Read the Docs build information
Build id: 665145
Project: cyverse-visual-interactive-computing-environment
Version: latest
Commit: a67f294c54ab94a4541346c2be2c5e0647e815b6
Date: 2021-06-28T14:25:42.617563Z
State: finished
Success: True


[rtd-command-info] start-time: 2021-06-28T14:27:46.658027Z, end-time: 2021-06-28T14:27:56.204504Z, duration: 9, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/Visual_Interactive_Computing_Environment.git .
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[rtd-command-info] start-time: 2021-06-28T14:27:56.350272Z, end-time: 2021-06-28T14:27:56.717063Z, 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 a67f294 Update index.rst

[rtd-command-info] start-time: 2021-06-28T14:27:56.964798Z, end-time: 2021-06-28T14:27:57.069260Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-06-28T14:27:57.179625Z, end-time: 2021-06-28T14:27:57.254559Z, duration: 0, exit-code: 0
git rev-parse HEAD
a67f294c54ab94a4541346c2be2c5e0647e815b6

[rtd-command-info] start-time: 2021-06-28T14:27:59.451065Z, end-time: 2021-06-28T14:28:13.454355Z, duration: 14, 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: 2021-06-28T14:28:13.589435Z, end-time: 2021-06-28T14:28:15.532884Z, 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 Please upgrade your Python as Python 2.7 is no longer maintained.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: 2021-06-28T14:28:15.635797Z, end-time: 2021-06-28T14:28:24.359281Z, duration: 8, 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
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Building wheels for collected packages: mock, future
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  Stored in directory: /tmp/pip-ephem-wheel-cache-pKDEga/wheels/ad/62/e0/a06cc957652749e64c7904e899eca3ecb2ec47c60d52653660
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  Stored in directory: /tmp/pip-ephem-wheel-cache-pKDEga/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-2021.5.30 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 urllib3-1.26.6

[rtd-command-info] start-time: 2021-06-28T14:28:24.464696Z, end-time: 2021-06-28T14:28:33.586177Z, duration: 9, 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.
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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==1.8->-r requirements.txt (line 1)) (20.9)
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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==1.8->-r requirements.txt (line 1)) (2.1.0)
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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==1.8->-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==1.8->-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==1.8->-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==1.8->-r requirements.txt (line 1)) (1.1.2)
Collecting traitlets
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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 3)) (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==1.8->-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==1.8->-r requirements.txt (line 1)) (2.4.7)
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  Building wheel for pyrsistent (setup.py): started
  Building wheel for pyrsistent (setup.py): finished with status 'done'
  Created wheel for pyrsistent: filename=pyrsistent-0.16.1-cp27-cp27mu-linux_x86_64.whl size=111634 sha256=d8d65a99005233c323b0b38103f235775f35a4a52b83f4d986911f4a8222b942
  Stored in directory: /tmp/pip-ephem-wheel-cache-9anaLq/wheels/b4/1b/d5/48db6e04aae1867820bc658b00f177b4e59ba8244f0133b351
  Building wheel for scandir (setup.py): started
  Building wheel for scandir (setup.py): finished with status 'done'
  Created wheel for scandir: filename=scandir-1.10.0-cp27-cp27mu-linux_x86_64.whl size=41653 sha256=9a6602599f26aaed9b3642a2930ea6f55ef309afa15b9e7419e71deb732b37ce
  Stored in directory: /tmp/pip-ephem-wheel-cache-9anaLq/wheels/58/2c/26/52406f7d1f19bcc47a6fbd1037a5f293492f5cf1d58c539edb
Successfully built sphinx-bootstrap-theme guzzle-sphinx-theme pandocfilters functools32 pyrsistent scandir
Installing collected packages: sphinx, enum34, decorator, ipython-genutils, traitlets, functools32, attrs, pyrsistent, contextlib2, zipp, configparser, scandir, pathlib2, importlib-metadata, jsonschema, jupyter-core, nbformat, entrypoints, mistune, testpath, pandocfilters, defusedxml, webencodings, bleach, nbconvert, nbsphinx, sphinxcontrib-images, sphinx-bootstrap-theme, guzzle-sphinx-theme
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
      Successfully uninstalled Sphinx-1.8.5
ERROR: pip's legacy dependency resolver does not consider dependency conflicts when selecting packages. This behaviour is the source of the following dependency conflicts.
sphinxcontrib-images 0.9.3 requires sphinx<2.0,>=1.8.5; python_version < "3.0", but you'll have sphinx 1.8.0 which is incompatible.
Successfully installed attrs-21.2.0 bleach-3.3.0 configparser-4.0.2 contextlib2-0.6.0.post1 decorator-4.4.2 defusedxml-0.7.1 entrypoints-0.3 enum34-1.1.10 functools32-3.2.3.post2 guzzle-sphinx-theme-0.7.11 importlib-metadata-2.1.1 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-core-4.6.3 mistune-0.8.4 nbconvert-5.6.1 nbformat-4.4.0 nbsphinx-0.5.1 pandocfilters-1.4.3 pathlib2-2.3.5 pyrsistent-0.16.1 scandir-1.10.0 sphinx-1.8.0 sphinx-bootstrap-theme-0.7.1 sphinxcontrib-images-0.9.3 testpath-0.4.4 traitlets-4.3.3 webencodings-0.5.1 zipp-1.2.0

[rtd-command-info] start-time: 2021-06-28T14:28:34.367571Z, end-time: 2021-06-28T14:28:34.433962Z, duration: 0, exit-code: 0
git rev-parse HEAD
a67f294c54ab94a4541346c2be2c5e0647e815b6

[rtd-command-info] start-time: 2021-06-28T14:28:34.736421Z, end-time: 2021-06-28T14:28:34.815022Z, 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': 'a67f294c',
}

# 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/665145/'

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: 2021-06-28T14:28:34.930838Z, end-time: 2021-06-28T14:28:42.320020Z, duration: 7, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.0
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 73 source files that are out of date
updating environment: 73 added, 0 changed, 0 removed
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/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))
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/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... [ 15%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
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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/buildenv/lib/python3.7/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/python3.7/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)
cyverse_rst_defined_substitutions.txt <included from /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst>:123: WARNING: image file not readable: ../img/cyverse_learning.png
cyverse_rst_defined_substitutions.txt <included from /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst>:128: WARNING: image file not readable: ../img/homeicon.png
cyverse_rst_defined_substitutions.txt <included from /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/data.rst>:134: WARNING: image file not readable: ../img/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:36: WARNING: Undefined substitution referenced: "add-tool".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/developer_guide/building.rst:81: WARNING: Undefined substitution referenced: "vice-do-not-pass".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/prerequisites.rst:16: WARNING: Undefined substitution referenced: "ORCID".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:28: WARNING: toctree contains reference to nonexisting document u'.. user_guide/quick-rshiny'
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:81: WARNING: Duplicate substitution definition name: "CyVerse_logo".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:86: WARNING: Duplicate substitution definition name: "Home_Icon".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:92: WARNING: Duplicate substitution definition name: "Intercom".
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1. Search for Rstudio App
======================
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6. Complete and Save Outputs
=======================
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6. Complete and Save Outputs
=======================
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copying TeX support files...
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build succeeded, 73 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).
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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: 2021-06-28T14:28:53.034439Z, end-time: 2021-06-28T14:29:41.182671Z, duration: 48, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-visual-interactive-computing-environment -interaction=nonstopmode
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homeicon3.png> <./cyverse_learning2.png> <./homeicon2.png>] [2]
Chapter 1.
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Chapter 2.

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[][][]\T1/ptm/m/n/10 Cy-

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Chapter 3.

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[7] [8] [9 <./homeicon4.png>] [10]
Chapter 4.

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Chapter 5.

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Chapter 6.

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Chapter 7.

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Chapter 8.
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Chapter 9.
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Chapter 10.
[45] [46]
Chapter 11.
[47] [48]
Chapter 12.

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[49 <./cyverse_learning1.png> <./homeicon1.png>] [50]
Chapter 13.
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Chapter 14.
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Chapter 15.
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[58]
Chapter 16.

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Chapter 1.
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Chapter 2.

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Chapter 3.

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Chapter 4.

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Chapter 5.

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Chapter 9.
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Chapter 10.
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Chapter 11.
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Chapter 12.

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Chapter 13.
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Chapter 14.
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Chapter 16.

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Chapter 1.
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Chapter 2.

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[][][]\T1/ptm/m/n/10 Reg-is-

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[][][]\T1/ptm/m/n/10 Cy-

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[5] [6]
Chapter 3.

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Chapter 4.

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Chapter 5.

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Chapter 6.

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Chapter 7.

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Chapter 8.
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Chapter 9.
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Chapter 10.
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Chapter 11.
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Chapter 12.

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[49 <./cyverse_learning1.png> <./homeicon1.png>] [50]
Chapter 13.
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Chapter 14.
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Chapter 15.
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Chapter 16.

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