Read the Docs build information
Build id: 765745
Project: cyverse-visual-interactive-computing-environment
Version: latest
Commit: 036b86e0674abee713ed9540ce323f6d110c2169
Date: 2021-11-05T15:44:13.303341Z
State: finished
Success: False


[rtd-command-info] start-time: 2021-11-05T15:44:15.270988Z, end-time: 2021-11-05T15:44:23.933252Z, duration: 8, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/Visual_Interactive_Computing_Environment.git .
Cloning into '.'...

[rtd-command-info] start-time: 2021-11-05T15:44:24.067062Z, end-time: 2021-11-05T15:44:24.425315Z, duration: 0, exit-code: 0
git checkout --force origin/main
Note: checking out 'origin/main'.

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 036b86e Update sharing.rst

[rtd-command-info] start-time: 2021-11-05T15:44:24.531479Z, end-time: 2021-11-05T15:44:24.598816Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-11-05T15:44:25.992920Z, end-time: 2021-11-05T15:44:31.118225Z, duration: 5, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-11-05T15:44:31.230154Z, end-time: 2021-11-05T15:44:32.387532Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (21.3.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (58.5.3)

[rtd-command-info] start-time: 2021-11-05T15:44:32.523461Z, end-time: 2021-11-05T15:44:40.483887Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting pillow==5.4.1
  Downloading Pillow-5.4.1-cp37-cp37m-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<2.2
  Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB)
Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting docutils>=0.11
  Downloading docutils-0.18-py2.py3-none-any.whl (569 kB)
Collecting Jinja2>=2.3
  Downloading Jinja2-3.0.2-py3-none-any.whl (133 kB)
Collecting six>=1.5
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx<2) (58.5.3)
Collecting packaging
  Downloading packaging-21.2-py3-none-any.whl (40 kB)
Collecting Pygments>=2.0
  Downloading Pygments-2.10.0-py3-none-any.whl (1.0 MB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB)
Collecting sphinxcontrib-websupport
  Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB)
Collecting requests>=2.0.0
  Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB)
Collecting imagesize
  Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB)
Collecting pytz>=2015.7
  Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB)
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (31 kB)
Collecting idna<4,>=2.5
  Downloading idna-3.3-py3-none-any.whl (61 kB)
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB)
Collecting certifi>=2017.4.17
  Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
Collecting charset-normalizer~=2.0.0
  Downloading charset_normalizer-2.0.7-py3-none-any.whl (38 kB)
Collecting pyparsing<3,>=2.0.2
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting sphinxcontrib-serializinghtml
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 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-py3-none-any.whl size=23772 sha256=8cd7cb508cc55ae1c0556e16eba4a564d1e7809f769628810e85b0709d408328
  Stored in directory: /tmp/pip-ephem-wheel-cache-sxi2a2ln/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=21b330efa5fbc7607bb3239fbe39bb6ab1d874eac95e3e5c862e25aea5fdd9f9
  Stored in directory: /tmp/pip-ephem-wheel-cache-sxi2a2ln/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
Successfully installed Jinja2-3.0.2 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.7 commonmark-0.8.1 docutils-0.18 future-0.18.2 idna-3.3 imagesize-1.2.0 mock-1.0.1 packaging-21.2 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.7

[rtd-command-info] start-time: 2021-11-05T15:44:41.621544Z, end-time: 2021-11-05T15:44:41.684491Z, 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 = 'Visual Interactive Computing Environment'
copyright = '2021, CyVerse'
author = 'CyVerse'
version = '2.1'
version = '2.1'

epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright
exclude_patterns = ['README.md', 'License.md', 'Contributors_maintainers.md']




###########################################################################
#          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
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

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

from sphinx import version_info

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

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

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

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


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("main", "/en/main/"),
    ],
    'downloads': [ 
    ("pdf", "//learning.cyverse.org/_/downloads/vice/en/latest/pdf/"),
    ("html", "//learning.cyverse.org/_/downloads/vice/en/latest/htmlzip/"),
    ("epub", "//learning.cyverse.org/_/downloads/vice/en/latest/epub/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-visual-interactive-computing-environment',
    'name': u'Visual_Interactive_Computing_Environment',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://learning.cyverse.org/projects/vice/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': 'Visual_Interactive_Computing_Environment',
    'github_version': 'main',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'main',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'main',
    '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': '036b86e0',
}

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





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

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

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/cyverse-visual-interactive-computing-environment/builds/765745/'

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: 2021-11-05T15:44:41.794786Z, end-time: 2021-11-05T15:44:44.777778Z, duration: 2, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -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 [html]: targets for 19 source files that are out of date
updating environment: 19 added, 0 changed, 0 removed
reading sources... [  5%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
reading sources... [ 10%] data
reading sources... [ 15%] developer_guide/adding
reading sources... [ 21%] developer_guide/building
reading sources... [ 26%] developer_guide/examples
reading sources... [ 31%] developer_guide/workflow
reading sources... [ 36%] getting_help/bestpractices
reading sources... [ 42%] getting_help/contact
reading sources... [ 47%] getting_help/faq
reading sources... [ 52%] getting_help/tool_troubleshooting
reading sources... [ 57%] getting_started/about
reading sources... [ 63%] getting_started/apptypes
reading sources... [ 68%] getting_started/prerequisites
reading sources... [ 73%] index
reading sources... [ 78%] user_guide/quick-jupyter
reading sources... [ 84%] user_guide/quick-rshiny
reading sources... [ 89%] user_guide/quick-rstudio
reading sources... [ 94%] user_guide/sharing
reading sources... [100%] vice_apps/examples

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition.
custom_urls.txt:58: WARNING: image file not readable: ../img/vice/jupyter/jupyter2-1.png
custom_urls.txt:64: WARNING: image file not readable: ../img/vice/jupyter/jupyter2-3.png
custom_urls.txt:70: WARNING: image file not readable: ../img/vice/jupyter/jupyter2-5.png
custom_urls.txt:76: WARNING: image file not readable: ../img/vice/jupyter/jupyter2-7.png
custom_urls.txt:81: WARNING: image file not readable: ../img/vice/jupyter/app_loading.gif
custom_urls.txt:86: WARNING: image file not readable: ../img/vice/shiny/shiny1-1.png
custom_urls.txt:92: WARNING: image file not readable: ../img/vice/shiny/shiny1-3.png
custom_urls.txt:98: WARNING: image file not readable: ../img/vice/shiny/shiny1-5.png
custom_urls.txt:104: WARNING: image file not readable: ../img/vice/shiny/shiny1-7.png
custom_urls.txt:110: WARNING: image file not readable: ../img/vice/shiny/shiny1-9.png
custom_urls.txt:116: WARNING: image file not readable: ../img/vice/shiny/shiny1-11.png
custom_urls.txt:122: WARNING: image file not readable: ../img/vice/shiny/shiny1-13.png
cyverse_rst_defined_substitutions.txt:123: WARNING: image file not readable: ../img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt:128: WARNING: image file not readable: ../img/homeicon.png
cyverse_rst_defined_substitutions.txt:134: WARNING: image file not readable: ../img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:36: WARNING: Undefined substitution referenced: "add-tool".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:81: WARNING: Undefined substitution referenced: "vice-do-not-pass".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/prerequisites.rst:16: WARNING: Undefined substitution referenced: "ORCID".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:28: WARNING: toctree contains reference to nonexisting document '.. user_guide/quick-rshiny'
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:81: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:86: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:92: WARNING: Duplicate substitution definition name: "Intercom".
custom_urls.txt:58: WARNING: image file not readable: ../img/vice/jupyter/jupyter2-1.png
custom_urls.txt:64: WARNING: image file not readable: ../img/vice/jupyter/jupyter2-3.png
custom_urls.txt:70: WARNING: image file not readable: ../img/vice/jupyter/jupyter2-5.png
custom_urls.txt:76: WARNING: image file not readable: ../img/vice/jupyter/jupyter2-7.png
custom_urls.txt:81: WARNING: image file not readable: ../img/vice/jupyter/app_loading.gif
custom_urls.txt:86: WARNING: image file not readable: ../img/vice/shiny/shiny1-1.png
custom_urls.txt:92: WARNING: image file not readable: ../img/vice/shiny/shiny1-3.png
custom_urls.txt:98: WARNING: image file not readable: ../img/vice/shiny/shiny1-5.png
custom_urls.txt:104: WARNING: image file not readable: ../img/vice/shiny/shiny1-7.png
custom_urls.txt:110: WARNING: image file not readable: ../img/vice/shiny/shiny1-9.png
custom_urls.txt:116: WARNING: image file not readable: ../img/vice/shiny/shiny1-11.png
custom_urls.txt:122: WARNING: image file not readable: ../img/vice/shiny/shiny1-13.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:92: WARNING: image file not readable: ./img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:11: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:89: WARNING: Unknown target name: "github repo link".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:99: WARNING: image file not readable: user_guide/../img/vice-share-5.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:24: WARNING: Duplicate explicit target name: "github".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:24: WARNING: Duplicate explicit target name: "github".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:24: WARNING: Duplicate explicit target name: "github".
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pickling environment... done
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build succeeded, 47 warnings.

The HTML page is in _build/localmedia.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2021-11-05T15:44:47.961204Z, end-time: 2021-11-05T15:44:50.188702Z, duration: 2, exit-code: 2
python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.8.5
loading translations [en]... done
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building [mo]: targets for 0 po files that are out of date
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition.
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:36: WARNING: Undefined substitution referenced: "add-tool".
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/prerequisites.rst:16: WARNING: Undefined substitution referenced: "ORCID".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:28: WARNING: toctree contains reference to nonexisting document '.. user_guide/quick-rshiny'
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:81: WARNING: Duplicate substitution definition name: "CyVerse_logo".
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:11: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:89: WARNING: Unknown target name: "github repo link".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:99: WARNING: image file not readable: user_guide/../img/vice-share-5.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:24: WARNING: Duplicate explicit target name: "github".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:24: WARNING: Duplicate explicit target name: "github".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:24: WARNING: Duplicate explicit target name: "github".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/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-visual-interactive-computing-environment/checkouts/latest/data.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst: WARNING: document isn't included in any toctree
done
processing CyVerseDocumentation.tex...
Exception occurred:
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages/sphinx/builders/latex/__init__.py", line 201, in write
    if toctrees[0].get('maxdepth') > 0:
TypeError: 'generator' object is not subscriptable
The full traceback has been saved in /tmp/sphinx-err-6viqgcx3.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!