Read the Docs build information
Build id: 104263
Project: cyverse-astrocontainers-workshop-2018
Version: latest
Commit: e51641714e45a550c1c1ba746b6b4cd3461acc98
Date: 2018-04-25T16:06:25.261500Z
State: finished
Success: True


[rtd-command-info] start-time: 2018-04-25T21:06:25.753779Z, end-time: 2018-04-25T21:06:26.474324Z, duration: 0, exit-code: 0
git clone --recursive https://github.com/CyVerse-learning-materials/astrocontainers_workshop_2018.git .
Cloning into '.'...

[rtd-command-info] start-time: 2018-04-25T21:06:26.549021Z, end-time: 2018-04-25T21:06:26.624795Z, 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 e516417... Fixed misc folder

[rtd-command-info] start-time: 2018-04-25T21:06:26.701025Z, end-time: 2018-04-25T21:06:26.710492Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2018-04-25T21:06:26.804892Z, end-time: 2018-04-25T21:06:26.811492Z, duration: 0, exit-code: 0
git show-ref --tags


[rtd-command-info] start-time: 2018-04-25T21:06:26.879151Z, end-time: 2018-04-25T21:06:26.887802Z, duration: 0, exit-code: 0
git branch -r
origin/HEAD -> origin/master
  origin/master

[rtd-command-info] start-time: 2018-04-25T21:06:27.681562Z, end-time: 2018-04-25T21:06:29.291336Z, 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-astrocontainers-workshop-2018/envs/latest/bin/python2.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/bin/python
Installing setuptools, pip, wheel...done.

[rtd-command-info] start-time: 2018-04-25T21:06:29.359581Z, end-time: 2018-04-25T21:06:51.729367Z, duration: 22, exit-code: 0
python pip install --use-wheel --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/.cache/pip Pygments==2.2.0 setuptools<40 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
Collecting Pygments==2.2.0
  Downloading https://files.pythonhosted.org/packages/02/ee/b6e02dc6529e82b75bb06823ff7d005b141037cb1416b10c6f00fc419dca/Pygments-2.2.0-py2.py3-none-any.whl (841kB)
Collecting setuptools<40
  Downloading https://files.pythonhosted.org/packages/20/d7/04a0b689d3035143e2ff288f4b9ee4bf6ed80585cc121c90bfd85a1a8c2e/setuptools-39.0.1-py2.py3-none-any.whl (569kB)
Collecting docutils==0.13.1
  Downloading https://files.pythonhosted.org/packages/5f/6d/e864b3c61b81eec57386ac62082fccfe694c7c3046d8723258a37da6d5fc/docutils-0.13.1-py2-none-any.whl (537kB)
Collecting mock==1.0.1
  Downloading https://files.pythonhosted.org/packages/a2/52/7edcd94f0afb721a2d559a5b9aae8af4f8f2c79bc63fdbe8a8a6c9b23bbe/mock-1.0.1.tar.gz (818kB)
Collecting pillow==2.6.1
  Downloading https://files.pythonhosted.org/packages/9f/53/9dafa3a48ffa25f4e22f40df880b58b99ad53648f0990caf09b1824d5db2/Pillow-2.6.1.tar.gz (7.3MB)
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading https://files.pythonhosted.org/packages/2e/c3/9b7dcd8548cf2c00531763ba154e524af575e8f36701bacfe5bcadc67440/alabaster-0.7.10-py2.py3-none-any.whl
Collecting commonmark==0.5.4
  Downloading https://files.pythonhosted.org/packages/4d/93/3808cbcebe94d205f55a9a32857df733a603339d32c46cd32669d808d964/CommonMark-0.5.4.tar.gz (120kB)
Collecting recommonmark==0.4.0
  Downloading https://files.pythonhosted.org/packages/df/a5/8ee4b84af7f997dfdba71254a88008cfc19c49df98983c9a4919e798f8ce/recommonmark-0.4.0-py2.py3-none-any.whl
Collecting sphinx==1.6.5
  Downloading https://files.pythonhosted.org/packages/00/6a/7d463c2d1e95356caf2df5aacda13d0932efa0697506624df89db45223a3/Sphinx-1.6.5-py2.py3-none-any.whl (1.9MB)
Collecting sphinx-rtd-theme<0.3
  Downloading https://files.pythonhosted.org/packages/d7/50/849cd05961e7bafda2e0846ba80fa03f5a16a55fc5acc1d9f6bc79eb6fd9/sphinx_rtd_theme-0.2.4-py2.py3-none-any.whl (1.4MB)
Collecting readthedocs-sphinx-ext<0.6
  Downloading https://files.pythonhosted.org/packages/a5/79/6e0b733c544d157f977bba50c114040a59cc0620351d70e82476821954b1/readthedocs_sphinx_ext-0.5.10-py2-none-any.whl
Collecting sphinxcontrib-websupport (from sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/56/0f/3ee19ca5e5a1d9751cf4bbeb372d40a46421c4321fe55a4703ba66d0bafb/sphinxcontrib_websupport-1.0.1-py2.py3-none-any.whl
Collecting six>=1.5 (from sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/49/df/50aa1999ab9bde74656c2919d9c0c085fd2b3775fd3eca826012bef76d8c/requests-2.18.4-py2.py3-none-any.whl (88kB)
Collecting typing; python_version < "3.5" (from sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/0d/4d/4e5985d075d241d686a1663fa1f88b61d544658d08c1375c7c6aac32afc3/typing-3.6.4-py2-none-any.whl
Collecting imagesize (from sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/e9/79/31cc1c2e0daf575f8fd2b581e2975e6a6938bd439581f766b79c50479521/imagesize-1.0.0-py2.py3-none-any.whl
Collecting babel!=2.0,>=1.3 (from sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/94/03/14e68ad12e771a79cf96792f7158d68a7b3d8c7b2badf39e9ef1f65b57d6/Babel-2.5.3-py2.py3-none-any.whl (6.8MB)
Collecting snowballstemmer>=1.1 (from sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/d4/6c/8a935e2c7b54a37714656d753e4187ee0631988184ed50c0cf6476858566/snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB)
Collecting Jinja2>=2.3 (from sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl (126kB)
Collecting nilsimsa>=0.3.7 (from readthedocs-sphinx-ext<0.6)
  Downloading https://files.pythonhosted.org/packages/e9/e4/be3c435d1f553800ccd69a5bb5b1c5b08e38a47e623d87b4c9208a6eebc7/nilsimsa-0.3.8.tar.gz (276kB)
Collecting urllib3<1.23,>=1.21.1 (from requests>=2.0.0->sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/63/cb/6965947c13a94236f6d4b8223e21beb4d576dc72e8130bd7880f600839b8/urllib3-1.22-py2.py3-none-any.whl (132kB)
Collecting idna<2.7,>=2.5 (from requests>=2.0.0->sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/27/cc/6dd9a3869f15c2edfab863b992838277279ce92663d334df9ecf5106f5c6/idna-2.6-py2.py3-none-any.whl (56kB)
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB)
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/7c/e6/92ad559b7192d846975fc916b65f667c7b8c3a32bea7372340bfe9a15fa5/certifi-2018.4.16-py2.py3-none-any.whl (150kB)
Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/dc/83/15f7833b70d3e067ca91467ca245bae0f6fe56ddc7451aa0dc5606b120f2/pytz-2018.4-py2.py3-none-any.whl (510kB)
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.6.5)
  Downloading https://files.pythonhosted.org/packages/4d/de/32d741db316d8fdb7680822dd37001ef7a448255de9699ab4bfcbdf4172b/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-astrocontainers-workshop-2018/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6
  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-astrocontainers-workshop-2018/.cache/pip/wheels/de/0e/6b/556798d1ac8762a076ddff5b20f65b2e6cc2ae13b0e683c263
  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-astrocontainers-workshop-2018/.cache/pip/wheels/a0/f4/35/019d917f6875107ade3aad634c982f5c6b604c5631cddf20ac
  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-astrocontainers-workshop-2018/.cache/pip/wheels/64/48/61/8d7f0b227d16d55bdad76e3181b6a76eb00bbbd147305da14d
  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-astrocontainers-workshop-2018/.cache/pip/wheels/33/56/20/ebe49a5c612fffe1c5a632146b16596f9e64676768661e4e46
Successfully built mock pillow commonmark nilsimsa MarkupSafe
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, sphinxcontrib-websupport, six, urllib3, idna, chardet, certifi, requests, typing, imagesize, pytz, babel, snowballstemmer, MarkupSafe, Jinja2, sphinx, sphinx-rtd-theme, nilsimsa, readthedocs-sphinx-ext
  Found existing installation: setuptools 28.8.0
    Uninstalling setuptools-28.8.0:
      Successfully uninstalled setuptools-28.8.0
Successfully installed Jinja2-2.10 MarkupSafe-1.0 Pygments-2.2.0 alabaster-0.7.10 babel-2.5.3 certifi-2018.4.16 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.6 imagesize-1.0.0 mock-1.0.1 nilsimsa-0.3.8 pillow-2.6.1 pytz-2018.4 readthedocs-sphinx-ext-0.5.10 recommonmark-0.4.0 requests-2.18.4 setuptools-39.0.1 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.6.5 sphinx-rtd-theme-0.2.4 sphinxcontrib-websupport-1.0.1 typing-3.6.4 urllib3-1.22
You are using pip version 9.0.1, however version 10.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

[rtd-command-info] start-time: 2018-04-25T21:06:51.816622Z, end-time: 2018-04-25T21:06:55.783943Z, duration: 3, exit-code: 0
python pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/.cache/pip -r/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt
Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: recommonmark in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 2))
Collecting sphinxcontrib-images (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 3))
  Downloading https://files.pythonhosted.org/packages/07/47/3959ecf843fa30ae06346ff340bfd4e29ae4c46a0bac049bf0bd525d8b1a/sphinxcontrib_images-0.7.0-py2-none-any.whl (65kB)
Collecting sphinx_bootstrap_theme (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 4))
  Downloading https://files.pythonhosted.org/packages/8a/f6/e7dbc28e448817d2b103c57a3e4ee52f8edc143beab9595ced31e4789749/sphinx-bootstrap-theme-0.6.5.tar.gz (1.2MB)
Collecting guzzle_sphinx_theme==0.7.11 (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 5))
  Downloading https://files.pythonhosted.org/packages/f4/7d/aed8cd5e4ca52bb8550d2c33fcbb8d6dbd5c2cf5e1694202d2135b374eba/guzzle_sphinx_theme-0.7.11.tar.gz (2.5MB)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: commonmark<=0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from recommonmark->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 2))
Requirement already satisfied: urllib3<1.23,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: idna<2.7,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/requirements.txt (line 1))
Building wheels for collected packages: sphinx-bootstrap-theme, guzzle-sphinx-theme
  Running setup.py bdist_wheel for sphinx-bootstrap-theme: started
  Running setup.py bdist_wheel for sphinx-bootstrap-theme: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/.cache/pip/wheels/01/3c/98/f37c5ef813bb7262c17c566da10f9f7e4f6ff4b897d0a4209c
  Running setup.py bdist_wheel for guzzle-sphinx-theme: started
  Running setup.py bdist_wheel for guzzle-sphinx-theme: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/.cache/pip/wheels/6e/68/e9/4626607977db13794bfaf48afab2cf05487bb4d3612c09dcee
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-0.6.5 sphinxcontrib-images-0.7.0
You are using pip version 9.0.1, however version 10.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

[rtd-command-info] start-time: 2018-04-25T21:06:56.311189Z, end-time: 2018-04-25T21:06:56.378050Z, 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 = 'CyVerse AstroContainers Workshop: Learning Docker and Singularity'
copyright = '2018, CyVerse'
author = 'CyVerse'
version = '0.1.0'
release = '0.1.0'

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': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-astrocontainers-workshop-2018',
    'name': u'astrocontainers_workshop_2018',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://cyverse-astrocontainers-workshop-2018.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/./',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'github_repo': 'astrocontainers_workshop_2018',
    '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': 'e5164171',
    
}




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: 2018-04-25T21:06:56.445208Z, end-time: 2018-04-25T21:06:59.717977Z, duration: 3, 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 18 source files that are out of date
updating environment: 18 added, 0 changed, 0 removed
reading sources... [  5%] atmosphere/boot
reading sources... [ 11%] deploying_apps/de_docker
reading sources... [ 16%] docker/dockeradvanced
reading sources... [ 22%] docker/dockerintro
reading sources... [ 27%] getting_started/about_cyverse
reading sources... [ 33%] getting_started/agenda
reading sources... [ 38%] getting_started/installation
reading sources... [ 44%] getting_started/main
reading sources... [ 50%] index
reading sources... [ 55%] instructions_reporting/instructors
reading sources... [ 61%] instructions_reporting/problems
reading sources... [ 66%] singularity/singularityadvanced
reading sources... [ 72%] singularity/singularityintro
reading sources... [ 77%] topics/train_docker
reading sources... [ 83%] topics/train_singularity
reading sources... [ 88%] useful_resources/usefulresources_docker
reading sources... [ 94%] useful_resources/usefulresources_other
reading sources... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "github".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  5%] atmosphere/boot
writing output... [ 11%] deploying_apps/de_docker
writing output... [ 16%] docker/dockeradvanced
writing output... [ 22%] docker/dockerintro
writing output... [ 27%] getting_started/about_cyverse
writing output... [ 33%] getting_started/agenda
writing output... [ 38%] getting_started/installation
writing output... [ 44%] getting_started/main
writing output... [ 50%] index
writing output... [ 55%] instructions_reporting/instructors
writing output... [ 61%] instructions_reporting/problems
writing output... [ 66%] singularity/singularityadvanced
writing output... [ 72%] singularity/singularityintro
writing output... [ 77%] topics/train_docker
writing output... [ 83%] topics/train_singularity
writing output... [ 88%] useful_resources/usefulresources_docker
writing output... [ 94%] useful_resources/usefulresources_other
writing output... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:40: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:104: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
generating indices... genindex
writing additional pages... search
copying images... [  2%] docker/../img/tmpfs.png
copying images... [  4%] docker/../img/auto_build-1.png
copying images... [  6%] docker/../img/bind_mount.png
copying images... [  8%] atmosphere/../img/atmo-1.png
copying images... [ 10%] docker/../img/create_repo2.png
copying images... [ 12%] docker/../img/docker_image.png
copying images... [ 14%] docker/../img/dc-1.png
copying images... [ 16%] docker/../img/rstudio_login.png
copying images... [ 18%] docker/../img/static_site_docker1.png
copying images... [ 20%] deploying_apps/../img/f1000.png
copying images... [ 22%] atmosphere/../img/atmo_cp.png
copying images... [ 25%] docker/../img/auto_build-3.png
copying images... [ 27%] instructions_reporting/../img/static_site_docker.png
copying images... [ 29%] docker/../img/auto_build-2.png
copying images... [ 31%] docker/../img/create_repo.png
copying images... [ 33%] docker/../img/portainer_demo.png
copying images... [ 35%] docker/../img/rstudio_login2.png
copying images... [ 37%] docker/../img/volumes.png
copying images... [ 39%] docker/../img/jn_login.png
copying images... [ 41%] docker/../img/static_site_docker.png
copying images... [ 43%] atmosphere/../img/atmo-6.png
copying images... [ 45%] docker/../img/auto_build-4.png
copying images... [ 47%] docker/../img/pwd.png
copying images... [ 50%] docker/../img/auto_build-6.png
copying images... [ 52%] docker/../img/auto_build-7.png
copying images... [ 54%] atmosphere/../img/atmo_cp0.png
copying images... [ 56%] atmosphere/../img/atmo-9.png
copying images... [ 58%] docker/../img/jn_login2.png
copying images... [ 60%] docker/../img/private_registry.png
copying images... [ 62%] docker/../img/catpic-1.png
copying images... [ 64%] docker/../img/rstudio_ss.png
copying images... [ 66%] docker/../img/jn_login3.png
copying images... [ 68%] singularity/../img/singularity.png
copying images... [ 70%] docker/../img/jn_login3.5.png
copying images... [ 72%] deploying_apps/../img/img_building_1.png
copying images... [ 75%] docker/../img/docker.png
copying images... [ 77%] atmosphere/../img/atmo_launch0.png
copying images... [ 79%] atmosphere/../img/atmo_launch1.png
copying images... [ 81%] atmosphere/../img/atmo-7.png
copying images... [ 83%] docker/../img/jn_login4.png
copying images... [ 85%] docker/../img/auto_build-5.png
copying images... [ 87%] docker/../img/auto_build-2.1.png
copying images... [ 89%] atmosphere/../img/atmo-8.png
copying images... [ 91%] getting_started/../img/cyverse_rgb.png
copying images... [ 93%] deploying_apps/../img/img_building_3.png
copying images... [ 95%] docker/../img/jn_ss.png
copying images... [ 97%] deploying_apps/../img/img_building_4.png
copying images... [100%] atmosphere/../img/atmo_launch.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/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, 7 warnings.

[rtd-command-info] start-time: 2018-04-25T21:06:59.820129Z, end-time: 2018-04-25T21:07:02.314282Z, duration: 2, 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... not yet created
building [mo]: targets for 0 po files that are out of date
building [json]: targets for 18 source files that are out of date
updating environment: 18 added, 0 changed, 0 removed
reading sources... [  5%] atmosphere/boot
reading sources... [ 11%] deploying_apps/de_docker
reading sources... [ 16%] docker/dockeradvanced
reading sources... [ 22%] docker/dockerintro
reading sources... [ 27%] getting_started/about_cyverse
reading sources... [ 33%] getting_started/agenda
reading sources... [ 38%] getting_started/installation
reading sources... [ 44%] getting_started/main
reading sources... [ 50%] index
reading sources... [ 55%] instructions_reporting/instructors
reading sources... [ 61%] instructions_reporting/problems
reading sources... [ 66%] singularity/singularityadvanced
reading sources... [ 72%] singularity/singularityintro
reading sources... [ 77%] topics/train_docker
reading sources... [ 83%] topics/train_singularity
reading sources... [ 88%] useful_resources/usefulresources_docker
reading sources... [ 94%] useful_resources/usefulresources_other
reading sources... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "github".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  5%] atmosphere/boot
writing output... [ 11%] deploying_apps/de_docker
writing output... [ 16%] docker/dockeradvanced
writing output... [ 22%] docker/dockerintro
writing output... [ 27%] getting_started/about_cyverse
writing output... [ 33%] getting_started/agenda
writing output... [ 38%] getting_started/installation
writing output... [ 44%] getting_started/main
writing output... [ 50%] index
writing output... [ 55%] instructions_reporting/instructors
writing output... [ 61%] instructions_reporting/problems
writing output... [ 66%] singularity/singularityadvanced
writing output... [ 72%] singularity/singularityintro
writing output... [ 77%] topics/train_docker
writing output... [ 83%] topics/train_singularity
writing output... [ 88%] useful_resources/usefulresources_docker
writing output... [ 94%] useful_resources/usefulresources_other
writing output... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:40: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:104: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
generating indices... genindex
writing additional pages... search
copying images... [  2%] docker/../img/tmpfs.png
copying images... [  4%] docker/../img/auto_build-1.png
copying images... [  6%] docker/../img/bind_mount.png
copying images... [  8%] atmosphere/../img/atmo-1.png
copying images... [ 10%] docker/../img/create_repo2.png
copying images... [ 12%] docker/../img/docker_image.png
copying images... [ 14%] docker/../img/dc-1.png
copying images... [ 16%] docker/../img/rstudio_login.png
copying images... [ 18%] docker/../img/static_site_docker1.png
copying images... [ 20%] deploying_apps/../img/f1000.png
copying images... [ 22%] atmosphere/../img/atmo_cp.png
copying images... [ 25%] docker/../img/auto_build-3.png
copying images... [ 27%] instructions_reporting/../img/static_site_docker.png
copying images... [ 29%] docker/../img/auto_build-2.png
copying images... [ 31%] docker/../img/create_repo.png
copying images... [ 33%] docker/../img/portainer_demo.png
copying images... [ 35%] docker/../img/rstudio_login2.png
copying images... [ 37%] docker/../img/volumes.png
copying images... [ 39%] docker/../img/jn_login.png
copying images... [ 41%] docker/../img/static_site_docker.png
copying images... [ 43%] atmosphere/../img/atmo-6.png
copying images... [ 45%] docker/../img/auto_build-4.png
copying images... [ 47%] docker/../img/pwd.png
copying images... [ 50%] docker/../img/auto_build-6.png
copying images... [ 52%] docker/../img/auto_build-7.png
copying images... [ 54%] atmosphere/../img/atmo_cp0.png
copying images... [ 56%] atmosphere/../img/atmo-9.png
copying images... [ 58%] docker/../img/jn_login2.png
copying images... [ 60%] docker/../img/private_registry.png
copying images... [ 62%] docker/../img/catpic-1.png
copying images... [ 64%] docker/../img/rstudio_ss.png
copying images... [ 66%] docker/../img/jn_login3.png
copying images... [ 68%] singularity/../img/singularity.png
copying images... [ 70%] docker/../img/jn_login3.5.png
copying images... [ 72%] deploying_apps/../img/img_building_1.png
copying images... [ 75%] docker/../img/docker.png
copying images... [ 77%] atmosphere/../img/atmo_launch0.png
copying images... [ 79%] atmosphere/../img/atmo_launch1.png
copying images... [ 81%] atmosphere/../img/atmo-7.png
copying images... [ 83%] docker/../img/jn_login4.png
copying images... [ 85%] docker/../img/auto_build-5.png
copying images... [ 87%] docker/../img/auto_build-2.1.png
copying images... [ 89%] atmosphere/../img/atmo-8.png
copying images... [ 91%] getting_started/../img/cyverse_rgb.png
copying images... [ 93%] deploying_apps/../img/img_building_3.png
copying images... [ 95%] docker/../img/jn_ss.png
copying images... [ 97%] deploying_apps/../img/img_building_4.png
copying images... [100%] atmosphere/../img/atmo_launch.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/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: 2018-04-25T21:07:02.440602Z, end-time: 2018-04-25T21:07:04.819974Z, duration: 2, 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... not yet created
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 18 added, 0 changed, 0 removed
reading sources... [  5%] atmosphere/boot
reading sources... [ 11%] deploying_apps/de_docker
reading sources... [ 16%] docker/dockeradvanced
reading sources... [ 22%] docker/dockerintro
reading sources... [ 27%] getting_started/about_cyverse
reading sources... [ 33%] getting_started/agenda
reading sources... [ 38%] getting_started/installation
reading sources... [ 44%] getting_started/main
reading sources... [ 50%] index
reading sources... [ 55%] instructions_reporting/instructors
reading sources... [ 61%] instructions_reporting/problems
reading sources... [ 66%] singularity/singularityadvanced
reading sources... [ 72%] singularity/singularityintro
reading sources... [ 77%] topics/train_docker
reading sources... [ 83%] topics/train_singularity
reading sources... [ 88%] useful_resources/usefulresources_docker
reading sources... [ 94%] useful_resources/usefulresources_other
reading sources... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "github".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... getting_started/main getting_started/installation getting_started/agenda getting_started/about_cyverse topics/train_docker topics/train_singularity atmosphere/boot docker/dockerintro docker/dockeradvanced singularity/singularityintro singularity/singularityadvanced deploying_apps/de_docker useful_resources/usefulresources_docker useful_resources/usefulresources_singularity useful_resources/usefulresources_other instructions_reporting/instructors instructions_reporting/problems 
writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/index.rst:40: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/index.rst:104: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
done
writing additional files...
copying images... [  2%] docker/../img/tmpfs.png
copying images... [  4%] docker/../img/auto_build-1.png
copying images... [  6%] docker/../img/bind_mount.png
copying images... [  8%] atmosphere/../img/atmo-1.png
copying images... [ 10%] docker/../img/create_repo2.png
copying images... [ 12%] docker/../img/docker_image.png
copying images... [ 14%] docker/../img/dc-1.png
copying images... [ 16%] docker/../img/rstudio_login.png
copying images... [ 18%] docker/../img/static_site_docker1.png
copying images... [ 20%] deploying_apps/../img/f1000.png
copying images... [ 22%] atmosphere/../img/atmo_cp.png
copying images... [ 25%] instructions_reporting/../img/static_site_docker.png
copying images... [ 27%] docker/../img/auto_build-2.png
copying images... [ 29%] docker/../img/jn_login3.png
copying images... [ 31%] docker/../img/portainer_demo.png
copying images... [ 33%] deploying_apps/../img/img_building_1.png
copying images... [ 35%] docker/../img/jn_login2.png
copying images... [ 37%] docker/../img/rstudio_login2.png
copying images... [ 39%] docker/../img/volumes.png
copying images... [ 41%] docker/../img/jn_login.png
copying images... [ 43%] docker/../img/static_site_docker.png
copying images... [ 45%] atmosphere/../img/atmo-6.png
copying images... [ 47%] docker/../img/auto_build-4.png
copying images... [ 50%] docker/../img/pwd.png
copying images... [ 52%] docker/../img/auto_build-6.png
copying images... [ 54%] docker/../img/auto_build-7.png
copying images... [ 56%] atmosphere/../img/atmo_cp0.png
copying images... [ 58%] atmosphere/../img/atmo-9.png
copying images... [ 60%] docker/../img/catpic-1.png
copying images... [ 62%] docker/../img/private_registry.png
copying images... [ 64%] docker/../img/rstudio_ss.png
copying images... [ 66%] docker/../img/auto_build-3.png
copying images... [ 68%] singularity/../img/singularity.png
copying images... [ 70%] docker/../img/jn_login3.5.png
copying images... [ 72%] docker/../img/create_repo.png
copying images... [ 75%] docker/../img/docker.png
copying images... [ 77%] atmosphere/../img/atmo_launch0.png
copying images... [ 79%] atmosphere/../img/atmo_launch1.png
copying images... [ 81%] atmosphere/../img/atmo-7.png
copying images... [ 83%] docker/../img/jn_login4.png
copying images... [ 85%] docker/../img/auto_build-5.png
copying images... [ 87%] docker/../img/auto_build-2.1.png
copying images... [ 89%] atmosphere/../img/atmo-8.png
copying images... [ 91%] deploying_apps/../img/img_building_4.png
copying images... [ 93%] deploying_apps/../img/img_building_3.png
copying images... [ 95%] docker/../img/jn_ss.png
copying images... [ 97%] getting_started/../img/cyverse_rgb.png
copying images... [100%] atmosphere/../img/atmo_launch.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/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.

[rtd-command-info] start-time: 2018-04-25T21:07:05.000825Z, end-time: 2018-04-25T21:07:07.396175Z, duration: 2, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.6.5
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 [latex]: all documents
updating environment: 18 added, 0 changed, 0 removed
reading sources... [  5%] atmosphere/boot
reading sources... [ 11%] deploying_apps/de_docker
reading sources... [ 16%] docker/dockeradvanced
reading sources... [ 22%] docker/dockerintro
reading sources... [ 27%] getting_started/about_cyverse
reading sources... [ 33%] getting_started/agenda
reading sources... [ 38%] getting_started/installation
reading sources... [ 44%] getting_started/main
reading sources... [ 50%] index
reading sources... [ 55%] instructions_reporting/instructors
reading sources... [ 61%] instructions_reporting/problems
reading sources... [ 66%] singularity/singularityadvanced
reading sources... [ 72%] singularity/singularityintro
reading sources... [ 77%] topics/train_docker
reading sources... [ 83%] topics/train_singularity
reading sources... [ 88%] useful_resources/usefulresources_docker
reading sources... [ 94%] useful_resources/usefulresources_other
reading sources... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "github".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
processing CyVerseDocumentation.tex...index getting_started/main getting_started/installation getting_started/agenda getting_started/about_cyverse topics/train_docker topics/train_singularity atmosphere/boot docker/dockerintro docker/dockeradvanced singularity/singularityintro singularity/singularityadvanced deploying_apps/de_docker useful_resources/usefulresources_docker useful_resources/usefulresources_singularity useful_resources/usefulresources_other instructions_reporting/instructors instructions_reporting/problems 
resolving references...
writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:40: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:104: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
done
copying images... [  2%] docker/../img/tmpfs.png
copying images... [  4%] docker/../img/auto_build-1.png
copying images... [  6%] docker/../img/bind_mount.png
copying images... [  8%] atmosphere/../img/atmo-1.png
copying images... [ 10%] docker/../img/create_repo2.png
copying images... [ 12%] docker/../img/docker_image.png
copying images... [ 14%] docker/../img/dc-1.png
copying images... [ 16%] docker/../img/rstudio_login.png
copying images... [ 18%] docker/../img/static_site_docker1.png
copying images... [ 20%] deploying_apps/../img/f1000.png
copying images... [ 22%] atmosphere/../img/atmo_cp.png
copying images... [ 24%] instructions_reporting/../img/static_site_docker.png
copying images... [ 26%] docker/../img/auto_build-2.png
copying images... [ 28%] docker/../img/jn_login3.png
copying images... [ 30%] docker/../img/portainer_demo.png
copying images... [ 32%] deploying_apps/../img/img_building_1.png
copying images... [ 34%] docker/../img/jn_login2.png
copying images... [ 36%] docker/../img/rstudio_login2.png
copying images... [ 38%] docker/../img/volumes.png
copying images... [ 40%] docker/../img/jn_login.png
copying images... [ 42%] docker/../img/static_site_docker.png
copying images... [ 44%] atmosphere/../img/atmo-6.png
copying images... [ 46%] docker/../img/auto_build-4.png
copying images... [ 48%] docker/../img/pwd.png
copying images... [ 51%] docker/../img/auto_build-6.png
copying images... [ 53%] docker/../img/auto_build-7.png
copying images... [ 55%] atmosphere/../img/atmo_cp0.png
copying images... [ 57%] atmosphere/../img/atmo-9.png
copying images... [ 59%] docker/../img/catpic-1.png
copying images... [ 61%] docker/../img/private_registry.png
copying images... [ 63%] docker/../img/rstudio_ss.png
copying images... [ 65%] docker/../img/auto_build-3.png
copying images... [ 67%] singularity/../img/singularity.png
copying images... [ 69%] docker/../img/jn_login3.5.png
copying images... [ 71%] docker/../img/create_repo.png
copying images... [ 73%] docker/../img/docker.png
copying images... [ 75%] atmosphere/../img/atmo_launch0.png
copying images... [ 77%] atmosphere/../img/atmo_launch1.png
copying images... [ 79%] http://singularity.lbl.gov/assets/img/diagram/singularity-2.4-flow.png
copying images... [ 81%] atmosphere/../img/atmo-7.png
copying images... [ 83%] docker/../img/jn_login4.png
copying images... [ 85%] docker/../img/auto_build-5.png
copying images... [ 87%] docker/../img/auto_build-2.1.png
copying images... [ 89%] atmosphere/../img/atmo-8.png
copying images... [ 91%] deploying_apps/../img/img_building_4.png
copying images... [ 93%] deploying_apps/../img/img_building_3.png
copying images... [ 95%] docker/../img/jn_ss.png
copying images... [ 97%] getting_started/../img/cyverse_rgb.png
copying images... [100%] atmosphere/../img/atmo_launch.png

copying TeX support files...
done
build succeeded, 5 warnings.

[rtd-command-info] start-time: 2018-04-25T21:07:07.487923Z, end-time: 2018-04-25T21:07:19.425976Z, duration: 11, exit-code: 0
pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/_build/latex/CyVerseDocumentation.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

(/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-works
hop-2018/checkouts/latest/_build/latex/CyVerseDocumentation.tex
LaTeX2e <2016/02/01>
Babel <3.9q> and hyphenation patterns for 81 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2017/03/26 v1.6 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-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.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/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty))))
(/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/etoolbox/etoolbox.sty)

 Package Sphinx Info: 
 **** titlesec 2.10.1 successfully patched for bugfix ****

(/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/latexconfig/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)
(./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/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))

Package hyperref Message: Driver (autodetected): hpdftex.

(/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 CyVerseDocumentation.idx
No file CyVerseDocumentation.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/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]
<cyverse_rgb.png, id=28, 1093.686pt x 238.0092pt> <use cyverse_rgb.png>
[1 <./cyverse_rgb.png>] [2]
Chapter 1.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 75.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4]
Chapter 2.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 136.


Underfull \hbox (badness 7344) in paragraph at lines 155--159
\T1/ptm/m/n/10 We \T1/ptm/b/n/10 strongly rec-om-mend \T1/ptm/m/n/10 Fire-
[5]
Underfull \hbox (badness 5189) in paragraph at lines 2--287
[][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber-
[6] [7] [8]
Chapter 3.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 304.


Underfull \hbox (badness 5802) in paragraph at lines 329--330
[]|\T1/ptm/m/n/10 General in-tro-duc-tion to

Underfull \hbox (badness 6675) in paragraph at lines 336--337
\T1/ptm/m/n/10 tainer tech-nol-ogy land-

Underfull \hbox (badness 6675) in paragraph at lines 378--379
\T1/ptm/m/n/10 af-ter-noon ses-sion plan-

Underfull \hbox (badness 10000) in paragraph at lines 383--384
[]|\T1/ptm/m/n/10 BYOD/A (Hands-on

Underfull \hbox (badness 10000) in paragraph at lines 2--394
[]|[][]\T1/ptm/m/n/10 Singularity Overview

Underfull \hbox (badness 10000) in paragraph at lines 397--398
[]|\T1/ptm/m/n/10 Singularity setup (CK

Underfull \hbox (badness 10000) in paragraph at lines 414--415
[]|\T1/ptm/m/n/10 Introductory Sin-gu-lar-ity

Underfull \hbox (badness 10000) in paragraph at lines 435--436
[]|\T1/ptm/m/n/10 Advanced Sin-gu-lar-ity

Underfull \hbox (badness 6675) in paragraph at lines 442--443
\T1/ptm/m/n/10 af-ter-noon ses-sion plan-

Underfull \hbox (badness 10000) in paragraph at lines 447--448
[]|\T1/ptm/m/n/10 BYOD/A (Hands-on
[9] [10]
Chapter 4.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 455.

[11] [12]
Chapter 5.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 489.

[13] [14]
Chapter 6.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 510.

[15] [16]
Chapter 7.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 531.

<atmo-1.png, id=159, 974.64125pt x 561.09625pt> <use atmo-1.png>
Overfull \hbox (94.8532pt too wide) in paragraph at lines 553--554
[][] 
[17] <atmo_cp0.png, id=167, 1310.8975pt x 220.825pt> <use atmo_cp0.png>
Overfull \hbox (94.84006pt too wide) in paragraph at lines 572--573
[][] 
[18 <./atmo-1.png>] <atmo_cp.png, id=174, 1698.345pt x 1411.2725pt>
<use atmo_cp.png>
Overfull \hbox (94.84691pt too wide) in paragraph at lines 579--580
[][] 
[19 <./atmo_cp0.png>] <atmo_launch0.png, id=180, 1303.87125pt x 406.51875pt>
<use atmo_launch0.png>
Overfull \hbox (94.8579pt too wide) in paragraph at lines 595--596
[][] 
[20 <./atmo_cp.png>] <atmo_launch1.png, id=187, 2244.385pt x 1274.7625pt>
<use atmo_launch1.png>
Overfull \hbox (94.83301pt too wide) in paragraph at lines 602--603
[][] 
[21 <./atmo_launch0.png>] <atmo_launch.png, id=194, 2198.2125pt x 1531.7225pt>
<use atmo_launch.png>
Overfull \hbox (94.82356pt too wide) in paragraph at lines 612--613
[][] 
[22 <./atmo_launch1.png>] <atmo-6.png, id=200, 1119.18124pt x 663.47874pt>
<use atmo-6.png>
Overfull \hbox (94.87204pt too wide) in paragraph at lines 622--623
[][] 
[23 <./atmo_launch.png>] <atmo-7.png, id=206, 1041.8925pt x 615.29875pt>
<use atmo-7.png>
Overfull \hbox (94.84581pt too wide) in paragraph at lines 632--633
[][] 
[24 <./atmo-6.png>] <atmo-8.png, id=212, 1764.5925pt x 1174.3875pt>
<use atmo-8.png>
Overfull \hbox (94.84535pt too wide) in paragraph at lines 644--645
[][] 
[25 <./atmo-7.png>] <atmo-9.png, id=218, 1774.63pt x 1499.6025pt>
<use atmo-9.png>
Overfull \hbox (94.8346pt too wide) in paragraph at lines 651--652
[][] 
[26 <./atmo-8.png>] [27 <./atmo-9.png>] [28]
Chapter 8.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 658.

<docker.png, id=234, 289.08pt x 97.8054pt> <use docker.png>
Overfull \hbox (94.87941pt too wide) in paragraph at lines 660--661
[] 
[29]
Overfull \vbox (136.83218pt too high) has occurred while \output is active
[30 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [31]
Overfull \vbox (1.82733pt too high) detected at line 771
[32] [33] [34]

! Package inputenc Error: Unicode char ☺ (U+263A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.882 ...to answer any of these questions yet! ☺
                                                   In this case, the client ...

<static_site_docker.png, id=281, 1858.945pt x 1184.425pt>
<use static_site_docker.png>
Overfull \hbox (94.82553pt too wide) in paragraph at lines 942--943
[][] 
[35] <static_site_docker1.png, id=286, 2244.385pt x 1274.7625pt>
<use static_site_docker1.png>
Overfull \hbox (94.83301pt too wide) in paragraph at lines 949--950
[][] 
[36 <./static_site_docker.png>]
Underfull \hbox (badness 10000) in paragraph at lines 951--953
\T1/pcr/m/n/10 Docker host. However if you want to assign a fixed port then you
 can use \TS1/pcr/m/n/10 ``\T1/pcr/m/n/10 -p

Underfull \hbox (badness 10000) in paragraph at lines 961--962
[]\T1/ptm/m/n/10 If you are run-ning Docker on At-mo-sphere/Jetstream or on any
 other cloud, you can open
[37 <./static_site_docker1.png>] [38]
Underfull \vbox (badness 1184) detected at line 1054

Overfull \vbox (3.56996pt too high) detected at line 1054
[39]

LaTeX Warning: Hyper reference `docker/dockerintro:create-a-python-flask-app-th
at-displays-random-cat' on page 40 undefined on input line 1074.


LaTeX Warning: Hyper reference `docker/dockerintro:build-the-image' on page 40 
undefined on input line 1077.


LaTeX Warning: Hyper reference `docker/dockerintro:run-your-image' on page 40 u
ndefined on input line 1080.


LaTeX Warning: Hyper reference `docker/dockerintro:app-py' on page 40 undefined
 on input line 1098.


LaTeX Warning: Hyper reference `docker/dockerintro:requirements-txt' on page 40
 undefined on input line 1101.


LaTeX Warning: Hyper reference `docker/dockerintro:templates-index-html' on pag
e 40 undefined on input line 1104.


LaTeX Warning: Hyper reference `docker/dockerintro:dockerfile' on page 40 undef
ined on input line 1107.

[40] [41]
Overfull \vbox (1.36995pt too high) detected at line 1236
[42] [43]
Underfull \hbox (badness 10000) in paragraph at lines 1290--1292
\T1/ptm/b/n/10 Note:  \T1/ptm/m/n/10 When you run the \T1/pcr/m/n/10 docker bui
ld \T1/ptm/m/n/10 com-mand given be-low, make sure to re-place

Overfull \vbox (2.56995pt too high) detected at line 1355
[44] <catpic-1.png, id=343, 2041.6275pt x 1371.1225pt> <use catpic-1.png>
Overfull \hbox (94.85628pt too wide) in paragraph at lines 1373--1374
[][] 
[45] [46 <./catpic-1.png>] [47]
<portainer_demo.png, id=368, 2294.5725pt x 1419.3025pt>
<use portainer_demo.png>
Overfull \hbox (94.81851pt too wide) in paragraph at lines 1479--1480
[][] 
[48] [49 <./portainer_demo.png>] <pwd.png, id=383, 2495.3225pt x 1640.1275pt>
<use pwd.png>
Overfull \hbox (94.82858pt too wide) in paragraph at lines 1495--1496
[][] 
[50 <./pwd.png>]
Chapter 9.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 1498.

[51] <docker_image.png, id=403, 2142.0025pt x 1202.4925pt>
<use docker_image.png>
Overfull \hbox (94.866pt too wide) in paragraph at lines 1580--1581
[][] 
[52] [53 <./docker_image.png>]
<private_registry.png, id=419, 2045.6425pt x 1059.96pt>
<use private_registry.png>
Overfull \hbox (94.84293pt too wide) in paragraph at lines 1619--1620
[][] 
[54]
Overfull \vbox (8.54036pt too high) detected at line 1633
[55 <./private_registry.png>] [56]
<auto_build-1.png, id=444, 2637.855pt x 1481.535pt> <use auto_build-1.png>
Overfull \hbox (94.83699pt too wide) in paragraph at lines 1731--1732
[][] 
[57] [58 <./auto_build-1.png>]
<create_repo.png, id=464, 2953.0325pt x 1674.255pt> <use create_repo.png>
Overfull \hbox (94.84164pt too wide) in paragraph at lines 1779--1780
[][] 
[59] <create_repo2.png, id=470, 2834.59pt x 758.835pt> <use create_repo2.png>
Overfull \hbox (94.81732pt too wide) in paragraph at lines 1787--1788
[][] 
[60 <./create_repo.png>]
Overfull \vbox (1.54773pt too high) detected at line 1801
[61 <./create_repo2.png>] <auto_build-2.png, id=482, 2115.905pt x 1330.9725pt>
<use auto_build-2.png>
Overfull \hbox (94.83147pt too wide) in paragraph at lines 1823--1824
[][] 
[62] <auto_build-2.1.png, id=488, 2115.905pt x 1330.9725pt>
<use auto_build-2.1.png>
Overfull \hbox (94.83147pt too wide) in paragraph at lines 1835--1836
[][] 
[63 <./auto_build-2.png>] [64 <./auto_build-2.1.png>]
<auto_build-5.png, id=501, 1152.305pt x 738.76pt> <use auto_build-5.png>
Overfull \hbox (94.86179pt too wide) in paragraph at lines 1881--1882
[][] 
[65] <auto_build-6.png, id=508, 1213.53375pt x 655.44875pt>
<use auto_build-6.png>
Overfull \hbox (94.84714pt too wide) in paragraph at lines 1889--1890
[][] 
[66 <./auto_build-5.png>]
<auto_build-7.png, id=514, 1213.53375pt x 655.44875pt> <use auto_build-7.png>
Overfull \hbox (94.84714pt too wide) in paragraph at lines 1905--1906
[][] 
[67 <./auto_build-6.png>] [68 <./auto_build-7.png>]
<volumes.png, id=528, 503.8825pt x 255.95625pt> <use volumes.png>
Overfull \hbox (94.85095pt too wide) in paragraph at lines 1947--1948
[][] 
[69] [70 <./volumes.png>] [71] [72]
<bind_mount.png, id=552, 503.8825pt x 256.96pt> <use bind_mount.png>
Overfull \hbox (94.85095pt too wide) in paragraph at lines 2121--2122
[][] 
[73] [74 <./bind_mount.png>] [75]
<tmpfs.png, id=570, 502.87875pt x 259.97125pt> <use tmpfs.png>
Overfull \hbox (94.84653pt too wide) in paragraph at lines 2206--2207
[][] 
[76] [77 <./tmpfs.png>] [78] [79] [80]
<dc-1.png, id=602, 1254.6875pt x 714.67pt> <use dc-1.png>
Overfull \hbox (94.86829pt too wide) in paragraph at lines 2449--2450
[][] 
[81] [82 <./dc-1.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2529 ...your version of Linux/Windows/OSX/OS9 
                                                  — well this is where D...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2529 ...ersion of Linux/Windows/OSX/OS9 — 
                                                  well this is where Docker ...

[83] <jn_ss.png, id=632, 2471.2325pt x 1078.0275pt> <use jn_ss.png>
Overfull \hbox (94.84572pt too wide) in paragraph at lines 2565--2566
[][] 
[84]
Overfull \vbox (19.54147pt too high) detected at line 2590
[85 <./jn_ss.png>] <jn_login.png, id=643, 1796.7125pt x 754.82pt>
<use jn_login.png>
Overfull \hbox (94.84164pt too wide) in paragraph at lines 2604--2605
[][] 
[86] <jn_login2.png, id=648, 1852.9225pt x 1009.7725pt> <use jn_login2.png>
Overfull \hbox (94.86247pt too wide) in paragraph at lines 2608--2609
[][] 
[87 <./jn_login.png>] <jn_login3.png, id=655, 2210.2575pt x 1290.8225pt>
<use jn_login3.png>
Overfull \hbox (94.84811pt too wide) in paragraph at lines 2612--2613
[][] 
<jn_login3.5.png, id=656, 2210.2575pt x 1290.8225pt> [88 <./jn_login2.png>]
<use jn_login3.5.png>
Overfull \hbox (94.84811pt too wide) in paragraph at lines 2614--2615
[][] 
[89 <./jn_login3.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2616 ...r compose file. And there you have it 
                                                  — a quick and easy way...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2616 ...ose file. And there you have it — 
                                                  a quick and easy way to st...

<rstudio_ss.png, id=667, 2700.0875pt x 1065.9825pt> <use rstudio_ss.png>
Overfull \hbox (94.8493pt too wide) in paragraph at lines 2626--2627
[][] 
[90 <./jn_login3.5.png>] <rstudio_login2.png, id=675, 1858.945pt x 1144.275pt>
<use rstudio_login2.png>
Overfull \hbox (94.82553pt too wide) in paragraph at lines 2638--2639
[][] 
[91 <./rstudio_ss.png>] <rstudio_login.png, id=682, 2310.6325pt x 1276.77pt>
<use rstudio_login.png>
Overfull \hbox (94.82121pt too wide) in paragraph at lines 2642--2643
[][] 
[92 <./rstudio_login2.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2665 ...te \sphinxcode{requirements.txt} file 
                                                  — Contains python modu...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2665 ...hinxcode{requirements.txt} file — 
                                                  Contains python modules an...

[93 <./rstudio_login.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2677 ...\sphinxcode{app.py} inside the folder 
                                                  — \sphinxcode{scikit\_do...

[94] [95] [96]
Chapter 10.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 2818.

<singularity.png, id=714, 225.84375pt x 225.84375pt> <use singularity.png>
[97 <./singularity.png>]
<singularity-2.4-flow.png, id=725, 3539.2225pt x 1258.7025pt>
<use singularity-2.4-flow.png>
Overfull \hbox (800.25983pt too wide) in paragraph at lines 2862--2863
[][] 
[98 <./singularity-2.4-flow.png>] [99] [100] [101] [102] [103]
Overfull \vbox (7.8273pt too high) detected at line 3244
[104] [105] [106] [107] [108] [109] [110] [111] [112]
Chapter 11.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 3678.

<use singularity.png> [113] [114] [115] [116] [117] [118]
Chapter 12.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 3874.

<f1000.png, id=865, 1006.76125pt x 349.305pt> <use f1000.png>
Overfull \hbox (94.84161pt too wide) in paragraph at lines 3885--3886
[][] 
[119]

LaTeX Warning: Hyper reference `deploying_apps/de_docker:build-and-test-your-do
cker-images' on page 120 undefined on input line 3894.


LaTeX Warning: Hyper reference `deploying_apps/de_docker:push-your-docker-image
-to-public-repositories' on page 120 undefined on input line 3897.

[120 <./f1000.png>]

LaTeX Warning: Hyper reference `deploying_apps/de_docker:add-docker-images-as-t
ool-in-de' on page 121 undefined on input line 3900.


LaTeX Warning: Hyper reference `deploying_apps/de_docker:create-a-ui-for-the-to
ol-in-de' on page 121 undefined on input line 3903.


LaTeX Warning: Hyper reference `deploying_apps/de_docker:test-the-app-using-app
ropriate-test-data' on page 121 undefined on input line 3906.

[121] <img_building_1.png, id=892, 2983.145pt x 1445.4pt>
<use img_building_1.png>
Overfull \hbox (94.818pt too wide) in paragraph at lines 3990--3991
[][] 
[122 <./img_building_1.png>]
<img_building_4.png, id=899, 1761.58125pt x 904.37875pt>
<use img_building_4.png>
Overfull \hbox (94.84953pt too wide) in paragraph at lines 4015--4016
[][] 
[123] <img_building_3.png, id=905, 2983.145pt x 1445.4pt>
<use img_building_3.png>
Overfull \hbox (94.818pt too wide) in paragraph at lines 4023--4026
[][]
[124 <./img_building_4.png>] [125 <./img_building_3.png>] [126]
Chapter 13.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 4038.

[127] [128]
Chapter 14.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 4081.

[129] [130]
Chapter 15.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 4101.

[131] [132]
Chapter 16.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 4123.


Underfull \hbox (badness 10000) in paragraph at lines 1--4171
[]\T1/pcr/m/n/10 git clone https://github.com/CyVerse-learning-materials/
[133] <static_site_docker2.png, id=996, 1858.945pt x 1184.425pt>
<use static_site_docker2.png>
Overfull \hbox (94.82553pt too wide) in paragraph at lines 4217--4218
[][] 
[134] [135 <./static_site_docker2.png>] [136]
Chapter 17.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 4230.

No file CyVerseDocumentation.ind.
[137] (./CyVerseDocumentation.aux)

Package rerunfilecheck Warning: File `CyVerseDocumentation.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.


LaTeX Warning: There were undefined references.


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/ucrb8a
.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/helvetic/uhvb8a.pfb></usr/share/texlive/texmf-dist/f
onts/type1/urw/helvetic/uhvbo8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on CyVerseDocumentation.pdf (141 pages, 7258008 bytes).
Transcript written on CyVerseDocumentation.log.

[rtd-command-info] start-time: 2018-04-25T21:07:19.496321Z, end-time: 2018-04-25T21:07:19.626596Z, duration: 0, exit-code: 0
makeindex -s python.ist CyVerseDocumentation.idx
This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support).
Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored).
Scanning input file CyVerseDocumentation.idx...done (0 entries accepted, 0 rejected).
Nothing written in CyVerseDocumentation.ind.
Transcript written in CyVerseDocumentation.ilg.

[rtd-command-info] start-time: 2018-04-25T21:07:19.696759Z, end-time: 2018-04-25T21:07:31.743854Z, duration: 12, exit-code: 0
pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/_build/latex/CyVerseDocumentation.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

(/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-works
hop-2018/checkouts/latest/_build/latex/CyVerseDocumentation.tex
LaTeX2e <2016/02/01>
Babel <3.9q> and hyphenation patterns for 81 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2017/03/26 v1.6 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-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.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/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty))))
(/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/etoolbox/etoolbox.sty)

 Package Sphinx Info: 
 **** titlesec 2.10.1 successfully patched for bugfix ****

(/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/latexconfig/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)
(./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/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))

Package hyperref Message: Driver (autodetected): hpdftex.

(/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 CyVerseDocumentation.idx
(./CyVerseDocumentation.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/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))
(./CyVerseDocumentation.out) (./CyVerseDocumentation.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] (./CyVerseDocumentation.toc) [1]
[2] <cyverse_rgb.png, id=114, 1093.686pt x 238.0092pt> <use cyverse_rgb.png>
[1 <./cyverse_rgb.png>] [2]
Chapter 1.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 75.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4]
Chapter 2.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 136.


Underfull \hbox (badness 7344) in paragraph at lines 155--159
\T1/ptm/m/n/10 We \T1/ptm/b/n/10 strongly rec-om-mend \T1/ptm/m/n/10 Fire-
[5]
Underfull \hbox (badness 5189) in paragraph at lines 2--287
[][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber-
[6] [7] [8]
Chapter 3.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 304.


Underfull \hbox (badness 5802) in paragraph at lines 329--330
[]|\T1/ptm/m/n/10 General in-tro-duc-tion to

Underfull \hbox (badness 6675) in paragraph at lines 336--337
\T1/ptm/m/n/10 tainer tech-nol-ogy land-

Underfull \hbox (badness 6675) in paragraph at lines 378--379
\T1/ptm/m/n/10 af-ter-noon ses-sion plan-

Underfull \hbox (badness 10000) in paragraph at lines 383--384
[]|\T1/ptm/m/n/10 BYOD/A (Hands-on

Underfull \hbox (badness 10000) in paragraph at lines 2--394
[]|[][]\T1/ptm/m/n/10 Singularity Overview

Underfull \hbox (badness 10000) in paragraph at lines 397--398
[]|\T1/ptm/m/n/10 Singularity setup (CK

Underfull \hbox (badness 10000) in paragraph at lines 414--415
[]|\T1/ptm/m/n/10 Introductory Sin-gu-lar-ity

Underfull \hbox (badness 10000) in paragraph at lines 435--436
[]|\T1/ptm/m/n/10 Advanced Sin-gu-lar-ity

Underfull \hbox (badness 6675) in paragraph at lines 442--443
\T1/ptm/m/n/10 af-ter-noon ses-sion plan-

Underfull \hbox (badness 10000) in paragraph at lines 447--448
[]|\T1/ptm/m/n/10 BYOD/A (Hands-on
[9] [10]
Chapter 4.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 455.

[11] [12]
Chapter 5.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 489.

[13] [14]
Chapter 6.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 510.

[15] [16]
Chapter 7.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 531.

<atmo-1.png, id=238, 974.64125pt x 561.09625pt> <use atmo-1.png>
Overfull \hbox (94.8532pt too wide) in paragraph at lines 553--554
[][] 
[17] <atmo_cp0.png, id=245, 1310.8975pt x 220.825pt> <use atmo_cp0.png>
Overfull \hbox (94.84006pt too wide) in paragraph at lines 572--573
[][] 
[18 <./atmo-1.png>] <atmo_cp.png, id=252, 1698.345pt x 1411.2725pt>
<use atmo_cp.png>
Overfull \hbox (94.84691pt too wide) in paragraph at lines 579--580
[][] 
[19 <./atmo_cp0.png>] <atmo_launch0.png, id=258, 1303.87125pt x 406.51875pt>
<use atmo_launch0.png>
Overfull \hbox (94.8579pt too wide) in paragraph at lines 595--596
[][] 
[20 <./atmo_cp.png>] <atmo_launch1.png, id=265, 2244.385pt x 1274.7625pt>
<use atmo_launch1.png>
Overfull \hbox (94.83301pt too wide) in paragraph at lines 602--603
[][] 
[21 <./atmo_launch0.png>] <atmo_launch.png, id=272, 2198.2125pt x 1531.7225pt>
<use atmo_launch.png>
Overfull \hbox (94.82356pt too wide) in paragraph at lines 612--613
[][] 
[22 <./atmo_launch1.png>] <atmo-6.png, id=278, 1119.18124pt x 663.47874pt>
<use atmo-6.png>
Overfull \hbox (94.87204pt too wide) in paragraph at lines 622--623
[][] 
[23 <./atmo_launch.png>] <atmo-7.png, id=284, 1041.8925pt x 615.29875pt>
<use atmo-7.png>
Overfull \hbox (94.84581pt too wide) in paragraph at lines 632--633
[][] 
[24 <./atmo-6.png>] <atmo-8.png, id=290, 1764.5925pt x 1174.3875pt>
<use atmo-8.png>
Overfull \hbox (94.84535pt too wide) in paragraph at lines 644--645
[][] 
[25 <./atmo-7.png>] <atmo-9.png, id=297, 1774.63pt x 1499.6025pt>
<use atmo-9.png>
Overfull \hbox (94.8346pt too wide) in paragraph at lines 651--652
[][] 
[26 <./atmo-8.png>] [27 <./atmo-9.png>] [28]
Chapter 8.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 658.

<docker.png, id=313, 289.08pt x 97.8054pt> <use docker.png>
Overfull \hbox (94.87941pt too wide) in paragraph at lines 660--661
[] 
[29]
Overfull \vbox (136.83218pt too high) has occurred while \output is active
[30 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [31]
Overfull \vbox (1.82733pt too high) detected at line 771
[32] [33] [34]

! Package inputenc Error: Unicode char ☺ (U+263A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.882 ...to answer any of these questions yet! ☺
                                                   In this case, the client ...

<static_site_docker.png, id=359, 1858.945pt x 1184.425pt>
<use static_site_docker.png>
Overfull \hbox (94.82553pt too wide) in paragraph at lines 942--943
[][] 
[35] <static_site_docker1.png, id=364, 2244.385pt x 1274.7625pt>
<use static_site_docker1.png>
Overfull \hbox (94.83301pt too wide) in paragraph at lines 949--950
[][] 
[36 <./static_site_docker.png>]
Underfull \hbox (badness 10000) in paragraph at lines 951--953
\T1/pcr/m/n/10 Docker host. However if you want to assign a fixed port then you
 can use \TS1/pcr/m/n/10 ``\T1/pcr/m/n/10 -p

Underfull \hbox (badness 10000) in paragraph at lines 961--962
[]\T1/ptm/m/n/10 If you are run-ning Docker on At-mo-sphere/Jetstream or on any
 other cloud, you can open
[37 <./static_site_docker1.png>] [38]
Underfull \vbox (badness 1184) detected at line 1054

Overfull \vbox (3.56996pt too high) detected at line 1054
[39] [40] [41]
Overfull \vbox (1.36995pt too high) detected at line 1236
[42] [43]
Underfull \hbox (badness 10000) in paragraph at lines 1290--1292
\T1/ptm/b/n/10 Note:  \T1/ptm/m/n/10 When you run the \T1/pcr/m/n/10 docker bui
ld \T1/ptm/m/n/10 com-mand given be-low, make sure to re-place

Overfull \vbox (2.56995pt too high) detected at line 1355
[44] <catpic-1.png, id=428, 2041.6275pt x 1371.1225pt> <use catpic-1.png>
Overfull \hbox (94.85628pt too wide) in paragraph at lines 1373--1374
[][] 
[45] [46 <./catpic-1.png>] [47]
<portainer_demo.png, id=453, 2294.5725pt x 1419.3025pt>
<use portainer_demo.png>
Overfull \hbox (94.81851pt too wide) in paragraph at lines 1479--1480
[][] 
[48] [49 <./portainer_demo.png>] <pwd.png, id=468, 2495.3225pt x 1640.1275pt>
<use pwd.png>
Overfull \hbox (94.82858pt too wide) in paragraph at lines 1495--1496
[][] 
[50 <./pwd.png>]
Chapter 9.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 1498.

[51] <docker_image.png, id=487, 2142.0025pt x 1202.4925pt>
<use docker_image.png>
Overfull \hbox (94.866pt too wide) in paragraph at lines 1580--1581
[][] 
[52] [53 <./docker_image.png>]
<private_registry.png, id=503, 2045.6425pt x 1059.96pt>
<use private_registry.png>
Overfull \hbox (94.84293pt too wide) in paragraph at lines 1619--1620
[][] 
[54]
Overfull \vbox (8.54036pt too high) detected at line 1633
[55 <./private_registry.png>] [56]
<auto_build-1.png, id=527, 2637.855pt x 1481.535pt> <use auto_build-1.png>
Overfull \hbox (94.83699pt too wide) in paragraph at lines 1731--1732
[][] 
[57] [58 <./auto_build-1.png>]
<create_repo.png, id=547, 2953.0325pt x 1674.255pt> <use create_repo.png>
Overfull \hbox (94.84164pt too wide) in paragraph at lines 1779--1780
[][] 
[59] <create_repo2.png, id=553, 2834.59pt x 758.835pt> <use create_repo2.png>
Overfull \hbox (94.81732pt too wide) in paragraph at lines 1787--1788
[][] 
[60 <./create_repo.png>]
Overfull \vbox (1.54773pt too high) detected at line 1801
[61 <./create_repo2.png>] <auto_build-2.png, id=565, 2115.905pt x 1330.9725pt>
<use auto_build-2.png>
Overfull \hbox (94.83147pt too wide) in paragraph at lines 1823--1824
[][] 
[62] <auto_build-2.1.png, id=572, 2115.905pt x 1330.9725pt>
<use auto_build-2.1.png>
Overfull \hbox (94.83147pt too wide) in paragraph at lines 1835--1836
[][] 
[63 <./auto_build-2.png>] [64 <./auto_build-2.1.png>]
<auto_build-5.png, id=585, 1152.305pt x 738.76pt> <use auto_build-5.png>
Overfull \hbox (94.86179pt too wide) in paragraph at lines 1881--1882
[][] 
[65] <auto_build-6.png, id=592, 1213.53375pt x 655.44875pt>
<use auto_build-6.png>
Overfull \hbox (94.84714pt too wide) in paragraph at lines 1889--1890
[][] 
[66 <./auto_build-5.png>]
<auto_build-7.png, id=598, 1213.53375pt x 655.44875pt> <use auto_build-7.png>
Overfull \hbox (94.84714pt too wide) in paragraph at lines 1905--1906
[][] 
[67 <./auto_build-6.png>] [68 <./auto_build-7.png>]
<volumes.png, id=612, 503.8825pt x 255.95625pt> <use volumes.png>
Overfull \hbox (94.85095pt too wide) in paragraph at lines 1947--1948
[][] 
[69] [70 <./volumes.png>] [71] [72]
<bind_mount.png, id=636, 503.8825pt x 256.96pt> <use bind_mount.png>
Overfull \hbox (94.85095pt too wide) in paragraph at lines 2121--2122
[][] 
[73] [74 <./bind_mount.png>] [75]
<tmpfs.png, id=654, 502.87875pt x 259.97125pt> <use tmpfs.png>
Overfull \hbox (94.84653pt too wide) in paragraph at lines 2206--2207
[][] 
[76] [77 <./tmpfs.png>] [78] [79] [80]
<dc-1.png, id=685, 1254.6875pt x 714.67pt> <use dc-1.png>
Overfull \hbox (94.86829pt too wide) in paragraph at lines 2449--2450
[][] 
[81] [82 <./dc-1.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2529 ...your version of Linux/Windows/OSX/OS9 
                                                  — well this is where D...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2529 ...ersion of Linux/Windows/OSX/OS9 — 
                                                  well this is where Docker ...

[83] <jn_ss.png, id=716, 2471.2325pt x 1078.0275pt> <use jn_ss.png>
Overfull \hbox (94.84572pt too wide) in paragraph at lines 2565--2566
[][] 
[84]
Overfull \vbox (19.54147pt too high) detected at line 2590
[85 <./jn_ss.png>] <jn_login.png, id=727, 1796.7125pt x 754.82pt>
<use jn_login.png>
Overfull \hbox (94.84164pt too wide) in paragraph at lines 2604--2605
[][] 
[86] <jn_login2.png, id=732, 1852.9225pt x 1009.7725pt> <use jn_login2.png>
Overfull \hbox (94.86247pt too wide) in paragraph at lines 2608--2609
[][] 
[87 <./jn_login.png>] <jn_login3.png, id=739, 2210.2575pt x 1290.8225pt>
<use jn_login3.png>
Overfull \hbox (94.84811pt too wide) in paragraph at lines 2612--2613
[][] 
<jn_login3.5.png, id=740, 2210.2575pt x 1290.8225pt> [88 <./jn_login2.png>]
<use jn_login3.5.png>
Overfull \hbox (94.84811pt too wide) in paragraph at lines 2614--2615
[][] 
[89 <./jn_login3.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2616 ...r compose file. And there you have it 
                                                  — a quick and easy way...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2616 ...ose file. And there you have it — 
                                                  a quick and easy way to st...

<rstudio_ss.png, id=751, 2700.0875pt x 1065.9825pt> <use rstudio_ss.png>
Overfull \hbox (94.8493pt too wide) in paragraph at lines 2626--2627
[][] 
[90 <./jn_login3.5.png>] <rstudio_login2.png, id=759, 1858.945pt x 1144.275pt>
<use rstudio_login2.png>
Overfull \hbox (94.82553pt too wide) in paragraph at lines 2638--2639
[][] 
[91 <./rstudio_ss.png>] <rstudio_login.png, id=766, 2310.6325pt x 1276.77pt>
<use rstudio_login.png>
Overfull \hbox (94.82121pt too wide) in paragraph at lines 2642--2643
[][] 
[92 <./rstudio_login2.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2665 ...te \sphinxcode{requirements.txt} file 
                                                  — Contains python modu...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2665 ...hinxcode{requirements.txt} file — 
                                                  Contains python modules an...

[93 <./rstudio_login.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.2677 ...\sphinxcode{app.py} inside the folder 
                                                  — \sphinxcode{scikit\_do...

[94] [95] [96]
Chapter 10.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 2818.

<singularity.png, id=798, 225.84375pt x 225.84375pt> <use singularity.png>
[97 <./singularity.png>]
<singularity-2.4-flow.png, id=807, 3539.2225pt x 1258.7025pt>
<use singularity-2.4-flow.png>
Overfull \hbox (800.25983pt too wide) in paragraph at lines 2862--2863
[][] 
[98 <./singularity-2.4-flow.png>] [99] [100] [101] [102] [103]
Overfull \vbox (7.8273pt too high) detected at line 3244
[104] [105] [106] [107] [108] [109] [110] [111] [112]
Chapter 11.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 3678.

<use singularity.png> [113] [114] [115] [116] [117] [118]
Chapter 12.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 3874.

<f1000.png, id=946, 1006.76125pt x 349.305pt> <use f1000.png>
Overfull \hbox (94.84161pt too wide) in paragraph at lines 3885--3886
[][] 
[119] [120 <./f1000.png>] [121]
<img_building_1.png, id=980, 2983.145pt x 1445.4pt> <use img_building_1.png>
Overfull \hbox (94.818pt too wide) in paragraph at lines 3990--3991
[][] 
[122 <./img_building_1.png>]
<img_building_4.png, id=986, 1761.58125pt x 904.37875pt>
<use img_building_4.png>
Overfull \hbox (94.84953pt too wide) in paragraph at lines 4015--4016
[][] 
[123] <img_building_3.png, id=992, 2983.145pt x 1445.4pt>
<use img_building_3.png>
Overfull \hbox (94.818pt too wide) in paragraph at lines 4023--4026
[][]
[124 <./img_building_4.png>] [125 <./img_building_3.png>] [126]
Chapter 13.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 4038.

[127] [128]
Chapter 14.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 4081.

[129] [130]
Chapter 15.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 4101.

[131] [132]
Chapter 16.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 4123.


Underfull \hbox (badness 10000) in paragraph at lines 1--4171
[]\T1/pcr/m/n/10 git clone https://github.com/CyVerse-learning-materials/
[133] <static_site_docker2.png, id=1077, 1858.945pt x 1184.425pt>
<use static_site_docker2.png>
Overfull \hbox (94.82553pt too wide) in paragraph at lines 4217--4218
[][] 
[134] [135 <./static_site_docker2.png>] [136]
Chapter 17.

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `\sphinxstylestrong' on input line 4230.

(./CyVerseDocumentation.ind) [137] (./CyVerseDocumentation.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/ucrb8a
.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/helvetic/uhvb8a.pfb></usr/share/texlive/texmf-dist/f
onts/type1/urw/helvetic/uhvbo8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on CyVerseDocumentation.pdf (141 pages, 7174717 bytes).
Transcript written on CyVerseDocumentation.log.

[rtd-command-info] start-time: 2018-04-25T21:07:31.857518Z, end-time: 2018-04-25T21:07:31.934910Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/_build/latex/CyVerseDocumentation.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/artifacts/latest/sphinx_pdf/cyverse-astrocontainers-workshop-2018.pdf


[rtd-command-info] start-time: 2018-04-25T21:07:32.010361Z, end-time: 2018-04-25T21:07:34.986184Z, duration: 2, exit-code: 0
python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub
Running Sphinx v1.6.5
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 [epub]: targets for 18 source files that are out of date
updating environment: 18 added, 0 changed, 0 removed
reading sources... [  5%] atmosphere/boot
reading sources... [ 11%] deploying_apps/de_docker
reading sources... [ 16%] docker/dockeradvanced
reading sources... [ 22%] docker/dockerintro
reading sources... [ 27%] getting_started/about_cyverse
reading sources... [ 33%] getting_started/agenda
reading sources... [ 38%] getting_started/installation
reading sources... [ 44%] getting_started/main
reading sources... [ 50%] index
reading sources... [ 55%] instructions_reporting/instructors
reading sources... [ 61%] instructions_reporting/problems
reading sources... [ 66%] singularity/singularityadvanced
reading sources... [ 72%] singularity/singularityintro
reading sources... [ 77%] topics/train_docker
reading sources... [ 83%] topics/train_singularity
reading sources... [ 88%] useful_resources/usefulresources_docker
reading sources... [ 94%] useful_resources/usefulresources_other
reading sources... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "github".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  5%] atmosphere/boot
writing output... [ 11%] deploying_apps/de_docker
writing output... [ 16%] docker/dockeradvanced
writing output... [ 22%] docker/dockerintro
writing output... [ 27%] getting_started/about_cyverse
writing output... [ 33%] getting_started/agenda
writing output... [ 38%] getting_started/installation
writing output... [ 44%] getting_started/main
writing output... [ 50%] index
writing output... [ 55%] instructions_reporting/instructors
writing output... [ 61%] instructions_reporting/problems
writing output... [ 66%] singularity/singularityadvanced
writing output... [ 72%] singularity/singularityintro
writing output... [ 77%] topics/train_docker
writing output... [ 83%] topics/train_singularity
writing output... [ 88%] useful_resources/usefulresources_docker
writing output... [ 94%] useful_resources/usefulresources_other
writing output... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:40: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:104: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
generating indices... genindex
writing additional pages...
copying images... [  2%] docker/../img/tmpfs.png
copying images... [  4%] docker/../img/auto_build-1.png
copying images... [  6%] docker/../img/bind_mount.png
copying images... [  8%] atmosphere/../img/atmo-1.png
copying images... [ 10%] docker/../img/create_repo2.png
copying images... [ 12%] docker/../img/docker_image.png
copying images... [ 14%] docker/../img/dc-1.png
copying images... [ 16%] docker/../img/rstudio_login.png
copying images... [ 18%] docker/../img/static_site_docker1.png
copying images... [ 20%] deploying_apps/../img/f1000.png
copying images... [ 22%] atmosphere/../img/atmo_cp.png
copying images... [ 24%] docker/../img/auto_build-3.png
copying images... [ 26%] instructions_reporting/../img/static_site_docker.png
copying images... [ 28%] docker/../img/auto_build-2.png
copying images... [ 30%] docker/../img/create_repo.png
copying images... [ 32%] docker/../img/portainer_demo.png
copying images... [ 34%] docker/../img/rstudio_login2.png
copying images... [ 36%] docker/../img/volumes.png
copying images... [ 38%] docker/../img/jn_login.png
copying images... [ 40%] docker/../img/static_site_docker.png
copying images... [ 42%] atmosphere/../img/atmo-6.png
copying images... [ 44%] docker/../img/auto_build-4.png
copying images... [ 46%] docker/../img/pwd.png
copying images... [ 48%] docker/../img/auto_build-6.png
copying images... [ 51%] docker/../img/auto_build-7.png
copying images... [ 53%] atmosphere/../img/atmo_cp0.png
copying images... [ 55%] atmosphere/../img/atmo-9.png
copying images... [ 57%] docker/../img/jn_login2.png
copying images... [ 59%] docker/../img/private_registry.png
copying images... [ 61%] docker/../img/catpic-1.png
copying images... [ 63%] docker/../img/rstudio_ss.png
copying images... [ 65%] docker/../img/jn_login3.png
copying images... [ 67%] singularity/../img/singularity.png
copying images... [ 69%] docker/../img/jn_login3.5.png
copying images... [ 71%] deploying_apps/../img/img_building_1.png
copying images... [ 73%] docker/../img/docker.png
copying images... [ 75%] atmosphere/../img/atmo_launch0.png
copying images... [ 77%] atmosphere/../img/atmo_launch1.png
copying images... [ 79%] atmosphere/../img/atmo-7.png
copying images... [ 81%] http://singularity.lbl.gov/assets/img/diagram/singularity-2.4-flow.png
copying images... [ 83%] docker/../img/jn_login4.png
copying images... [ 85%] docker/../img/auto_build-5.png
copying images... [ 87%] docker/../img/auto_build-2.1.png
copying images... [ 89%] atmosphere/../img/atmo-8.png
copying images... [ 91%] getting_started/../img/cyverse_rgb.png
copying images... [ 93%] deploying_apps/../img/img_building_3.png
copying images... [ 95%] docker/../img/jn_ss.png
copying images... [ 97%] deploying_apps/../img/img_building_4.png
copying images... [100%] atmosphere/../img/atmo_launch.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/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
writing mimetype file...
writing META-INF/container.xml file...
writing content.opf file...
writing nav.xhtml file...
writing toc.ncx file...
writing CyVerseAstroContainersWorkshopLearningDockerandSingularity.epub file...
build succeeded, 7 warnings.

[rtd-command-info] start-time: 2018-04-25T21:07:35.087752Z, end-time: 2018-04-25T21:07:35.153062Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/_build/epub/CyVerseAstroContainersWorkshopLearningDockerandSingularity.epub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/artifacts/latest/sphinx_epub/cyverse-astrocontainers-workshop-2018.epub