Read the Docs build information Build id: 86798 Project: cyverse-dnasubway-guide Version: latest Commit: 9b0aca170bf306e3e07c24e190948d61cd9ff632 Date: 2018-02-15T18:04:10.713452Z State: finished Success: True [rtd-command-info] start-time: 2018-02-16T00:04:13.035279Z, end-time: 2018-02-16T00:04:14.792462Z, 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 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2018-02-16T00:04:14.918606Z, end-time: 2018-02-16T00:04:38.968223Z, duration: 24, exit-code: 0 python pip install --use-wheel --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip Pygments==2.2.0 setuptools==37.0.0 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx==1.6.5 sphinx-rtd-theme<0.3 readthedocs-sphinx-ext<0.6 Collecting Pygments==2.2.0 Downloading Pygments-2.2.0-py2.py3-none-any.whl (841kB) Collecting setuptools==37.0.0 Downloading setuptools-37.0.0-py2.py3-none-any.whl (481kB) Collecting docutils==0.13.1 Downloading docutils-0.13.1-py2-none-any.whl (537kB) Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861kB) Collecting pillow==2.6.1 Downloading Pillow-2.6.1.zip (7.5MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.10-py2.py3-none-any.whl Collecting commonmark==0.5.4 Downloading CommonMark-0.5.4.tar.gz (120kB) Collecting recommonmark==0.4.0 Downloading recommonmark-0.4.0-py2.py3-none-any.whl Collecting sphinx==1.6.5 Downloading Sphinx-1.6.5-py2.py3-none-any.whl (1.9MB) Collecting sphinx-rtd-theme<0.3 Downloading sphinx_rtd_theme-0.2.4-py2.py3-none-any.whl (1.4MB) Collecting readthedocs-sphinx-ext<0.6 Downloading readthedocs_sphinx_ext-0.5.8-py2-none-any.whl Collecting sphinxcontrib-websupport (from sphinx==1.6.5) Downloading sphinxcontrib_websupport-1.0.1-py2.py3-none-any.whl Collecting six>=1.5 (from sphinx==1.6.5) Downloading six-1.11.0-py2.py3-none-any.whl Collecting requests>=2.0.0 (from sphinx==1.6.5) Downloading requests-2.18.4-py2.py3-none-any.whl (88kB) Collecting typing; python_version < "3.5" (from sphinx==1.6.5) Downloading typing-3.6.4-py2-none-any.whl Collecting imagesize (from sphinx==1.6.5) Downloading imagesize-0.7.1-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 (from sphinx==1.6.5) Downloading Babel-2.5.3-py2.py3-none-any.whl (6.8MB) Collecting snowballstemmer>=1.1 (from sphinx==1.6.5) Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB) Collecting Jinja2>=2.3 (from sphinx==1.6.5) Downloading Jinja2-2.10-py2.py3-none-any.whl (126kB) Collecting nilsimsa>=0.3.7 (from readthedocs-sphinx-ext<0.6) Downloading nilsimsa-0.3.8.tar.gz (276kB) Collecting urllib3<1.23,>=1.21.1 (from requests>=2.0.0->sphinx==1.6.5) Downloading urllib3-1.22-py2.py3-none-any.whl (132kB) Collecting idna<2.7,>=2.5 (from requests>=2.0.0->sphinx==1.6.5) Downloading idna-2.6-py2.py3-none-any.whl (56kB) Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx==1.6.5) Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB) Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx==1.6.5) Downloading certifi-2018.1.18-py2.py3-none-any.whl (151kB) Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.6.5) Downloading pytz-2018.3-py2.py3-none-any.whl (509kB) Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.6.5) Downloading MarkupSafe-1.0.tar.gz Building wheels for collected packages: mock, pillow, commonmark, nilsimsa, MarkupSafe Running setup.py bdist_wheel for mock: started Running setup.py bdist_wheel for mock: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip/wheels/b2/f8/fe/920b7d3b279878045354cde14646f73864cf944501f19e4a1b Running setup.py bdist_wheel for pillow: started Running setup.py bdist_wheel for pillow: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip/wheels/d0/3d/6f/4a3dbe290c7053073e6c32734c146d7174f2ad7675030b6137 Running setup.py bdist_wheel for commonmark: started Running setup.py bdist_wheel for commonmark: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip/wheels/fd/3a/ea/9ead7944d8ba3771888487ca4f6ef39bcde9fd4e986c32f442 Running setup.py bdist_wheel for nilsimsa: started Running setup.py bdist_wheel for nilsimsa: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip/wheels/77/f8/25/539c7b52ecbfcb7ed9b6c7189f9fdde48706c41fe529a64c9f Running setup.py bdist_wheel for MarkupSafe: started Running setup.py bdist_wheel for MarkupSafe: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip/wheels/88/a7/30/e39a54a87bcbe25308fa3ca64e8ddc75d9b3e5afa21ee32d57 Successfully built mock pillow commonmark nilsimsa MarkupSafe Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, sphinxcontrib-websupport, six, urllib3, idna, chardet, certifi, requests, typing, imagesize, pytz, babel, snowballstemmer, MarkupSafe, Jinja2, sphinx, sphinx-rtd-theme, nilsimsa, readthedocs-sphinx-ext Found existing installation: setuptools 28.8.0 Uninstalling setuptools-28.8.0: Successfully uninstalled setuptools-28.8.0 Successfully installed Jinja2-2.10 MarkupSafe-1.0 Pygments-2.2.0 alabaster-0.7.10 babel-2.5.3 certifi-2018.1.18 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.6 imagesize-0.7.1 mock-1.0.1 nilsimsa-0.3.8 pillow-2.6.1 pytz-2018.3 readthedocs-sphinx-ext-0.5.8 recommonmark-0.4.0 requests-2.18.4 setuptools-37.0.0 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.6.5 sphinx-rtd-theme-0.2.4 sphinxcontrib-websupport-1.0.1 typing-3.6.4 urllib3-1.22 [rtd-command-info] start-time: 2018-02-16T00:04:39.810149Z, end-time: 2018-02-16T00:04:39.865801Z, 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 sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix else: SUFFIX = source_suffix[0] else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = False if 'html_theme' in globals(): if html_theme in ['default']: # Allow people to bail with a hack of having an html_style if not 'html_style' in globals(): import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True else: import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' if 'http' not in settings.MEDIA_URL: websupport2_static_url = 'https://media.readthedocs.com/' else: websupport2_static_url = 'https://media.readthedocs.com/media//static' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("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, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '9b0aca17', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): extensions.append("readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] [rtd-command-info] start-time: 2018-02-16T00:04:39.939732Z, end-time: 2018-02-16T00:04:41.788709Z, duration: 1, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.6.5 making output directory... loading translations [en]... done building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 9 source files that are out of date updating environment: 9 added, 0 changed, 0 removed reading sources... [ 11%] Contributors_maintainers reading sources... [ 22%] License reading sources... [ 33%] index reading sources... [ 44%] step1 reading sources... [ 55%] step2 reading sources... [ 66%] step3 reading sources... [ 77%] step4 reading sources... [ 88%] step5 reading sources... [100%] step6 looking for now-outdated files... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:179: WARNING: Enumerated list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:181: WARNING: Block quote ends without a blank line; unexpected unindent. 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... [ 11%] Contributors_maintainers writing output... [ 22%] License writing output... [ 33%] index writing output... [ 44%] step1 writing output... [ 55%] step2 writing output... [ 66%] step3 writing output... [ 77%] step4 writing output... [ 88%] step5 writing output... [100%] step6 generating indices... genindex writing additional pages... search copying images... [ 5%] ./img/dna_subway/dnasubway-icon.png copying images... [ 11%] ./img/dna_subway/project_info_tab.png copying images... [ 16%] ./img/dna_subway/private_projects.png copying images... [ 22%] ./img/dna_subway/blue_align.png copying images... [ 27%] ./img/dna_subway/jbrowse.png copying images... [ 33%] ./img/dna_subway/blue_blast.png copying images... [ 38%] ./img/dna_subway/blue_trace.png copying images... [ 44%] ./img/dna_subway/yellow_tree.png copying images... [ 50%] ./img/dna_subway/yellow_alignment.png copying images... [ 55%] ./img/dna_subway/repeat_results.png copying images... [ 61%] ./img/cyverse_rgb.png copying images... [ 66%] ./img/dna_subway/blue_ml.png copying images... [ 72%] ./img/dna_subway/apollo_1.png copying images... [ 77%] ./img/dna_subway/apollo_3.png copying images... [ 83%] ./img/dna_subway/apollo_2.png copying images... [ 88%] ./img/dna_subway/apollo_4.png copying images... [ 94%] ./img/homeicon.png copying images... [100%] ./img/dna_subway/blue_nj.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 WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 6 warnings. [rtd-command-info] start-time: 2018-02-16T00:04:42.092430Z, end-time: 2018-02-16T00:04:43.604066Z, duration: 1, exit-code: 0 python sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json Running Sphinx v1.6.5 making output directory... loading translations [en]... done loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [json]: targets for 9 source files that are out of date updating environment: 9 added, 0 changed, 0 removed reading sources... [ 11%] Contributors_maintainers reading sources... [ 22%] License reading sources... [ 33%] index reading sources... [ 44%] step1 reading sources... [ 55%] step2 reading sources... [ 66%] step3 reading sources... [ 77%] step4 reading sources... [ 88%] step5 reading sources... [100%] step6 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:179: WARNING: Enumerated list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:181: 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... [ 11%] Contributors_maintainers writing output... [ 22%] License writing output... [ 33%] index writing output... [ 44%] step1 writing output... [ 55%] step2 writing output... [ 66%] step3 writing output... [ 77%] step4 writing output... [ 88%] step5 writing output... [100%] step6 generating indices... genindex writing additional pages... search copying images... [ 5%] ./img/dna_subway/dnasubway-icon.png copying images... [ 11%] ./img/dna_subway/project_info_tab.png copying images... [ 16%] ./img/dna_subway/private_projects.png copying images... [ 22%] ./img/dna_subway/blue_align.png copying images... [ 27%] ./img/dna_subway/jbrowse.png copying images... [ 33%] ./img/dna_subway/blue_blast.png copying images... [ 38%] ./img/dna_subway/blue_trace.png copying images... [ 44%] ./img/dna_subway/yellow_tree.png copying images... [ 50%] ./img/dna_subway/yellow_alignment.png copying images... [ 55%] ./img/dna_subway/repeat_results.png copying images... [ 61%] ./img/cyverse_rgb.png copying images... [ 66%] ./img/dna_subway/blue_ml.png copying images... [ 72%] ./img/dna_subway/apollo_1.png copying images... [ 77%] ./img/dna_subway/apollo_3.png copying images... [ 83%] ./img/dna_subway/apollo_2.png copying images... [ 88%] ./img/dna_subway/apollo_4.png copying images... [ 94%] ./img/homeicon.png copying images... [100%] ./img/dna_subway/blue_nj.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 WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 6 warnings. [rtd-command-info] start-time: 2018-02-16T00:04:43.694745Z, end-time: 2018-02-16T00:04:45.230188Z, duration: 1, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.6.5 making output directory... loading translations [en]... done loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 9 added, 0 changed, 0 removed reading sources... [ 11%] Contributors_maintainers reading sources... [ 22%] License reading sources... [ 33%] index reading sources... [ 44%] step1 reading sources... [ 55%] step2 reading sources... [ 66%] step3 reading sources... [ 77%] step4 reading sources... [ 88%] step5 reading sources... [100%] step6 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:179: WARNING: Enumerated list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:181: 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 writing... done writing additional files... copying images... 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[100%] ./img/dna_subway/blue_nj.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 WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 6 warnings.