Read the Docs build information Build id: 173108 Project: cyverse-atmosphere-guide Version: latest Commit: 2a494c3b94d5288867027305707e7eb077793616 Date: 2019-01-09T21:48:49.618994Z State: finished Success: True [rtd-command-info] start-time: 2019-01-09T21:50:31.124856Z, end-time: 2019-01-09T21:50:31.724505Z, duration: 0, exit-code: 0 git clone --depth 50 --no-single-branch https://github.com/CyVerse-learning-materials/atmosphere_guide.git . Cloning into '.'... [rtd-command-info] start-time: 2019-01-09T21:50:31.887640Z, end-time: 2019-01-09T21:50:31.945137Z, 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 HEAD is now at 2a494c3 Add files via upload [rtd-command-info] start-time: 2019-01-09T21:50:32.006806Z, end-time: 2019-01-09T21:50:32.013773Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-01-09T21:50:32.745631Z, end-time: 2019-01-09T21:50:34.621903Z, 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-atmosphere-guide/envs/latest/bin/python2.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/envs/latest/bin/python Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2019-01-09T21:50:34.693158Z, end-time: 2019-01-09T21:50:36.722553Z, duration: 2, exit-code: 0 python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip pip Collecting pip Downloading https://files.pythonhosted.org/packages/c2/d7/90f34cb0d83a6c5631cf71dfe64cc1054598c843a92b400e55675cc2ac37/pip-18.1-py2.py3-none-any.whl (1.3MB) Installing collected packages: pip Found existing installation: pip 9.0.1 Uninstalling pip-9.0.1: Successfully uninstalled pip-9.0.1 Successfully installed pip-18.1 [rtd-command-info] start-time: 2019-01-09T21:50:36.780176Z, end-time: 2019-01-09T21:50:55.994634Z, duration: 19, exit-code: 0 python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.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<1.8 sphinx-rtd-theme<0.5 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/7f/e1/820d941153923aac1d49d7fc37e17b6e73bfbd2904959fffbad77900cf92/setuptools-39.2.0-py2.py3-none-any.whl (567kB) 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/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-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<1.8 Downloading https://files.pythonhosted.org/packages/90/f9/a0babe32c78480994e4f1b93315558f5ed756104054a7029c672a8d77b72/Sphinx-1.7.9-py2.py3-none-any.whl (1.9MB) Collecting sphinx-rtd-theme<0.5 Downloading https://files.pythonhosted.org/packages/ef/0c/e4a462190506bc4bff6ca8cf93da07b2d13e540466d2e8a760352d0c69b0/sphinx_rtd_theme-0.4.2-py2.py3-none-any.whl (6.4MB) Collecting readthedocs-sphinx-ext<0.6 Downloading https://files.pythonhosted.org/packages/a5/19/abebb2ac7554119cc56d77ce03abcb17b200d6cc3b04dce05cd31248f06f/readthedocs_sphinx_ext-0.5.16-py2.py3-none-any.whl Collecting sphinxcontrib-websupport (from sphinx<1.8) Downloading https://files.pythonhosted.org/packages/52/69/3c2fbdc3702358c5b34ee25e387b24838597ef099761fc9a42c166796e8f/sphinxcontrib_websupport-1.1.0-py2.py3-none-any.whl Collecting six>=1.5 (from sphinx<1.8) Downloading https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl Collecting requests>=2.0.0 (from sphinx<1.8) Downloading https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl (57kB) Collecting packaging (from sphinx<1.8) Downloading https://files.pythonhosted.org/packages/89/d1/92e6df2e503a69df9faab187c684585f0136662c12bb1f36901d426f3fab/packaging-18.0-py2.py3-none-any.whl Collecting typing; python_version < "3.5" (from sphinx<1.8) Downloading https://files.pythonhosted.org/packages/cc/3e/29f92b7aeda5b078c86d14f550bf85cff809042e3429ace7af6193c3bc9f/typing-3.6.6-py2-none-any.whl Collecting imagesize (from sphinx<1.8) Downloading https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 (from sphinx<1.8) Downloading https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl (8.1MB) Collecting snowballstemmer>=1.1 (from sphinx<1.8) 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<1.8) Downloading https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl (126kB) Collecting urllib3<1.25,>=1.21.1 (from requests>=2.0.0->sphinx<1.8) Downloading https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl (118kB) Collecting idna<2.9,>=2.5 (from requests>=2.0.0->sphinx<1.8) Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB) Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx<1.8) 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<1.8) Downloading https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl (154kB) Collecting pyparsing>=2.0.2 (from packaging->sphinx<1.8) Downloading https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl (59kB) Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx<1.8) Downloading https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl (510kB) Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<1.8) Downloading https://files.pythonhosted.org/packages/bc/3a/6bfd7b4b202fa33bdda8e4e3d3acc719f381fd730f9a0e7c5f34e845bd4d/MarkupSafe-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl Building wheels for collected packages: mock, pillow, commonmark 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-atmosphere-guide/.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-atmosphere-guide/.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-atmosphere-guide/.cache/pip/wheels/a0/f4/35/019d917f6875107ade3aad634c982f5c6b604c5631cddf20ac Successfully built mock pillow commonmark Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, sphinxcontrib-websupport, six, urllib3, idna, chardet, certifi, requests, pyparsing, packaging, typing, imagesize, pytz, babel, snowballstemmer, MarkupSafe, Jinja2, sphinx, sphinx-rtd-theme, 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-1.1.0 Pygments-2.2.0 alabaster-0.7.12 babel-2.6.0 certifi-2018.11.29 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-18.0 pillow-2.6.1 pyparsing-2.3.0 pytz-2018.9 readthedocs-sphinx-ext-0.5.16 recommonmark-0.4.0 requests-2.21.0 setuptools-39.2.0 six-1.12.0 snowballstemmer-1.2.1 sphinx-1.7.9 sphinx-rtd-theme-0.4.2 sphinxcontrib-websupport-1.1.0 typing-3.6.6 urllib3-1.24.1 [rtd-command-info] start-time: 2019-01-09T21:50:56.605823Z, end-time: 2019-01-09T21:50:56.664973Z, 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 = 'Atmosphere Guide' copyright = '2017, CyVerse' author = 'CyVerse' version = '1.0' release = '1.0' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib 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 = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("htmlzip", "//readthedocs.com/projects/cyverse-atmosphere-guide/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-atmosphere-guide', 'name': u'atmosphere_guide', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/projects/atmosphere-guide/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'atmosphere_guide', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '2a494c3b', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] [rtd-command-info] start-time: 2019-01-09T21:50:56.724355Z, end-time: 2019-01-09T21:50:58.187909Z, duration: 1, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.7.9 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 10 source files that are out of date updating environment: 10 added, 0 changed, 0 removed reading sources... [ 10%] Contributors_maintainers reading sources... [ 20%] License reading sources... [ 30%] README reading sources... [ 40%] index reading sources... [ 50%] slides/README reading sources... [ 60%] step1 reading sources... [ 70%] step2 reading sources... [ 80%] step3 reading sources... [ 90%] step4 reading sources... [100%] step5 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step4.rst:8: WARNING: Title underline too short. **Transferring Data to and from an Instance** -------------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step4.rst:8: WARNING: Duplicate explicit target name: "link". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/slides/README.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 10%] Contributors_maintainers writing output... [ 20%] License writing output... [ 30%] README writing output... [ 40%] index writing output... [ 50%] slides/README writing output... [ 60%] step1 writing output... [ 70%] step2 writing output... [ 80%] step3 writing output... [ 90%] step4 writing output... [100%] step5 generating indices... genindex writing additional pages... search copying images... [ 12%] ./img/atmosphere/atmosphere-icon.png copying images... [ 25%] ./img/atmosphere/project_icon.png copying images... [ 37%] ./img/atmosphere/vnc_desktop.png copying images... [ 50%] ./img/atmosphere/launch_window.png copying images... [ 62%] ./img/cyverse_rgb.png copying images... [ 75%] ./img/atmosphere/instance_status.png copying images... [ 87%] ./img/atmosphere/need_more.png copying images... [100%] ./img/homeicon.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 8 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2019-01-09T21:50:58.276227Z, end-time: 2019-01-09T21:50:59.499386Z, duration: 1, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.7.9 loading translations [en]... done making output directory... loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 10 added, 0 changed, 0 removed reading sources... [ 10%] Contributors_maintainers reading sources... [ 20%] License reading sources... [ 30%] README reading sources... [ 40%] index reading sources... [ 50%] slides/README reading sources... [ 60%] step1 reading sources... [ 70%] step2 reading sources... [ 80%] step3 reading sources... [ 90%] step4 reading sources... [100%] step5 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step4.rst:8: WARNING: Title underline too short. **Transferring Data to and from an Instance** -------------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step4.rst:8: WARNING: Duplicate explicit target name: "link". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/slides/README.md: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... step1 step2 step3 step4 step5 writing... done writing additional files... copying images... [ 12%] ./img/atmosphere/atmosphere-icon.png copying images... [ 25%] ./img/atmosphere/project_icon.png copying images... [ 37%] ./img/atmosphere/vnc_desktop.png copying images... [ 50%] ./img/atmosphere/launch_window.png copying images... [ 62%] ./img/cyverse_rgb.png copying images... [ 75%] ./img/atmosphere/instance_status.png copying images... [ 87%] ./img/atmosphere/need_more.png copying images... [100%] ./img/homeicon.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 8 warnings. The HTML page is in _build/localmedia.