Read the Docs build information
Build id: 633177
Project: cyverse-visual-interactive-computing-environment
Version: latest
Commit: 378782c26a33ad15bc2ab2a7938829691ac2471d
Date: 2021-05-14T03:14:50.747286Z
State: finished
Success: True


[rtd-command-info] start-time: 2021-05-14T03:14:52.214979Z, end-time: 2021-05-14T03:14:57.164742Z, duration: 4, 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: 2021-05-14T03:14:57.336965Z, end-time: 2021-05-14T03:14:57.628282Z, 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 378782c Update cyverse_rst_defined_substitutions.txt

[rtd-command-info] start-time: 2021-05-14T03:14:57.761679Z, end-time: 2021-05-14T03:14:57.836881Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-05-14T03:15:00.478326Z, end-time: 2021-05-14T03:15:14.322264Z, duration: 13, exit-code: 0
python2.7 -mvirtualenv 
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python2.7
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: 2021-05-14T03:15:14.446029Z, end-time: 2021-05-14T03:15:16.294203Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
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 Please upgrade your Python as Python 2.7 is no longer maintained.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-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (20.3.4)
Requirement already up-to-date: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (44.1.1)

[rtd-command-info] start-time: 2021-05-14T03:15:16.406933Z, end-time: 2021-05-14T03:15:25.414370Z, duration: 9, 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
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 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<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)
Collecting docutils>=0.11
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
Collecting imagesize
  Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB)
Collecting typing; python_version < "3.5"
  Downloading typing-3.10.0.0-py2-none-any.whl (26 kB)
Collecting Pygments>=2.0
  Downloading Pygments-2.5.2-py2.py3-none-any.whl (896 kB)
Collecting Jinja2>=2.3
  Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
Collecting packaging
  Downloading packaging-20.9-py2.py3-none-any.whl (40 kB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB)
Requirement already satisfied, skipping upgrade: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<2) (44.1.1)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB)
Collecting six>=1.5
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting requests>=2.0.0
  Downloading requests-2.25.1-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-2021.1-py2.py3-none-any.whl (510 kB)
Collecting chardet<5,>=3.0.2
  Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB)
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.4-py2.py3-none-any.whl (153 kB)
Collecting idna<3,>=2.5
  Downloading idna-2.10-py2.py3-none-any.whl (58 kB)
Collecting certifi>=2017.4.17
  Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 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=23756 sha256=5b18f3ff5de2995a39a7e2a6659609618f7db328c82e5d0fc8bb65311e024838
  Stored in directory: /tmp/pip-ephem-wheel-cache-cR3TNl/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=a91379c6479ade48c403b47622c2edbb9cb076f88f99166c07b69ff4cc7e6975
  Stored in directory: /tmp/pip-ephem-wheel-cache-cR3TNl/wheels/5f/11/0c/aad680baf5ef4fbcbab992c9f03e1130357e0c173a4fdabfff
Successfully built mock future
Installing collected packages: mock, pillow, alabaster, future, commonmark, imagesize, typing, Pygments, docutils, MarkupSafe, Jinja2, pyparsing, packaging, snowballstemmer, pytz, babel, six, chardet, urllib3, idna, certifi, requests, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.5.2 alabaster-0.7.12 babel-2.9.1 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 typing-3.10.0.0 urllib3-1.26.4

[rtd-command-info] start-time: 2021-05-14T03:15:25.534802Z, end-time: 2021-05-14T03:15:28.473383Z, duration: 2, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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 satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 1)) (1.8.5)
Requirement already satisfied: recommonmark in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 2)) (0.5.0)
Collecting sphinxcontrib-images
  Downloading sphinxcontrib_images-0.9.3-py2.py3-none-any.whl (67 kB)
Collecting sphinx_bootstrap_theme
  Downloading sphinx-bootstrap-theme-0.7.1.tar.gz (1.2 MB)
Collecting guzzle_sphinx_theme==0.7.11
  Downloading guzzle_sphinx_theme-0.7.11.tar.gz (2.5 MB)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.2.0)
Requirement already satisfied: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (3.10.0.0)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.5.2)
Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.17.1)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.11.3)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (20.9)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.7.12)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.1.0)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (44.1.1)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.9.1)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.16.0)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.25.1)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.1.2)
Requirement already satisfied: commonmark>=0.7.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from recommonmark->-r requirements.txt (line 2)) (0.8.1)
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx->-r requirements.txt (line 1)) (1.1.1)
Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from packaging->sphinx->-r requirements.txt (line 1)) (2.4.7)
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx->-r requirements.txt (line 1)) (2021.1)
Requirement already satisfied: chardet<5,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (4.0.0)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (1.26.4)
Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2.10)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2020.12.5)
Requirement already satisfied: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from commonmark>=0.7.3->recommonmark->-r requirements.txt (line 2)) (0.18.2)
Building wheels for collected packages: sphinx-bootstrap-theme, guzzle-sphinx-theme
  Building wheel for sphinx-bootstrap-theme (setup.py): started
  Building wheel for sphinx-bootstrap-theme (setup.py): finished with status 'done'
  Created wheel for sphinx-bootstrap-theme: filename=sphinx_bootstrap_theme-0.7.1-py2-none-any.whl size=1250222 sha256=0f6b82f1ab76ee0d516dea630e65cadd19524e88e82f1c4ceaddadddb0b0202b
  Stored in directory: /tmp/pip-ephem-wheel-cache-tS2HLZ/wheels/95/93/4e/ce6bc27771a672df0da2021feb26f922e8a74bacdeb9195838
  Building wheel for guzzle-sphinx-theme (setup.py): started
  Building wheel for guzzle-sphinx-theme (setup.py): finished with status 'done'
  Created wheel for guzzle-sphinx-theme: filename=guzzle_sphinx_theme-0.7.11-py2-none-any.whl size=2555156 sha256=1c5c5ed0f235e001526f5fd8ef79853a8c8afab6892e6b4606f5be719fa71797
  Stored in directory: /tmp/pip-ephem-wheel-cache-tS2HLZ/wheels/9d/61/03/c574afdc16ce34de1d382f4d4cdb1eb624fafabe9e0a6988c2
Successfully built sphinx-bootstrap-theme guzzle-sphinx-theme
Installing collected packages: sphinxcontrib-images, sphinx-bootstrap-theme, guzzle-sphinx-theme
Successfully installed guzzle-sphinx-theme-0.7.11 sphinx-bootstrap-theme-0.7.1 sphinxcontrib-images-0.9.3

[rtd-command-info] start-time: 2021-05-14T03:15:29.354270Z, end-time: 2021-05-14T03:15:29.425489Z, 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 = '2020, CyVerse'
author = 'CyVerse'
version = '2.0'
version = '2.0'

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 should't rely on extra depencies.

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/"),
    ],
    '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': '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': '378782c2',
}

# 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/633177/'

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: 2021-05-14T03:15:29.531554Z, end-time: 2021-05-14T03:15:34.946627Z, duration: 5, 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 49 source files that are out of date
updating environment: 49 added, 0 changed, 0 removed
reading sources... [  2%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/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... [  4%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
reading sources... [  6%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
reading sources... [  8%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
reading sources... [ 10%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
reading sources... [ 12%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
reading sources... [ 14%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
reading sources... [ 16%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
reading sources... [ 18%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
reading sources... [ 20%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
reading sources... [ 22%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
reading sources... [ 24%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
reading sources... [ 26%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
reading sources... [ 28%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
reading sources... [ 30%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
reading sources... [ 32%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
reading sources... [ 34%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
reading sources... [ 36%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
reading sources... [ 38%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
reading sources... [ 40%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
reading sources... [ 42%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
reading sources... [ 44%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
reading sources... [ 46%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
reading sources... [ 48%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
reading sources... [ 51%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
reading sources... [ 53%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
reading sources... [ 55%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
reading sources... [ 57%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
reading sources... [ 59%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
reading sources... [ 61%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
reading sources... [ 63%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
reading sources... [ 65%] data
reading sources... [ 67%] developer_guide/adding
reading sources... [ 69%] developer_guide/building
reading sources... [ 71%] developer_guide/examples
reading sources... [ 73%] developer_guide/workflow
reading sources... [ 75%] getting_help/bestpractices
reading sources... [ 77%] getting_help/contact
reading sources... [ 79%] getting_help/faq
reading sources... [ 81%] getting_help/tool_troubleshooting
reading sources... [ 83%] getting_started/about
reading sources... [ 85%] getting_started/apptypes
reading sources... [ 87%] getting_started/prerequisites
reading sources... [ 89%] index
reading sources... [ 91%] user_guide/quick-jupyter
reading sources... [ 93%] user_guide/quick-rshiny
reading sources... [ 95%] user_guide/quick-rstudio
reading sources... [ 97%] user_guide/sharing
reading sources... [100%] vice_apps/examples

/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.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
WARNING: invalid signature for autoclass (u'{{ objname }}')
WARNING: don't know which module to import for autodocumenting u'{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
WARNING: invalid signature for automodule (u'{{ fullname }}')
WARNING: don't know which module to import for autodocumenting u'{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst:63: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst:48: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:123: WARNING: image file not readable: ../img/cyverse_learning.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/adding.rst:57: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:60: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:62: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:98: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:102: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:75: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:78: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:80: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:31: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:34: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:36: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:29: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:31: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:33: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:11: WARNING: Title underline too short.

**Contact**
----------
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:36: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:38: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:40: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:41: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:43: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:45: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/about.rst:41: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:92: WARNING: Title underline too short.

4. What is Ubuntu Desktop?
=========================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:92: WARNING: Title underline too short.

4. What is Ubuntu Desktop?
=========================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:118: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:120: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:122: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:4: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:82: WARNING: Duplicate substitution definition name: "Home_Icon".
cyverse_rst_defined_substitutions.txt:123: WARNING: image file not readable: ../img/cyverse_learning.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/user_guide/quick-jupyter.rst:8: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:107: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:109: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:111: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:114: WARNING: Duplicate explicit target name: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:104: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:10: 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:68: WARNING: Title underline too short.

6. Complete your analysis
=======================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:68: WARNING: Title underline too short.

6. Complete your analysis
=======================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:79: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:91: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:94: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:96: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:99: WARNING: Duplicate explicit target name: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:88: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:102: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:105: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:107: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
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/buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION.rst: 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
done
preparing documents... done
writing output... [  2%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
writing output... [  4%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
writing output... [  6%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
writing output... [  8%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
writing output... [ 10%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
writing output... [ 12%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
writing output... [ 14%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
writing output... [ 16%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
writing output... [ 18%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
writing output... [ 20%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
writing output... [ 22%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
writing output... [ 24%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
writing output... [ 26%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
writing output... [ 28%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
writing output... [ 30%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
writing output... [ 32%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
writing output... [ 34%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
writing output... [ 36%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
writing output... [ 38%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
writing output... [ 40%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
writing output... [ 42%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
writing output... [ 44%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
writing output... [ 46%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
writing output... [ 48%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
writing output... [ 51%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
writing output... [ 53%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
writing output... [ 55%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
writing output... [ 57%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
writing output... [ 59%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
writing output... [ 61%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
writing output... [ 63%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
writing output... [ 65%] data
writing output... [ 67%] developer_guide/adding
writing output... [ 69%] developer_guide/building
writing output... [ 71%] developer_guide/examples
writing output... [ 73%] developer_guide/workflow
writing output... [ 75%] getting_help/bestpractices
writing output... [ 77%] getting_help/contact
writing output... [ 79%] getting_help/faq
writing output... [ 81%] getting_help/tool_troubleshooting
writing output... [ 83%] getting_started/about
writing output... [ 85%] getting_started/apptypes
writing output... [ 87%] getting_started/prerequisites
writing output... [ 89%] index
writing output... [ 91%] user_guide/quick-jupyter
writing output... [ 93%] user_guide/quick-rshiny
writing output... [ 95%] user_guide/quick-rstudio
writing output... [ 97%] user_guide/sharing
writing output... [100%] vice_apps/examples

generating indices... genindex
writing additional pages... search
copying images... [  1%] user_guide/../img/vice/shiny/shiny1-6.png
copying images... [  3%] user_guide/../img/vice/shiny/shiny1-4.png
copying images... [  5%] user_guide/../img/vice-share-5.png
copying images... [  7%] vice_apps/../img/cyverse_learning.png
copying images... [  9%] user_guide/../img/vice-share-7.png
copying images... [ 11%] user_guide/../img/vice/jupyter/jupyter2-0.png
copying images... [ 13%] developer_guide/../img/flow_new.png
copying images... [ 15%] user_guide/../img/vice/rstudio/rstudio3-1.png
copying images... [ 16%] getting_started/../img/vice_diagram.png
copying images... [ 18%] user_guide/../img/quick_launch/create_quick_launch.png
copying images... [ 20%] user_guide/../img/vice/rstudio/rstudio3-2.png
copying images... [ 22%] user_guide/../img/vice/shiny/shiny1-8.png
copying images... [ 24%] user_guide/../img/vice/rstudio/rstudio3-5.png
copying images... [ 26%] user_guide/../img/vice/shiny/shiny1-10.png
copying images... [ 28%] user_guide/../img/vice/rstudio/rstudio3-4.png
copying images... [ 30%] getting_started/../img/cyverse_learning.png
copying images... [ 32%] user_guide/../img/vice/jupyter/jupyter2-2.png
copying images... [ 33%] user_guide/../img/vice-share-6.png
copying images... [ 35%] user_guide/../img/vice/jupyter/jupyter2-5.png
copying images... [ 37%] user_guide/../img/vice/jupyter/jupyter2-6.png
copying images... [ 39%] user_guide/../img/vice/jupyter/jupyter2-7.png
copying images... [ 41%] user_guide/../img/vice/shiny/shiny1-13.png
copying images... [ 43%] user_guide/../img/homeicon.png
copying images... [ 45%] user_guide/../img/vice/rstudio/rstudio3-6.png
copying images... [ 47%] user_guide/../img/quick_launch/create_quick_launch_dialog.png
copying images... [ 49%] getting_started/../img/homeicon.png
copying images... [ 50%] user_guide/../img/quick_launch/use_quick_launch.png
copying images... [ 52%] user_guide/../img/vice/rstudio/rstudio3-9.png
copying images... [ 54%] user_guide/../img/vice/shiny/shiny1-7.png
copying images... [ 56%] user_guide/../img/vice-share-2.png
copying images... [ 58%] user_guide/../img/vice/shiny/shiny1-11.png
copying images... [ 60%] user_guide/../img/vice/shiny/shiny1-1.png
copying images... [ 62%] user_guide/../img/vice/shiny/shiny1-12.png
copying images... [ 64%] user_guide/../img/vice/jupyter/jupyter2-1.png
copying images... [ 66%] user_guide/../img/vice/jupyter/jupyter2-3.png
copying images... [ 67%] user_guide/../img/vice-share-3.png
copying images... [ 69%] user_guide/../img/vice/jupyter/app_loading.gif
copying images... [ 71%] user_guide/../img/vice/rstudio/rstudio3-7.png
copying images... [ 73%] vice_apps/../img/homeicon.png
copying images... [ 75%] user_guide/../img/vice/shiny/shiny1-9.png
copying images... [ 77%] developer_guide/../img/add-tool.png
copying images... [ 79%] developer_guide/../img/do_not_pass.png
copying images... [ 81%] ./img/homeicon.png
copying images... [ 83%] user_guide/../img/vice-share-4.png
copying images... [ 84%] user_guide/../img/vice-share-1.png
copying images... [ 86%] user_guide/../img/vice/shiny/shiny1-5.png
copying images... [ 88%] user_guide/../img/vice/rstudio/rstudio3-10.png
copying images... [ 90%] user_guide/../img/vice/shiny/shiny1-3.png
copying images... [ 92%] user_guide/../img/vice/shiny/shiny1-2.png
copying images... [ 94%] user_guide/../img/vice/rstudio/rstudio3-8.png
copying images... [ 96%] developer_guide/../img/homeicon.png
copying images... [ 98%] user_guide/../img/vice/rstudio/rstudio3-3.png
copying images... [100%] getting_help/../img/homeicon.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/_static' does not exist
done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 107 warnings.

The HTML pages are in _build/html.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2021-05-14T03:15:35.175725Z, end-time: 2021-05-14T03:15:38.793056Z, duration: 3, exit-code: 0
python -m sphinx -T -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 49 added, 0 changed, 0 removed
reading sources... [  2%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/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... [  4%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
reading sources... [  6%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
reading sources... [  8%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
reading sources... [ 10%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
reading sources... [ 12%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
reading sources... [ 14%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
reading sources... [ 16%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
reading sources... [ 18%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
reading sources... [ 20%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
reading sources... [ 22%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
reading sources... [ 24%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
reading sources... [ 26%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
reading sources... [ 28%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
reading sources... [ 30%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
reading sources... [ 32%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
reading sources... [ 34%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
reading sources... [ 36%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
reading sources... [ 38%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
reading sources... [ 40%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
reading sources... [ 42%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
reading sources... [ 44%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
reading sources... [ 46%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
reading sources... [ 48%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
reading sources... [ 51%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
reading sources... [ 53%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
reading sources... [ 55%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
reading sources... [ 57%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
reading sources... [ 59%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
reading sources... [ 61%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
reading sources... [ 63%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
reading sources... [ 65%] data
reading sources... [ 67%] developer_guide/adding
reading sources... [ 69%] developer_guide/building
reading sources... [ 71%] developer_guide/examples
reading sources... [ 73%] developer_guide/workflow
reading sources... [ 75%] getting_help/bestpractices
reading sources... [ 77%] getting_help/contact
reading sources... [ 79%] getting_help/faq
reading sources... [ 81%] getting_help/tool_troubleshooting
reading sources... [ 83%] getting_started/about
reading sources... [ 85%] getting_started/apptypes
reading sources... [ 87%] getting_started/prerequisites
reading sources... [ 89%] index
reading sources... [ 91%] user_guide/quick-jupyter
reading sources... [ 93%] user_guide/quick-rshiny
reading sources... [ 95%] user_guide/quick-rstudio
reading sources... [ 97%] user_guide/sharing
reading sources... [100%] vice_apps/examples

/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.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
WARNING: invalid signature for autoclass (u'{{ objname }}')
WARNING: don't know which module to import for autodocumenting u'{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
WARNING: invalid signature for automodule (u'{{ fullname }}')
WARNING: don't know which module to import for autodocumenting u'{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst:63: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst:48: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:123: WARNING: image file not readable: ../img/cyverse_learning.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/adding.rst:57: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:60: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:62: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:98: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:102: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:75: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:78: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:80: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:31: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:34: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:36: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:29: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:31: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:33: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:11: WARNING: Title underline too short.

**Contact**
----------
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:36: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:38: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:40: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:41: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:43: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:45: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/about.rst:41: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:92: WARNING: Title underline too short.

4. What is Ubuntu Desktop?
=========================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:92: WARNING: Title underline too short.

4. What is Ubuntu Desktop?
=========================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:118: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:120: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:122: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:4: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:82: WARNING: Duplicate substitution definition name: "Home_Icon".
cyverse_rst_defined_substitutions.txt:123: WARNING: image file not readable: ../img/cyverse_learning.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/user_guide/quick-jupyter.rst:8: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:107: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:109: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:111: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:114: WARNING: Duplicate explicit target name: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:104: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:10: 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:68: WARNING: Title underline too short.

6. Complete your analysis
=======================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:68: WARNING: Title underline too short.

6. Complete your analysis
=======================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:79: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:91: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:94: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:96: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:99: WARNING: Duplicate explicit target name: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:88: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:102: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:105: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:107: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
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/buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION.rst: 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
done
preparing documents... done
assembling single document... getting_started/about getting_started/prerequisites getting_started/apptypes user_guide/quick-jupyter user_guide/quick-rstudio user_guide/quick-rshiny user_guide/sharing developer_guide/workflow developer_guide/adding developer_guide/building vice_apps/examples getting_help/faq getting_help/bestpractices getting_help/tool_troubleshooting getting_help/contact 
writing... done
writing additional files...
copying images... [  1%] user_guide/../img/vice/shiny/shiny1-6.png
copying images... [  3%] user_guide/../img/vice/shiny/shiny1-4.png
copying images... [  5%] user_guide/../img/vice-share-5.png
copying images... [  7%] user_guide/../img/vice-share-7.png
copying images... [  9%] user_guide/../img/vice/jupyter/jupyter2-0.png
copying images... [ 11%] getting_help/../img/homeicon.png
copying images... [ 13%] user_guide/../img/vice/shiny/shiny1-9.png
copying images... [ 15%] user_guide/../img/vice/rstudio/rstudio3-1.png
copying images... [ 16%] getting_started/../img/vice_diagram.png
copying images... [ 18%] vice_apps/../img/cyverse_learning.png
copying images... [ 20%] user_guide/../img/vice/rstudio/rstudio3-2.png
copying images... [ 22%] user_guide/../img/vice/shiny/shiny1-8.png
copying images... [ 24%] user_guide/../img/vice/shiny/shiny1-10.png
copying images... [ 26%] user_guide/../img/homeicon.png
copying images... [ 28%] getting_started/../img/cyverse_learning.png
copying images... [ 30%] user_guide/../img/vice/jupyter/jupyter2-2.png
copying images... [ 32%] user_guide/../img/vice-share-6.png
copying images... [ 33%] user_guide/../img/vice/jupyter/jupyter2-5.png
copying images... [ 35%] user_guide/../img/vice/jupyter/jupyter2-6.png
copying images... [ 37%] user_guide/../img/vice/jupyter/jupyter2-7.png
copying images... [ 39%] user_guide/../img/vice/rstudio/rstudio3-5.png
copying images... [ 41%] user_guide/../img/vice/rstudio/rstudio3-4.png
copying images... [ 43%] user_guide/../img/vice/rstudio/rstudio3-6.png
copying images... [ 45%] user_guide/../img/quick_launch/create_quick_launch_dialog.png
copying images... [ 47%] developer_guide/../img/flow_new.png
copying images... [ 49%] getting_started/../img/homeicon.png
copying images... [ 50%] user_guide/../img/quick_launch/use_quick_launch.png
copying images... [ 52%] user_guide/../img/vice/rstudio/rstudio3-9.png
copying images... [ 54%] user_guide/../img/vice/shiny/shiny1-7.png
copying images... [ 56%] user_guide/../img/vice-share-2.png
copying images... [ 58%] user_guide/../img/vice/shiny/shiny1-11.png
copying images... [ 60%] user_guide/../img/vice/shiny/shiny1-1.png
copying images... [ 62%] user_guide/../img/vice/shiny/shiny1-12.png
copying images... [ 64%] user_guide/../img/vice/shiny/shiny1-13.png
copying images... [ 66%] user_guide/../img/vice/jupyter/jupyter2-1.png
copying images... [ 67%] user_guide/../img/vice/jupyter/jupyter2-3.png
copying images... [ 69%] user_guide/../img/vice-share-3.png
copying images... [ 71%] user_guide/../img/vice/jupyter/app_loading.gif
copying images... [ 73%] user_guide/../img/vice/rstudio/rstudio3-7.png
copying images... [ 75%] vice_apps/../img/homeicon.png
copying images... [ 77%] user_guide/../img/quick_launch/create_quick_launch.png
copying images... [ 79%] user_guide/../img/vice/rstudio/rstudio3-8.png
copying images... [ 81%] ./img/homeicon.png
copying images... [ 83%] user_guide/../img/vice-share-4.png
copying images... [ 84%] user_guide/../img/vice-share-1.png
copying images... [ 86%] user_guide/../img/vice/shiny/shiny1-5.png
copying images... [ 88%] user_guide/../img/vice/rstudio/rstudio3-10.png
copying images... [ 90%] user_guide/../img/vice/shiny/shiny1-3.png
copying images... [ 92%] user_guide/../img/vice/shiny/shiny1-2.png
copying images... [ 94%] developer_guide/../img/homeicon.png
copying images... [ 96%] developer_guide/../img/do_not_pass.png
copying images... [ 98%] user_guide/../img/vice/rstudio/rstudio3-3.png
copying images... [100%] developer_guide/../img/add-tool.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/_static' does not exist
done
copying extra files... done
dumping object inventory... done
build succeeded, 107 warnings.

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

[rtd-command-info] start-time: 2021-05-14T03:15:39.006113Z, end-time: 2021-05-14T03:15:43.524332Z, duration: 4, exit-code: 0
python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 49 added, 0 changed, 0 removed
reading sources... [  2%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/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... [  4%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
reading sources... [  6%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
reading sources... [  8%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
reading sources... [ 10%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
reading sources... [ 12%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
reading sources... [ 14%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
reading sources... [ 16%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
reading sources... [ 18%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
reading sources... [ 20%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
reading sources... [ 22%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
reading sources... [ 24%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
reading sources... [ 26%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
reading sources... [ 28%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
reading sources... [ 30%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
reading sources... [ 32%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
reading sources... [ 34%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
reading sources... [ 36%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
reading sources... [ 38%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
reading sources... [ 40%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
reading sources... [ 42%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
reading sources... [ 44%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
reading sources... [ 46%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
reading sources... [ 48%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
reading sources... [ 51%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
reading sources... [ 53%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
reading sources... [ 55%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
reading sources... [ 57%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
reading sources... [ 59%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
reading sources... [ 61%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
reading sources... [ 63%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
reading sources... [ 65%] data
reading sources... [ 67%] developer_guide/adding
reading sources... [ 69%] developer_guide/building
reading sources... [ 71%] developer_guide/examples
reading sources... [ 73%] developer_guide/workflow
reading sources... [ 75%] getting_help/bestpractices
reading sources... [ 77%] getting_help/contact
reading sources... [ 79%] getting_help/faq
reading sources... [ 81%] getting_help/tool_troubleshooting
reading sources... [ 83%] getting_started/about
reading sources... [ 85%] getting_started/apptypes
reading sources... [ 87%] getting_started/prerequisites
reading sources... [ 89%] index
reading sources... [ 91%] user_guide/quick-jupyter
reading sources... [ 93%] user_guide/quick-rshiny
reading sources... [ 95%] user_guide/quick-rstudio
reading sources... [ 97%] user_guide/sharing
reading sources... [100%] vice_apps/examples

/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.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
WARNING: invalid signature for autoclass (u'{{ objname }}')
WARNING: don't know which module to import for autodocumenting u'{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
WARNING: invalid signature for automodule (u'{{ fullname }}')
WARNING: don't know which module to import for autodocumenting u'{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst:63: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst:48: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:123: WARNING: image file not readable: ../img/cyverse_learning.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/adding.rst:57: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:60: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:62: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:98: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:102: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:75: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:78: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:80: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:31: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:34: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:36: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:29: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:31: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:33: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:11: WARNING: Title underline too short.

**Contact**
----------
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:36: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:38: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:40: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:41: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:43: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:45: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/about.rst:41: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:92: WARNING: Title underline too short.

4. What is Ubuntu Desktop?
=========================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:92: WARNING: Title underline too short.

4. What is Ubuntu Desktop?
=========================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:118: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:120: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:122: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:4: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:82: WARNING: Duplicate substitution definition name: "Home_Icon".
cyverse_rst_defined_substitutions.txt:123: WARNING: image file not readable: ../img/cyverse_learning.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/user_guide/quick-jupyter.rst:8: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:107: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:109: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:111: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:114: WARNING: Duplicate explicit target name: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:104: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:10: 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:68: WARNING: Title underline too short.

6. Complete your analysis
=======================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:68: WARNING: Title underline too short.

6. Complete your analysis
=======================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:79: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:91: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:94: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:96: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:99: WARNING: Duplicate explicit target name: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:88: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:102: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:105: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:107: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
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/buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION.rst: 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
done
processing CyVerseDocumentation.tex.../home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/builders/latex/__init__.py:201: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  if toctrees[0].get('maxdepth') > 0:
index getting_started/about getting_started/prerequisites getting_started/apptypes user_guide/quick-jupyter user_guide/quick-rstudio user_guide/quick-rshiny user_guide/sharing developer_guide/workflow developer_guide/adding developer_guide/building vice_apps/examples getting_help/faq getting_help/bestpractices getting_help/tool_troubleshooting getting_help/contact 
resolving references...
custom_urls.txt:14: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://de.cyverse.org/Powered-By-CyVerse-blue.svg)
custom_urls.txt:17: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://de.cyverse.org/Powered-By-CyVerse-blue.svg)
custom_urls.txt:23: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://de.cyverse.org/Powered-By-CyVerse-blue.svg)
custom_urls.txt:20: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://de.cyverse.org/Powered-By-CyVerse-blue.svg)
writing... done
copying images... [  1%] user_guide/../img/vice/shiny/shiny1-6.png
copying images... [  3%] user_guide/../img/vice/shiny/shiny1-4.png
copying images... [  5%] user_guide/../img/vice-share-5.png
copying images... [  7%] user_guide/../img/vice-share-7.png
copying images... [  9%] user_guide/../img/vice/jupyter/jupyter2-0.png
copying images... [ 11%] getting_help/../img/homeicon.png
copying images... [ 13%] user_guide/../img/vice/shiny/shiny1-9.png
copying images... [ 15%] user_guide/../img/vice/rstudio/rstudio3-1.png
copying images... [ 16%] getting_started/../img/vice_diagram.png
copying images... [ 18%] vice_apps/../img/cyverse_learning.png
copying images... [ 20%] user_guide/../img/vice/rstudio/rstudio3-2.png
copying images... [ 22%] user_guide/../img/vice/shiny/shiny1-8.png
copying images... [ 24%] user_guide/../img/vice/shiny/shiny1-10.png
copying images... [ 26%] user_guide/../img/homeicon.png
copying images... [ 28%] getting_started/../img/cyverse_learning.png
copying images... [ 30%] user_guide/../img/vice/jupyter/jupyter2-2.png
copying images... [ 32%] user_guide/../img/vice-share-6.png
copying images... [ 33%] user_guide/../img/vice/jupyter/jupyter2-5.png
copying images... [ 35%] user_guide/../img/vice/jupyter/jupyter2-6.png
copying images... [ 37%] user_guide/../img/vice/jupyter/jupyter2-7.png
copying images... [ 39%] user_guide/../img/vice/rstudio/rstudio3-5.png
copying images... [ 41%] user_guide/../img/vice/rstudio/rstudio3-4.png
copying images... [ 43%] user_guide/../img/vice/rstudio/rstudio3-6.png
copying images... [ 45%] user_guide/../img/quick_launch/create_quick_launch_dialog.png
copying images... [ 47%] developer_guide/../img/flow_new.png
copying images... [ 49%] getting_started/../img/homeicon.png
copying images... [ 50%] user_guide/../img/quick_launch/use_quick_launch.png
copying images... [ 52%] user_guide/../img/vice/rstudio/rstudio3-9.png
copying images... [ 54%] user_guide/../img/vice/shiny/shiny1-7.png
copying images... [ 56%] user_guide/../img/vice-share-2.png
copying images... [ 58%] user_guide/../img/vice/shiny/shiny1-11.png
copying images... [ 60%] user_guide/../img/vice/shiny/shiny1-1.png
copying images... [ 62%] user_guide/../img/vice/shiny/shiny1-12.png
copying images... [ 64%] user_guide/../img/vice/shiny/shiny1-13.png
copying images... [ 66%] user_guide/../img/vice/jupyter/jupyter2-1.png
copying images... [ 67%] user_guide/../img/vice/jupyter/jupyter2-3.png
copying images... [ 69%] user_guide/../img/vice-share-3.png
copying images... [ 71%] user_guide/../img/vice/jupyter/app_loading.gif
copying images... [ 73%] user_guide/../img/vice/rstudio/rstudio3-7.png
copying images... [ 75%] vice_apps/../img/homeicon.png
copying images... [ 77%] user_guide/../img/quick_launch/create_quick_launch.png
copying images... [ 79%] user_guide/../img/vice/rstudio/rstudio3-8.png
copying images... [ 81%] ./img/homeicon.png
copying images... [ 83%] user_guide/../img/vice-share-4.png
copying images... [ 84%] user_guide/../img/vice-share-1.png
copying images... [ 86%] user_guide/../img/vice/shiny/shiny1-5.png
copying images... [ 88%] user_guide/../img/vice/rstudio/rstudio3-10.png
copying images... [ 90%] user_guide/../img/vice/shiny/shiny1-3.png
copying images... [ 92%] user_guide/../img/vice/shiny/shiny1-2.png
copying images... [ 94%] developer_guide/../img/homeicon.png
copying images... [ 96%] developer_guide/../img/do_not_pass.png
copying images... [ 98%] user_guide/../img/vice/rstudio/rstudio3-3.png
copying images... [100%] developer_guide/../img/add-tool.png

copying TeX support files...
done
build succeeded, 110 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).
WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/_build/latex/_static/searchtools.js

[rtd-command-info] start-time: 2021-05-14T03:15:53.071653Z, end-time: 2021-05-14T03:15:53.154333Z, 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: 2021-05-14T03:15:53.266021Z, end-time: 2021-05-14T03:16:52.442609Z, duration: 59, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-visual-interactive-computing-environment -interaction=nonstopmode
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, <GEN1> chunk 1.
Subroutine makeglo redefined at (eval 11) line 7, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, <GEN2> chunk 1.
Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
Latexmk: applying rule 'pdflatex'...
------------
Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="cyverse-visual-interactive-computing-environment"  "CyVerseDocumentation.tex"'
------------
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./CyVerseDocumentation.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)
(./sphinxmulticell.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (./footnotehyper-sphinx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty)
(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty)
(./sphinxhighlight.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty)
Writing index file cyverse-visual-interactive-computing-environment.idx
(./cyverse-visual-interactive-computing-environment.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<<ot1.cmap>><<oml.cmap
>><<oms.cmap>><<omx.cmap>>
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2]

LaTeX Warning: File `{../img/cyverse_learning}.png' not found on input line 2.


! Package pdftex.def Error: File `../img/cyverse_learning.png' not found: using
 draft setting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.83 ...nxpxdimen]{{../img/cyverse_learning}.png}}
                                                  ^^M
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1 <./homeicon.png> <
./cyverse_learning.png> <./homeicon3.png>] [2]
Chapter 1.

Overfull \hbox (132.49107pt too wide) in paragraph at lines 108--109
[][] 
[3] [4 <./vice_diagram.png>] [5] [6]
Chapter 2.

Underfull \hbox (badness 10000) in paragraph at lines 175--175
[]\T1/phv/m/n/10 Pre-req-ui-

Overfull \hbox (32.78404pt too wide) in paragraph at lines 175--175
[]\T1/phv/m/n/10 Link/Download| 

Underfull \hbox (badness 10000) in paragraph at lines 2--175
[][][]\T1/ptm/m/n/10 Reg-is-

Underfull \hbox (badness 10000) in paragraph at lines 175--175
[]\T1/ptm/m/n/10 Dis-cov-ery

Underfull \hbox (badness 10000) in paragraph at lines 175--175
\T1/ptm/m/n/10 En-vi-ron-

Underfull \hbox (badness 10000) in paragraph at lines 2--175
[][][]\T1/ptm/m/n/10 Cy-

Underfull \hbox (badness 10000) in paragraph at lines 2--175
\T1/ptm/m/n/10 Verse

Underfull \hbox (badness 10000) in paragraph at lines 2--175
\T1/ptm/m/n/10 User
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [7] [8]
Chapter 3.
[9] [10] [11 <./homeicon4.png>] [12]
Chapter 4.

Overfull \hbox (57.21245pt too wide) in paragraph at lines 406--407
[][] 

Overfull \hbox (57.21245pt too wide) in paragraph at lines 411--412
[] 
[13 <./jupyter2-0.png>]
Overfull \hbox (57.21245pt too wide) in paragraph at lines 423--424
[][] 
[14 <./jupyter2-1.png>]

! LaTeX Error: Unknown graphics extension: .gif.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.438 ...dth=700\sphinxpxdimen]{{app_loading}.gif}
                                                  

Overfull \hbox (57.21245pt too wide) in paragraph at lines 446--447
[][] 
[15 <./jupyter2-2.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 465--466
[][] 
[16 <./jupyter2-3.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 476--477
[][] 
[17 <./jupyter2-5.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 483--484
[][] 
[18 <./jupyter2-6.png>] [19 <./jupyter2-7.png>] [20]
Chapter 5.

Overfull \hbox (57.23264pt too wide) in paragraph at lines 514--515
[][] 
[21]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 516--517
[][] 
[22 <./rstudio3-1.png> <./rstudio3-2.png>]
Overfull \hbox (163.14012pt too wide) in paragraph at lines 527--529
[]\T1/ptm/m/it/10 To use a file as an in-put... [] 

Overfull \hbox (174.8303pt too wide) in paragraph at lines 530--532
[]\T1/ptm/m/it/10 To use a folder as an in-put... [] 
[23 <./rstudio3-3.png>]
Underfull \hbox (badness 10000) in paragraph at lines 537--539
[]\T1/ptm/m/n/10 Launch the anal-y-sis af-ter you are fin-ished se-lect-ing the
 in-put files (if any).

Overfull \hbox (57.20068pt too wide) in paragraph at lines 537--539
[] 
[24 <./rstudio3-4.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 545--546
[][] 
[25 <./rstudio3-5.png>]
Overfull \hbox (57.2051pt too wide) in paragraph at lines 552--553
[][] 
[26 <./rstudio3-6.png>]
Overfull \hbox (57.2051pt too wide) in paragraph at lines 563--564
[][] 
[27 <./rstudio3-7.png>]
Overfull \hbox (57.20729pt too wide) in paragraph at lines 565--566
[][] 
[28 <./rstudio3-8.png> <./rstudio3-9.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 572--573
[][] 
[29 <./rstudio3-10.png>] [30]
Chapter 6.

Overfull \hbox (57.20361pt too wide) in paragraph at lines 616--617
[][] 
[31]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 623--624
[][] 
[32 <./shiny1-1.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 630--631
[][] 
[33 <./shiny1-2.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 632--633
[][] 
[34 <./shiny1-3.png> <./shiny1-4.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 639--640
[][] 

Overfull \hbox (57.20361pt too wide) in paragraph at lines 641--642
[][] 
[35 <./shiny1-5.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 648--649
[][] 
[36 <./shiny1-6.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 655--656
[][] 
[37 <./shiny1-7.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 662--663
[][] 
[38 <./shiny1-8.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 669--670
[][] 
[39 <./shiny1-9.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 671--672
[][] 
[40 <./shiny1-10.png> <./shiny1-11.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 678--679
[][] 

Overfull \hbox (57.20361pt too wide) in paragraph at lines 680--681
[][] 
[41 <./shiny1-12.png>] [42 <./shiny1-13.png>]
Chapter 7.

Overfull \hbox (94.8507pt too wide) in paragraph at lines 735--736
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 737--738
[][] 
[43 <./vice-share-1.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 739--740
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 741--742
[][] 
[44 <./vice-share-2.png> <./vice-share-3.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 743--744
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 747--748
[][] 
[45 <./vice-share-4.png> <./vice-share-5.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 749--750
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 751--752
[][] 
[46 <./vice-share-6.png>]
Overfull \hbox (12.04185pt too wide) in paragraph at lines 785--786
[][] 
[47 <./vice-share-7.png>] [48 <./create_quick_launch.png> <./create_quick_launc
h_dialog.png>] [49 <./use_quick_launch.png> <./homeicon1.png>] [50]
Chapter 8.

Overfull \hbox (57.21684pt too wide) in paragraph at lines 838--839
[][] 
[51 <./flow_new.png>] [52]
Chapter 9.
[53] [54]
Chapter 10.
[55] [56 <./add-tool.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 1046--1047
[][] 
[57] [58 <./do_not_pass.png> <./cyverse_learning1.png> <./homeicon5.png>]
Chapter 11.

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M
[59 <./homeicon2.png>] [60]
Chapter 12.
[61] [62]
Chapter 13.
[63] [64]
Chapter 14.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [65] [66] [67]
[68]
Chapter 15.

LaTeX Warning: File `{../img/intercom}.png' not found on input line 1447.


! Package pdftex.def Error: File `../img/intercom.png' not found: using draft s
etting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1447 ...25\sphinxpxdimen]{{../img/intercom}.png}
                                                   on the lower right-hand s...

No file cyverse-visual-interactive-computing-environment.ind.
[69] (./cyverse-visual-interactive-computing-environment.aux)

Package rerunfilecheck Warning: File `cyverse-visual-interactive-computing-envi
ronment.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmsy5.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a
.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvb8a.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvbo8a.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a
.pfb>
Output written on cyverse-visual-interactive-computing-environment.pdf (73 page
s, 11214952 bytes).
Transcript written on cyverse-visual-interactive-computing-environment.log.
Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written
Latexmk: Missing input file: '{../img/cyverse_learning}.png' from line
  'LaTeX Warning: File `{../img/cyverse_learning}.png' not found on input line 2.'
Latexmk: Missing input file: '{../img/intercom}.png' from line
  'LaTeX Warning: File `{../img/intercom}.png' not found on input line 1447.'
Latexmk: Missing input file: 'cyverse-visual-interactive-computing-environment.ind' from line
  'No file cyverse-visual-interactive-computing-environment.ind.'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf'
Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf'
Rule 'makeindex cyverse-visual-interactive-computing-environment.idx': File changes, etc:
   Non-existent destination files:
      'cyverse-visual-interactive-computing-environment.ind'
------------
Run number 1 of rule 'makeindex cyverse-visual-interactive-computing-environment.idx'
------------
------------
Running 'makeindex -s python.ist  -o "cyverse-visual-interactive-computing-environment.ind" "cyverse-visual-interactive-computing-environment.idx"'
------------
Latexmk: applying rule 'makeindex cyverse-visual-interactive-computing-environment.idx'...
This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored).
Scanning input file cyverse-visual-interactive-computing-environment.idx...done (0 entries accepted, 0 rejected).
Nothing written in cyverse-visual-interactive-computing-environment.ind.
Transcript written in cyverse-visual-interactive-computing-environment.ilg.
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'cyverse-visual-interactive-computing-environment.aux'
      'cyverse-visual-interactive-computing-environment.ind'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="cyverse-visual-interactive-computing-environment"  "CyVerseDocumentation.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./CyVerseDocumentation.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)
(./sphinxmulticell.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (./footnotehyper-sphinx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty)
(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty)
(./sphinxhighlight.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty)
Writing index file cyverse-visual-interactive-computing-environment.idx
(./cyverse-visual-interactive-computing-environment.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./cyverse-visual-interactive-computing-environment.out)
(./cyverse-visual-interactive-computing-environment.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<<ot1.cmap>><<oml.cmap
>><<oms.cmap>><<omx.cmap>>
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2]
(./cyverse-visual-interactive-computing-environment.toc) [1] [2]

LaTeX Warning: File `{../img/cyverse_learning}.png' not found on input line 2.


! Package pdftex.def Error: File `../img/cyverse_learning.png' not found: using
 draft setting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.83 ...nxpxdimen]{{../img/cyverse_learning}.png}}
                                                  ^^M
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1 <./homeicon.png> <
./cyverse_learning.png> <./homeicon3.png>] [2]
Chapter 1.

Overfull \hbox (132.49107pt too wide) in paragraph at lines 108--109
[][] 
[3] [4 <./vice_diagram.png>] [5] [6]
Chapter 2.

Underfull \hbox (badness 10000) in paragraph at lines 175--175
[]\T1/phv/m/n/10 Pre-req-ui-

Overfull \hbox (32.78404pt too wide) in paragraph at lines 175--175
[]\T1/phv/m/n/10 Link/Download| 

Underfull \hbox (badness 10000) in paragraph at lines 2--175
[][][]\T1/ptm/m/n/10 Reg-is-

Underfull \hbox (badness 10000) in paragraph at lines 175--175
[]\T1/ptm/m/n/10 Dis-cov-ery

Underfull \hbox (badness 10000) in paragraph at lines 175--175
\T1/ptm/m/n/10 En-vi-ron-

Underfull \hbox (badness 10000) in paragraph at lines 2--175
[][][]\T1/ptm/m/n/10 Cy-

Underfull \hbox (badness 10000) in paragraph at lines 2--175
\T1/ptm/m/n/10 Verse

Underfull \hbox (badness 10000) in paragraph at lines 2--175
\T1/ptm/m/n/10 User
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [7] [8]
Chapter 3.
[9] [10] [11 <./homeicon4.png>] [12]
Chapter 4.

Overfull \hbox (57.21245pt too wide) in paragraph at lines 406--407
[][] 

Overfull \hbox (57.21245pt too wide) in paragraph at lines 411--412
[] 
[13 <./jupyter2-0.png>]
Overfull \hbox (57.21245pt too wide) in paragraph at lines 423--424
[][] 
[14 <./jupyter2-1.png>]

! LaTeX Error: Unknown graphics extension: .gif.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.438 ...dth=700\sphinxpxdimen]{{app_loading}.gif}
                                                  

Overfull \hbox (57.21245pt too wide) in paragraph at lines 446--447
[][] 
[15 <./jupyter2-2.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 465--466
[][] 
[16 <./jupyter2-3.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 476--477
[][] 
[17 <./jupyter2-5.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 483--484
[][] 
[18 <./jupyter2-6.png>] [19 <./jupyter2-7.png>] [20]
Chapter 5.

Overfull \hbox (57.23264pt too wide) in paragraph at lines 514--515
[][] 
[21]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 516--517
[][] 
[22 <./rstudio3-1.png> <./rstudio3-2.png>]
Overfull \hbox (163.14012pt too wide) in paragraph at lines 527--529
[]\T1/ptm/m/it/10 To use a file as an in-put... [] 

Overfull \hbox (174.8303pt too wide) in paragraph at lines 530--532
[]\T1/ptm/m/it/10 To use a folder as an in-put... [] 
[23 <./rstudio3-3.png>]
Underfull \hbox (badness 10000) in paragraph at lines 537--539
[]\T1/ptm/m/n/10 Launch the anal-y-sis af-ter you are fin-ished se-lect-ing the
 in-put files (if any).

Overfull \hbox (57.20068pt too wide) in paragraph at lines 537--539
[] 
[24 <./rstudio3-4.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 545--546
[][] 
[25 <./rstudio3-5.png>]
Overfull \hbox (57.2051pt too wide) in paragraph at lines 552--553
[][] 
[26 <./rstudio3-6.png>]
Overfull \hbox (57.2051pt too wide) in paragraph at lines 563--564
[][] 
[27 <./rstudio3-7.png>]
Overfull \hbox (57.20729pt too wide) in paragraph at lines 565--566
[][] 
[28 <./rstudio3-8.png> <./rstudio3-9.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 572--573
[][] 
[29 <./rstudio3-10.png>] [30]
Chapter 6.

Overfull \hbox (57.20361pt too wide) in paragraph at lines 616--617
[][] 
[31]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 623--624
[][] 
[32 <./shiny1-1.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 630--631
[][] 
[33 <./shiny1-2.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 632--633
[][] 
[34 <./shiny1-3.png> <./shiny1-4.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 639--640
[][] 

Overfull \hbox (57.20361pt too wide) in paragraph at lines 641--642
[][] 
[35 <./shiny1-5.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 648--649
[][] 
[36 <./shiny1-6.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 655--656
[][] 
[37 <./shiny1-7.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 662--663
[][] 
[38 <./shiny1-8.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 669--670
[][] 
[39 <./shiny1-9.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 671--672
[][] 
[40 <./shiny1-10.png> <./shiny1-11.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 678--679
[][] 

Overfull \hbox (57.20361pt too wide) in paragraph at lines 680--681
[][] 
[41 <./shiny1-12.png>] [42 <./shiny1-13.png>]
Chapter 7.

Overfull \hbox (94.8507pt too wide) in paragraph at lines 735--736
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 737--738
[][] 
[43 <./vice-share-1.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 739--740
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 741--742
[][] 
[44 <./vice-share-2.png> <./vice-share-3.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 743--744
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 747--748
[][] 
[45 <./vice-share-4.png> <./vice-share-5.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 749--750
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 751--752
[][] 
[46 <./vice-share-6.png>]
Overfull \hbox (12.04185pt too wide) in paragraph at lines 785--786
[][] 
[47 <./vice-share-7.png>] [48 <./create_quick_launch.png> <./create_quick_launc
h_dialog.png>] [49 <./use_quick_launch.png> <./homeicon1.png>] [50]
Chapter 8.

Overfull \hbox (57.21684pt too wide) in paragraph at lines 838--839
[][] 
[51 <./flow_new.png>] [52]
Chapter 9.
[53] [54]
Chapter 10.
[55] [56 <./add-tool.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 1046--1047
[][] 
[57] [58 <./do_not_pass.png> <./cyverse_learning1.png> <./homeicon5.png>]
Chapter 11.

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M
[59 <./homeicon2.png>] [60]
Chapter 12.
[61] [62]
Chapter 13.
[63] [64]
Chapter 14.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [65] [66] [67]
[68]
Chapter 15.

LaTeX Warning: File `{../img/intercom}.png' not found on input line 1447.


! Package pdftex.def Error: File `../img/intercom.png' not found: using draft s
etting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1447 ...25\sphinxpxdimen]{{../img/intercom}.png}
                                                   on the lower right-hand s...

(./cyverse-visual-interactive-computing-environment.ind) [69]
(./cyverse-visual-interactive-computing-environment.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmsy5.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a
.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvb8a.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvbo8a.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a
.pfb>
Output written on cyverse-visual-interactive-computing-environment.pdf (73 page
s, 11220058 bytes).
Transcript written on cyverse-visual-interactive-computing-environment.log.
Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written
Latexmk: Missing input file: '{../img/cyverse_learning}.png' from line
  'LaTeX Warning: File `{../img/cyverse_learning}.png' not found on input line 2.'
Latexmk: Missing input file: '{../img/intercom}.png' from line
  'LaTeX Warning: File `{../img/intercom}.png' not found on input line 1447.'
Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf'
Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf'
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'cyverse-visual-interactive-computing-environment.out'
      'cyverse-visual-interactive-computing-environment.toc'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="cyverse-visual-interactive-computing-environment"  "CyVerseDocumentation.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./CyVerseDocumentation.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)
(./sphinxmulticell.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (./footnotehyper-sphinx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty)
(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty)
(./sphinxhighlight.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty)
Writing index file cyverse-visual-interactive-computing-environment.idx
(./cyverse-visual-interactive-computing-environment.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./cyverse-visual-interactive-computing-environment.out)
(./cyverse-visual-interactive-computing-environment.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<<ot1.cmap>><<oml.cmap
>><<oms.cmap>><<omx.cmap>>
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2]
(./cyverse-visual-interactive-computing-environment.toc) [1] [2]

LaTeX Warning: File `{../img/cyverse_learning}.png' not found on input line 2.


! Package pdftex.def Error: File `../img/cyverse_learning.png' not found: using
 draft setting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.83 ...nxpxdimen]{{../img/cyverse_learning}.png}}
                                                  ^^M
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1 <./homeicon.png> <
./cyverse_learning.png> <./homeicon3.png>] [2]
Chapter 1.

Overfull \hbox (132.49107pt too wide) in paragraph at lines 108--109
[][] 
[3] [4 <./vice_diagram.png>] [5] [6]
Chapter 2.

Underfull \hbox (badness 10000) in paragraph at lines 175--175
[]\T1/phv/m/n/10 Pre-req-ui-

Overfull \hbox (32.78404pt too wide) in paragraph at lines 175--175
[]\T1/phv/m/n/10 Link/Download| 

Underfull \hbox (badness 10000) in paragraph at lines 2--175
[][][]\T1/ptm/m/n/10 Reg-is-

Underfull \hbox (badness 10000) in paragraph at lines 175--175
[]\T1/ptm/m/n/10 Dis-cov-ery

Underfull \hbox (badness 10000) in paragraph at lines 175--175
\T1/ptm/m/n/10 En-vi-ron-

Underfull \hbox (badness 10000) in paragraph at lines 2--175
[][][]\T1/ptm/m/n/10 Cy-

Underfull \hbox (badness 10000) in paragraph at lines 2--175
\T1/ptm/m/n/10 Verse

Underfull \hbox (badness 10000) in paragraph at lines 2--175
\T1/ptm/m/n/10 User
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [7] [8]
Chapter 3.
[9] [10] [11 <./homeicon4.png>] [12]
Chapter 4.

Overfull \hbox (57.21245pt too wide) in paragraph at lines 406--407
[][] 

Overfull \hbox (57.21245pt too wide) in paragraph at lines 411--412
[] 
[13 <./jupyter2-0.png>]
Overfull \hbox (57.21245pt too wide) in paragraph at lines 423--424
[][] 
[14 <./jupyter2-1.png>]

! LaTeX Error: Unknown graphics extension: .gif.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.438 ...dth=700\sphinxpxdimen]{{app_loading}.gif}
                                                  

Overfull \hbox (57.21245pt too wide) in paragraph at lines 446--447
[][] 
[15 <./jupyter2-2.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 465--466
[][] 
[16 <./jupyter2-3.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 476--477
[][] 
[17 <./jupyter2-5.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 483--484
[][] 
[18 <./jupyter2-6.png>] [19 <./jupyter2-7.png>] [20]
Chapter 5.

Overfull \hbox (57.23264pt too wide) in paragraph at lines 514--515
[][] 
[21]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 516--517
[][] 
[22 <./rstudio3-1.png> <./rstudio3-2.png>]
Overfull \hbox (163.14012pt too wide) in paragraph at lines 527--529
[]\T1/ptm/m/it/10 To use a file as an in-put... [] 

Overfull \hbox (174.8303pt too wide) in paragraph at lines 530--532
[]\T1/ptm/m/it/10 To use a folder as an in-put... [] 
[23 <./rstudio3-3.png>]
Underfull \hbox (badness 10000) in paragraph at lines 537--539
[]\T1/ptm/m/n/10 Launch the anal-y-sis af-ter you are fin-ished se-lect-ing the
 in-put files (if any).

Overfull \hbox (57.20068pt too wide) in paragraph at lines 537--539
[] 
[24 <./rstudio3-4.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 545--546
[][] 
[25 <./rstudio3-5.png>]
Overfull \hbox (57.2051pt too wide) in paragraph at lines 552--553
[][] 
[26 <./rstudio3-6.png>]
Overfull \hbox (57.2051pt too wide) in paragraph at lines 563--564
[][] 
[27 <./rstudio3-7.png>]
Overfull \hbox (57.20729pt too wide) in paragraph at lines 565--566
[][] 
[28 <./rstudio3-8.png> <./rstudio3-9.png>]
Overfull \hbox (57.20068pt too wide) in paragraph at lines 572--573
[][] 
[29 <./rstudio3-10.png>] [30]
Chapter 6.

Overfull \hbox (57.20361pt too wide) in paragraph at lines 616--617
[][] 
[31]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 623--624
[][] 
[32 <./shiny1-1.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 630--631
[][] 
[33 <./shiny1-2.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 632--633
[][] 
[34 <./shiny1-3.png> <./shiny1-4.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 639--640
[][] 

Overfull \hbox (57.20361pt too wide) in paragraph at lines 641--642
[][] 
[35 <./shiny1-5.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 648--649
[][] 
[36 <./shiny1-6.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 655--656
[][] 
[37 <./shiny1-7.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 662--663
[][] 
[38 <./shiny1-8.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 669--670
[][] 
[39 <./shiny1-9.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 671--672
[][] 
[40 <./shiny1-10.png> <./shiny1-11.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 678--679
[][] 

Overfull \hbox (57.20361pt too wide) in paragraph at lines 680--681
[][] 
[41 <./shiny1-12.png>] [42 <./shiny1-13.png>]
Chapter 7.

Overfull \hbox (94.8507pt too wide) in paragraph at lines 735--736
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 737--738
[][] 
[43 <./vice-share-1.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 739--740
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 741--742
[][] 
[44 <./vice-share-2.png> <./vice-share-3.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 743--744
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 747--748
[][] 
[45 <./vice-share-4.png> <./vice-share-5.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 749--750
[][] 

Overfull \hbox (94.8507pt too wide) in paragraph at lines 751--752
[][] 
[46 <./vice-share-6.png>]
Overfull \hbox (12.04185pt too wide) in paragraph at lines 785--786
[][] 
[47 <./vice-share-7.png>] [48 <./create_quick_launch.png> <./create_quick_launc
h_dialog.png>] [49 <./use_quick_launch.png> <./homeicon1.png>] [50]
Chapter 8.

Overfull \hbox (57.21684pt too wide) in paragraph at lines 838--839
[][] 
[51 <./flow_new.png>] [52]
Chapter 9.
[53] [54]
Chapter 10.
[55] [56 <./add-tool.png>]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 1046--1047
[][] 
[57] [58 <./do_not_pass.png> <./cyverse_learning1.png> <./homeicon5.png>]
Chapter 11.

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M

! LaTeX Error: Unknown graphics extension: .svg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1143 \end{tabulary}
                     ^^M
[59 <./homeicon2.png>] [60]
Chapter 12.
[61] [62]
Chapter 13.
[63] [64]
Chapter 14.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [65] [66] [67]
[68]
Chapter 15.

LaTeX Warning: File `{../img/intercom}.png' not found on input line 1447.


! Package pdftex.def Error: File `../img/intercom.png' not found: using draft s
etting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1447 ...25\sphinxpxdimen]{{../img/intercom}.png}
                                                   on the lower right-hand s...

(./cyverse-visual-interactive-computing-environment.ind) [69]
(./cyverse-visual-interactive-computing-environment.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmsy5.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a
.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvb8a.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvbo8a.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a
.pfb>
Output written on cyverse-visual-interactive-computing-environment.pdf (73 page
s, 11220058 bytes).
Transcript written on cyverse-visual-interactive-computing-environment.log.
Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written
Latexmk: Missing input file: '{../img/cyverse_learning}.png' from line
  'LaTeX Warning: File `{../img/cyverse_learning}.png' not found on input line 2.'
Latexmk: Missing input file: '{../img/intercom}.png' from line
  'LaTeX Warning: File `{../img/intercom}.png' not found on input line 1447.'
Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf'
Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.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

[rtd-command-info] start-time: 2021-05-14T03:16:52.568334Z, end-time: 2021-05-14T03:16:52.641144Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/./_build/latex/cyverse-visual-interactive-computing-environment.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/artifacts/latest/sphinx_pdf/cyverse-visual-interactive-computing-environment.pdf


[rtd-command-info] start-time: 2021-05-14T03:16:52.747733Z, end-time: 2021-05-14T03:17:14.853859Z, duration: 22, exit-code: 0
python -m sphinx -T -b epub -d _build/doctrees -D language=en . _build/epub
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [epub]: targets for 49 source files that are out of date
updating environment: 49 added, 0 changed, 0 removed
reading sources... [  2%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/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... [  4%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
reading sources... [  6%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
reading sources... [  8%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
reading sources... [ 10%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
reading sources... [ 12%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
reading sources... [ 14%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
reading sources... [ 16%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
reading sources... [ 18%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
reading sources... [ 20%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
reading sources... [ 22%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
reading sources... [ 24%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
reading sources... [ 26%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
reading sources... [ 28%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
reading sources... [ 30%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
reading sources... [ 32%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
reading sources... [ 34%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
reading sources... [ 36%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
reading sources... [ 38%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
reading sources... [ 40%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
reading sources... [ 42%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
reading sources... [ 44%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
reading sources... [ 46%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
reading sources... [ 48%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
reading sources... [ 51%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
reading sources... [ 53%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
reading sources... [ 55%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
reading sources... [ 57%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
reading sources... [ 59%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
reading sources... [ 61%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
reading sources... [ 63%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
reading sources... [ 65%] data
reading sources... [ 67%] developer_guide/adding
reading sources... [ 69%] developer_guide/building
reading sources... [ 71%] developer_guide/examples
reading sources... [ 73%] developer_guide/workflow
reading sources... [ 75%] getting_help/bestpractices
reading sources... [ 77%] getting_help/contact
reading sources... [ 79%] getting_help/faq
reading sources... [ 81%] getting_help/tool_troubleshooting
reading sources... [ 83%] getting_started/about
reading sources... [ 85%] getting_started/apptypes
reading sources... [ 87%] getting_started/prerequisites
reading sources... [ 89%] index
reading sources... [ 91%] user_guide/quick-jupyter
reading sources... [ 93%] user_guide/quick-rshiny
reading sources... [ 95%] user_guide/quick-rstudio
reading sources... [ 97%] user_guide/sharing
reading sources... [100%] vice_apps/examples

/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.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
WARNING: invalid signature for autoclass (u'{{ objname }}')
WARNING: don't know which module to import for autodocumenting u'{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
WARNING: invalid signature for automodule (u'{{ fullname }}')
WARNING: don't know which module to import for autodocumenting u'{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst:63: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst:48: WARNING: Undefined substitution referenced: "Github Repo Link".
cyverse_rst_defined_substitutions.txt:123: WARNING: image file not readable: ../img/cyverse_learning.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/adding.rst:57: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:60: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:62: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/adding.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:98: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:102: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:75: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:78: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:80: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/examples.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:31: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:34: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:36: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/workflow.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:29: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:31: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:33: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/bestpractices.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:11: WARNING: Title underline too short.

**Contact**
----------
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:36: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:38: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:40: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:41: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:43: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:45: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/faq.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/about.rst:41: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:92: WARNING: Title underline too short.

4. What is Ubuntu Desktop?
=========================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:92: WARNING: Title underline too short.

4. What is Ubuntu Desktop?
=========================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:118: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:120: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:122: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:4: WARNING: Duplicate target name, cannot be used as a unique reference: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:82: WARNING: Duplicate substitution definition name: "Home_Icon".
cyverse_rst_defined_substitutions.txt:123: WARNING: image file not readable: ../img/cyverse_learning.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/user_guide/quick-jupyter.rst:8: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:107: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:109: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:111: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:114: WARNING: Duplicate explicit target name: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rshiny.rst:104: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:10: 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:68: WARNING: Title underline too short.

6. Complete your analysis
=======================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:68: WARNING: Title underline too short.

6. Complete your analysis
=======================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:79: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:91: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:94: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:96: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:99: WARNING: Duplicate explicit target name: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:5: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:88: WARNING: Duplicate target name, cannot be used as a unique reference: "home_icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:102: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:105: WARNING: Duplicate explicit target name: "cyverse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/sharing.rst:107: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/vice_apps/examples.rst:10: WARNING: Duplicate explicit target name: "dockerfiles".
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/buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION.rst: 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
done
preparing documents... done
writing output... [  2%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
writing output... [  4%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
writing output... [  6%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
writing output... [  8%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
writing output... [ 10%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
writing output... [ 12%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
writing output... [ 14%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
writing output... [ 16%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
writing output... [ 18%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
writing output... [ 20%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
writing output... [ 22%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
writing output... [ 24%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
writing output... [ 26%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
writing output... [ 28%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
writing output... [ 30%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
writing output... [ 32%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
writing output... [ 34%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
writing output... [ 36%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
writing output... [ 38%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
writing output... [ 40%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
writing output... [ 42%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
writing output... [ 44%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
writing output... [ 46%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
writing output... [ 48%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
writing output... [ 51%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
writing output... [ 53%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
writing output... [ 55%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
writing output... [ 57%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
writing output... [ 59%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
writing output... [ 61%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
writing output... [ 63%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
writing output... [ 65%] data
writing output... [ 67%] developer_guide/adding
writing output... [ 69%] developer_guide/building
writing output... [ 71%] developer_guide/examples
writing output... [ 73%] developer_guide/workflow
writing output... [ 75%] getting_help/bestpractices
writing output... [ 77%] getting_help/contact
writing output... [ 79%] getting_help/faq
writing output... [ 81%] getting_help/tool_troubleshooting
writing output... [ 83%] getting_started/about
writing output... [ 85%] getting_started/apptypes
writing output... [ 87%] getting_started/prerequisites
writing output... [ 89%] index
writing output... [ 91%] user_guide/quick-jupyter
writing output... [ 93%] user_guide/quick-rshiny
writing output... [ 95%] user_guide/quick-rstudio
writing output... [ 97%] user_guide/sharing
writing output... [100%] vice_apps/examples

WARNING: Could not fetch remote image: https://raw.githubusercontent.com/requests/requests/master/docs/_static/requests-logo-small.png [404]
generating indices... genindex
writing additional pages...
copying images... [  1%] user_guide/../img/vice/shiny/shiny1-6.png
copying images... [  2%] https://travis-ci.org/benjaminp/six.svg?branch=master
copying images... [  3%] user_guide/../img/vice-share-5.png
copying images... [  4%] https://img.shields.io/pypi/pyversions/setuptools.svg
copying images... [  5%] user_guide/../img/vice-share-7.png
copying images... [  7%] user_guide/../img/vice/jupyter/jupyter2-0.png
copying images... [  8%] https://badge.fury.io/py/idna.svg
copying images... [  9%] user_guide/../img/quick_launch/create_quick_launch_dialog.png
copying images... [ 10%] user_guide/../img/vice/rstudio/rstudio3-2.png
copying images... [ 11%] user_guide/../img/vice/rstudio/rstudio3-4.png
copying images... [ 12%] developer_guide/../img/flow_new.png
copying images... [ 14%] user_guide/../img/vice/jupyter/jupyter2-5.png
copying images... [ 15%] https://img.shields.io/pypi/l/requests.svg
copying images... [ 16%] https://img.shields.io/appveyor/ci/shazow/urllib3/master.svg
copying images... [ 17%] user_guide/../img/vice/rstudio/rstudio3-1.png
copying images... [ 18%] developer_guide/../img/add-tool.png
copying images... [ 20%] user_guide/../img/quick_launch/create_quick_launch.png
copying images... [ 21%] https://img.shields.io/pypi/v/setuptools.svg
copying images... [ 22%] user_guide/../img/vice/shiny/shiny1-11.png
copying images... [ 23%] user_guide/../img/vice/jupyter/jupyter2-7.png
copying images... [ 24%] user_guide/../img/vice-share-4.png
copying images... [ 25%] user_guide/../img/vice/rstudio/rstudio3-5.png
copying images... [ 27%] https://de.cyverse.org/Powered-By-CyVerse-blue.svg
copying images... [ 28%] user_guide/../img/vice/shiny/shiny1-10.png
copying images... [ 29%] https://img.shields.io/appveyor/ci/jaraco/setuptools/master.svg?label=Windows%20build%20%40%20Appveyor
copying images... [ 30%] getting_started/../img/cyverse_learning.png
copying images... [ 31%] user_guide/../img/vice/shiny/shiny1-8.png
copying images... [ 32%] developer_guide/../img/do_not_pass.png
copying images... [ 34%] https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg
copying images... [ 35%] https://img.shields.io/pypi/l/chardet.svg
copying images... [ 36%] user_guide/../img/vice/jupyter/jupyter2-6.png
copying images... [ 37%] http://img.shields.io/pypi/v/six.svg
copying images... [ 38%] user_guide/../img/vice/shiny/shiny1-13.png
copying images... [ 40%] user_guide/../img/homeicon.png
copying images... [ 41%] https://img.shields.io/pypi/v/requests.svg
copying images... [ 42%] user_guide/../img/vice/rstudio/rstudio3-6.png
copying images... [ 43%] user_guide/../img/vice-share-3.png
copying images... [ 44%] https://readthedocs.org/projects/urllib3/badge/?version=latest
copying images... [ 45%] getting_started/../img/homeicon.png
copying images... [ 47%] https://readthedocs.org/projects/setuptools/badge/?version=latest
copying images... [ 48%] user_guide/../img/vice/rstudio/rstudio3-9.png
copying images... [ 49%] https://img.shields.io/travis/pypa/pip/master.svg
copying images... [ 50%] https://www.bountysource.com/badge/tracker?tracker_id=192525
copying images... [ 51%] https://img.shields.io/travis/pypa/setuptools/master.svg?label=Linux%20build%20%40%20Travis%20CI
copying images... [ 52%] user_guide/../img/vice-share-1.png
copying images... [ 54%] user_guide/../img/vice-share-2.png
copying images... [ 55%] getting_started/../img/vice_diagram.png
copying images... [ 56%] https://img.shields.io/github/contributors/requests/requests.svg
copying images... [ 57%] user_guide/../img/vice/shiny/shiny1-1.png
copying images... [ 58%] user_guide/../img/vice/shiny/shiny1-12.png
copying images... [ 60%] user_guide/../img/vice/jupyter/jupyter2-1.png
copying images... [ 61%] user_guide/../img/vice/jupyter/jupyter2-3.png
copying images... [ 62%] user_guide/../img/quick_launch/use_quick_launch.png
copying images... [ 63%] https://travis-ci.org/spinus/sphinxcontrib-images.svg?branch=master
copying images... [ 64%] user_guide/../img/vice/jupyter/app_loading.gif
copying images... [ 65%] user_guide/../img/vice/rstudio/rstudio3-7.png
copying images... [ 67%] vice_apps/../img/homeicon.png
copying images... [ 68%] user_guide/../img/vice/shiny/shiny1-9.png
copying images... [ 69%] http://img.shields.io/badge/license-MIT-green.svg
copying images... [ 70%] https://img.shields.io/coveralls/chardet/chardet/stable.svg
copying images... [ 71%] https://codecov.io/github/requests/requests/coverage.svg?branch=master
copying images... [ 72%] ./img/homeicon.png
copying images... [ 74%] user_guide/../img/vice/shiny/shiny1-2.png
copying images... [ 75%] getting_help/../img/homeicon.png
copying images... [ 76%] https://readthedocs.org/projects/pip/badge/?version=stable
copying images... [ 77%] user_guide/../img/vice/shiny/shiny1-5.png
copying images... [ 78%] user_guide/../img/vice/rstudio/rstudio3-10.png
copying images... [ 80%] user_guide/../img/vice/shiny/shiny1-3.png
copying images... [ 81%] https://img.shields.io/codecov/c/github/shazow/urllib3.svg
copying images... [ 82%] vice_apps/../img/cyverse_learning.png
copying images... [ 83%] https://img.shields.io/pypi/v/chardet.svg
copying images... [ 84%] https://travis-ci.org/shazow/urllib3.svg?branch=master
copying images... [ 85%] user_guide/../img/vice/rstudio/rstudio3-8.png
copying images... [ 87%] https://img.shields.io/appveyor/ci/pypa/pip.svg
copying images... [ 88%] user_guide/../img/vice/shiny/shiny1-7.png
copying images... [ 89%] developer_guide/../img/homeicon.png
copying images... [ 90%] user_guide/../img/vice-share-6.png
copying images... [ 91%] https://img.shields.io/pypi/pyversions/requests.svg
copying images... [ 92%] https://img.shields.io/pypi/v/pip.svg
copying images... [ 94%] user_guide/../img/vice/rstudio/rstudio3-3.png
copying images... [ 95%] https://img.shields.io/travis/chardet/chardet/stable.svg
copying images... [ 96%] user_guide/../img/vice/shiny/shiny1-4.png
copying images... [ 97%] user_guide/../img/vice/jupyter/jupyter2-2.png
copying images... [ 98%] https://travis-ci.org/kjd/idna.svg?branch=master
copying images... [100%] https://img.shields.io/pypi/v/urllib3.svg?maxAge=86400

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/_static' does not exist
done
copying extra files... done
writing mimetype file...
writing META-INF/container.xml file...
writing content.opf file...
writing nav.xhtml file...
writing toc.ncx file...
writing VisualInteractiveComputingEnvironment.epub file...
build succeeded, 108 warnings.

The ePub file is in _build/epub.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2021-05-14T03:17:14.975610Z, end-time: 2021-05-14T03:17:15.041540Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/./_build/epub/VisualInteractiveComputingEnvironment.epub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/artifacts/latest/sphinx_epub/cyverse-visual-interactive-computing-environment.epub