Read the Docs build information
Build id: 99648
Project: cyverse-ez-quickstart
Version: latest
Commit: daef141739a88e1007a1a3531d95c55700a346c3
Date: 2018-04-07T03:32:28.473134Z
State: finished
Success: True
[rtd-command-info] start-time: 2018-04-07T08:32:28.907381Z, end-time: 2018-04-07T08:32:28.913712Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/CyVerse-learning-materials/ez_quickstart.git
[rtd-command-info] start-time: 2018-04-07T08:32:28.976388Z, end-time: 2018-04-07T08:32:29.229765Z, duration: 0, exit-code: 0
git fetch --tags --prune
From https://github.com/CyVerse-learning-materials/ez_quickstart
0cba493..daef141 master -> origin/master
[rtd-command-info] start-time: 2018-04-07T08:32:29.302746Z, end-time: 2018-04-07T08:32:29.310981Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 0cba493... Update index.rst
HEAD is now at daef141... Create anaconda.rst
[rtd-command-info] start-time: 2018-04-07T08:32:29.374059Z, end-time: 2018-04-07T08:32:29.382354Z, duration: 0, exit-code: 0
git clean -d -f -f
[rtd-command-info] start-time: 2018-04-07T08:32:29.476935Z, end-time: 2018-04-07T08:32:29.484983Z, duration: 0, exit-code: 0
git show-ref --tags
[rtd-command-info] start-time: 2018-04-07T08:32:29.548056Z, end-time: 2018-04-07T08:32:29.556865Z, duration: 0, exit-code: 0
git branch -r
origin/HEAD -> origin/master
origin/master
[rtd-command-info] start-time: 2018-04-07T08:32:30.437263Z, end-time: 2018-04-07T08:32:32.207575Z, 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-ez-quickstart/envs/latest/bin/python2.7
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/bin/python2.7)
Installing setuptools, pip, wheel...done.
[rtd-command-info] start-time: 2018-04-07T08:32:32.274351Z, end-time: 2018-04-07T08:32:34.197046Z, duration: 1, exit-code: 0
python pip install --use-wheel --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/.cache/pip Pygments==2.2.0 setuptools==37.0.0 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==1.6.5 sphinx-rtd-theme<0.3 readthedocs-sphinx-ext<0.6
Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: setuptools==37.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: docutils==0.13.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: pillow==2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: commonmark==0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: recommonmark==0.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: sphinx==1.6.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: sphinx-rtd-theme<0.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5)
Requirement already up-to-date: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5)
Requirement already up-to-date: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5)
Requirement already up-to-date: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5)
Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5)
Requirement already up-to-date: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5)
Requirement already up-to-date: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5)
Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5)
Requirement already up-to-date: nilsimsa>=0.3.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from readthedocs-sphinx-ext<0.6)
Requirement already up-to-date: urllib3<1.23,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.6.5)
Requirement already up-to-date: idna<2.7,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.6.5)
Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.6.5)
Requirement already up-to-date: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.6.5)
Requirement already up-to-date: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx==1.6.5)
Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx==1.6.5)
You are using pip version 9.0.1, however version 9.0.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
[rtd-command-info] start-time: 2018-04-07T08:32:34.701339Z, end-time: 2018-04-07T08:32:34.759177Z, 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 = 'EZ Installation Quickstart'
copyright = '2017, CyVerse'
author = 'Blake Joyce'
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",
'version_slug': "latest",
'MEDIA_URL': "https://media.readthedocs.com/media/",
'PRODUCTION_DOMAIN': "readthedocs.com",
'versions': [
("latest", "/en/latest/"),
],
'downloads': [
("htmlzip", "//readthedocs.com/projects/cyverse-ez-quickstart/downloads/htmlzip/latest/"),
],
'subprojects': [
],
'slug': 'cyverse-ez-quickstart',
'name': u'ez_quickstart',
'rtd_language': u'en',
'programming_language': u'words',
'canonical_url': 'https://cyverse-ez-quickstart.readthedocs-hosted.com/en/latest/',
'analytics_code': '',
'single_version': False,
'conf_py_path': '/./',
'api_host': 'https://readthedocs.com',
'github_user': 'CyVerse-learning-materials',
'github_repo': 'ez_quickstart',
'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,
'user_analytics_code': '',
'global_analytics_code': 'UA-17997319-2',
'commit': 'daef1417',
}
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: 2018-04-07T08:32:34.828786Z, end-time: 2018-04-07T08:32:36.333333Z, duration: 1, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.6.5
making output directory...
loading translations [en]... done
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 8 source files that are out of date
updating environment: 8 added, 0 changed, 0 removed
reading sources... [ 12%] Contributors_maintainers
reading sources... [ 25%] License
reading sources... [ 37%] README
reading sources... [ 50%] anaconda
reading sources... [ 62%] docker
reading sources... [ 75%] index
reading sources... [ 87%] rstudio
reading sources... [100%] slides/README
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:7: WARNING: Duplicate explicit target name: "request access".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:65: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 3 does not contain the same number of items as row 1 (1 vs 3).
.. list-table::
:header-rows: 1
* - Prerequisite
- Preparation/Notes
- Link/Download
* - CyVerse account
- You will need a CyVerse account to complete this exercise
- `Register `_
* - Atmosphere Access
- `Request Access `_
* - Jetstream Access
- `Request Access `_
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:111: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 2 does not contain the same number of items as row 1 (1 vs 2).
.. list-table::
:header-rows: 1
* - A running Atmosphere instance using a featured image.
- Notes
* - `A running Atmosphere or Jetstream Image `__
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:7: WARNING: Duplicate explicit target name: "atmosphere".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:7: WARNING: Duplicate explicit target name: "jetstream".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:215: WARNING: Unknown target name: "connect to atmosphere via ssh".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:18: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:21: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:24: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:31: WARNING: Unknown directive type "Ubuntu".
.. Ubuntu::
- In a terminal, reset the symbolic link for `libfortran.so`:
``sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/libgfortran.so``
- Install Dependencies
``sudo apt-get install gdebi-core g++``
- Change to the `/opt` folder
``cd /opt``
``sudo wget https://download2.rstudio.org/rstudio-server-1.0.153-amd64.deb``
``sudo gdebi -n rstudio-server-1.0.153-amd64.deb``
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:45: WARNING: Unknown directive type "Centos".
.. Centos::
``cd /opt``
``sudo wget https://download2.rstudio.org/rstudio-server-rhel-1.0.153-x86_64.rpm``
``sudo yum install --nogpgcheck rstudio-server-rhel-1.0.153-x86_64.rpm``
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/License.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/anaconda.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/slides/README.md: WARNING: document isn't included in any toctree
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 12%] Contributors_maintainers
writing output... [ 25%] License
writing output... [ 37%] README
writing output... [ 50%] anaconda
writing output... [ 62%] docker
writing output... [ 75%] index
writing output... [ 87%] rstudio
writing output... [100%] slides/README
generating indices... genindex
writing additional pages... search
copying images... [ 50%] ./img/homeicon.png
copying images... [100%] ./img/cyverse_rgb.png
copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/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, 18 warnings.
[rtd-command-info] start-time: 2018-04-07T08:32:36.423457Z, end-time: 2018-04-07T08:32:37.408562Z, duration: 0, exit-code: 0
python sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json
Running Sphinx v1.6.5
making output directory...
loading translations [en]... done
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [json]: targets for 7 source files that are out of date
updating environment: 1 added, 0 changed, 0 removed
reading sources... [100%] anaconda
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/License.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/anaconda.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/slides/README.md: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [ 12%] Contributors_maintainers
writing output... [ 25%] License
writing output... [ 37%] README
writing output... [ 50%] anaconda
writing output... [ 62%] docker
writing output... [ 75%] index
writing output... [ 87%] rstudio
writing output... [100%] slides/README
generating indices... genindex
writing additional pages... search
copying images... [ 50%] ./img/homeicon.png
copying images... [100%] ./img/cyverse_rgb.png
copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/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, 7 warnings.
[rtd-command-info] start-time: 2018-04-07T08:32:37.490983Z, end-time: 2018-04-07T08:32:38.422076Z, duration: 0, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.6.5
making output directory...
loading translations [en]... done
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 1 added, 0 changed, 0 removed
reading sources... [100%] anaconda
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/License.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/anaconda.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/slides/README.md: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... rstudio docker
writing... done
writing additional files...
copying images... [ 50%] ./img/homeicon.png
copying images... [100%] ./img/cyverse_rgb.png
copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/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, 7 warnings.