Read the Docs build information Build id: 106828 Project: cyverse-astrocontainers-workshop-2018 Version: latest Commit: e0cea08b0684ec2b1b1b269c32091cbac321c4e0 Date: 2018-05-07T16:52:51.864908Z State: finished Success: True [rtd-command-info] start-time: 2018-05-07T21:52:52.818619Z, end-time: 2018-05-07T21:52:52.827018Z, 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: 2018-05-07T21:52:52.895536Z, end-time: 2018-05-07T21:52:53.208156Z, duration: 0, exit-code: 0 git fetch --tags --prune From https://github.com/CyVerse-learning-materials/astrocontainers_workshop_2018 e786f12..e0cea08 master -> origin/master [rtd-command-info] start-time: 2018-05-07T21:52:53.307044Z, end-time: 2018-05-07T21:52:53.319032Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was e786f12... Simply the introduction session HEAD is now at e0cea08... Add a nice Galaxy figure [rtd-command-info] start-time: 2018-05-07T21:52:53.398191Z, end-time: 2018-05-07T21:52:53.407774Z, 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: 2018-05-07T21:52:53.513622Z, end-time: 2018-05-07T21:52:53.526327Z, duration: 0, exit-code: 0 git show-ref --tags [rtd-command-info] start-time: 2018-05-07T21:52:53.599375Z, end-time: 2018-05-07T21:52:53.608839Z, duration: 0, exit-code: 0 git branch -r origin/HEAD -> origin/master origin/master [rtd-command-info] start-time: 2018-05-07T21:52:54.508747Z, end-time: 2018-05-07T21:52:56.187498Z, 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 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: 2018-05-07T21:52:56.253597Z, end-time: 2018-05-07T21:52:58.542027Z, 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: 2018-05-07T21:52:58.619560Z, end-time: 2018-05-07T21:52:59.162012Z, 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: 2018-05-07T21:52:59.714965Z, end-time: 2018-05-07T21:52:59.790152Z, 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': 'e0cea08b', } 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: 2018-05-07T21:52:59.872360Z, end-time: 2018-05-07T21:53:03.088947Z, 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... 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[100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:214: WARNING: Unexpected section title or transition. ________________________________ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:215: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:217: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:217: WARNING: Unexpected section title or transition. -------------------------------- /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/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:490: WARNING: Title underline too short. 4.1: Docker2Singularity & Singularity2Docker ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... 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[rtd-command-info] start-time: 2018-05-07T21:53:03.217978Z, end-time: 2018-05-07T21:53:04.760595Z, duration: 1, exit-code: 0 python sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json Running Sphinx v1.6.5 making output directory... loading translations [en]... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [json]: targets for 18 source files that are out of date updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] docker/dockerintro looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 5%] atmosphere/boot writing output... [ 11%] docker/dockeradvanced writing output... [ 16%] docker/dockerdemos writing output... [ 22%] docker/dockerintro writing output... [ 27%] getting_started/about_cyverse writing output... [ 33%] getting_started/agenda writing output... 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Highlighting skipped. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:108: WARNING: Could not lex literal_block as "bash". Highlighting skipped. generating indices... genindex writing additional pages... search copying images... [ 3%] docker/../img/auto_build-1.png copying images... [ 6%] docker/../img/bind_mount.png copying images... [ 9%] atmosphere/../img/atmo-1.png copying images... [ 12%] docker/../img/create_repo2.png copying images... [ 16%] docker/../img/docker_image.png copying images... [ 19%] docker/../img/dc-1.png copying images... [ 22%] docker/../img/jn_galaxy.png copying images... [ 25%] atmosphere/../img/atmo_cp.png copying images... [ 29%] instructions_reporting/../img/static_site_docker.png copying images... [ 32%] docker/../img/auto_build-2.png copying images... [ 35%] docker/../img/portainer_demo.png copying images... [ 38%] docker/../img/jn_login.png copying images... 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[rtd-command-info] start-time: 2018-05-07T21:53:04.884809Z, end-time: 2018-05-07T21:53:06.233005Z, duration: 1, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.6.5 making output directory... loading translations [en]... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 1 changed, 0 removed reading sources... 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[ 96%] getting_started/../img/cyverse_rgb.png copying images... [100%] atmosphere/../img/atmo_launch.png copying TeX support files... done build succeeded, 2 warnings. [rtd-command-info] start-time: 2018-05-07T21:53:07.840827Z, end-time: 2018-05-07T21:53:14.503050Z, duration: 6, 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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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- Underfull \hbox (badness 7944) in paragraph at lines 181--183 []|\T1/ptm/m/n/10 The At-mo-sphere Cloud ser-vice [5] Underfull \hbox (badness 5189) in paragraph at lines 2--295 [][][]\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 312. Underfull \hbox (badness 10000) in paragraph at lines 344--345 \T1/ptm/m/n/10 com-pu-ta-tion re-sources Underfull \hbox (badness 6675) in paragraph at lines 386--387 \T1/ptm/m/n/10 af-ter-noon ses-sion plan- Underfull \hbox (badness 10000) in paragraph at lines 391--392 []|\T1/ptm/m/n/10 BYOD/A (Hands-on Underfull \hbox (badness 10000) in paragraph at lines 2--402 []|[][]\T1/ptm/m/n/10 Singularity Overview Underfull \hbox (badness 10000) in paragraph at lines 422--423 []|\T1/ptm/m/n/10 Introductory Sin-gu-lar-ity Underfull \hbox (badness 10000) in paragraph at lines 443--444 []|\T1/ptm/m/n/10 Advanced Sin-gu-lar-ity Underfull \hbox (badness 6675) in paragraph at lines 450--451 \T1/ptm/m/n/10 af-ter-noon ses-sion plan- Underfull \hbox (badness 10000) in paragraph at lines 455--456 []|\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 463. [11] [12] Chapter 5. 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[17 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [18] [19] [20] [21] Underfull \hbox (badness 10000) in paragraph at lines 774--775 []\T1/ptm/m/n/10 We can then \T1/pcr/m/n/10 cd \T1/ptm/m/n/10 into the HOPS wor k di-rec-tory, and mount it to \T1/pcr/m/n/10 /root \T1/ptm/m/n/10 as we launch the [22 <./bind_mount.png>] [23] Overfull \hbox (57.20003pt too wide) in paragraph at lines 890--891 | []| [24] Overfull \hbox (57.22421pt too wide) in paragraph at lines 894--895 | []| [25 <./jn_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 for immediate help. ... l.896 ...er 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.896 ...pose file. And there you have it —  a quick and easy way to st... [26 <./jn_galaxy.png>] Chapter 8. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 899. 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Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 1913. [57] [58 <./portainer_demo.png>] [59 <./pwd.png>] [60] Chapter 10. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 1970. [61 <./singularity.png>] Overfull \hbox (800.25983pt too wide) in paragraph at lines 2014--2015 [][] [62 <./singularity-2.4-flow.png>] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Chapter 11. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2846. [77] [78] [79] [80] [81] [82] Chapter 12. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3042. 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Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3368. No file CyVerseDocumentation.ind. [105] (./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 (109 pages, 3413252 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2018-05-07T21:53:14.573986Z, end-time: 2018-05-07T21:53:14.707417Z, 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: 2018-05-07T21:53:14.796878Z, end-time: 2018-05-07T21:53:21.470787Z, duration: 6, 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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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- Underfull \hbox (badness 7944) in paragraph at lines 181--183 []|\T1/ptm/m/n/10 The At-mo-sphere Cloud ser-vice [5] Underfull \hbox (badness 5189) in paragraph at lines 2--295 [][][]\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 312. Underfull \hbox (badness 10000) in paragraph at lines 344--345 \T1/ptm/m/n/10 com-pu-ta-tion re-sources Underfull \hbox (badness 6675) in paragraph at lines 386--387 \T1/ptm/m/n/10 af-ter-noon ses-sion plan- Underfull \hbox (badness 10000) in paragraph at lines 391--392 []|\T1/ptm/m/n/10 BYOD/A (Hands-on Underfull \hbox (badness 10000) in paragraph at lines 2--402 []|[][]\T1/ptm/m/n/10 Singularity Overview Underfull \hbox (badness 10000) in paragraph at lines 422--423 []|\T1/ptm/m/n/10 Introductory Sin-gu-lar-ity Underfull \hbox (badness 10000) in paragraph at lines 443--444 []|\T1/ptm/m/n/10 Advanced Sin-gu-lar-ity Underfull \hbox (badness 6675) in paragraph at lines 450--451 \T1/ptm/m/n/10 af-ter-noon ses-sion plan- Underfull \hbox (badness 10000) in paragraph at lines 455--456 []|\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 463. [11] [12] Chapter 5. 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[17 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [18] [19] [20] [21] Underfull \hbox (badness 10000) in paragraph at lines 774--775 []\T1/ptm/m/n/10 We can then \T1/pcr/m/n/10 cd \T1/ptm/m/n/10 into the HOPS wor k di-rec-tory, and mount it to \T1/pcr/m/n/10 /root \T1/ptm/m/n/10 as we launch the [22 <./bind_mount.png>] [23] Overfull \hbox (57.20003pt too wide) in paragraph at lines 890--891 | []| [24] Overfull \hbox (57.22421pt too wide) in paragraph at lines 894--895 | []| [25 <./jn_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 for immediate help. ... l.896 ...er 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.896 ...pose file. And there you have it —  a quick and easy way to st... [26 <./jn_galaxy.png>] Chapter 8. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 899. 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Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 1913. [57] [58 <./portainer_demo.png>] [59 <./pwd.png>] [60] Chapter 10. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 1970. [61 <./singularity.png>] Overfull \hbox (800.25983pt too wide) in paragraph at lines 2014--2015 [][] [62 <./singularity-2.4-flow.png>] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Chapter 11. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2846. [77] [78] [79] [80] [81] [82] Chapter 12. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3042. Overfull \hbox (94.855pt too wide) in paragraph at lines 3064--3065 [][] [83] Overfull \hbox (94.855pt too wide) in paragraph at lines 3083--3084 [][] [84 <./atmo-1.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3090--3091 [][] [85 <./atmo_cp0.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3106--3107 [][] [86 <./atmo_cp.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3113--3114 [][] [87 <./atmo_launch0.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3123--3124 [][] [88 <./atmo_launch1.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3133--3134 [][] [89 <./atmo_launch.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3146--3147 [][] [90 <./atmo-6.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3162--3163 [][] [91 <./atmo-7.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3169--3170 [][] [92 <./atmo-8.png>] [93 <./atmo-9.png>] [94] Chapter 13. 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Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3368. (./CyVerseDocumentation.ind) [105] (./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 (109 pages, 3411134 bytes). Transcript written on CyVerseDocumentation.log. 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