Read the Docs build information
Build id: 425604
Project: cyverse-dnasubway-guide
Version: latest
Commit: 85bdb58a9caa54ae15db3e91acfdabbfada3beac
Date: 2020-09-18T15:28:45.425306Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-09-18T15:34:41.736382Z, end-time: 2020-09-18T15:34:43.308931Z, duration: 1, 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: 2020-09-18T15:34:44.055384Z, end-time: 2020-09-18T15:34:44.341942Z, 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 85bdb58 add triage issue template

[rtd-command-info] start-time: 2020-09-18T15:34:44.532513Z, end-time: 2020-09-18T15:34:44.580638Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-09-18T15:34:46.127812Z, end-time: 2020-09-18T15:34:49.469667Z, duration: 3, exit-code: 0
python2.7 -mvirtualenv 
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: 2020-09-18T15:34:50.002448Z, end-time: 2020-09-18T15:34:50.657947Z, duration: 0, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (20.2.3)

[rtd-command-info] start-time: 2020-09-18T15:34:50.971113Z, end-time: 2020-09-18T15:34:58.962596Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
Collecting Pygments==2.3.1
  Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB)
Collecting setuptools==41.0.1
  Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB)
Collecting docutils==0.14
  Downloading docutils-0.14-py2-none-any.whl (543 kB)
Collecting mock==1.0.1
  Downloading mock-1.0.1.tar.gz (818 kB)
Collecting pillow==5.4.1
  Downloading Pillow-5.4.1-cp27-cp27mu-manylinux1_x86_64.whl (2.0 MB)
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB)
Collecting commonmark==0.8.1
  Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB)
Collecting recommonmark==0.5.0
  Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx<2
  Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB)
Collecting sphinx-rtd-theme<0.5
  Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB)
Collecting readthedocs-sphinx-ext<1.1
  Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB)
Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
Collecting imagesize
  Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB)
Collecting typing; python_version < "3.5"
  Downloading typing-3.7.4.3-py2-none-any.whl (26 kB)
Collecting Jinja2>=2.3
  Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
Collecting packaging
  Downloading packaging-20.4-py2.py3-none-any.whl (37 kB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB)
Collecting six>=1.5
  Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting requests>=2.0.0
  Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB)
Collecting sphinxcontrib-websupport
  Downloading sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl (39 kB)
Collecting MarkupSafe>=0.23
  Downloading MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl (24 kB)
Collecting pyparsing>=2.0.2
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting pytz>=2015.7
  Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB)
Collecting certifi>=2017.4.17
  Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
  Downloading urllib3-1.25.10-py2.py3-none-any.whl (127 kB)
Collecting idna<3,>=2.5
  Downloading idna-2.10-py2.py3-none-any.whl (58 kB)
Collecting chardet<4,>=3.0.2
  Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py2-none-any.whl size=23754 sha256=7da532649030526b7da87ee79ddfdde82c6290667606200c415fca25d2099be3
  Stored in directory: /tmp/pip-ephem-wheel-cache-HcTQL8/wheels/ad/62/e0/a06cc957652749e64c7904e899eca3ecb2ec47c60d52653660
  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-py2-none-any.whl size=502566 sha256=5a249de5449f312120f36bd470c4798999c47deae373fcfe5ea2854835111888
  Stored in directory: /tmp/pip-ephem-wheel-cache-HcTQL8/wheels/5f/11/0c/aad680baf5ef4fbcbab992c9f03e1130357e0c173a4fdabfff
Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, typing, MarkupSafe, Jinja2, six, pyparsing, packaging, snowballstemmer, pytz, babel, certifi, urllib3, idna, chardet, requests, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
    Found existing installation: setuptools 44.1.1
    Uninstalling setuptools-44.1.1:
      Successfully uninstalled setuptools-44.1.1
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 typing-3.7.4.3 urllib3-1.25.10

[rtd-command-info] start-time: 2020-09-18T15:35:00.932474Z, end-time: 2020-09-18T15:35:01.000406Z, 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 = '2.0'
version = '2.0'

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 multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

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

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

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


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("html", "//learning.cyverse.org/_/downloads/dnasubway_guide/en/latest/htmlzip/"),
    ],
    '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': 'UA-72224033-6',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'proxied_api_host': '/_',
    '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,
    'docsearch_disabled': False,
    'user_analytics_code': 'UA-72224033-6',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '85bdb58a',
}




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

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

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

project_language = 'en'

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

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

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

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

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

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

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

[rtd-command-info] start-time: 2020-09-18T15:35:01.556676Z, end-time: 2020-09-18T15:35:03.921953Z, 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 12 source files that are out of date
updating environment: 12 added, 0 changed, 0 removed
reading sources... [  8%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
/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... [ 16%] Contributors_maintainers
reading sources... [ 25%] License
reading sources... [ 33%] index
reading sources... [ 41%] step1
reading sources... [ 50%] step2
reading sources... [ 58%] step3
reading sources... [ 66%] step4
reading sources... [ 75%] step5
reading sources... [ 83%] step6
reading sources... [ 91%] step7
reading sources... [100%] step8

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/index.rst:90: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/index.rst:75: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step1.rst:115: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step1.rst:100: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step2.rst:99: WARNING: Duplicate substitution definition name: "Home_Icon".
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cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
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cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step4.rst:126: WARNING: Duplicate substitution definition name: "Home_Icon".
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cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step5.rst:303: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step5.rst:288: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:195: WARNING: Enumerated list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:197: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:255: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:243: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:512: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:500: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:822: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:893: WARNING: Duplicate substitution definition name: "CyVerse User Portal".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:810: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md: WARNING: document isn't included in any toctree
/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
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  8%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
writing output... [ 16%] Contributors_maintainers
writing output... [ 25%] License
writing output... [ 33%] index
writing output... [ 41%] step1
writing output... [ 50%] step2
writing output... [ 58%] step3
writing output... [ 66%] step4
writing output... [ 75%] step5
writing output... [ 83%] step6
writing output... [ 91%] step7
writing output... [100%] step8

generating indices... genindex
writing additional pages... search
copying images... [  2%] ./img/dna_subway/sleuth_heatmap_1.png
copying images... [  5%] ./img/dna_subway/metadata_error.gif
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copying images... [ 24%] ./img/dna_subway/dnasubway-icon.png
copying images... [ 27%] ./img/dna_subway/project_info_tab.png
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copying images... [100%] ./img/dna_subway/overview_tab.gif

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, 45 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2020-09-18T15:35:04.480164Z, end-time: 2020-09-18T15:35:06.577408Z, 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: 12 added, 0 changed, 0 removed
reading sources... [  8%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
/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... [ 16%] Contributors_maintainers
reading sources... [ 25%] License
reading sources... [ 33%] index
reading sources... [ 41%] step1
reading sources... [ 50%] step2
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reading sources... [ 66%] step4
reading sources... [ 75%] step5
reading sources... [ 83%] step6
reading sources... [ 91%] step7
reading sources... [100%] step8

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/index.rst:90: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/index.rst:75: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step1.rst:115: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step1.rst:100: WARNING: Undefined substitution referenced: "Github Repo Link".
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cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
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cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
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cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step5.rst:303: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step5.rst:288: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:195: WARNING: Enumerated list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:197: WARNING: Block quote ends without a blank line; unexpected unindent.
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:243: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:512: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:500: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:822: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:893: WARNING: Duplicate substitution definition name: "CyVerse User Portal".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:810: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md: WARNING: document isn't included in any toctree
/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
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... step1 step2 step3 step4 step5 step7 step8 
writing... done
writing additional files...
copying images... [  2%] ./img/dna_subway/sleuth_heatmap_1.png
copying images... [  5%] ./img/dna_subway/metadata_error.gif
copying images... [  8%] ./img/dna_subway/blue_trace.png
copying images... [ 10%] ./img/dna_subway/histogram_poor.png
copying images... [ 13%] ./img/dna_subway/sleuth_bootstrap_1.png
copying images... [ 16%] ./img/dna_subway/sleuth_pca_1.png
copying images... [ 18%] ./img/dna_subway/apollo_2.png
copying images... [ 21%] ./img/dna_subway/sleuth_results_1.png
copying images... [ 24%] ./img/dna_subway/dnasubway-icon.png
copying images... [ 27%] ./img/dna_subway/project_info_tab.png
copying images... [ 29%] ./img/dna_subway/private_projects.png
copying images... [ 32%] ./img/dna_subway/blue_align.png
copying images... [ 35%] ./img/dna_subway/emperor_plots.gif
copying images... [ 37%] ./img/dna_subway/yellow_tree.png
copying images... [ 40%] ./img/dna_subway/taxonomic_barplots.gif
copying images... [ 43%] ./img/dna_subway/blue_blast.png
copying images... [ 45%] ./img/dna_subway/blue_ml.png
copying images... [ 48%] ./img/dna_subway/apollo_4.png
copying images... [ 51%] ./img/dna_subway/histogram_good.png
copying images... [ 54%] ./img/dna_subway/sleuth_volcano_1.png
copying images... [ 56%] ./img/dna_subway/metadata_add_column.gif
copying images... [ 59%] ./img/dna_subway/yellow_alignment.png
copying images... [ 62%] ./img/dna_subway/blue_nj.png
copying images... [ 64%] ./img/dna_subway/apollo_1.png
copying images... [ 67%] ./img/dna_subway/metadata_add_samples.gif
copying images... [ 70%] ./img/dna_subway/apollo_5.png
copying images... [ 72%] ./img/dna_subway/apollo_3.png
copying images... [ 75%] ./img/homeicon.png
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copying images... [ 81%] ./img/dna_subway/jbrowse.png
copying images... [ 83%] ./img/dna_subway/quality_plot.gif
copying images... [ 86%] ./img/dna_subway/repeat_results.png
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copying images... [ 97%] ./img/dna_subway/metadata_rows.gif
copying images... [100%] ./img/dna_subway/overview_tab.gif

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, 45 warnings.

The HTML page is in _build/localmedia.