Read the Docs build information Build id: 257921 Project: cyverse-learning-materials-home Version: latest Commit: fb78956a783ff0abdcd61ec22e5b796adce02322 Date: 2019-11-08T18:48:40.373459Z State: finished Success: True [rtd-command-info] start-time: 2019-11-08T18:48:41.213465Z, end-time: 2019-11-08T18:48:41.247769Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/learning-materials-home.git [rtd-command-info] start-time: 2019-11-08T18:48:41.332888Z, end-time: 2019-11-08T18:48:41.973242Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/CyVerse-learning-materials/learning-materials-home 0274074..fb78956 master -> origin/master [rtd-command-info] start-time: 2019-11-08T18:48:42.225449Z, end-time: 2019-11-08T18:48:42.261987Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 0274074 Update workshops.rst HEAD is now at fb78956 Update webinars.rst [rtd-command-info] start-time: 2019-11-08T18:48:42.341691Z, end-time: 2019-11-08T18:48:42.381108Z, duration: 0, exit-code: 0 git clean -d -f -f Removing _build/ Removing misc/__init__.pyc Removing misc/cyverse_sphinx_conf.pyc [rtd-command-info] start-time: 2019-11-08T18:48:43.608087Z, end-time: 2019-11-08T18:48:46.143840Z, duration: 2, exit-code: 0 python2.7 -mvirtualenv --no-site-packages --no-download New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/bin/python2.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-11-08T18:48:46.231714Z, end-time: 2019-11-08T18:48:48.626319Z, duration: 2, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip pip Collecting pip Using cached https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl Installing collected packages: pip Found existing installation: pip 18.1 Uninstalling pip-18.1: Successfully uninstalled pip-18.1 Successfully installed pip-19.3.1 [rtd-command-info] start-time: 2019-11-08T18:48:48.712904Z, end-time: 2019-11-08T18:49:00.380335Z, duration: 11, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip 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 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. 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 Using cached https://files.pythonhosted.org/packages/13/e5/6d710c9cf96c31ac82657bcfb441df328b22df8564d58d0c4cd62612674c/Pygments-2.3.1-py2.py3-none-any.whl Collecting setuptools==41.0.1 Using cached https://files.pythonhosted.org/packages/ec/51/f45cea425fd5cb0b0380f5b0f048ebc1da5b417e48d304838c02d6288a1e/setuptools-41.0.1-py2.py3-none-any.whl Collecting docutils==0.14 Using cached https://files.pythonhosted.org/packages/50/09/c53398e0005b11f7ffb27b7aa720c617aba53be4fb4f4f3f06b9b5c60f28/docutils-0.14-py2-none-any.whl Processing /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6/mock-1.0.1-cp27-none-any.whl Collecting pillow==5.4.1 Using cached https://files.pythonhosted.org/packages/0d/f3/421598450cb9503f4565d936860763b5af413a61009d87a5ab1e34139672/Pillow-5.4.1-cp27-cp27mu-manylinux1_x86_64.whl Collecting alabaster!=0.7.5,<0.8,>=0.7 Using cached https://files.pythonhosted.org/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-py2.py3-none-any.whl Collecting commonmark==0.8.1 Using cached https://files.pythonhosted.org/packages/ab/ca/439c88039583a29564a0043186875258e9a4f041fb5c422cd387b8e10175/commonmark-0.8.1-py2.py3-none-any.whl Collecting recommonmark==0.5.0 Using cached https://files.pythonhosted.org/packages/9b/3d/92ea48401622510e57b4bdaa74dc9db2fb9e9e892324b48f9c02d716a93a/recommonmark-0.5.0-py2.py3-none-any.whl Collecting sphinx<2 Using cached https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl Collecting sphinx-rtd-theme<0.5 Using cached https://files.pythonhosted.org/packages/60/b4/4df37087a1d36755e3a3bfd2a30263f358d2dea21938240fa02313d45f51/sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl Collecting readthedocs-sphinx-ext<1.1 Using cached https://files.pythonhosted.org/packages/51/43/a5a98d9aec325b2824bdf504fa446ae876d0909d03e28667018f9eb01bcd/readthedocs_sphinx_ext-1.0.0-py2.py3-none-any.whl Processing /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip/wheels/8b/99/a0/81daf51dcd359a9377b110a8a886b3895921802d2fc1b2397e/future-0.18.2-cp27-none-any.whl Collecting snowballstemmer>=1.1 Using cached https://files.pythonhosted.org/packages/7d/4b/cdf1113a0e88b641893b814e9c36f69a6fda28cd88b62c7f0d858cde3166/snowballstemmer-2.0.0-py2.py3-none-any.whl Collecting sphinxcontrib-websupport Using cached https://files.pythonhosted.org/packages/2a/59/d64bda9b7480a84a3569be4dde267c0f6675b255ba63b4c8e84469940457/sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl Collecting packaging Using cached https://files.pythonhosted.org/packages/cf/94/9672c2d4b126e74c4496c6b3c58a8b51d6419267be9e70660ba23374c875/packaging-19.2-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 Using cached https://files.pythonhosted.org/packages/2c/60/f2af68eb046c5de5b1fe6dd4743bf42c074f7141fe7b2737d3061533b093/Babel-2.7.0-py2.py3-none-any.whl Collecting requests>=2.0.0 Using cached https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl Collecting Jinja2>=2.3 Using cached https://files.pythonhosted.org/packages/65/e0/eb35e762802015cab1ccee04e8a277b03f1d8e53da3ec3106882ec42558b/Jinja2-2.10.3-py2.py3-none-any.whl Collecting typing; python_version < "3.5" Using cached https://files.pythonhosted.org/packages/22/30/64ca29543375759dc589ade14a6cd36382abf2bec17d67de8481bc9814d7/typing-3.7.4.1-py2-none-any.whl Collecting imagesize Using cached https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl Collecting six>=1.5 Using cached https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl Collecting pyparsing>=2.0.2 Using cached https://files.pythonhosted.org/packages/a3/c4/7828cf9e71ce8fbd43c1e502f3fdd0498f069fcf9d1c268205ce278ae201/pyparsing-2.4.4-py2.py3-none-any.whl Collecting pytz>=2015.7 Using cached https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Using cached https://files.pythonhosted.org/packages/e0/da/55f51ea951e1b7c63a579c09dd7db825bb730ec1fe9c0180fc77bfb31448/urllib3-1.25.6-py2.py3-none-any.whl Collecting certifi>=2017.4.17 Using cached https://files.pythonhosted.org/packages/18/b0/8146a4f8dd402f60744fa380bc73ca47303cccf8b9190fd16a827281eac2/certifi-2019.9.11-py2.py3-none-any.whl Collecting chardet<3.1.0,>=3.0.2 Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl Collecting idna<2.9,>=2.5 Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl Collecting MarkupSafe>=0.23 Using cached https://files.pythonhosted.org/packages/fb/40/f3adb7cf24a8012813c5edb20329eb22d5d8e2a0ecf73d21d6b85865da11/MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, snowballstemmer, sphinxcontrib-websupport, pyparsing, six, packaging, pytz, babel, urllib3, certifi, chardet, idna, requests, MarkupSafe, Jinja2, typing, imagesize, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Found existing installation: setuptools 40.6.3 Uninstalling setuptools-40.6.3: Successfully uninstalled setuptools-40.6.3 Successfully installed Jinja2-2.10.3 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.7.0 certifi-2019.9.11 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.2 pillow-5.4.1 pyparsing-2.4.4 pytz-2019.3 readthedocs-sphinx-ext-1.0.0 recommonmark-0.5.0 requests-2.22.0 setuptools-41.0.1 six-1.13.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 typing-3.7.4.1 urllib3-1.25.6 [rtd-command-info] start-time: 2019-11-08T18:49:02.667022Z, end-time: 2019-11-08T18:49:02.999973Z, 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 Center Home' copyright = '2019, CyVerse' author = 'CyVerse' version = '0.1b.0' release = '0.1b.0' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright # html theme configuration -- see https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html html_theme_options = { # Table of Content options 'collapse_navigation': True, 'sticky_navigation': True, 'navigation_depth': 4, 'includehidden': True, 'titles_only': False } ########################################################################### # 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://media.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://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("html", "//readthedocs.com/projects/cyverse-learning-materials-home/downloads/htmlzip/latest/"), ], 'subprojects': [ ("cyverse-discovery-environment-guide", "https://learning.cyverse.org/projects/discovery-environment-guide/en/latest/"), ("cyverse-atmosphere-guide", "https://learning.cyverse.org/projects/atmosphere-guide/en/latest/"), ("cyverse-account-creation-quickstart", "https://learning.cyverse.org/projects/cyverse-account-creation-quickstart/en/latest/"), ("cyverse-importing-sradata-quickstart", "https://learning.cyverse.org/projects/cyverse-importing-sradata-quickstart/en/latest/"), ("cyverse-dnasubway-guide", "https://learning.cyverse.org/projects/dnasubway_guide/en/latest/"), ("cyverse-trimmomatic-quickstart", "https://learning.cyverse.org/projects/trimmomatic_quickstart/en/latest/"), ("cyverse-data-store-guide", "https://learning.cyverse.org/projects/data_store_guide/en/latest/"), ("cyverse-fastqc-quickstart", "https://learning.cyverse.org/projects/fastqc_quickstart/en/latest/"), ("cyverse-kallisto-tutorial", "https://learning.cyverse.org/projects/kallisto_tutorial/en/latest/"), ("cyverse-sra-submission-quickstart", "https://learning.cyverse.org/projects/sra_submission_quickstart/en/latest/"), ("cyverse-sciapps-guide", "https://learning.cyverse.org/projects/SciApps Guide/en/latest/"), ("cyverse-documentation-quickstart", "https://learning.cyverse.org/projects/Documentation-Quickstart/en/latest/"), ("cyverse-group-project-quickstart", "https://learning.cyverse.org/projects/cyverse-group-project-quickstart/en/latest/"), ("cyverse-container-camp-workshop-2019", "https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/"), ("cyverse-creating-docker-containers-quickstart", "https://learning.cyverse.org/projects/cyverse-creating-docker-containers-quickstart/en/latest/"), ("cyverse-learning-center-faq", "https://learning.cyverse.org/projects/faq/en/latest/"), ("cyverse-240-minute-r-tutorial", "https://learning.cyverse.org/projects/cyverse-240-minute-r-tutorial/en/latest/"), ("cyverse-git-for-mere-mortals", "https://learning.cyverse.org/projects/cyverse-git-for-mere-mortals/en/latest/"), ("cyverse-cyverse-tools-and-services-workshop", "https://learning.cyverse.org/projects/cyverse-cyverse-tools-and-services-workshop/en/latest/"), ("cyverse-visual-interactive-computing-environment", "https://learning.cyverse.org/projects/vice/en/latest/"), ("cyverse-doi-request-quickstart", "https://learning.cyverse.org/projects/cyverse-doi-request-quickstart/en/latest/"), ("cyverse-foundational-open-science-skills-2020", "https://learning.cyverse.org/projects/foss-2020/en/latest/"), ("cyverse-austria-workshop", "https://learning.cyverse.org/projects/cyverse-austria-workshop/en/latest/"), ], 'slug': 'cyverse-learning-materials-home', 'name': u'learning-materials-home', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'learning-materials-home', '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': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'fb78956a', } 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: 2019-11-08T18:49:03.081731Z, end-time: 2019-11-08T18:49:06.081248Z, duration: 2, 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 10 source files that are out of date updating environment: 10 added, 0 changed, 0 removed reading sources... [ 10%] README reading sources... [ 20%] contributing reading sources... [ 30%] index reading sources... [ 40%] platform_guides reading sources... [ 50%] power_users reading sources... [ 60%] quick_starts reading sources... [ 70%] tools_and_apps reading sources... [ 80%] tutorials reading sources... [ 90%] webinars reading sources... [100%] workshops /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/README.rst:21: WARNING: Duplicate explicit target name: "tutorials@cyverse.org". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/README.rst:170: WARNING: Duplicate substitution definition name: "Powered by CyVerse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/contributing.rst:39: WARNING: Duplicate substitution definition name: "Github Repo Link". README.rst:21: WARNING: Duplicate explicit target name: "tutorials@cyverse.org". README.rst:170: WARNING: Duplicate substitution definition name: "Powered by CyVerse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/platform_guides.rst:100: WARNING: Duplicate substitution definition name: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/power_users.rst:36: WARNING: Undefined substitution referenced: "External Collaborative Partnership". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/power_users.rst:36: WARNING: Undefined substitution referenced: "ECP Request web form". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/quick_starts.rst:125: WARNING: Duplicate substitution definition name: "Data Store". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tools_and_apps.rst:11: WARNING: Title underline too short. Tool and App Integration ----------- cyverse_rst_defined_substitutions.txt:32: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tutorials.rst:131: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tutorials.rst:145: WARNING: Duplicate substitution definition name: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tutorials.rst:59: WARNING: Undefined substitution referenced: "Discover Variants Using SAM Tools". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/webinars.rst:12: WARNING: Title underline too short. Follow this link to upcoming and past CyVerse Webinars (also know as CyVerse Focus Forums): https://cyverse.org/ffw>`_) ---- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/webinars.rst:12: WARNING: Title underline too short. Follow this link to upcoming and past CyVerse Webinars (also know as CyVerse Focus Forums): https://cyverse.org/ffw>`_) ---- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/webinars.rst:19: WARNING: Document may not end with a transition. cyverse_rst_defined_substitutions.txt:52: WARNING: Document may not end with a transition. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 10%] README writing output... [ 20%] contributing writing output... [ 30%] index writing output... [ 40%] platform_guides writing output... [ 50%] power_users writing output... [ 60%] quick_starts writing output... [ 70%] tools_and_apps writing output... [ 80%] tutorials writing output... [ 90%] webinars writing output... [100%] workshops generating indices... genindex writing additional pages... search copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_cmyk.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/_static' does not exist done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 19 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2019-11-08T18:49:06.217547Z, end-time: 2019-11-08T18:49:09.183138Z, duration: 2, 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: 10 added, 0 changed, 0 removed reading sources... [ 10%] README reading sources... [ 20%] contributing reading sources... [ 30%] index reading sources... [ 40%] platform_guides reading sources... [ 50%] power_users reading sources... [ 60%] quick_starts reading sources... [ 70%] tools_and_apps reading sources... [ 80%] tutorials reading sources... [ 90%] webinars reading sources... [100%] workshops /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/README.rst:21: WARNING: Duplicate explicit target name: "tutorials@cyverse.org". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/README.rst:170: WARNING: Duplicate substitution definition name: "Powered by CyVerse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/contributing.rst:39: WARNING: Duplicate substitution definition name: "Github Repo Link". README.rst:21: WARNING: Duplicate explicit target name: "tutorials@cyverse.org". README.rst:170: WARNING: Duplicate substitution definition name: "Powered by CyVerse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/platform_guides.rst:100: WARNING: Duplicate substitution definition name: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/power_users.rst:36: WARNING: Undefined substitution referenced: "External Collaborative Partnership". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/power_users.rst:36: WARNING: Undefined substitution referenced: "ECP Request web form". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/quick_starts.rst:125: WARNING: Duplicate substitution definition name: "Data Store". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tools_and_apps.rst:11: WARNING: Title underline too short. Tool and App Integration ----------- cyverse_rst_defined_substitutions.txt:32: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tutorials.rst:131: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tutorials.rst:145: WARNING: Duplicate substitution definition name: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tutorials.rst:59: WARNING: Undefined substitution referenced: "Discover Variants Using SAM Tools". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/webinars.rst:12: WARNING: Title underline too short. Follow this link to upcoming and past CyVerse Webinars (also know as CyVerse Focus Forums): https://cyverse.org/ffw>`_) ---- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/webinars.rst:12: WARNING: Title underline too short. Follow this link to upcoming and past CyVerse Webinars (also know as CyVerse Focus Forums): https://cyverse.org/ffw>`_) ---- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/webinars.rst:19: WARNING: Document may not end with a transition. cyverse_rst_defined_substitutions.txt:52: WARNING: Document may not end with a transition. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... README platform_guides tools_and_apps quick_starts tutorials workshops webinars contributing power_users writing... done writing additional files... copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_cmyk.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 19 warnings. The HTML page is in _build/localmedia.