Read the Docs build information Build id: 147112 Project: cyverse-visual-interactive-computing-environment Version: latest Commit: e7f1e028b7c2c7a70feff1a5decf8896fb5b54f3 Date: 2018-10-03T20:30:58.430613Z State: finished Success: True [rtd-command-info] start-time: 2018-10-04T01:30:59.011035Z, end-time: 2018-10-04T01:30:59.021185Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/Visual_Interactive_Computing_Environment.git [rtd-command-info] start-time: 2018-10-04T01:30:59.077709Z, end-time: 2018-10-04T01:30:59.357053Z, duration: 0, exit-code: 0 git fetch --tags --prune From https://github.com/CyVerse-learning-materials/Visual_Interactive_Computing_Environment a3da245..e7f1e02 master -> origin/master [rtd-command-info] start-time: 2018-10-04T01:30:59.427692Z, end-time: 2018-10-04T01:30:59.460018Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was a3da245... added draft VICE diagram HEAD is now at e7f1e02... Update about.rst [rtd-command-info] start-time: 2018-10-04T01:30:59.516234Z, end-time: 2018-10-04T01:30:59.536716Z, duration: 0, exit-code: 0 git clean -d -f -f Removing misc/__init__.pyc Removing misc/cyverse_sphinx_conf.pyc [rtd-command-info] start-time: 2018-10-04T01:30:59.631107Z, end-time: 2018-10-04T01:30:59.637746Z, duration: 0, exit-code: 0 git branch -r origin/HEAD -> origin/master origin/master [rtd-command-info] start-time: 2018-10-04T01:31:00.341121Z, end-time: 2018-10-04T01:31:01.981119Z, 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-visual-interactive-computing-environment/envs/latest/bin/python2.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python2.7) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2018-10-04T01:31:02.113286Z, end-time: 2018-10-04T01:31:04.527287Z, duration: 2, exit-code: 0 python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.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 Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: setuptools<40 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: docutils==0.13.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: pillow==2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: commonmark==0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: recommonmark==0.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: sphinx<1.8 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: idna<2.8,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Requirement already up-to-date: urllib3<1.24,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Requirement already up-to-date: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Requirement already up-to-date: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from packaging->sphinx<1.8) Requirement already up-to-date: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx<1.8) Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx<1.8) You are using pip version 9.0.1, however version 18.0 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2018-10-04T01:31:04.647359Z, end-time: 2018-10-04T01:31:05.209792Z, duration: 0, exit-code: 0 python pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.cache/pip -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: recommonmark in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 2)) Requirement already satisfied: sphinxcontrib-images in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 3)) Requirement already satisfied: sphinx_bootstrap_theme in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 4)) Requirement already satisfied: guzzle_sphinx_theme==0.7.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 5)) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: commonmark<=0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from recommonmark->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 2)) Requirement already satisfied: idna<2.8,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: urllib3<1.24,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/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-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from packaging->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) You are using pip version 9.0.1, however version 18.0 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2018-10-04T01:31:05.928299Z, end-time: 2018-10-04T01:31:05.991186Z, duration: 0, exit-code: 0 cat conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # General information about the project. import sys import os sys.path.insert(0, os.path.dirname(__file__)) from misc.cyverse_sphinx_conf import * # noqa project = 'Visual Interactive Computing Environment' copyright = '2018, CyVerse' author = 'CyVerse' version = '1.0' release = '1.0' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright exclude_patterns = ['README.md', 'License.md', 'Contributors_maintainers.md'] ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # 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' 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': [ ("pdf", "//readthedocs.com/projects/cyverse-visual-interactive-computing-environment/downloads/pdf/latest/"), ("htmlzip", "//readthedocs.com/projects/cyverse-visual-interactive-computing-environment/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/cyverse-visual-interactive-computing-environment/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-visual-interactive-computing-environment', 'name': u'Visual_Interactive_Computing_Environment', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-visual-interactive-computing-environment.readthedocs-hosted.com/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/./', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'Visual_Interactive_Computing_Environment', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'e7f1e028', } 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: 2018-10-04T01:31:06.127629Z, end-time: 2018-10-04T01:31:10.639349Z, duration: 4, 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 41 source files that are out of date updating environment: 41 added, 0 changed, 0 removed reading sources... 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[45] Overfull \vbox (136.54112pt too high) has occurred while \output is active [46 <./flow.png>] [47] [48] Chapter 10. [49] [50] Chapter 11. Underfull \hbox (badness 10000) in paragraph at lines 789--789 []\T1/phv/m/n/10 Pre-req-ui- Overfull \hbox (32.78404pt too wide) in paragraph at lines 789--789 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2--789 [][][]\T1/ptm/m/n/10 Reg-is- Underfull \hbox (badness 10000) in paragraph at lines 789--789 []\T1/ptm/m/n/10 Dis-cov-ery Underfull \hbox (badness 10000) in paragraph at lines 789--789 \T1/ptm/m/n/10 En-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 2--789 [][][]\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2--789 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2--789 \T1/ptm/m/n/10 User No file CyVerseDocumentation.ind. [51] (./CyVerseDocumentation.aux) Package rerunfilecheck Warning: File `CyVerseDocumentation.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. 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} Output written on CyVerseDocumentation.pdf (55 pages, 9385480 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2018-10-04T01:31:30.899883Z, end-time: 2018-10-04T01:31:31.027258Z, 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. 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[3] [4] Chapter 2. [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] [7] [8] Chapter 3. Overfull \hbox (57.20361pt too wide) in paragraph at lines 285--286 [][] [9] Overfull \hbox (57.20361pt too wide) in paragraph at lines 292--293 [][] [10 <./jupyter1-1.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 294--295 [][] [11 <./jupyter1-2.png> <./ju pyter1-3.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 301--302 [][] Overfull \hbox (57.20361pt too wide) in paragraph at lines 308--309 [][] [12 <./jupyter1-4.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 315--316 [][] [13 <./jupyter1-5.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 322--323 [][] [14 <./jupyter1-6.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 324--325 [][] [15 <./jupyter1-7.png> <./jupyter1-8.png>] [16] Chapter 4. Overfull \hbox (57.20361pt too wide) in paragraph at lines 358--359 [][] [17] Overfull \hbox (57.20361pt too wide) in paragraph at lines 365--366 [][] [18 <./rstudio1-1.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 367--368 [][] [19 <./rstudio1-2.png> <./rs tudio1-2.5.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 374--375 [][] Overfull \hbox (57.20361pt too wide) in paragraph at lines 381--382 [][] [20 <./rstudio1-3.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 388--389 [][] [21 <./rstudio1-4.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 390--391 [][] [22 <./rstudio1-5.png> <./rs tudio1-6.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 397--398 [][] [23 <./rstudio1-7.p ng>] [24] Chapter 5. Overfull \hbox (57.20361pt too wide) in paragraph at lines 445--446 [][] [25] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 448. 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Overfull \hbox (57.20361pt too wide) in paragraph at lines 484--485 [][] [31 <./shiny1-7.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 491--492 [][] [32 <./shiny1-8.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 498--499 [][] [33 <./shiny1-9.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 500--501 [][] [34 <./shiny1-10.png> <./shin y1-11.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 507--508 [][] Overfull \hbox (57.20361pt too wide) in paragraph at lines 509--510 [][] [35 <./shiny1-12.png>] [36 <./shiny1-13.png>] [37] [38] Chapter 6. [39] [40] Chapter 7. Underfull \hbox (badness 10000) in paragraph at lines 1--643 [][][]$\T1/ptm/m/n/10 https : / / github . com / cyverse-[]de / docker^^\les / tree / master / shiny$[][] [][]$https : / / github . com / cyverse-[]de / docke r^^\les / tree / master / [41] [42] Chapter 8. [43] [44] Chapter 9. [45] Overfull \vbox (136.54112pt too high) has occurred while \output is active [46 <./flow.png>] [47] [48] Chapter 10. [49] [50] Chapter 11. Underfull \hbox (badness 10000) in paragraph at lines 789--789 []\T1/phv/m/n/10 Pre-req-ui- Overfull \hbox (32.78404pt too wide) in paragraph at lines 789--789 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2--789 [][][]\T1/ptm/m/n/10 Reg-is- Underfull \hbox (badness 10000) in paragraph at lines 789--789 []\T1/ptm/m/n/10 Dis-cov-ery Underfull \hbox (badness 10000) in paragraph at lines 789--789 \T1/ptm/m/n/10 En-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 2--789 [][][]\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2--789 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2--789 \T1/ptm/m/n/10 User (./CyVerseDocumentation.ind) [51] (./CyVerseDocumentation.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on CyVerseDocumentation.pdf (55 pages, 9319835 bytes). Transcript written on CyVerseDocumentation.log. 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