception was raised:
No module named 'sklearn'
WARNING: autodoc: failed to import module 'methylcheck'; the following exception was raised:
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:10: WARNING: toctree contains reference to nonexisting document 'docs/demo-methylprep-to-methylcheck-example'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:10: WARNING: toctree contains reference to nonexisting document 'docs/methylprep_methylcheck_example'
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generating indices... genindex
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The ePub file is in _build/epub.

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