Read the Docs build information Build id: 179490 Project: cyverse-dnasubway-guide Version: latest Commit: 9b17116d4212b95de88852fc4149ae7fda192e53 Date: 2019-01-31T21:36:07.496444Z State: finished Success: True [rtd-command-info] start-time: 2019-01-31T21:38:50.439996Z, end-time: 2019-01-31T21:38:50.450376Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/dnasubway_guide.git [rtd-command-info] start-time: 2019-01-31T21:38:50.518716Z, end-time: 2019-01-31T21:38:50.767903Z, duration: 0, exit-code: 0 git fetch --tags --prune --prune-tags --depth 50 [rtd-command-info] start-time: 2019-01-31T21:38:50.946657Z, end-time: 2019-01-31T21:38:51.031091Z, duration: 0, exit-code: 0 git checkout --force origin/master HEAD is now at 9b17116 add pyc [rtd-command-info] start-time: 2019-01-31T21:38:51.111634Z, end-time: 2019-01-31T21:38:51.128397Z, 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: 2019-01-31T21:38:52.022018Z, end-time: 2019-01-31T21:38:53.717393Z, duration: 1, exit-code: 0 python2.7 -mvirtualenv --no-site-packages --no-download New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python2.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python2.7) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2019-01-31T21:38:53.789353Z, end-time: 2019-01-31T21:38:54.472720Z, duration: 0, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip pip Cache entry deserialization failed, entry ignored Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages [rtd-command-info] start-time: 2019-01-31T21:38:54.531439Z, end-time: 2019-01-31T21:38:58.562731Z, duration: 4, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6 Cache entry deserialization failed, entry ignored Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: setuptools<40 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: docutils==0.13.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: pillow==2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: commonmark==0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: recommonmark==0.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: sphinx<1.8 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages Cache entry deserialization failed, entry ignored Requirement already up-to-date: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: urllib3<1.25,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from packaging->sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx<1.8) [rtd-command-info] start-time: 2019-01-31T21:38:59.079643Z, end-time: 2019-01-31T21:38:59.134443Z, 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 = 'DNA Subway Guide' copyright = '2016, CyVerse' author = 'CyVerse' version = '1.0' release = '1.0' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import 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 else: SUFFIX = source_suffix[0] else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # 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': [ ("htmlzip", "//readthedocs.com/projects/cyverse-dnasubway-guide/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-dnasubway-guide', 'name': u'dnasubway_guide', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/projects/dnasubway_guide/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'dnasubway_guide', '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': '9b17116d', } 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"] [rtd-command-info] start-time: 2019-01-31T21:38:59.211262Z, end-time: 2019-01-31T21:39:01.595752Z, duration: 2, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.7.9 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 11 source files that are out of date updating environment: 11 added, 0 changed, 0 removed reading sources... 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[100%] step8 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:194: WARNING: Enumerated list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:196: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:488: WARNING: Duplicate substitution definition name: "CyVerse logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:492: WARNING: Duplicate substitution definition name: "Home_Icon". cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:64: WARNING: Block quote ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/License.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 9%] Contributors_maintainers writing output... [ 18%] License writing output... [ 27%] index writing output... [ 36%] step1 writing output... [ 45%] step2 writing output... [ 54%] step3 writing output... [ 63%] step4 writing output... [ 72%] step5 writing output... [ 81%] step6 writing output... [ 90%] step7 writing output... [100%] step8 generating indices... genindex writing additional pages... search copying images... [ 2%] ./img/dna_subway/sleuth_heatmap_1.png copying images... [ 5%] ./img/dna_subway/blue_trace.png copying images... [ 8%] ./img/dna_subway/histogram_poor.png copying images... [ 11%] ./img/dna_subway/sleuth_bootstrap_1.png copying images... [ 13%] ./img/dna_subway/sleuth_pca_1.png copying images... [ 16%] ./img/dna_subway/apollo_2.png copying images... [ 19%] ./img/dna_subway/sleuth_results_1.png copying images... [ 22%] ./img/dna_subway/dnasubway-icon.png copying images... [ 25%] ./img/dna_subway/project_info_tab.png copying images... 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[rtd-command-info] start-time: 2019-01-31T21:39:01.727838Z, end-time: 2019-01-31T21:39:04.015319Z, duration: 2, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.7.9 loading translations [en]... done making output directory... loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 11 added, 0 changed, 0 removed reading sources... [ 9%] Contributors_maintainers reading sources... [ 18%] License reading sources... [ 27%] index reading sources... [ 36%] step1 reading sources... [ 45%] step2 reading sources... [ 54%] step3 reading sources... [ 63%] step4 reading sources... [ 72%] step5 reading sources... [ 81%] step6 reading sources... [ 90%] step7 reading sources... [100%] step8 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:194: WARNING: Enumerated list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:196: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:488: WARNING: Duplicate substitution definition name: "CyVerse logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:492: WARNING: Duplicate substitution definition name: "Home_Icon". cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:64: WARNING: Block quote ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/License.md: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... step1 step2 step3 step4 step5 step6 step7 step8 writing... done writing additional files... copying images... 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[ 94%] ./img/dna_subway/sleuth_loadings_1.png copying images... [ 97%] ./img/dna_subway/faith.png copying images... [100%] ./img/dna_subway/unweighted.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 9 warnings. The HTML page is in _build/localmedia.