Read the Docs build information Build id: 424501 Project: cyverse-cc-2020 Version: latest Commit: 41a43dc64c78be0ca2ede884b6254e82eb5e25ac Date: 2020-09-17T18:44:31.889623Z State: finished Success: True [rtd-command-info] start-time: 2020-09-17T18:45:29.685601Z, end-time: 2020-09-17T18:45:33.927720Z, duration: 4, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/container_camp_workshop_2020.git . Cloning into '.'... [rtd-command-info] start-time: 2020-09-17T18:45:34.529489Z, end-time: 2020-09-17T18:45:35.536162Z, duration: 1, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 41a43dc add triage issue template [rtd-command-info] start-time: 2020-09-17T18:45:35.648854Z, end-time: 2020-09-17T18:45:35.711803Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-09-17T18:45:37.952587Z, end-time: 2020-09-17T18:45:41.886249Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-09-17T18:45:42.524087Z, end-time: 2020-09-17T18:45:43.200983Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (20.2.3) [rtd-command-info] start-time: 2020-09-17T18:45:43.497732Z, end-time: 2020-09-17T18:45:51.760419Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.10-py2.py3-none-any.whl (127 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=6d6244f0f2d2e023076b534431d9f11a54003228408af6d0185111501af3e5d6 Stored in directory: /tmp/pip-ephem-wheel-cache-uyv39chy/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=482fa810e9194391d6271906b6d3c8e420bd0c723a7f0dc596651257e8fbf534 Stored in directory: /tmp/pip-ephem-wheel-cache-uyv39chy/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, pytz, babel, imagesize, snowballstemmer, six, pyparsing, packaging, MarkupSafe, Jinja2, urllib3, certifi, chardet, idna, requests, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 50.3.0 Uninstalling setuptools-50.3.0: Successfully uninstalled setuptools-50.3.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.10 [rtd-command-info] start-time: 2020-09-17T18:45:51.943448Z, end-time: 2020-09-17T18:45:55.021128Z, duration: 3, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (1.8.5) Requirement already satisfied: recommonmark in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 2)) (0.5.0) Collecting sphinxcontrib-images Downloading sphinxcontrib_images-0.9.2-py2.py3-none-any.whl (63 kB) Collecting sphinx_bootstrap_theme Downloading sphinx-bootstrap-theme-0.7.1.tar.gz (1.2 MB) Collecting guzzle_sphinx_theme==0.7.11 Downloading guzzle_sphinx_theme-0.7.11.tar.gz (2.5 MB) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.14) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.15.0) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.11.2) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.0.0) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.8.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (20.4) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.2.4) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (41.0.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.7.12) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.2.0) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.24.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.3.1) Requirement already satisfied: commonmark>=0.7.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from recommonmark->-r requirements.txt (line 2)) (0.8.1) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx->-r requirements.txt (line 1)) (1.1.1) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx->-r requirements.txt (line 1)) (2020.1) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from packaging->sphinx->-r requirements.txt (line 1)) (2.4.7) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->sphinx->-r requirements.txt (line 1)) (1.1.4) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2.10) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (3.0.4) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (1.25.10) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2020.6.20) Requirement already satisfied: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages (from commonmark>=0.7.3->recommonmark->-r requirements.txt (line 2)) (0.18.2) Building wheels for collected packages: sphinx-bootstrap-theme, guzzle-sphinx-theme Building wheel for sphinx-bootstrap-theme (setup.py): started Building wheel for sphinx-bootstrap-theme (setup.py): finished with status 'done' Created wheel for sphinx-bootstrap-theme: filename=sphinx_bootstrap_theme-0.7.1-py3-none-any.whl size=1250222 sha256=a9b3ec1a8ba3b83b1e3e9da45e3e73cd3519a9967515a90865a09c1a1091f89e Stored in directory: /tmp/pip-ephem-wheel-cache-yaorm1cv/wheels/08/be/f3/01d145bc6faf769e37d9fb6f1d2f078bc8cd9725c9d883699c Building wheel for guzzle-sphinx-theme (setup.py): started Building wheel for guzzle-sphinx-theme (setup.py): finished with status 'done' Created wheel for guzzle-sphinx-theme: filename=guzzle_sphinx_theme-0.7.11-py3-none-any.whl size=2555156 sha256=b68d9d6fc4adc8e5a059d2bf93497ecdd1dde719e09fdab58866e8f808918c3e Stored in directory: /tmp/pip-ephem-wheel-cache-yaorm1cv/wheels/5c/d1/84/25697025762e126f3a2eba16cae45f22432fe99669b05df5c0 Successfully built sphinx-bootstrap-theme guzzle-sphinx-theme Installing collected packages: sphinxcontrib-images, sphinx-bootstrap-theme, guzzle-sphinx-theme ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts. We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default. sphinxcontrib-images 0.9.2 requires sphinx>=2.0; python_version >= "3.0", but you'll have sphinx 1.8.5 which is incompatible. Successfully installed guzzle-sphinx-theme-0.7.11 sphinx-bootstrap-theme-0.7.1 sphinxcontrib-images-0.9.2 [rtd-command-info] start-time: 2020-09-17T18:45:56.829882Z, end-time: 2020-09-17T18:45:56.901401Z, 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 Learning Institute - Container Camp 2020' copyright = '2020, CyVerse' author = 'CyVerse' version = '0.3.0' release = '0.3.0' epub_title = 'CyVerse Learning Institute - Container Camp 2020' epub_author = 'Amanda Cooksey, Upendra Devisetty, Sateesh Peri, Julian Pistorius, Tyson L. Swetnam, Reetu Tujeeta, Jason Williams' epub_publisher = 'CyVerse' epub_copyright = 'CC0 - Open Source' ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' 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') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//learning.cyverse.org/_/downloads/Container-camp-2020/en/latest/pdf/"), ("html", "//learning.cyverse.org/_/downloads/Container-camp-2020/en/latest/htmlzip/"), ("epub", "//learning.cyverse.org/_/downloads/Container-camp-2020/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'cyverse-cc-2020', 'name': u'cc-2020', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/projects/Container-camp-2020/en/latest/', 'analytics_code': 'UA-72224033-6', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'proxied_api_host': '/_', 'github_repo': 'container_camp_workshop_2020', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-72224033-6', 'global_analytics_code': 'UA-17997319-2', 'commit': '41a43dc6', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2020-09-17T18:45:57.751774Z, end-time: 2020-09-17T18:46:03.656107Z, duration: 5, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 63 source files that are out of date updating environment: 63 added, 0 changed, 0 removed reading sources... 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[100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/biocontainers.rst:177: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/datascience.rst:2: WARNING: Title underline too short. **Docker for Data Science** -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:18: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:16: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:46: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:51: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:62: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} WARNING: invalid signature for autoclass ('{{ objname }}') WARNING: don't know which module to import for autodocumenting '{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) WARNING: invalid signature for automodule ('{{ fullname }}') WARNING: don't know which module to import for autodocumenting '{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'cyverse/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:75: WARNING: Content block expected for the "important" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:5: WARNING: Undefined substitution referenced: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:5: WARNING: Unknown target name: "home_icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/de_docker.rst:4: WARNING: Duplicate explicit target name: "dockerhub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:104: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:111: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:144: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/vice_docker.rst:4: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:260: WARNING: Title underline too short. 3.1 Log into the Docker Hub Registry ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:311: WARNING: Title underline too short. 3.3 Private repositories ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:311: WARNING: Title underline too short. 3.3 Private repositories ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:316: WARNING: Title underline too short. 3.4 Pull down the Registry Image ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:376: WARNING: Title underline too short. 4.0 Automated Docker image building from GitHub ============================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:376: WARNING: Title underline too short. 4.0 Automated Docker image building from GitHub ============================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:568: WARNING: Title level inconsistent: 5.1 Bind mounts ^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:582: WARNING: Title level inconsistent: 5.2 Create and manage volumes ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:632: WARNING: Title level inconsistent: Populate a volume using a container ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:651: WARNING: Error in "code-block" directive: 1 argument(s) required, 0 supplied. .. code-block:: HOSTNAME=790e13bba28a SHLVL=1 HOME=/root PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:725: WARNING: Title underline too short. 6.0 Docker Compose for multi-container apps ========================================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:725: WARNING: Title underline too short. 6.0 Docker Compose for multi-container apps ========================================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerintro.rst:498: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerintro.rst:391: WARNING: Undefined substitution referenced: "volumes". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:9: WARNING: Title underline too short. **Finding the perfect container** ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:39: WARNING: Title underline too short. Docker Registries ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:9: WARNING: Duplicate explicit target name: "nvidia gpu cloud". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:111: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/about_cyverse.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/agenda.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/code_conduct.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/code_conduct.rst:9: WARNING: Title underline too short. **Code of Conduct** ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/installation.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:9: WARNING: Title underline too short. **Location** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:48: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:52: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:8: WARNING: Title underline too short. **Learning objectives** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:20: WARNING: Title underline too short. **FAIR Data principles** ======================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:20: WARNING: Title underline too short. **FAIR Data principles** ======================= 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name: "Ask CyVerse". cyverse_rst_defined_substitutions.txt:95: WARNING: Duplicate substitution definition name: "CyVerse Learning Center". cyverse_rst_defined_substitutions.txt:99: WARNING: Duplicate substitution definition name: "CyVerse Wiki". cyverse_rst_defined_substitutions.txt:106: WARNING: Duplicate substitution definition name: "CyVerse_logo". cyverse_rst_defined_substitutions.txt:111: WARNING: Duplicate substitution definition name: "CyVerse_logo2". cyverse_rst_defined_substitutions.txt:115: WARNING: Duplicate substitution definition name: "Home_Icon". cyverse_rst_defined_substitutions.txt:120: WARNING: Duplicate substitution definition name: "Home_Icon2". cyverse_rst_defined_substitutions.txt:125: WARNING: Duplicate substitution definition name: "Intercom". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:23: WARNING: toctree contains reference to nonexisting document 'getting_started/glossary' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:96: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:100: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short. 5.0 Building your own Containers from scratch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short. 5.2 Building Singularity containers ================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:221: WARNING: Error in "image" directive: no content permitted. image:: ../img/singularity.png :height: 200 :width: 200 singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:221: WARNING: Substitution definition "singularity" empty or invalid. .. |singularity| image:: ../img/singularity.png :height: 200 :width: 200 singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:4: WARNING: Undefined substitution referenced: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityhpc.rst:2: WARNING: Duplicate explicit target name: "user guide". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityhpc.rst:76: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 7 supplied. .. code-block:: bash BootStrap: debootstrap OSVersion: xenial MirrorURL: http://us.archive.ubuntu.com/ubuntu/ %runscript echo "This is what happens when you run the container..." %post echo "Hello from inside the container" sed -i 's/$/ universe/' /etc/apt/sources.list apt update apt -y --allow-unauthenticated install vim build-essential wget gfortran bison libibverbs-dev libibmad-dev libibumad-dev librdmacm-dev libmlx5-dev libmlx4-dev wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz tar xvf mvapich2-2.1.tar.gz cd mvapich2-2.1 ./configure --prefix=/usr/local make -j4 make install /usr/local/bin/mpicc examples/hellow.c -o /usr/bin/hellow /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityintro.rst:308: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:16: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:30: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:30: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:33: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:41: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:41: WARNING: Title underline 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[rtd-command-info] start-time: 2020-09-17T18:46:04.354194Z, end-time: 2020-09-17T18:46:08.339355Z, duration: 3, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 63 added, 0 changed, 0 removed reading sources... [ 1%] .github/ISSUE_TEMPLATE/triage-for-2-0-release reading sources... [ 3%] README reading sources... [ 4%] breakout/biocontainers reading sources... [ 6%] breakout/datascience reading sources... [ 7%] breakout/workflows reading sources... [ 9%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION reading sources... [ 11%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION reading sources... 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[100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/biocontainers.rst:177: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/datascience.rst:2: WARNING: Title underline too short. **Docker for Data Science** -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:18: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:16: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:46: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:51: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:62: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} WARNING: invalid signature for autoclass ('{{ objname }}') WARNING: don't know which module to import for autodocumenting '{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) WARNING: invalid signature for automodule ('{{ fullname }}') WARNING: don't know which module to import for autodocumenting '{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'cyverse/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:75: WARNING: Content block expected for the "important" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:5: WARNING: Undefined substitution referenced: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:5: WARNING: Unknown target name: "home_icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/de_docker.rst:4: WARNING: Duplicate explicit target name: "dockerhub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:104: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:111: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:144: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/vice_docker.rst:4: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:260: WARNING: Title underline too short. 3.1 Log into the Docker Hub Registry ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:311: WARNING: Title underline too short. 3.3 Private repositories ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:311: WARNING: Title underline too short. 3.3 Private repositories ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:316: WARNING: Title underline too short. 3.4 Pull down the Registry Image ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:376: WARNING: Title underline too short. 4.0 Automated Docker image building from GitHub ============================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:376: WARNING: Title underline too short. 4.0 Automated Docker image building from GitHub ============================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:568: WARNING: Title level inconsistent: 5.1 Bind mounts ^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:582: WARNING: Title level inconsistent: 5.2 Create and manage volumes ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:632: WARNING: Title level inconsistent: Populate a volume using a container ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:651: WARNING: Error in "code-block" directive: 1 argument(s) required, 0 supplied. .. code-block:: HOSTNAME=790e13bba28a SHLVL=1 HOME=/root PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:725: WARNING: Title underline too short. 6.0 Docker Compose for multi-container apps ========================================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:725: WARNING: Title underline too short. 6.0 Docker Compose for multi-container apps ========================================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerintro.rst:498: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerintro.rst:391: WARNING: Undefined substitution referenced: "volumes". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:9: WARNING: Title underline too short. **Finding the perfect container** ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:39: WARNING: Title underline too short. Docker Registries ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:9: WARNING: Duplicate explicit target name: "nvidia gpu cloud". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:111: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/about_cyverse.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/agenda.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/code_conduct.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/code_conduct.rst:9: WARNING: Title underline too short. **Code of Conduct** ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/installation.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:9: WARNING: Title underline too short. **Location** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:48: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:52: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:8: WARNING: Title underline too short. **Learning objectives** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:20: WARNING: Title underline too short. **FAIR Data principles** ======================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:20: WARNING: Title underline too short. **FAIR Data principles** ======================= 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name: "Ask CyVerse". cyverse_rst_defined_substitutions.txt:95: WARNING: Duplicate substitution definition name: "CyVerse Learning Center". cyverse_rst_defined_substitutions.txt:99: WARNING: Duplicate substitution definition name: "CyVerse Wiki". cyverse_rst_defined_substitutions.txt:106: WARNING: Duplicate substitution definition name: "CyVerse_logo". cyverse_rst_defined_substitutions.txt:111: WARNING: Duplicate substitution definition name: "CyVerse_logo2". cyverse_rst_defined_substitutions.txt:115: WARNING: Duplicate substitution definition name: "Home_Icon". cyverse_rst_defined_substitutions.txt:120: WARNING: Duplicate substitution definition name: "Home_Icon2". cyverse_rst_defined_substitutions.txt:125: WARNING: Duplicate substitution definition name: "Intercom". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:23: WARNING: toctree contains reference to nonexisting document 'getting_started/glossary' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:96: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:100: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short. 5.0 Building your own Containers from scratch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short. 5.2 Building Singularity containers ================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:221: WARNING: Error in "image" directive: no content permitted. image:: ../img/singularity.png :height: 200 :width: 200 singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:221: WARNING: Substitution definition "singularity" empty or invalid. .. |singularity| image:: ../img/singularity.png :height: 200 :width: 200 singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:4: WARNING: Undefined substitution referenced: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityhpc.rst:2: WARNING: Duplicate explicit target name: "user guide". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityhpc.rst:76: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 7 supplied. .. code-block:: bash BootStrap: debootstrap OSVersion: xenial MirrorURL: http://us.archive.ubuntu.com/ubuntu/ %runscript echo "This is what happens when you run the container..." %post echo "Hello from inside the container" sed -i 's/$/ universe/' /etc/apt/sources.list apt update apt -y --allow-unauthenticated install vim build-essential wget gfortran bison libibverbs-dev libibmad-dev libibumad-dev librdmacm-dev libmlx5-dev libmlx4-dev wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz tar xvf mvapich2-2.1.tar.gz cd mvapich2-2.1 ./configure --prefix=/usr/local make -j4 make install /usr/local/bin/mpicc examples/hellow.c -o /usr/bin/hellow /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityintro.rst:308: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:16: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:30: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:30: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:33: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:41: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:41: WARNING: Title underline 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[100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/biocontainers.rst:177: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/datascience.rst:2: WARNING: Title underline too short. **Docker for Data Science** -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:18: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:16: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:46: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:51: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:62: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} WARNING: invalid signature for autoclass ('{{ objname }}') WARNING: don't know which module to import for autodocumenting '{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) WARNING: invalid signature for automodule ('{{ fullname }}') WARNING: don't know which module to import for autodocumenting '{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'cyverse/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:75: WARNING: Content block expected for the "important" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:5: WARNING: Undefined substitution referenced: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:5: WARNING: Unknown target name: "home_icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/de_docker.rst:4: WARNING: Duplicate explicit target name: "dockerhub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:104: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:111: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:144: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/vice_docker.rst:4: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:260: WARNING: Title underline too short. 3.1 Log into the Docker Hub Registry ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:311: WARNING: Title underline too short. 3.3 Private repositories ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:311: WARNING: Title underline too short. 3.3 Private repositories ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:316: WARNING: Title underline too short. 3.4 Pull down the Registry Image ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:376: WARNING: Title underline too short. 4.0 Automated Docker image building from GitHub ============================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:376: WARNING: Title underline too short. 4.0 Automated Docker image building from GitHub ============================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:568: WARNING: Title level inconsistent: 5.1 Bind mounts ^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:582: WARNING: Title level inconsistent: 5.2 Create and manage volumes ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:632: WARNING: Title level inconsistent: Populate a volume using a container ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:651: WARNING: Error in "code-block" directive: 1 argument(s) required, 0 supplied. .. code-block:: HOSTNAME=790e13bba28a SHLVL=1 HOME=/root PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:725: WARNING: Title underline too short. 6.0 Docker Compose for multi-container apps ========================================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:725: WARNING: Title underline too short. 6.0 Docker Compose for multi-container apps ========================================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerintro.rst:498: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerintro.rst:391: WARNING: Undefined substitution referenced: "volumes". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:9: WARNING: Title underline too short. **Finding the perfect container** ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:39: WARNING: Title underline too short. Docker Registries ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:9: WARNING: Duplicate explicit target name: "nvidia gpu cloud". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:111: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/about_cyverse.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/agenda.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/code_conduct.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/code_conduct.rst:9: WARNING: Title underline too short. **Code of Conduct** ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/installation.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:9: WARNING: Title underline too short. **Location** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:48: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:52: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:8: WARNING: Title underline too short. **Learning objectives** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:20: WARNING: Title underline too short. **FAIR Data principles** ======================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:20: WARNING: Title underline too short. **FAIR Data principles** ======================= 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name: "Ask CyVerse". cyverse_rst_defined_substitutions.txt:95: WARNING: Duplicate substitution definition name: "CyVerse Learning Center". cyverse_rst_defined_substitutions.txt:99: WARNING: Duplicate substitution definition name: "CyVerse Wiki". cyverse_rst_defined_substitutions.txt:106: WARNING: Duplicate substitution definition name: "CyVerse_logo". cyverse_rst_defined_substitutions.txt:111: WARNING: Duplicate substitution definition name: "CyVerse_logo2". cyverse_rst_defined_substitutions.txt:115: WARNING: Duplicate substitution definition name: "Home_Icon". cyverse_rst_defined_substitutions.txt:120: WARNING: Duplicate substitution definition name: "Home_Icon2". cyverse_rst_defined_substitutions.txt:125: WARNING: Duplicate substitution definition name: "Intercom". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:23: WARNING: toctree contains reference to nonexisting document 'getting_started/glossary' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:96: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:100: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short. 5.0 Building your own Containers from scratch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short. 5.2 Building Singularity containers ================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:221: WARNING: Error in "image" directive: no content permitted. image:: ../img/singularity.png :height: 200 :width: 200 singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:221: WARNING: Substitution definition "singularity" empty or invalid. .. |singularity| image:: ../img/singularity.png :height: 200 :width: 200 singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:4: WARNING: 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--prefix=/usr/local make -j4 make install /usr/local/bin/mpicc examples/hellow.c -o /usr/bin/hellow /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityintro.rst:308: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:16: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:30: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:30: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:33: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:41: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:41: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:46: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:46: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Duplicate explicit target name: "mint". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:54: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ 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[100%] instructions_reporting/../img/instructors_code.png copying TeX support files... done build succeeded, 157 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2020-09-17T18:46:25.040935Z, end-time: 2020-09-17T18:46:25.102751Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2020-09-17T18:46:25.345183Z, end-time: 2020-09-17T18:47:09.350467Z, duration: 44, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-cc-2020 -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. 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[3] [4] Chapter 2. [5] [6] Chapter 3. [7] [8] Chapter 4. [9] Underfull \hbox (badness 5189) in paragraph at lines 2--309 [][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber- (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [10] Chapter 5. [11] [12] Chapter 6. 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[17 <./cyverse_cmyk3.png> <./homeicon5.png>] [18] Chapter 8. [19] Overfull \hbox (31.92583pt too wide) in paragraph at lines 831--832 [][] [20 <./reproducibility-spectrum.png>] Chapter 9. [21] [22] Chapter 10. [23] [24] Chapter 11. [25] [26] Chapter 12. [27 <./cyverse_cmyk2.png>] [28 <./homeicon2.png>] Chapter 13. [29] [30] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1201--1202 [][] [31 <./biocontainers5a1.png (PNG copy)>] [32 <./dff16156a2fac35ba7650c7bae20c56 1e0b8d2e8.png>] Overfull \hbox (69.56999pt too wide) in paragraph at lines 1257--1258 [][] Overfull \hbox (44.56996pt too wide) in paragraph at lines 1286--1287 [][] Overfull \hbox (44.56996pt too wide) in paragraph at lines 1291--1292 [][] [33 <./atmoactive.png (PNG copy)> <./atmoauth.png (PNG copy)>] Overfull \hbox (19.56993pt too wide) in paragraph at lines 1311--1312 [][] [34 <./atmosuccess.png (PNG copy)>] [35 <./hubfind1.png (PNG copy)>] [36] Chapter 14. [37 <./docker.png>] [38] Underfull \hbox (badness 10000) in paragraph at lines 1485--1486 []\T1/ptm/m/n/10 You can change the en-try-point of a con-tainer by mak-ing a s tate-ment af-ter the \T1/pcr/m/n/10 repository/ [39] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [40] [41] [42] [43] [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 1864--1867 []|\T1/ptm/m/it/10 Usage: \T1/pcr/m/n/10 docker run -it user/image:tag Overfull \hbox (6.70221pt too wide) in paragraph at lines 1870--1873 [] [46] [47] [48 <./portainer_demo.png>] [49 <./pwd.png>] [50] Chapter 15. [51] [52] [53] [54] [55] [56 <./docker_image.png>] [57 <./private_registry.png> ] [58] Overfull \hbox (132.49107pt too wide) in paragraph at lines 2462--2463 [][] Overfull \hbox (132.49107pt too wide) in paragraph at lines 2473--2474 [][] [59 <./dockerhub_create.png> <./dockerhub_createrepo.png>] Overfull \hbox (132.49107pt too wide) in paragraph at lines 2487--2488 [][] [60 <./dockerhub_buildsettings.png>] Overfull \hbox (132.49107pt too wide) in paragraph at lines 2491--2492 [][] [61 <./dockerhub_autobuild.png>] [62 <./create_repo.png> <./create_repo2.png>] Overfull \hbox (132.49107pt too wide) in paragraph at lines 2595--2596 [][] [63] Overfull \vbox (90.47859pt too high) has occurred while \output is active [64 <./dockerhub_autobuilds.png>] [65 <./auto_build-2.1.png>] [66 <./auto_build -5.png> <./auto_build-6.png>] [67 <./auto_build-7.png>] Underfull \hbox (badness 10000) in paragraph at lines 2727--2729 \T1/ptm/b/n/10 Note: \T1/ptm/m/n/10 File lo-ca-tion on Mac OS X is a bit dif-f er-ent: [][]$https : / / timonweb . com / posts / [68] [69 <./bind_mount.png>] [70] [71] [72 <./dc-1.png>] Chapter 16. 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[83] [84] [85] [86] Chapter 18. [87] [88] Chapter 19. [89] [90] [91] [92] [93 <./cyverse_cmyk.png> <./homeicon.png>] [94] Chapter 20. [95 <./biocontainers5a.png (PNG copy)>] [96 <./biocontainers13.png (PNG copy)>] Overfull \hbox (94.8507pt too wide) in paragraph at lines 4030--4031 [][] Overfull \hbox (94.8507pt too wide) in paragraph at lines 4034--4035 [][] LaTeX Warning: Hyper reference `breakout/biocontainers:how-to-request-a-biocont ainer' on page 97 undefined on input line 4041. LaTeX Warning: Hyper reference `breakout/biocontainers:how-to-build-a-biocontai ner' on page 97 undefined on input line 4041. [97 <./biocontainers15.png (PNG copy)> <./biocontainers19.png (PNG copy)>] Overfull \hbox (94.8507pt too wide) in paragraph at lines 4059--4060 [][] LaTeX Warning: Hyper reference `breakout/biocontainers:how-to-request-a-biocont ainer' on page 98 undefined on input line 4062. 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See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4341 ...87086e249/Powered-By-CyVerse-blue}.svg}} ^^M [109] [110] Chapter 23. [111] [112] Chapter 24. [113] [114] Chapter 25. [115] ! 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.4482 ...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.4482 ...ersion of Linux/Windows/OSX/OS9 —  well this is where Docker ... 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[161] Overfull \hbox (94.8507pt too wide) in paragraph at lines 5391--5392 [][] [162] Overfull \hbox (94.8507pt too wide) in paragraph at lines 5395--5396 [][] [163 <./static_site_docker.png> <./instructors_code.png>] [164] Chapter 34. No file cyverse-cc-2020.ind. [165] (./cyverse-cc-2020.aux) Package rerunfilecheck Warning: File `cyverse-cc-2020.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-cc-2020.pdf (169 pages, 11077094 bytes). Transcript written on cyverse-cc-2020.log. Latexmk: Index file 'cyverse-cc-2020.idx' was written Latexmk: Missing input file: 'cyverse-cc-2020.ind' from line 'No file cyverse-cc-2020.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-cc-2020.pdf' Rule 'makeindex cyverse-cc-2020.idx': File changes, etc: Non-existent destination files: 'cyverse-cc-2020.ind' ------------ Run number 1 of rule 'makeindex cyverse-cc-2020.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-cc-2020.ind" "cyverse-cc-2020.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-cc-2020.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file cyverse-cc-2020.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-cc-2020.ind. Transcript written in cyverse-cc-2020.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-cc-2020.aux' 'cyverse-cc-2020.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-cc-2020" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./CyVerseDocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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(./cyverse-cc-2020.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] (./cyverse-cc-2020.toc [1]) [2] Overfull \hbox (132.49107pt too wide) in paragraph at lines 88--89 [][] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1 <./cyverse_learni ng2.png> <./homeicon4.png> <./cc-boat.png (PNG copy)> <./cyverse_learning1.png> <./homeicon3.png>] [2] Chapter 1. [3] [4] Chapter 2. [5] [6] Chapter 3. [7] [8] Chapter 4. [9] Underfull \hbox (badness 5189) in paragraph at lines 2--309 [][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber- (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [10] Chapter 5. [11] [12] Chapter 6. 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[37 <./docker.png>] [38] Underfull \hbox (badness 10000) in paragraph at lines 1485--1486 []\T1/ptm/m/n/10 You can change the en-try-point of a con-tainer by mak-ing a s tate-ment af-ter the \T1/pcr/m/n/10 repository/ [39] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [40] [41] [42] [43] [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 1864--1867 []|\T1/ptm/m/it/10 Usage: \T1/pcr/m/n/10 docker run -it user/image:tag Overfull \hbox (6.70221pt too wide) in paragraph at lines 1870--1873 [] [46] [47] [48 <./portainer_demo.png>] [49 <./pwd.png>] [50] Chapter 15. 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[83] [84] [85] [86] Chapter 18. [87] [88] Chapter 19. [89] [90] [91] [92] [93 <./cyverse_cmyk.png> <./homeicon.png>] [94] Chapter 20. 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Type H for immediate help. ... l.4482 ...ersion of Linux/Windows/OSX/OS9 —  well this is where Docker ... Overfull \hbox (57.21031pt too wide) in paragraph at lines 4495--4496 [][] Overfull \hbox (57.21031pt too wide) in paragraph at lines 4499--4500 [][] [116 <./jn_login.png>] Overfull \hbox (57.21031pt too wide) in paragraph at lines 4503--4504 [][] Overfull \hbox (57.21031pt too wide) in paragraph at lines 4505--4506 [][] [117 <./jn_login2.png> <./jn_login3.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.4525 ...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.4525 ...ose file. And there you have it —  a quick and easy way to st... 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[3] [4] Chapter 2. [5] [6] Chapter 3. [7] [8] Chapter 4. [9] Underfull \hbox (badness 5189) in paragraph at lines 2--309 [][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber- (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [10] Chapter 5. [11] [12] Chapter 6. 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[17 <./cyverse_cmyk3.png> <./homeicon5.png>] [18] Chapter 8. [19] Overfull \hbox (31.92583pt too wide) in paragraph at lines 831--832 [][] [20 <./reproducibility-spectrum.png>] Chapter 9. [21] [22] Chapter 10. [23] [24] Chapter 11. [25] [26] Chapter 12. [27 <./cyverse_cmyk2.png>] [28 <./homeicon2.png>] Chapter 13. [29] [30] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1201--1202 [][] [31 <./biocontainers5a1.png (PNG copy)>] [32 <./dff16156a2fac35ba7650c7bae20c56 1e0b8d2e8.png>] Overfull \hbox (69.56999pt too wide) in paragraph at lines 1257--1258 [][] Overfull \hbox (44.56996pt too wide) in paragraph at lines 1286--1287 [][] Overfull \hbox (44.56996pt too wide) in paragraph at lines 1291--1292 [][] [33 <./atmoactive.png (PNG copy)> <./atmoauth.png (PNG copy)>] Overfull \hbox (19.56993pt too wide) in paragraph at lines 1311--1312 [][] [34 <./atmosuccess.png (PNG copy)>] [35 <./hubfind1.png (PNG copy)>] [36] Chapter 14. [37 <./docker.png>] [38] Underfull \hbox (badness 10000) in paragraph at lines 1485--1486 []\T1/ptm/m/n/10 You can change the en-try-point of a con-tainer by mak-ing a s tate-ment af-ter the \T1/pcr/m/n/10 repository/ [39] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [40] [41] [42] [43] [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 1864--1867 []|\T1/ptm/m/it/10 Usage: \T1/pcr/m/n/10 docker run -it user/image:tag Overfull \hbox (6.70221pt too wide) in paragraph at lines 1870--1873 [] [46] [47] [48 <./portainer_demo.png>] [49 <./pwd.png>] [50] Chapter 15. 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[83] [84] [85] [86] Chapter 18. [87] [88] Chapter 19. [89] [90] [91] [92] [93 <./cyverse_cmyk.png> <./homeicon.png>] [94] Chapter 20. 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Type H for immediate help. ... l.4482 ...ersion of Linux/Windows/OSX/OS9 —  well this is where Docker ... Overfull \hbox (57.21031pt too wide) in paragraph at lines 4495--4496 [][] Overfull \hbox (57.21031pt too wide) in paragraph at lines 4499--4500 [][] [116 <./jn_login.png>] Overfull \hbox (57.21031pt too wide) in paragraph at lines 4503--4504 [][] Overfull \hbox (57.21031pt too wide) in paragraph at lines 4505--4506 [][] [117 <./jn_login2.png> <./jn_login3.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.4525 ...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.4525 ...ose file. And there you have it —  a quick and easy way to st... 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[161] Overfull \hbox (94.8507pt too wide) in paragraph at lines 5391--5392 [][] [162] Overfull \hbox (94.8507pt too wide) in paragraph at lines 5395--5396 [][] [163 <./static_site_docker.png> <./instructors_code.png>] [164] Chapter 34. (./cyverse-cc-2020.ind) [165] (./cyverse-cc-2020.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-cc-2020.pdf (169 pages, 11082906 bytes). Transcript written on cyverse-cc-2020.log. Latexmk: Index file 'cyverse-cc-2020.idx' was written Latexmk: Log file says output to 'cyverse-cc-2020.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2020-09-17T18:47:09.481603Z, end-time: 2020-09-17T18:47:09.542366Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/./_build/latex/cyverse-cc-2020.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/artifacts/latest/sphinx_pdf/cyverse-cc-2020.pdf [rtd-command-info] start-time: 2020-09-17T18:47:09.906217Z, end-time: 2020-09-17T18:47:25.269718Z, duration: 15, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [epub]: targets for 63 source files that are out of date updating environment: 63 added, 0 changed, 0 removed reading sources... 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[100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/biocontainers.rst:177: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/datascience.rst:2: WARNING: Title underline too short. **Docker for Data Science** -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:18: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:16: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:46: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:51: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/breakout/workflows.rst:62: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} WARNING: invalid signature for autoclass ('{{ objname }}') WARNING: don't know which module to import for autodocumenting '{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) WARNING: invalid signature for automodule ('{{ fullname }}') WARNING: don't know which module to import for autodocumenting '{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'cyverse/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:75: WARNING: Content block expected for the "important" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:5: WARNING: Undefined substitution referenced: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/boot.rst:5: WARNING: Unknown target name: "home_icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/de_docker.rst:4: WARNING: Duplicate explicit target name: "dockerhub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:104: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:111: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/tool_integration_app_building_DE.rst:144: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/cyverse/vice_docker.rst:4: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:260: WARNING: Title underline too short. 3.1 Log into the Docker Hub Registry ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:311: WARNING: Title underline too short. 3.3 Private repositories ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:311: WARNING: Title underline too short. 3.3 Private repositories ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:316: WARNING: Title underline too short. 3.4 Pull down the Registry Image ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:376: WARNING: Title underline too short. 4.0 Automated Docker image building from GitHub ============================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:376: WARNING: Title underline too short. 4.0 Automated Docker image building from GitHub ============================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:568: WARNING: Title level inconsistent: 5.1 Bind mounts ^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:582: WARNING: Title level inconsistent: 5.2 Create and manage volumes ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:632: WARNING: Title level inconsistent: Populate a volume using a container ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:651: WARNING: Error in "code-block" directive: 1 argument(s) required, 0 supplied. .. code-block:: HOSTNAME=790e13bba28a SHLVL=1 HOME=/root PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:725: WARNING: Title underline too short. 6.0 Docker Compose for multi-container apps ========================================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockeradvanced.rst:725: WARNING: Title underline too short. 6.0 Docker Compose for multi-container apps ========================================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerintro.rst:498: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/dockerintro.rst:391: WARNING: Undefined substitution referenced: "volumes". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:9: WARNING: Title underline too short. **Finding the perfect container** ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:39: WARNING: Title underline too short. Docker Registries ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:9: WARNING: Duplicate explicit target name: "nvidia gpu cloud". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/docker/findingcontainers.rst:111: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/about_cyverse.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/agenda.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/code_conduct.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/code_conduct.rst:9: WARNING: Title underline too short. **Code of Conduct** ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/installation.rst:1: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'getting_started/cyverse_rst_defined_substitutions.txt'. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:9: WARNING: Title underline too short. **Location** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:48: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/location.rst:52: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:8: WARNING: Title underline too short. **Learning objectives** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:20: WARNING: Title underline too short. **FAIR Data principles** ======================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/getting_started/main.rst:20: WARNING: Title underline too short. **FAIR Data principles** ======================= 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name: "Ask CyVerse". cyverse_rst_defined_substitutions.txt:95: WARNING: Duplicate substitution definition name: "CyVerse Learning Center". cyverse_rst_defined_substitutions.txt:99: WARNING: Duplicate substitution definition name: "CyVerse Wiki". cyverse_rst_defined_substitutions.txt:106: WARNING: Duplicate substitution definition name: "CyVerse_logo". cyverse_rst_defined_substitutions.txt:111: WARNING: Duplicate substitution definition name: "CyVerse_logo2". cyverse_rst_defined_substitutions.txt:115: WARNING: Duplicate substitution definition name: "Home_Icon". cyverse_rst_defined_substitutions.txt:120: WARNING: Duplicate substitution definition name: "Home_Icon2". cyverse_rst_defined_substitutions.txt:125: WARNING: Duplicate substitution definition name: "Intercom". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:23: WARNING: toctree contains reference to nonexisting document 'getting_started/glossary' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:96: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/index.rst:100: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short. 5.0 Building your own Containers from scratch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short. 5.2 Building Singularity containers ================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:221: WARNING: Error in "image" directive: no content permitted. image:: ../img/singularity.png :height: 200 :width: 200 singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:221: WARNING: Substitution definition "singularity" empty or invalid. .. |singularity| image:: ../img/singularity.png :height: 200 :width: 200 singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityadvanced.rst:4: WARNING: 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--prefix=/usr/local make -j4 make install /usr/local/bin/mpicc examples/hellow.c -o /usr/bin/hellow /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/singularity/singularityintro.rst:308: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:7: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:16: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cc-2020/checkouts/latest/topics/linux.rst:30: WARNING: Title underline too short. *Installing Linux* 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