Read the Docs build information Build id: 106816 Project: cyverse-astrocontainers-workshop-2018 Version: latest Commit: 1374f483c6f47651acc03a88a6a7247c26f2ea62 Date: 2018-05-07T15:17:11.513680Z State: finished Success: True [rtd-command-info] start-time: 2018-05-07T20:17:12.177836Z, end-time: 2018-05-07T20:17:12.187118Z, 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: 2018-05-07T20:17:12.275595Z, end-time: 2018-05-07T20:17:12.703761Z, duration: 0, exit-code: 0 git fetch --tags --prune From https://github.com/CyVerse-learning-materials/astrocontainers_workshop_2018 fb3f23d..1374f48 master -> origin/master [rtd-command-info] start-time: 2018-05-07T20:17:12.778680Z, end-time: 2018-05-07T20:17:12.813259Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was fb3f23d... Update singularityintro.rst HEAD is now at 1374f48... Update file [rtd-command-info] start-time: 2018-05-07T20:17:12.877329Z, end-time: 2018-05-07T20:17:12.886066Z, 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: 2018-05-07T20:17:12.988267Z, end-time: 2018-05-07T20:17:12.995374Z, duration: 0, exit-code: 0 git show-ref --tags [rtd-command-info] start-time: 2018-05-07T20:17:13.060843Z, end-time: 2018-05-07T20:17:13.070034Z, duration: 0, exit-code: 0 git branch -r origin/HEAD -> origin/master origin/master [rtd-command-info] start-time: 2018-05-07T20:17:14.193269Z, end-time: 2018-05-07T20:17:16.186728Z, 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: 2018-05-07T20:17:16.255036Z, end-time: 2018-05-07T20:17:19.258443Z, duration: 3, 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: 2018-05-07T20:17:19.388242Z, end-time: 2018-05-07T20:17:19.936394Z, 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: 2018-05-07T20:17:20.537835Z, end-time: 2018-05-07T20:17:20.602796Z, 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': '1374f483', } 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: 2018-05-07T20:17:20.685530Z, end-time: 2018-05-07T20:17:27.111133Z, duration: 6, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.6.5 making output directory... loading translations [en]... done building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 18 source files that are out of date updating environment: 18 added, 0 changed, 0 removed reading sources... [ 5%] atmosphere/boot reading sources... [ 11%] docker/dockeradvanced reading sources... [ 16%] docker/dockerdemos reading sources... [ 22%] docker/dockerintro reading sources... [ 27%] getting_started/about_cyverse reading sources... [ 33%] getting_started/agenda reading sources... [ 38%] getting_started/installation reading sources... [ 44%] getting_started/main reading sources... [ 50%] index reading sources... [ 55%] instructions_reporting/instructors reading sources... [ 61%] instructions_reporting/problems reading sources... [ 66%] singularity/singularityadvanced reading sources... [ 72%] singularity/singularityintro reading sources... [ 77%] topics/train_docker reading sources... [ 83%] topics/train_singularity reading sources... [ 88%] useful_resources/usefulresources_docker reading sources... [ 94%] useful_resources/usefulresources_other reading sources... [100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst: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... [ 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... [ 38%] getting_started/installation writing output... [ 44%] getting_started/main writing output... [ 50%] index writing output... [ 55%] instructions_reporting/instructors writing output... [ 61%] instructions_reporting/problems writing output... [ 66%] singularity/singularityadvanced writing output... [ 72%] singularity/singularityintro writing output... [ 77%] topics/train_docker writing output... [ 83%] topics/train_singularity writing output... [ 88%] useful_resources/usefulresources_docker writing output... [ 94%] useful_resources/usefulresources_other writing output... [100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:150: WARNING: Could not lex literal_block as "bash". Highlighting skipped. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:108: WARNING: Could not lex literal_block as "bash". Highlighting skipped. generating indices... genindex writing additional pages... search copying images... [ 2%] docker/../img/auto_build-1.png copying images... [ 5%] docker/../img/bind_mount.png copying images... [ 8%] atmosphere/../img/atmo-1.png copying images... [ 11%] docker/../img/create_repo2.png copying images... [ 14%] docker/../img/docker_image.png copying images... [ 17%] docker/../img/dc-1.png copying images... [ 20%] docker/../img/static_site_docker1.png copying images... [ 22%] atmosphere/../img/atmo_cp.png copying images... [ 25%] instructions_reporting/../img/static_site_docker.png copying images... [ 28%] docker/../img/auto_build-2.png copying images... [ 31%] docker/../img/jn_login3.png copying images... [ 34%] docker/../img/portainer_demo.png copying images... [ 37%] docker/../img/jn_login2.png copying images... [ 40%] docker/../img/jn_login.png copying images... [ 42%] docker/../img/static_site_docker.png copying images... [ 45%] atmosphere/../img/atmo-6.png copying images... [ 48%] docker/../img/pwd.png copying images... [ 51%] docker/../img/auto_build-6.png copying images... [ 54%] docker/../img/auto_build-7.png copying images... [ 57%] atmosphere/../img/atmo_cp0.png copying images... [ 60%] atmosphere/../img/atmo-9.png copying images... [ 62%] docker/../img/catpic-1.png copying images... [ 65%] docker/../img/private_registry.png copying images... [ 68%] singularity/../img/singularity.png copying images... [ 71%] docker/../img/jn_login3.5.png copying images... [ 74%] docker/../img/create_repo.png copying images... [ 77%] docker/../img/docker.png copying images... [ 80%] atmosphere/../img/atmo_launch0.png copying images... [ 82%] atmosphere/../img/atmo_launch1.png copying images... [ 85%] atmosphere/../img/atmo-7.png copying images... [ 88%] docker/../img/auto_build-5.png copying images... [ 91%] docker/../img/auto_build-2.1.png copying images... [ 94%] atmosphere/../img/atmo-8.png copying images... [ 97%] getting_started/../img/cyverse_rgb.png copying images... [100%] atmosphere/../img/atmo_launch.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 11 warnings. [rtd-command-info] start-time: 2018-05-07T20:17:27.318202Z, end-time: 2018-05-07T20:17:30.404985Z, duration: 3, 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, 3 changed, 0 removed reading sources... [ 33%] docker/dockeradvanced reading sources... [ 66%] docker/dockerintro reading sources... [100%] getting_started/agenda /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". 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... [ 38%] getting_started/installation writing output... [ 44%] getting_started/main writing output... [ 50%] index writing output... [ 55%] instructions_reporting/instructors writing output... [ 61%] instructions_reporting/problems writing output... [ 66%] singularity/singularityadvanced writing output... [ 72%] singularity/singularityintro writing output... [ 77%] topics/train_docker writing output... [ 83%] topics/train_singularity writing output... [ 88%] useful_resources/usefulresources_docker writing output... [ 94%] useful_resources/usefulresources_other writing output... [100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:150: WARNING: Could not lex literal_block as "bash". Highlighting skipped. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:108: WARNING: Could not lex literal_block as "bash". Highlighting skipped. generating indices... genindex writing additional pages... search copying images... [ 2%] docker/../img/auto_build-1.png copying images... [ 5%] docker/../img/bind_mount.png copying images... [ 8%] atmosphere/../img/atmo-1.png copying images... [ 11%] docker/../img/create_repo2.png copying images... [ 14%] docker/../img/docker_image.png copying images... [ 17%] docker/../img/dc-1.png copying images... [ 20%] docker/../img/static_site_docker1.png copying images... [ 22%] atmosphere/../img/atmo_cp.png copying images... [ 25%] instructions_reporting/../img/static_site_docker.png copying images... [ 28%] docker/../img/auto_build-2.png copying images... [ 31%] docker/../img/jn_login3.png copying images... [ 34%] docker/../img/portainer_demo.png copying images... [ 37%] docker/../img/jn_login2.png copying images... [ 40%] docker/../img/jn_login.png copying images... [ 42%] docker/../img/static_site_docker.png copying images... [ 45%] atmosphere/../img/atmo-6.png copying images... [ 48%] docker/../img/pwd.png copying images... [ 51%] docker/../img/auto_build-6.png copying images... [ 54%] docker/../img/auto_build-7.png copying images... [ 57%] atmosphere/../img/atmo_cp0.png copying images... [ 60%] atmosphere/../img/atmo-9.png copying images... [ 62%] docker/../img/catpic-1.png copying images... [ 65%] docker/../img/private_registry.png copying images... [ 68%] singularity/../img/singularity.png copying images... [ 71%] docker/../img/jn_login3.5.png copying images... [ 74%] docker/../img/create_repo.png copying images... [ 77%] docker/../img/docker.png copying images... [ 80%] atmosphere/../img/atmo_launch0.png copying images... [ 82%] atmosphere/../img/atmo_launch1.png copying images... [ 85%] atmosphere/../img/atmo-7.png copying images... [ 88%] docker/../img/auto_build-5.png copying images... [ 91%] docker/../img/auto_build-2.1.png copying images... [ 94%] atmosphere/../img/atmo-8.png copying images... [ 97%] getting_started/../img/cyverse_rgb.png copying images... [100%] atmosphere/../img/atmo_launch.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 9 warnings. [rtd-command-info] start-time: 2018-05-07T20:17:30.588479Z, end-time: 2018-05-07T20:17:32.739705Z, duration: 2, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.6.5 making output directory... loading translations [en]... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 3 changed, 0 removed reading sources... [ 33%] docker/dockeradvanced reading sources... [ 66%] docker/dockerintro reading sources... [100%] getting_started/agenda /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". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... getting_started/main getting_started/installation getting_started/agenda getting_started/about_cyverse topics/train_docker topics/train_singularity docker/dockerintro docker/dockeradvanced docker/dockerdemos singularity/singularityintro singularity/singularityadvanced atmosphere/boot useful_resources/usefulresources_docker useful_resources/usefulresources_singularity useful_resources/usefulresources_other instructions_reporting/instructors instructions_reporting/problems writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/index.rst:150: WARNING: Could not lex literal_block as "bash". Highlighting skipped. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/index.rst:108: WARNING: Could not lex literal_block as "bash". Highlighting skipped. done writing additional files... copying images... [ 2%] docker/../img/auto_build-1.png copying images... [ 5%] docker/../img/bind_mount.png copying images... [ 8%] atmosphere/../img/atmo-1.png copying images... [ 11%] docker/../img/create_repo2.png copying images... [ 14%] docker/../img/docker_image.png copying images... [ 17%] docker/../img/dc-1.png copying images... [ 20%] docker/../img/static_site_docker1.png copying images... [ 22%] atmosphere/../img/atmo_cp.png copying images... [ 25%] instructions_reporting/../img/static_site_docker.png copying images... [ 28%] docker/../img/jn_login2.png copying images... [ 31%] docker/../img/jn_login3.png copying images... [ 34%] docker/../img/portainer_demo.png copying images... [ 37%] docker/../img/jn_login.png copying images... [ 40%] docker/../img/static_site_docker.png copying images... [ 42%] atmosphere/../img/atmo-6.png copying images... [ 45%] docker/../img/pwd.png copying images... [ 48%] docker/../img/auto_build-6.png copying images... [ 51%] docker/../img/auto_build-7.png copying images... [ 54%] atmosphere/../img/atmo_cp0.png copying images... [ 57%] atmosphere/../img/atmo-9.png copying images... [ 60%] docker/../img/catpic-1.png copying images... [ 62%] docker/../img/private_registry.png copying images... [ 65%] docker/../img/auto_build-2.png copying images... [ 68%] singularity/../img/singularity.png copying images... [ 71%] docker/../img/jn_login3.5.png copying images... [ 74%] docker/../img/create_repo.png copying images... [ 77%] docker/../img/docker.png copying images... [ 80%] atmosphere/../img/atmo_launch0.png copying images... [ 82%] atmosphere/../img/atmo_launch1.png copying images... [ 85%] atmosphere/../img/atmo-7.png copying images... [ 88%] docker/../img/auto_build-5.png copying images... [ 91%] docker/../img/auto_build-2.1.png copying images... [ 94%] atmosphere/../img/atmo-8.png copying images... [ 97%] getting_started/../img/cyverse_rgb.png copying images... [100%] atmosphere/../img/atmo_launch.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 9 warnings. [rtd-command-info] start-time: 2018-05-07T20:17:32.875060Z, end-time: 2018-05-07T20:17:34.728470Z, duration: 1, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.6.5 making output directory... loading translations [en]... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 3 changed, 0 removed reading sources... [ 33%] docker/dockeradvanced reading sources... [ 66%] docker/dockerintro reading sources... [100%] getting_started/agenda /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". looking for now-outdated files... none found pickling environment... done checking consistency... done processing CyVerseDocumentation.tex...index getting_started/main getting_started/installation getting_started/agenda getting_started/about_cyverse topics/train_docker topics/train_singularity docker/dockerintro docker/dockeradvanced docker/dockerdemos singularity/singularityintro singularity/singularityadvanced atmosphere/boot useful_resources/usefulresources_docker useful_resources/usefulresources_singularity useful_resources/usefulresources_other instructions_reporting/instructors instructions_reporting/problems resolving references... writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:150: WARNING: Could not lex literal_block as "bash". Highlighting skipped. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:108: WARNING: Could not lex literal_block as "bash". Highlighting skipped. done copying images... [ 2%] docker/../img/auto_build-1.png copying images... [ 5%] docker/../img/bind_mount.png copying images... [ 8%] atmosphere/../img/atmo-1.png copying images... [ 11%] docker/../img/create_repo2.png copying images... [ 13%] docker/../img/docker_image.png copying images... [ 16%] docker/../img/dc-1.png copying images... [ 19%] docker/../img/static_site_docker1.png copying images... [ 22%] atmosphere/../img/atmo_cp.png copying images... [ 25%] instructions_reporting/../img/static_site_docker.png copying images... [ 27%] docker/../img/jn_login2.png copying images... [ 30%] docker/../img/jn_login3.png copying images... [ 33%] docker/../img/portainer_demo.png copying images... [ 36%] docker/../img/jn_login.png copying images... [ 38%] docker/../img/static_site_docker.png copying images... [ 41%] atmosphere/../img/atmo-6.png copying images... [ 44%] docker/../img/pwd.png copying images... [ 47%] docker/../img/auto_build-6.png copying images... [ 50%] docker/../img/auto_build-7.png copying images... [ 52%] atmosphere/../img/atmo_cp0.png copying images... [ 55%] atmosphere/../img/atmo-9.png copying images... [ 58%] docker/../img/catpic-1.png copying images... [ 61%] docker/../img/private_registry.png copying images... [ 63%] docker/../img/auto_build-2.png copying images... [ 66%] singularity/../img/singularity.png copying images... [ 69%] docker/../img/jn_login3.5.png copying images... [ 72%] docker/../img/create_repo.png copying images... [ 75%] docker/../img/docker.png copying images... [ 77%] atmosphere/../img/atmo_launch0.png copying images... [ 80%] atmosphere/../img/atmo_launch1.png copying images... [ 83%] http://singularity.lbl.gov/assets/img/diagram/singularity-2.4-flow.png copying images... [ 86%] atmosphere/../img/atmo-7.png copying images... [ 88%] docker/../img/auto_build-5.png copying images... [ 91%] docker/../img/auto_build-2.1.png copying images... [ 94%] atmosphere/../img/atmo-8.png copying images... [ 97%] getting_started/../img/cyverse_rgb.png copying images... [100%] atmosphere/../img/atmo_launch.png copying TeX support files... done build succeeded, 7 warnings. [rtd-command-info] start-time: 2018-05-07T20:17:34.792813Z, end-time: 2018-05-07T20:17:42.140829Z, 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. (./sphinxmanual.cls Document Class: sphinxmanual 2017/03/26 v1.6 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) Package Sphinx Info: **** titlesec 2.10.1 successfully patched for bugfix **** (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file CyVerseDocumentation.idx No file CyVerseDocumentation.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] [1 <./cyverse_rgb.png>] [2] Chapter 1. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 75. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 136. Underfull \hbox (badness 7344) in paragraph at lines 155--159 \T1/ptm/m/n/10 We \T1/ptm/b/n/10 strongly rec-om-mend \T1/ptm/m/n/10 Fire- 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. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 497. [13] [14] Chapter 6. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 525. [15] [16] Chapter 7. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 546. [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] ! Package inputenc Error: Unicode char ☺ (U+263A) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. 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. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 1078. [31] Overfull \vbox (11.56995pt too high) detected at line 1152 [32] [33] [34] [35] [36] [37] Overfull \hbox (94.866pt too wide) in paragraph at lines 1521--1522 [][] [38] [39 <./docker_image.png>] Overfull \hbox (94.84293pt too wide) in paragraph at lines 1560--1561 [][] [40] Overfull \vbox (8.54036pt too high) detected at line 1574 [41 <./private_registry.png>] [42] Overfull \hbox (94.83699pt too wide) in paragraph at lines 1672--1673 [][] [43] [44 <./auto_build-1.png>] Overfull \hbox (94.84164pt too wide) in paragraph at lines 1720--1721 [][] [45] Overfull \hbox (94.81732pt too wide) in paragraph at lines 1728--1729 [][] [46 <./create_repo.png>] Overfull \vbox (1.54773pt too high) detected at line 1742 [47 <./create_repo2.png>] Overfull \hbox (94.83147pt too wide) in paragraph at lines 1764--1765 [][] [48] Overfull \hbox (94.83147pt too wide) in paragraph at lines 1776--1777 [][] [49 <./auto_build-2.png>] [50 <./auto_build-2.1.png>] Overfull \hbox (94.86179pt too wide) in paragraph at lines 1822--1823 [][] [51] Overfull \hbox (94.84714pt too wide) in paragraph at lines 1830--1831 [][] [52 <./auto_build-5.png>] Overfull \hbox (94.84714pt too wide) in paragraph at lines 1846--1847 [][] [53 <./auto_build-6.png>] [54 <./auto_build-7.png>] [55] [56] Overfull \hbox (94.86829pt too wide) in paragraph at lines 2072--2073 [][] [57] [58 <./dc-1.png>] [59] [60] Chapter 9. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2092. [61] [62 <./portainer_demo.png>] [63 <./pwd.png>] [64] Chapter 10. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2149. [65 <./singularity.png>] Overfull \hbox (800.25983pt too wide) in paragraph at lines 2193--2194 [][] [66 <./singularity-2.4-flow.png>] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] Chapter 11. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3025. [81] [82] [83] [84] [85] [86] Chapter 12. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3221. Overfull \hbox (94.855pt too wide) in paragraph at lines 3243--3244 [][] [87] Overfull \hbox (94.855pt too wide) in paragraph at lines 3262--3263 [][] [88 <./atmo-1.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3269--3270 [][] [89 <./atmo_cp0.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3285--3286 [][] [90 <./atmo_cp.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3292--3293 [][] [91 <./atmo_launch0.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3302--3303 [][] [92 <./atmo_launch1.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3312--3313 [][] [93 <./atmo_launch.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3325--3326 [][] [94 <./atmo-6.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3341--3342 [][] [95 <./atmo-7.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3348--3349 [][] [96 <./atmo-8.png>] [97 <./atmo-9.png>] [98] Chapter 13. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3355. [99] [100] Chapter 14. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3398. [101] [102] Chapter 15. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3418. [103] [104] Chapter 16. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3440. Underfull \hbox (badness 10000) in paragraph at lines 1--3488 []\T1/pcr/m/n/10 git clone https://github.com/CyVerse-learning-materials/ [105] Overfull \hbox (94.82553pt too wide) in paragraph at lines 3534--3535 [][] [106] [107 <./static_site_docker2.png>] [108] Chapter 17. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3547. No file CyVerseDocumentation.ind. [109] (./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 (113 pages, 3440721 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2018-05-07T20:17:42.231076Z, end-time: 2018-05-07T20:17:42.364986Z, 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: 2018-05-07T20:17:42.448716Z, end-time: 2018-05-07T20:17:49.794704Z, 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. (./sphinxmanual.cls Document Class: sphinxmanual 2017/03/26 v1.6 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) Package Sphinx Info: **** titlesec 2.10.1 successfully patched for bugfix **** (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file CyVerseDocumentation.idx (./CyVerseDocumentation.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./CyVerseDocumentation.out) (./CyVerseDocumentation.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./CyVerseDocumentation.toc) [1] [2] [1 <./cyverse_rgb.png>] [2] Chapter 1. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 75. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 136. Underfull \hbox (badness 7344) in paragraph at lines 155--159 \T1/ptm/m/n/10 We \T1/ptm/b/n/10 strongly rec-om-mend \T1/ptm/m/n/10 Fire- 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. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 497. [13] [14] Chapter 6. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 525. [15] [16] Chapter 7. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 546. [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] ! Package inputenc Error: Unicode char ☺ (U+263A) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. 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. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 1078. [31] Overfull \vbox (11.56995pt too high) detected at line 1152 [32] [33] [34] [35] [36] [37] Overfull \hbox (94.866pt too wide) in paragraph at lines 1521--1522 [][] [38] [39 <./docker_image.png>] Overfull \hbox (94.84293pt too wide) in paragraph at lines 1560--1561 [][] [40] Overfull \vbox (8.54036pt too high) detected at line 1574 [41 <./private_registry.png>] [42] Overfull \hbox (94.83699pt too wide) in paragraph at lines 1672--1673 [][] [43] [44 <./auto_build-1.png>] Overfull \hbox (94.84164pt too wide) in paragraph at lines 1720--1721 [][] [45] Overfull \hbox (94.81732pt too wide) in paragraph at lines 1728--1729 [][] [46 <./create_repo.png>] Overfull \vbox (1.54773pt too high) detected at line 1742 [47 <./create_repo2.png>] Overfull \hbox (94.83147pt too wide) in paragraph at lines 1764--1765 [][] [48] Overfull \hbox (94.83147pt too wide) in paragraph at lines 1776--1777 [][] [49 <./auto_build-2.png>] [50 <./auto_build-2.1.png>] Overfull \hbox (94.86179pt too wide) in paragraph at lines 1822--1823 [][] [51] Overfull \hbox (94.84714pt too wide) in paragraph at lines 1830--1831 [][] [52 <./auto_build-5.png>] Overfull \hbox (94.84714pt too wide) in paragraph at lines 1846--1847 [][] [53 <./auto_build-6.png>] [54 <./auto_build-7.png>] [55] [56] Overfull \hbox (94.86829pt too wide) in paragraph at lines 2072--2073 [][] [57] [58 <./dc-1.png>] [59] [60] Chapter 9. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2092. [61] [62 <./portainer_demo.png>] [63 <./pwd.png>] [64] Chapter 10. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2149. [65 <./singularity.png>] Overfull \hbox (800.25983pt too wide) in paragraph at lines 2193--2194 [][] [66 <./singularity-2.4-flow.png>] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] Chapter 11. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3025. [81] [82] [83] [84] [85] [86] Chapter 12. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3221. Overfull \hbox (94.855pt too wide) in paragraph at lines 3243--3244 [][] [87] Overfull \hbox (94.855pt too wide) in paragraph at lines 3262--3263 [][] [88 <./atmo-1.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3269--3270 [][] [89 <./atmo_cp0.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3285--3286 [][] [90 <./atmo_cp.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3292--3293 [][] [91 <./atmo_launch0.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3302--3303 [][] [92 <./atmo_launch1.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3312--3313 [][] [93 <./atmo_launch.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3325--3326 [][] [94 <./atmo-6.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3341--3342 [][] [95 <./atmo-7.png>] Overfull \hbox (94.855pt too wide) in paragraph at lines 3348--3349 [][] [96 <./atmo-8.png>] [97 <./atmo-9.png>] [98] Chapter 13. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3355. [99] [100] Chapter 14. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3398. [101] [102] Chapter 15. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3418. [103] [104] Chapter 16. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3440. Underfull \hbox (badness 10000) in paragraph at lines 1--3488 []\T1/pcr/m/n/10 git clone https://github.com/CyVerse-learning-materials/ [105] Overfull \hbox (94.82553pt too wide) in paragraph at lines 3534--3535 [][] [106] [107 <./static_site_docker2.png>] [108] Chapter 17. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 3547. (./CyVerseDocumentation.ind) [109] (./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 (113 pages, 3444593 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2018-05-07T20:17:49.865131Z, end-time: 2018-05-07T20:17:49.939175Z, 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: 2018-05-07T20:17:50.057668Z, end-time: 2018-05-07T20:17:53.284568Z, duration: 3, 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, 3 changed, 0 removed reading sources... [ 33%] docker/dockeradvanced reading sources... [ 66%] docker/dockerintro reading sources... [100%] getting_started/agenda /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". 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... [ 38%] getting_started/installation writing output... [ 44%] getting_started/main writing output... [ 50%] index writing output... [ 55%] instructions_reporting/instructors writing output... [ 61%] instructions_reporting/problems writing output... [ 66%] singularity/singularityadvanced writing output... [ 72%] singularity/singularityintro writing output... [ 77%] topics/train_docker writing output... [ 83%] topics/train_singularity writing output... [ 88%] useful_resources/usefulresources_docker writing output... [ 94%] useful_resources/usefulresources_other writing output... [100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/docker/dockeradvanced.rst:150: WARNING: Could not lex literal_block as "bash". Highlighting skipped. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/singularity/singularityintro.rst:108: WARNING: Could not lex literal_block as "bash". Highlighting skipped. generating indices... genindex writing additional pages... copying images... [ 2%] docker/../img/auto_build-1.png copying images... [ 5%] docker/../img/bind_mount.png copying images... [ 8%] atmosphere/../img/atmo-1.png copying images... [ 11%] docker/../img/create_repo2.png copying images... [ 13%] docker/../img/docker_image.png copying images... [ 16%] docker/../img/dc-1.png copying images... [ 19%] docker/../img/static_site_docker1.png copying images... [ 22%] atmosphere/../img/atmo_cp.png copying images... [ 25%] instructions_reporting/../img/static_site_docker.png copying images... [ 27%] docker/../img/auto_build-2.png copying images... [ 30%] docker/../img/jn_login3.png copying images... [ 33%] docker/../img/portainer_demo.png copying images... [ 36%] docker/../img/jn_login2.png copying images... [ 38%] docker/../img/jn_login.png copying images... [ 41%] docker/../img/static_site_docker.png copying images... [ 44%] atmosphere/../img/atmo-6.png copying images... [ 47%] docker/../img/pwd.png copying images... [ 50%] docker/../img/auto_build-6.png copying images... [ 52%] docker/../img/auto_build-7.png copying images... [ 55%] atmosphere/../img/atmo_cp0.png copying images... [ 58%] atmosphere/../img/atmo-9.png copying images... [ 61%] docker/../img/catpic-1.png copying images... [ 63%] docker/../img/private_registry.png copying images... [ 66%] singularity/../img/singularity.png copying images... [ 69%] docker/../img/jn_login3.5.png copying images... [ 72%] docker/../img/create_repo.png copying images... [ 75%] docker/../img/docker.png copying images... [ 77%] atmosphere/../img/atmo_launch0.png copying images... [ 80%] atmosphere/../img/atmo_launch1.png copying images... [ 83%] atmosphere/../img/atmo-7.png copying images... [ 86%] http://singularity.lbl.gov/assets/img/diagram/singularity-2.4-flow.png copying images... [ 88%] docker/../img/auto_build-5.png copying images... [ 91%] docker/../img/auto_build-2.1.png copying images... [ 94%] atmosphere/../img/atmo-8.png copying images... [ 97%] getting_started/../img/cyverse_rgb.png copying images... [100%] atmosphere/../img/atmo_launch.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying extra files... done writing mimetype file... writing META-INF/container.xml file... writing content.opf file... writing nav.xhtml file... writing toc.ncx file... writing CyVerseAstroContainersWorkshopLearningDockerandSingularity.epub file... build succeeded, 9 warnings. [rtd-command-info] start-time: 2018-05-07T20:17:53.380872Z, end-time: 2018-05-07T20:17:53.696033Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/checkouts/latest/_build/epub/CyVerseAstroContainersWorkshopLearningDockerandSingularity.epub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-astrocontainers-workshop-2018/artifacts/latest/sphinx_epub/cyverse-astrocontainers-workshop-2018.epub