Read the Docs build information
Build id: 71056
Project: cyverse-discovery-environment-guide
Version: latest
Commit: 891977ac251f755d95733fc8260ba678b7099e24
Date: 2017-11-21T20:57:38.944157Z
State: finished
Success: True


[rtd-command-info] start-time: 2017-11-22T02:54:26.413169Z, end-time: 2017-11-22T02:54:28.159995Z, duration: 1, exit-code: 0
python2.7 -mvirtualenv --no-site-packages --no-download 
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/bin/python2.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/bin/python
Installing setuptools, pip, wheel...done.

[rtd-command-info] start-time: 2017-11-22T02:54:28.287605Z, end-time: 2017-11-22T02:54:50.009246Z, duration: 21, exit-code: 0
python pip install --use-wheel -U --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/.cache/pip Pygments==2.2.0 setuptools==28.8.0 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx==1.5.3 sphinx-rtd-theme<0.3 readthedocs-sphinx-ext<0.6
Collecting Pygments==2.2.0
  Downloading Pygments-2.2.0-py2.py3-none-any.whl (841kB)
Requirement already up-to-date: setuptools==28.8.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages
Collecting docutils==0.13.1
  Downloading docutils-0.13.1-py2-none-any.whl (537kB)
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861kB)
Collecting pillow==2.6.1
  Downloading Pillow-2.6.1.zip (7.5MB)
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.10-py2.py3-none-any.whl
Collecting commonmark==0.5.4
  Downloading CommonMark-0.5.4.tar.gz (120kB)
Collecting recommonmark==0.4.0
  Downloading recommonmark-0.4.0-py2.py3-none-any.whl
Collecting sphinx==1.5.3
  Downloading Sphinx-1.5.3-py2.py3-none-any.whl (1.6MB)
Collecting sphinx-rtd-theme<0.3
  Downloading sphinx_rtd_theme-0.2.4-py2.py3-none-any.whl (1.4MB)
Collecting readthedocs-sphinx-ext<0.6
  Downloading readthedocs_sphinx_ext-0.5.5-py2.py3-none-any.whl
Collecting six>=1.5 (from sphinx==1.5.3)
  Downloading six-1.11.0-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx==1.5.3)
  Downloading requests-2.18.4-py2.py3-none-any.whl (88kB)
Collecting imagesize (from sphinx==1.5.3)
  Downloading imagesize-0.7.1-py2.py3-none-any.whl
Collecting babel!=2.0,>=1.3 (from sphinx==1.5.3)
  Downloading Babel-2.5.1-py2.py3-none-any.whl (6.8MB)
Collecting snowballstemmer>=1.1 (from sphinx==1.5.3)
  Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB)
Collecting Jinja2>=2.3 (from sphinx==1.5.3)
  Downloading Jinja2-2.10-py2.py3-none-any.whl (126kB)
Collecting nilsimsa>=0.3.7 (from readthedocs-sphinx-ext<0.6)
  Downloading nilsimsa-0.3.8.tar.gz (276kB)
Collecting urllib3<1.23,>=1.21.1 (from requests>=2.0.0->sphinx==1.5.3)
  Downloading urllib3-1.22-py2.py3-none-any.whl (132kB)
Collecting idna<2.7,>=2.5 (from requests>=2.0.0->sphinx==1.5.3)
  Downloading idna-2.6-py2.py3-none-any.whl (56kB)
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx==1.5.3)
  Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB)
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx==1.5.3)
  Downloading certifi-2017.11.5-py2.py3-none-any.whl (330kB)
Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.5.3)
  Downloading pytz-2017.3-py2.py3-none-any.whl (511kB)
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.5.3)
  Downloading MarkupSafe-1.0.tar.gz
Building wheels for collected packages: mock, pillow, commonmark, nilsimsa, MarkupSafe
  Running setup.py bdist_wheel for mock: started
  Running setup.py bdist_wheel for mock: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/.cache/pip/wheels/b2/f8/fe/920b7d3b279878045354cde14646f73864cf944501f19e4a1b
  Running setup.py bdist_wheel for pillow: started
  Running setup.py bdist_wheel for pillow: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/.cache/pip/wheels/d0/3d/6f/4a3dbe290c7053073e6c32734c146d7174f2ad7675030b6137
  Running setup.py bdist_wheel for commonmark: started
  Running setup.py bdist_wheel for commonmark: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/.cache/pip/wheels/fd/3a/ea/9ead7944d8ba3771888487ca4f6ef39bcde9fd4e986c32f442
  Running setup.py bdist_wheel for nilsimsa: started
  Running setup.py bdist_wheel for nilsimsa: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/.cache/pip/wheels/77/f8/25/539c7b52ecbfcb7ed9b6c7189f9fdde48706c41fe529a64c9f
  Running setup.py bdist_wheel for MarkupSafe: started
  Running setup.py bdist_wheel for MarkupSafe: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/.cache/pip/wheels/88/a7/30/e39a54a87bcbe25308fa3ca64e8ddc75d9b3e5afa21ee32d57
Successfully built mock pillow commonmark nilsimsa MarkupSafe
Installing collected packages: Pygments, docutils, mock, pillow, alabaster, commonmark, recommonmark, six, urllib3, idna, chardet, certifi, requests, imagesize, pytz, babel, snowballstemmer, MarkupSafe, Jinja2, sphinx, sphinx-rtd-theme, nilsimsa, readthedocs-sphinx-ext
Successfully installed Jinja2-2.10 MarkupSafe-1.0 Pygments-2.2.0 alabaster-0.7.10 babel-2.5.1 certifi-2017.11.5 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.6 imagesize-0.7.1 mock-1.0.1 nilsimsa-0.3.8 pillow-2.6.1 pytz-2017.3 readthedocs-sphinx-ext-0.5.5 recommonmark-0.4.0 requests-2.18.4 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.5.3 sphinx-rtd-theme-0.2.4 urllib3-1.22

[rtd-command-info] start-time: 2017-11-22T02:54:50.846311Z, end-time: 2017-11-22T02:54:50.904213Z, 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 = 'Discovery Environment Guide'
copyright = '2017, CyVerse'
author = 'CyVerse'
version = '1.0'
release = '1.0'

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




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


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


import sys
import os.path
from six import string_types

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    else:
        SUFFIX = source_suffix[0]
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')
html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static')

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

            using_rtd_theme = True
else:
    import sphinx_rtd_theme
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(sphinx_rtd_theme.get_html_theme_path())
    else:
        html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
    using_rtd_theme = True

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    if 'http' not in settings.MEDIA_URL:
        websupport2_static_url = 'https://media.readthedocs.com/'
    else:
        websupport2_static_url = 'https://media.readthedocs.com/media//static'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("htmlzip", "//readthedocs.com/projects/cyverse-discovery-environment-guide/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-discovery-environment-guide',
    'name': u'discovery_environment_guide',
    'rtd_language': u'en',
    'canonical_url': 'https://learning.cyverse.org/projects/discovery-environment-guide/en/latest/',
    'analytics_code': '',
    'single_version': False,
    'conf_py_path': '/./',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'github_repo': 'discovery_environment_guide',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    
    'commit': '891977ac',
    
}




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

# Add custom RTD extension
if 'extensions' in globals():
    extensions.append("readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

[rtd-command-info] start-time: 2017-11-22T02:54:51.017641Z, end-time: 2017-11-22T02:54:52.919930Z, duration: 1, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.5.3
making output directory...
loading translations [en]... done
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 5 source files that are out of date
updating environment: 5 added, 0 changed, 0 removed
reading sources... [ 20%] index
reading sources... [ 40%] step1
reading sources... [ 60%] step2
reading sources... [ 80%] step3
reading sources... [100%] step4

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step1.rst:84: WARNING: image file not readable: ./img/de/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step1.rst:84: WARNING: image file not readable: ./img/de/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:8: WARNING: Duplicate explicit target name: "de_sample_plants.fas".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:120: WARNING: image file not readable: ./img/de/dots.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:120: WARNING: image file not readable: ./img/de/dots.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step4.rst:46: WARNING: Explicit markup ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 20%] index
writing output... [ 40%] step1
writing output... [ 60%] step2
writing output... [ 80%] step3
writing output... [100%] step4

generating indices... genindex
writing additional pages... search
copying images... [  4%] ./img/de/data_window.png
copying images... [  9%] ./img/de/beta.png
copying images... [ 14%] ./img/de/de-icon.png
copying images... [ 19%] ./img/de/manage_sharing_menu.png
copying images... [ 23%] ./img/de/favorite.png
copying images... [ 28%] ./img/de/manage_data_links.png
copying images... [ 33%] ./img/de/apps_icon.png
copying images... [ 38%] ./img/de/info.png
copying images... [ 42%] ./img/de/muscle_app_window.png
copying images... [ 47%] ./img/de/person_icon.png
copying images... [ 52%] ./img/de/data_icon.png
copying images... [ 57%] ./img/de/comment.png
copying images... [ 61%] ./img/de/viewing_window.png
copying images... [ 66%] ./img/de/unavailable.png
copying images... [ 71%] ./img/de/de_app_icon.png
copying images... [ 76%] ./img/cyverse_rgb.png
copying images... [ 80%] ./img/de/rating.png
copying images... [ 85%] ./img/de/link_icon.png
copying images... [ 90%] ./img/de/delete_icon.png
copying images... [ 95%] ./img/homeicon.png
copying images... [100%] ./img/de/private.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/_static' does not exist
WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist
done
copying readthedocs static files... done
copying searchtools... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 8 warnings.

[rtd-command-info] start-time: 2017-11-22T02:54:53.077597Z, end-time: 2017-11-22T02:54:54.190428Z, duration: 1, exit-code: 0
python sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json
Running Sphinx v1.5.3
making output directory...
loading translations [en]... done
loading pickled environment... not yet created
building [mo]: targets for 0 po files that are out of date
building [json]: targets for 5 source files that are out of date
updating environment: 5 added, 0 changed, 0 removed
reading sources... [ 20%] index
reading sources... [ 40%] step1
reading sources... [ 60%] step2
reading sources... [ 80%] step3
reading sources... [100%] step4

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step1.rst:84: WARNING: image file not readable: ./img/de/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step1.rst:84: WARNING: image file not readable: ./img/de/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:8: WARNING: Duplicate explicit target name: "de_sample_plants.fas".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:120: WARNING: image file not readable: ./img/de/dots.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:120: WARNING: image file not readable: ./img/de/dots.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step4.rst:46: WARNING: Explicit markup ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 20%] index
writing output... [ 40%] step1
writing output... [ 60%] step2
writing output... [ 80%] step3
writing output... [100%] step4

generating indices... genindex
writing additional pages... search
copying images... [  4%] ./img/de/data_window.png
copying images... [  9%] ./img/de/beta.png
copying images... [ 14%] ./img/de/de-icon.png
copying images... [ 19%] ./img/de/manage_sharing_menu.png
copying images... [ 23%] ./img/de/favorite.png
copying images... [ 28%] ./img/de/manage_data_links.png
copying images... [ 33%] ./img/de/apps_icon.png
copying images... [ 38%] ./img/de/info.png
copying images... [ 42%] ./img/de/muscle_app_window.png
copying images... [ 47%] ./img/de/person_icon.png
copying images... [ 52%] ./img/de/data_icon.png
copying images... [ 57%] ./img/de/comment.png
copying images... [ 61%] ./img/de/viewing_window.png
copying images... [ 66%] ./img/de/unavailable.png
copying images... [ 71%] ./img/de/de_app_icon.png
copying images... [ 76%] ./img/cyverse_rgb.png
copying images... [ 80%] ./img/de/rating.png
copying images... [ 85%] ./img/de/link_icon.png
copying images... [ 90%] ./img/de/delete_icon.png
copying images... [ 95%] ./img/homeicon.png
copying images... [100%] ./img/de/private.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/_static' does not exist
WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist
done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 8 warnings.

[rtd-command-info] start-time: 2017-11-22T02:54:54.337395Z, end-time: 2017-11-22T02:54:55.507005Z, duration: 1, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.5.3
making output directory...
loading translations [en]... done
loading pickled environment... not yet created
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 5 added, 0 changed, 0 removed
reading sources... [ 20%] index
reading sources... [ 40%] step1
reading sources... [ 60%] step2
reading sources... [ 80%] step3
reading sources... [100%] step4

looking for now-outdated files... none found
pickling environment... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step1.rst:84: WARNING: image file not readable: ./img/de/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step1.rst:84: WARNING: image file not readable: ./img/de/intercom.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:8: WARNING: Duplicate explicit target name: "de_sample_plants.fas".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:120: WARNING: image file not readable: ./img/de/dots.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:120: WARNING: image file not readable: ./img/de/dots.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step4.rst:46: WARNING: Explicit markup ends without a blank line; unexpected unindent.
done
checking consistency... done
preparing documents... done
assembling single document... step1 step2 step3 step4 
writing... done
writing additional files...
copying images... [  4%] ./img/de/data_window.png
copying images... [  9%] ./img/de/beta.png
copying images... [ 14%] ./img/de/de-icon.png
copying images... [ 19%] ./img/de/manage_sharing_menu.png
copying images... [ 23%] ./img/de/favorite.png
copying images... [ 28%] ./img/de/manage_data_links.png
copying images... [ 33%] ./img/de/apps_icon.png
copying images... [ 38%] ./img/de/info.png
copying images... [ 42%] ./img/de/muscle_app_window.png
copying images... [ 47%] ./img/de/person_icon.png
copying images... [ 52%] ./img/de/data_icon.png
copying images... [ 57%] ./img/de/comment.png
copying images... [ 61%] ./img/de/viewing_window.png
copying images... [ 66%] ./img/de/unavailable.png
copying images... [ 71%] ./img/de/de_app_icon.png
copying images... [ 76%] ./img/cyverse_rgb.png
copying images... [ 80%] ./img/de/rating.png
copying images... [ 85%] ./img/de/link_icon.png
copying images... [ 90%] ./img/de/delete_icon.png
copying images... [ 95%] ./img/homeicon.png
copying images... [100%] ./img/de/private.png

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