Read the Docs build information
Build id: 200996
Project: cyverse-dnasubway-guide
Version: latest
Commit: a0119f7226fc89c4d4e3237b93023130b915209e
Date: 2019-04-12T19:41:51.494718Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-04-12T19:41:52.004362Z, end-time: 2019-04-12T19:41:52.670160Z, duration: 0, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/dnasubway_guide.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-04-12T19:41:52.847307Z, end-time: 2019-04-12T19:41:52.932562Z, 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 a0119f7 remove hoover feature from volcano plot

[rtd-command-info] start-time: 2019-04-12T19:41:52.994916Z, end-time: 2019-04-12T19:41:53.003730Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-04-12T19:41:53.652743Z, end-time: 2019-04-12T19:41:55.721673Z, duration: 2, exit-code: 0
python2.7 -mvirtualenv --no-site-packages --no-download 
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python2.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-04-12T19:41:55.782994Z, end-time: 2019-04-12T19:41:57.756813Z, duration: 1, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip pip
Collecting pip
  Downloading https://files.pythonhosted.org/packages/d8/f3/413bab4ff08e1fc4828dfc59996d721917df8e8583ea85385d51125dceff/pip-19.0.3-py2.py3-none-any.whl (1.4MB)
Installing collected packages: pip
  Found existing installation: pip 18.1
    Uninstalling pip-18.1:
      Successfully uninstalled pip-18.1
Successfully installed pip-19.0.3

[rtd-command-info] start-time: 2019-04-12T19:41:57.815477Z, end-time: 2019-04-12T19:42:07.836456Z, duration: 10, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip Pygments==2.3.1 setuptools<41 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting Pygments==2.3.1
  Downloading https://files.pythonhosted.org/packages/13/e5/6d710c9cf96c31ac82657bcfb441df328b22df8564d58d0c4cd62612674c/Pygments-2.3.1-py2.py3-none-any.whl (849kB)
Collecting setuptools<41
  Downloading https://files.pythonhosted.org/packages/44/56/75e64a8fbbe9e0bd30cfdd58ca1856bc0dc15a43e41504a58d8373f34213/setuptools-40.9.0-py2.py3-none-any.whl (575kB)
Collecting docutils==0.14
  Downloading https://files.pythonhosted.org/packages/50/09/c53398e0005b11f7ffb27b7aa720c617aba53be4fb4f4f3f06b9b5c60f28/docutils-0.14-py2-none-any.whl (543kB)
Collecting mock==1.0.1
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Collecting recommonmark==0.5.0
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Collecting sphinx<2
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Collecting sphinx-rtd-theme<0.5
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Collecting readthedocs-sphinx-ext<0.6
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Collecting future (from commonmark==0.8.1)
  Downloading https://files.pythonhosted.org/packages/90/52/e20466b85000a181e1e144fd8305caf2cf475e2f9674e797b222f8105f5f/future-0.17.1.tar.gz (829kB)
Collecting snowballstemmer>=1.1 (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/d4/6c/8a935e2c7b54a37714656d753e4187ee0631988184ed50c0cf6476858566/snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB)
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Collecting babel!=2.0,>=1.3 (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl (8.1MB)
Collecting requests>=2.0.0 (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl (57kB)
Collecting Jinja2>=2.3 (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl (124kB)
Collecting typing; python_version < "3.5" (from sphinx<2)
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Collecting packaging (from sphinx<2)
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Collecting imagesize (from sphinx<2)
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Collecting six>=1.5 (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx<2)
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Collecting urllib3<1.25,>=1.21.1 (from requests>=2.0.0->sphinx<2)
  Downloading https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl (118kB)
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<2)
  Downloading https://files.pythonhosted.org/packages/60/75/f692a584e85b7eaba0e03827b3d51f45f571c2e793dd731e598828d380aa/certifi-2019.3.9-py2.py3-none-any.whl (158kB)
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx<2)
  Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB)
Collecting idna<2.9,>=2.5 (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 pyparsing>=2.0.2 (from packaging->sphinx<2)
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip/wheels/0c/61/d2/d6b7317325828fbb39ee6ad559dbe4664d0896da4721bf379e
Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, snowballstemmer, sphinxcontrib-websupport, pytz, babel, urllib3, certifi, chardet, idna, requests, MarkupSafe, Jinja2, typing, pyparsing, six, packaging, imagesize, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Found existing installation: setuptools 40.6.3
    Uninstalling setuptools-40.6.3:
      Successfully uninstalled setuptools-40.6.3
Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.6.0 certifi-2019.3.9 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-19.0 pillow-5.4.1 pyparsing-2.4.0 pytz-2019.1 readthedocs-sphinx-ext-0.5.17 recommonmark-0.5.0 requests-2.21.0 setuptools-40.9.0 six-1.12.0 snowballstemmer-1.2.1 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.0 typing-3.6.6 urllib3-1.24.1

[rtd-command-info] start-time: 2019-04-12T19:42:08.371527Z, end-time: 2019-04-12T19:42:08.431597Z, duration: 0, exit-code: 0
cat conf.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# General information about the project.

import sys
import os
sys.path.insert(0, os.path.dirname(__file__))

from misc.cyverse_sphinx_conf import *  # noqa

project = 'DNA Subway Guide'
copyright = '2016, CyVerse'
author = 'CyVerse'
version = '1.0'
release = '1.0'

epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright




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


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


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

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for mulitple 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': [ 
    ("htmlzip", "//readthedocs.com/projects/cyverse-dnasubway-guide/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-dnasubway-guide',
    'name': u'dnasubway_guide',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://learning.cyverse.org/projects/dnasubway_guide/en/latest/',
    'analytics_code': '',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'github_repo': 'dnasubway_guide',
    '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': 'a0119f72',
}




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"]

[rtd-command-info] start-time: 2019-04-12T19:42:08.502199Z, end-time: 2019-04-12T19:42:10.958835Z, duration: 2, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 11 source files that are out of date
updating environment: 11 added, 0 changed, 0 removed
reading sources... [  9%] Contributors_maintainers
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
reading sources... [ 18%] License
reading sources... [ 27%] index
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reading sources... [100%] step8

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:194: WARNING: Enumerated list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:196: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:488: WARNING: Duplicate substitution definition name: "CyVerse logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:492: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:64: WARNING: Block quote ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/License.md: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  9%] Contributors_maintainers
writing output... [ 18%] License
writing output... [ 27%] index
writing output... [ 36%] step1
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generating indices... genindex
writing additional pages... search
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copying images... [ 83%] ./img/dna_subway/bray.png
copying images... [ 86%] ./img/dna_subway/jbrowse.png
copying images... [ 88%] ./img/dna_subway/repeat_results.png
copying images... [ 91%] ./img/cyverse_rgb.png
copying images... [ 94%] ./img/dna_subway/sleuth_loadings_1.png
copying images... [ 97%] ./img/dna_subway/faith.png
copying images... [100%] ./img/dna_subway/unweighted.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/_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, 8 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2019-04-12T19:42:11.059874Z, end-time: 2019-04-12T19:42:13.394979Z, duration: 2, 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...
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 11 added, 0 changed, 0 removed
reading sources... [  9%] Contributors_maintainers
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
reading sources... [ 18%] License
reading sources... [ 27%] index
reading sources... [ 36%] step1
reading sources... [ 45%] step2
reading sources... [ 54%] step3
reading sources... [ 63%] step4
reading sources... [ 72%] step5
reading sources... [ 81%] step6
reading sources... [ 90%] step7
reading sources... [100%] step8

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:194: WARNING: Enumerated list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:196: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:488: WARNING: Duplicate substitution definition name: "CyVerse logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:492: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:64: WARNING: Block quote ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/License.md: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... step1 step2 step3 step4 step5 step6 step7 step8 
writing... done
writing additional files...
copying images... [  2%] ./img/dna_subway/sleuth_heatmap_1.png
copying images... [  5%] ./img/dna_subway/blue_trace.png
copying images... [  8%] ./img/dna_subway/histogram_poor.png
copying images... [ 11%] ./img/dna_subway/sleuth_bootstrap_1.png
copying images... [ 13%] ./img/dna_subway/sleuth_pca_1.png
copying images... [ 16%] ./img/dna_subway/apollo_2.png
copying images... [ 19%] ./img/dna_subway/sleuth_results_1.png
copying images... [ 22%] ./img/dna_subway/dnasubway-icon.png
copying images... [ 25%] ./img/dna_subway/project_info_tab.png
copying images... [ 27%] ./img/dna_subway/private_projects.png
copying images... [ 30%] ./img/dna_subway/blue_align.png
copying images... [ 33%] ./img/dna_subway/faith_group.png
copying images... [ 36%] ./img/dna_subway/taxonomy.png
copying images... [ 38%] ./img/dna_subway/taxabar.png
copying images... [ 41%] ./img/dna_subway/yellow_tree.png
copying images... [ 44%] ./img/dna_subway/blue_blast.png
copying images... [ 47%] ./img/dna_subway/core_matrix.png
copying images... [ 50%] ./img/dna_subway/blue_ml.png
copying images... [ 52%] ./img/dna_subway/apollo_4.png
copying images... [ 55%] ./img/dna_subway/even_cor.png
copying images... [ 58%] ./img/dna_subway/histogram_good.png
copying images... [ 61%] ./img/dna_subway/sleuth_volcano_1.png
copying images... [ 63%] ./img/dna_subway/group_sig.png
copying images... [ 66%] ./img/dna_subway/yellow_alignment.png
copying images... [ 69%] ./img/dna_subway/blue_nj.png
copying images... [ 72%] ./img/dna_subway/apollo_1.png
copying images... [ 75%] ./img/dna_subway/apollo_5.png
copying images... [ 77%] ./img/dna_subway/apollo_3.png
copying images... [ 80%] ./img/homeicon.png
copying images... [ 83%] ./img/dna_subway/bray.png
copying images... [ 86%] ./img/dna_subway/jbrowse.png
copying images... [ 88%] ./img/dna_subway/repeat_results.png
copying images... [ 91%] ./img/cyverse_rgb.png
copying images... [ 94%] ./img/dna_subway/sleuth_loadings_1.png
copying images... [ 97%] ./img/dna_subway/faith.png
copying images... [100%] ./img/dna_subway/unweighted.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/_static' does not exist
done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded, 8 warnings.

The HTML page is in _build/localmedia.