Read the Docs build information Build id: 335889 Project: cyverse-container-camp-workshop-2019 Version: latest Commit: 5d193f47bac4371a2b15b6933ceb532b547854de Date: 2020-05-26T19:19:04.980591Z State: finished Success: True [rtd-command-info] start-time: 2020-05-26T19:19:17.937807Z, end-time: 2020-05-26T19:19:21.283571Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/container_camp_workshop_2019.git . Cloning into '.'... [rtd-command-info] start-time: 2020-05-26T19:19:21.605644Z, end-time: 2020-05-26T19:19:22.198864Z, duration: 0, 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 5d193f4 Merge pull request #6 from sanjanasudarshan/master [rtd-command-info] start-time: 2020-05-26T19:19:22.625530Z, end-time: 2020-05-26T19:19:22.833882Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-26T19:19:25.360908Z, end-time: 2020-05-26T19:19:28.566762Z, duration: 3, exit-code: 0 python2.7 -mvirtualenv New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/bin/python2.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-05-26T19:19:28.678142Z, end-time: 2020-05-26T19:19:29.444680Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (20.1.1) [rtd-command-info] start-time: 2020-05-26T19:19:29.698465Z, end-time: 2020-05-26T19:19:38.813373Z, duration: 9, 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 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support 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-py2-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-cp27-cp27mu-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 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 typing; python_version < "3.5" Downloading typing-3.7.4.1-py2-none-any.whl (26 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl (39 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl (24 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.4.5.1-py2.py3-none-any.whl (157 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 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-py2-none-any.whl size=23755 sha256=f05c3dad0e3a4b4fc3190b4d1eb38fc5ff3b93ffca4cda25888a27f96972d41b Stored in directory: /tmp/pip-ephem-wheel-cache-Kjn9pV/wheels/ad/62/e0/a06cc957652749e64c7904e899eca3ecb2ec47c60d52653660 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-py2-none-any.whl size=502566 sha256=e7e07fa7e69107ef2d2d3f28a7e09f271f0bf63e1e77447f802fa972802ab0ac Stored in directory: /tmp/pip-ephem-wheel-cache-Kjn9pV/wheels/5f/11/0c/aad680baf5ef4fbcbab992c9f03e1130357e0c173a4fdabfff Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, imagesize, typing, MarkupSafe, Jinja2, certifi, idna, chardet, urllib3, requests, six, pyparsing, packaging, snowballstemmer, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 44.1.0 Uninstalling setuptools-44.1.0: Successfully uninstalled setuptools-44.1.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.4.5.1 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 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-2.23.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 typing-3.7.4.1 urllib3-1.25.9 [rtd-command-info] start-time: 2020-05-26T19:19:38.923356Z, end-time: 2020-05-26T19:19:41.714102Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 1)) (1.8.5) Requirement already satisfied: recommonmark in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/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: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.8.0) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.2.0) Requirement already satisfied: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (3.7.4.1) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.14) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.11.2) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.23.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (20.4) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.3.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.7.12) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.0.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (41.0.1) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.15.0) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.1.2) Requirement already satisfied: commonmark>=0.7.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from recommonmark->-r requirements.txt (line 2)) (0.8.1) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx->-r requirements.txt (line 1)) (2020.1) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx->-r requirements.txt (line 1)) (1.1.1) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2020.4.5.1) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (1.25.9) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2.9) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (3.0.4) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from packaging->sphinx->-r requirements.txt (line 1)) (2.4.7) Requirement already satisfied: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/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-py2-none-any.whl size=1250222 sha256=d46cad9819182efadabc699d5ebcdb8822fbad93462fd528df648def176b174f Stored in directory: /tmp/pip-ephem-wheel-cache-YCdUXz/wheels/95/93/4e/ce6bc27771a672df0da2021feb26f922e8a74bacdeb9195838 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-py2-none-any.whl size=2555155 sha256=ed8034b89086d9bcf32ad1ee9463e20b3efff24348f78952380125f05a95fb23 Stored in directory: /tmp/pip-ephem-wheel-cache-YCdUXz/wheels/9d/61/03/c574afdc16ce34de1d382f4d4cdb1eb624fafabe9e0a6988c2 Successfully built sphinx-bootstrap-theme guzzle-sphinx-theme Installing collected packages: sphinxcontrib-images, sphinx-bootstrap-theme, guzzle-sphinx-theme Successfully installed guzzle-sphinx-theme-0.7.11 sphinx-bootstrap-theme-0.7.1 sphinxcontrib-images-0.9.2 [rtd-command-info] start-time: 2020-05-26T19:19:42.994771Z, end-time: 2020-05-26T19:19:43.211154Z, 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 Container Camp 2019' copyright = '2019, CyVerse' author = 'CyVerse' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import 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_workshop_2019/en/latest/pdf/"), ("html", "//learning.cyverse.org/_/downloads/container_camp_workshop_2019/en/latest/htmlzip/"), ("epub", "//learning.cyverse.org/_/downloads/container_camp_workshop_2019/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'cyverse-container-camp-workshop-2019', 'name': u'container_camp_workshop_2019', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/', 'analytics_code': 'UA-72224033-6', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'container_camp_workshop_2019', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': 'UA-72224033-6', 'global_analytics_code': 'UA-17997319-2', 'commit': '5d193f47', } 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' [rtd-command-info] start-time: 2020-05-26T19:19:43.343641Z, end-time: 2020-05-26T19:19:49.008033Z, duration: 5, exit-code: 0 python sphinx-build -T -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 55 source files that are out of date updating environment: 55 added, 0 changed, 0 removed reading sources... 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reference: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/agenda.rst:2: WARNING: Duplicate explicit target name: "slides". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/main.rst:4: WARNING: Title underline too short. **Workshop Code of Conduct and Other Information** ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/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-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short. 5.2 Building Singularity containers ================================== 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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-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". looking for now-outdated files... none found pickling environment... done checking consistency... 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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/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-container-camp-workshop-2019/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-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:140: WARNING: Duplicate explicit target name: "user guide". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:278: 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-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". looking for now-outdated files... none found pickling environment... done checking consistency... 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[3] [4] Chapter 2. [5] Underfull \hbox (badness 5189) in paragraph at lines 2--288 [][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber- [6] Chapter 3. Underfull \hbox (badness 5802) in paragraph at lines 332--333 []|\T1/ptm/m/n/10 General in-tro-duc-tion to Underfull \hbox (badness 6675) in paragraph at lines 339--340 \T1/ptm/m/n/10 tainer tech-nol-ogy land- Underfull \hbox (badness 10000) in paragraph at lines 353--354 []|\T1/ptm/m/n/10 Introduction to Docker Underfull \hbox (badness 6412) in paragraph at lines 360--361 []|\T1/ptm/m/n/10 Lunch break (on your Underfull \hbox (badness 10000) in paragraph at lines 379--380 []|\T1/ptm/m/n/10 Docker hands-on ex-er- Underfull \hbox (badness 10000) in paragraph at lines 2--383 []|[][]\T1/ptm/m/n/10 Docker hands-on ex-er- Underfull \hbox (badness 6961) in paragraph at lines 400--401 []|\T1/ptm/m/n/10 Review Day 1 (Ques- Underfull \hbox (badness 10000) in paragraph at lines 2--421 [][][]\T1/ptm/m/n/10 Non-interactive Underfull \hbox (badness 10000) in paragraph at lines 1--441 [][][]$\T1/ptm/m/n/10 https : / / mirrorlab . 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[15] [16] Chapter 8. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [17 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [18] [19] [20] [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1041--1043 \T1/ptm/b/n/10 Note: \T1/ptm/m/n/10 When you run the \T1/pcr/m/n/10 docker bui ld \T1/ptm/m/n/10 com-mand given be-low, make sure to re-place [24] Overfull \vbox (11.24115pt too high) detected at line 1126 [25] LaTeX Warning: Hyper reference `docker/dockerintro:create-a-python-file-contain ing-a-function' on page 26 undefined on input line 1134. [26] [27] [28] [29] [30 <./portainer_demo.png>] [31 <./pwd.png>] [32] Chapter 9. [33] [34] [35 <./docker_image.png>] [36 <./private_registry.png>] [37] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1699--1700 [][] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1710--1711 [][] [38 <./dockerhub_create.png>] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1724--1725 [][] [39 <./dockerhub_createrepo.png>] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1728--1729 [][] [40 <./dockerhub_buildsettings.png>] [41 <./dockerhub_autobuild.png>] [42 <./cr eate_repo.png> <./create_repo2.png>] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1832--1833 [][] [43] Overfull \vbox (90.47859pt too high) has occurred while \output is active [44 <./dockerhub_autobuilds.png>] [45 <./auto_build-2.1.png>] [46 <./auto_build -5.png> <./auto_build-6.png>] [47 <./auto_build-7.png>] [48 <./volumes.png>] Underfull \hbox (badness 10000) in paragraph at lines 2050--2052 \T1/ptm/b/n/10 Note: \T1/ptm/m/n/10 File lo-ca-tion on Mac OS X is a bit dif-f er-ent: [][]$https : / / timonweb . com / posts / [49] [50] [51 <./bind_mount.png>] [52] [53] [54] [55 <./dc-1.png>] [56] Chapter 10. 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Latexmk: Index file 'cyverse-container-camp-workshop-2019.idx' was written Latexmk: Missing input file: 'cyverse-container-camp-workshop-2019.ind' from line 'No file cyverse-container-camp-workshop-2019.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Rule 'makeindex cyverse-container-camp-workshop-2019.idx': File changes, etc: Non-existent destination files: 'cyverse-container-camp-workshop-2019.ind' ------------ Run number 1 of rule 'makeindex cyverse-container-camp-workshop-2019.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-container-camp-workshop-2019.ind" "cyverse-container-camp-workshop-2019.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-container-camp-workshop-2019.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). 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[3] [4] Chapter 2. [5] Underfull \hbox (badness 5189) in paragraph at lines 2--288 [][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber- [6] Chapter 3. Underfull \hbox (badness 5802) in paragraph at lines 332--333 []|\T1/ptm/m/n/10 General in-tro-duc-tion to Underfull \hbox (badness 6675) in paragraph at lines 339--340 \T1/ptm/m/n/10 tainer tech-nol-ogy land- Underfull \hbox (badness 10000) in paragraph at lines 353--354 []|\T1/ptm/m/n/10 Introduction to Docker Underfull \hbox (badness 6412) in paragraph at lines 360--361 []|\T1/ptm/m/n/10 Lunch break (on your Underfull \hbox (badness 10000) in paragraph at lines 379--380 []|\T1/ptm/m/n/10 Docker hands-on ex-er- Underfull \hbox (badness 10000) in paragraph at lines 2--383 []|[][]\T1/ptm/m/n/10 Docker hands-on ex-er- Underfull \hbox (badness 6961) in paragraph at lines 400--401 []|\T1/ptm/m/n/10 Review Day 1 (Ques- Underfull \hbox (badness 10000) in paragraph at lines 2--421 [][][]\T1/ptm/m/n/10 Non-interactive Underfull \hbox (badness 10000) in paragraph at lines 1--441 [][][]$\T1/ptm/m/n/10 https : / / mirrorlab . 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Latexmk: Index file 'cyverse-container-camp-workshop-2019.idx' was written Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-container-camp-workshop-2019.out' 'cyverse-container-camp-workshop-2019.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-container-camp-workshop-2019" "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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[3] [4] Chapter 2. [5] Underfull \hbox (badness 5189) in paragraph at lines 2--288 [][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber- [6] Chapter 3. Underfull \hbox (badness 5802) in paragraph at lines 332--333 []|\T1/ptm/m/n/10 General in-tro-duc-tion to Underfull \hbox (badness 6675) in paragraph at lines 339--340 \T1/ptm/m/n/10 tainer tech-nol-ogy land- Underfull \hbox (badness 10000) in paragraph at lines 353--354 []|\T1/ptm/m/n/10 Introduction to Docker Underfull \hbox (badness 6412) in paragraph at lines 360--361 []|\T1/ptm/m/n/10 Lunch break (on your Underfull \hbox (badness 10000) in paragraph at lines 379--380 []|\T1/ptm/m/n/10 Docker hands-on ex-er- Underfull \hbox (badness 10000) in paragraph at lines 2--383 []|[][]\T1/ptm/m/n/10 Docker hands-on ex-er- Underfull \hbox (badness 6961) in paragraph at lines 400--401 []|\T1/ptm/m/n/10 Review Day 1 (Ques- Underfull \hbox (badness 10000) in paragraph at lines 2--421 [][][]\T1/ptm/m/n/10 Non-interactive Underfull \hbox (badness 10000) in paragraph at lines 1--441 [][][]$\T1/ptm/m/n/10 https : / / mirrorlab . 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[15] [16] Chapter 8. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [17 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [18] [19] [20] [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1041--1043 \T1/ptm/b/n/10 Note: \T1/ptm/m/n/10 When you run the \T1/pcr/m/n/10 docker bui ld \T1/ptm/m/n/10 com-mand given be-low, make sure to re-place [24] Overfull \vbox (11.24115pt too high) detected at line 1126 [25] [26] [27] [28] [29] [30 <./portainer_demo.png>] [31 <./pwd.png>] [32] Chapter 9. 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See the inputenc package documentation for explanation. Type H for immediate help. ... l.3770 ...inxupquote{app.py}} inside the folder  — \sphinxcode{\sphinxupq... [96 <./rstudio_login.png>] [97] [98] [99 <./cyverse_rgb.png>] [100] Chapter 18. 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[135] Overfull \hbox (94.8507pt too wide) in paragraph at lines 4604--4605 [][] [136] Overfull \hbox (94.8507pt too wide) in paragraph at lines 4608--4609 [][] [137 <./static_site_docker.png> <./instructors_code.png>] [138] Chapter 25. (./cyverse-container-camp-workshop-2019.ind) [139] (./cyverse-container-camp-workshop-2019.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-container-camp-workshop-2019.pdf (143 pages, 9568607 bytes). Transcript written on cyverse-container-camp-workshop-2019.log. Latexmk: Index file 'cyverse-container-camp-workshop-2019.idx' was written Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.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: 2020-05-26T19:20:57.410652Z, end-time: 2020-05-26T19:20:57.610942Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/./_build/latex/cyverse-container-camp-workshop-2019.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/artifacts/latest/sphinx_pdf/cyverse-container-camp-workshop-2019.pdf [rtd-command-info] start-time: 2020-05-26T19:20:57.732353Z, end-time: 2020-05-26T19:21:13.875498Z, duration: 16, 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 55 source files that are out of date updating environment: 55 added, 0 changed, 0 removed reading sources... 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[100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/biocontainers.rst:2: WARNING: Title underline too short. **Biocontainers** ================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/datascience.rst:2: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/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-container-camp-workshop-2019/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 }} 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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-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". looking for now-outdated files... none found pickling environment... done checking consistency... 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