Read the Docs build information Build id: 106794 Project: cyverse-astrocontainers-workshop-2018 Version: latest Commit: 735349af90cac379d9a5fb761a221e6764999792 Date: 2018-05-07T14:02:56.093231Z State: finished Success: True [rtd-command-info] start-time: 2018-05-07T19:02:56.559972Z, end-time: 2018-05-07T19:02:56.567763Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/astrocontainers_workshop_2018.git [rtd-command-info] start-time: 2018-05-07T19:02:56.635952Z, end-time: 2018-05-07T19:02:57.136274Z, duration: 0, exit-code: 0 git fetch --tags --prune From https://github.com/CyVerse-learning-materials/astrocontainers_workshop_2018 af65245..735349a master -> origin/master [rtd-command-info] start-time: 2018-05-07T19:02:57.208648Z, end-time: 2018-05-07T19:02:57.216916Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was af65245... Will do data analysis instead of deploying web app HEAD is now at 735349a... Run the HOPS container and bind mount the host data directory [rtd-command-info] start-time: 2018-05-07T19:02:57.285434Z, end-time: 2018-05-07T19:02:57.294030Z, 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: 2018-05-07T19:02:57.383720Z, end-time: 2018-05-07T19:02:57.389937Z, duration: 0, exit-code: 0 git show-ref --tags [rtd-command-info] start-time: 2018-05-07T19:02:57.454973Z, end-time: 2018-05-07T19:02:57.462897Z, duration: 0, exit-code: 0 git branch -r origin/HEAD -> origin/master origin/master [rtd-command-info] start-time: 2018-05-07T19:02:58.282783Z, end-time: 2018-05-07T19:03:00.828312Z, duration: 2, 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 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/bin/python2.7) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2018-05-07T19:03:00.896826Z, end-time: 2018-05-07T19:03:03.416037Z, duration: 2, 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 Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: setuptools<40 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/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-astrocontainers-workshop-2018/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-astrocontainers-workshop-2018/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-astrocontainers-workshop-2018/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-astrocontainers-workshop-2018/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-astrocontainers-workshop-2018/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-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: sphinx==1.6.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: sphinx-rtd-theme<0.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/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-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5) Requirement already up-to-date: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5) Requirement already up-to-date: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5) Requirement already up-to-date: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5) Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5) Requirement already up-to-date: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5) Requirement already up-to-date: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5) Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx==1.6.5) Requirement already up-to-date: nilsimsa>=0.3.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from readthedocs-sphinx-ext<0.6) Requirement already up-to-date: urllib3<1.23,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.6.5) Requirement already up-to-date: idna<2.7,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.6.5) Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.6.5) Requirement already up-to-date: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.6.5) Requirement already up-to-date: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx==1.6.5) Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx==1.6.5) You are using pip version 9.0.1, however version 10.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2018-05-07T19:03:03.493092Z, end-time: 2018-05-07T19:03:04.364227Z, duration: 0, 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)) Requirement already satisfied: sphinxcontrib-images 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 3)) Requirement already satisfied: sphinx_bootstrap_theme 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 4)) Requirement already satisfied: guzzle_sphinx_theme==0.7.11 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 5)) 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)) 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: 2018-05-07T19:03:04.897439Z, end-time: 2018-05-07T19:03:04.965049Z, 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': [ ("pdf", "//readthedocs.com/projects/cyverse-astrocontainers-workshop-2018/downloads/pdf/latest/"), ("htmlzip", "//readthedocs.com/projects/cyverse-astrocontainers-workshop-2018/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/cyverse-astrocontainers-workshop-2018/downloads/epub/latest/"), ], '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': '', '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': '735349af', } 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: 2018-05-07T19:03:05.064017Z, end-time: 2018-05-07T19:03:12.384022Z, duration: 7, 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... 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Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3642. No file CyVerseDocumentation.ind. [111] (./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} Output written on CyVerseDocumentation.pdf (115 pages, 3841124 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2018-05-07T19:03:25.951222Z, end-time: 2018-05-07T19:03:26.078226Z, 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: 2018-05-07T19:03:26.139016Z, end-time: 2018-05-07T19:03:33.772445Z, duration: 7, 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. 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Type H for immediate help. ... l.843 ...to answer any of these questions yet! ☺ In this case, the client ... [24] [25 <./static_site_docker.png>] Underfull \hbox (badness 10000) in paragraph at lines 924--925 []\T1/ptm/m/n/10 If you are run-ning Docker on At-mo-sphere/Jetstream or on any other cloud, you can open [26 <./static_site_docker1.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 for immediate help. ... l.1009 ...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 for immediate help. ... l.1009 ...ersion of Linux/Windows/OSX/OS9 —  well this is where Docker ... [27] Overfull \hbox (57.20003pt too wide) in paragraph at lines 1056--1057 | []| [28] Overfull \hbox (132.50845pt too wide) in paragraph at lines 1060--1061 | []| Overfull \hbox (132.49976pt too wide) in paragraph at lines 1064--1065 | []| [29 <./jn_login.png> <./jn_login2.png>] Overfull \hbox (132.48445pt too wide) in paragraph at lines 1066--1067 | []| ! Package inputenc Error: Unicode char   (U+200A) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1075 ...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 for immediate help. ... l.1075 ...ose file. And there you have it —  a quick and easy way to st... [30 <./jn_login3.png> <./jn_login3.5.png>] Chapter 8. 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[31] Overfull \vbox (11.56995pt too high) detected at line 1152 [32] [33] [34] [35] [36] Underfull \hbox (badness 10000) in paragraph at lines 1388--1390 \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 [37] Overfull \hbox (94.85628pt too wide) in paragraph at lines 1471--1472 [][] [38] [39 <./catpic-1.png>] [40] [41] Overfull \hbox (94.866pt too wide) in paragraph at lines 1616--1617 [][] [42 <./docker_image.png>] Overfull \hbox (94.84293pt too wide) in paragraph at lines 1655--1656 [][] [43] Overfull \vbox (8.54036pt too high) detected at line 1669 [44 <./private_registry.png>] [45] Overfull \hbox (94.83699pt too wide) in paragraph at lines 1767--1768 [][] [46] [47 <./auto_build-1.png>] Overfull \hbox (94.84164pt too wide) in paragraph at lines 1815--1816 [][] [48] Overfull \hbox (94.81732pt too wide) in paragraph at lines 1823--1824 [][] [49 <./create_repo.png>] Overfull \vbox (1.54773pt too high) detected at line 1837 [50 <./create_repo2.png>] Overfull \hbox (94.83147pt too wide) in paragraph at lines 1859--1860 [][] [51] Overfull \hbox (94.83147pt too wide) in paragraph at lines 1871--1872 [][] [52 <./auto_build-2.png>] [53 <./auto_build-2.1.png>] Overfull \hbox (94.86179pt too wide) in paragraph at lines 1917--1918 [][] [54] Overfull \hbox (94.84714pt too wide) in paragraph at lines 1925--1926 [][] [55 <./auto_build-5.png>] Overfull \hbox (94.84714pt too wide) in paragraph at lines 1941--1942 [][] [56 <./auto_build-6.png>] [57 <./auto_build-7.png>] [58] [59] Overfull \hbox (94.86829pt too wide) in paragraph at lines 2167--2168 [][] [60] [61 <./dc-1.png>] [62] Chapter 9. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2187. [63] [64 <./portainer_demo.png>] [65 <./pwd.png>] [66] Chapter 10. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2244. [67 <./singularity.png>] Overfull \hbox (800.25983pt too wide) in paragraph at lines 2288--2289 [][] [68 <./singularity-2.4-flow.png>] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] Chapter 11. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3120. [83] [84] [85] [86] [87] [88] Chapter 12. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3316. Overfull \hbox (94.855pt too wide) in paragraph at lines 3338--3339 [][] [89] Overfull \hbox (94.855pt too wide) in paragraph at lines 3357--3358 [][] [90 <./atmo-1.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3364--3365 [][] [91 <./atmo_cp0.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3380--3381 [][] [92 <./atmo_cp.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3387--3388 [][] [93 <./atmo_launch0.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3397--3398 [][] [94 <./atmo_launch1.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3407--3408 [][] [95 <./atmo_launch.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3420--3421 [][] [96 <./atmo-6.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3436--3437 [][] [97 <./atmo-7.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3443--3444 [][] [98 <./atmo-8.png>] [99 <./atmo-9.png>] [100] Chapter 13. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3450. [101] [102] Chapter 14. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3493. [103] [104] Chapter 15. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3513. [105] [106] Chapter 16. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3535. Underfull \hbox (badness 10000) in paragraph at lines 1--3583 []\T1/pcr/m/n/10 git clone https://github.com/CyVerse-learning-materials/ [107] Overfull \hbox (94.82553pt too wide) in paragraph at lines 3629--3630 [][] [108] [109 <./static_site_docker2.png>] [110] Chapter 17. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3642. (./CyVerseDocumentation.ind) [111] (./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 (115 pages, 3857885 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2018-05-07T19:03:33.847550Z, end-time: 2018-05-07T19:03:33.924307Z, 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: 2018-05-07T19:03:34.013240Z, end-time: 2018-05-07T19:03:35.982044Z, duration: 1, 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... done 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: 0 added, 1 changed, 0 removed reading sources... 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