Read the Docs build information Build id: 55697 Project: cyverse-fastqc-quickstart Version: latest Commit: 531ca9a75c84955f396b55d7800702344068b8b0 Date: 2017-08-01T16:41:48.304378Z State: finished Success: True [rtd-command-info] start-time: 2017-08-01T21:40:57.332453Z, end-time: 2017-08-01T21:40:59.015598Z, 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-fastqc-quickstart/envs/latest/bin/python2.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/envs/latest/bin/python Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2017-08-01T21:40:59.121879Z, end-time: 2017-08-01T21:41:34.152824Z, duration: 35, exit-code: 0 python pip install --use-wheel -U --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/.cache/pip sphinx==1.5.3 Pygments==2.2.0 setuptools==28.8.0 docutils==0.13.1 mkdocs==0.15.0 mock==1.0.1 pillow==2.6.1 readthedocs-sphinx-ext<0.6 sphinx-rtd-theme<0.3 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 Collecting sphinx==1.5.3 Downloading Sphinx-1.5.3-py2.py3-none-any.whl (1.6MB) Collecting Pygments==2.2.0 Downloading Pygments-2.2.0-py2.py3-none-any.whl (841kB) Requirement already up-to-date: setuptools==28.8.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/envs/latest/lib/python2.7/site-packages Collecting docutils==0.13.1 Downloading docutils-0.13.1-py2-none-any.whl (537kB) Collecting mkdocs==0.15.0 Downloading mkdocs-0.15.0-py2.py3-none-any.whl (966kB) 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 readthedocs-sphinx-ext<0.6 Downloading readthedocs_sphinx_ext-0.5.5-py2.py3-none-any.whl Collecting sphinx-rtd-theme<0.3 Downloading sphinx_rtd_theme-0.2.4-py2.py3-none-any.whl (1.4MB) 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 six>=1.5 (from sphinx==1.5.3) Downloading six-1.10.0-py2.py3-none-any.whl Collecting requests>=2.0.0 (from sphinx==1.5.3) Downloading requests-2.18.2-py2.py3-none-any.whl (88kB) Collecting imagesize (from sphinx==1.5.3) Downloading imagesize-0.7.1-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 (from sphinx==1.5.3) Downloading Babel-2.4.0-py2.py3-none-any.whl (6.8MB) Collecting snowballstemmer>=1.1 (from sphinx==1.5.3) Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB) Collecting Jinja2>=2.3 (from sphinx==1.5.3) Downloading Jinja2-2.9.6-py2.py3-none-any.whl (340kB) Collecting tornado>=4.1 (from mkdocs==0.15.0) Downloading tornado-4.5.1.tar.gz (483kB) Collecting click>=4.0 (from mkdocs==0.15.0) Downloading click-6.7-py2.py3-none-any.whl (71kB) Collecting livereload>=2.3.2 (from mkdocs==0.15.0) Downloading livereload-2.5.1-py2-none-any.whl Collecting mkdocs-bootstrap>=0.1.1 (from mkdocs==0.15.0) Downloading mkdocs-bootstrap-0.1.1.tar.gz (363kB) Collecting mkdocs-bootswatch>=0.1.0 (from mkdocs==0.15.0) Downloading mkdocs-bootswatch-0.4.0.tar.gz (4.4MB) Collecting PyYAML>=3.10 (from mkdocs==0.15.0) Downloading PyYAML-3.12.tar.gz (253kB) Collecting Markdown>=2.3.1 (from mkdocs==0.15.0) Downloading Markdown-2.6.8.tar.gz (307kB) Collecting nilsimsa>=0.3.7 (from readthedocs-sphinx-ext<0.6) Downloading nilsimsa-0.3.8.tar.gz (276kB) Collecting idna<2.6,>=2.5 (from requests>=2.0.0->sphinx==1.5.3) Downloading idna-2.5-py2.py3-none-any.whl (55kB) Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx==1.5.3) Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB) Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx==1.5.3) Downloading certifi-2017.7.27.1-py2.py3-none-any.whl (349kB) Collecting urllib3<1.23,>=1.21.1 (from requests>=2.0.0->sphinx==1.5.3) Downloading urllib3-1.22-py2.py3-none-any.whl (132kB) Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.5.3) Downloading pytz-2017.2-py2.py3-none-any.whl (484kB) Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.5.3) Downloading MarkupSafe-1.0.tar.gz Collecting singledispatch (from tornado>=4.1->mkdocs==0.15.0) Downloading singledispatch-3.4.0.3-py2.py3-none-any.whl Collecting backports_abc>=0.4 (from tornado>=4.1->mkdocs==0.15.0) Downloading backports_abc-0.5-py2.py3-none-any.whl Building wheels for collected packages: mock, pillow, commonmark, tornado, mkdocs-bootstrap, mkdocs-bootswatch, PyYAML, Markdown, 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-fastqc-quickstart/.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-fastqc-quickstart/.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-fastqc-quickstart/.cache/pip/wheels/fd/3a/ea/9ead7944d8ba3771888487ca4f6ef39bcde9fd4e986c32f442 Running setup.py bdist_wheel for tornado: started Running setup.py bdist_wheel for tornado: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/.cache/pip/wheels/84/83/cd/6a04602633457269d161344755e6766d24307189b7a67ff4b7 Running setup.py bdist_wheel for mkdocs-bootstrap: started Running setup.py bdist_wheel for mkdocs-bootstrap: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/.cache/pip/wheels/6a/6b/d4/b947c6453aae64d38ab0e3b70cb71a60cb6bb7d0a184a4b727 Running setup.py bdist_wheel for mkdocs-bootswatch: started Running setup.py bdist_wheel for mkdocs-bootswatch: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/.cache/pip/wheels/cd/af/36/fbd242260aeadfc4d890450b2070d4e42ea129460d771d0e37 Running setup.py bdist_wheel for PyYAML: started Running setup.py bdist_wheel for PyYAML: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/.cache/pip/wheels/2c/f7/79/13f3a12cd723892437c0cfbde1230ab4d82947ff7b3839a4fc Running setup.py bdist_wheel for Markdown: started Running setup.py bdist_wheel for Markdown: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/.cache/pip/wheels/85/a7/08/33ee5cd488d0365d8bed79d1d4e5c28dd3fbfc7f6d0ad4bb09 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-fastqc-quickstart/.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-fastqc-quickstart/.cache/pip/wheels/88/a7/30/e39a54a87bcbe25308fa3ca64e8ddc75d9b3e5afa21ee32d57 Successfully built mock pillow commonmark tornado mkdocs-bootstrap mkdocs-bootswatch PyYAML Markdown nilsimsa MarkupSafe Installing collected packages: six, idna, chardet, certifi, urllib3, requests, docutils, Pygments, imagesize, pytz, babel, snowballstemmer, MarkupSafe, Jinja2, alabaster, sphinx, singledispatch, backports-abc, tornado, click, livereload, mkdocs-bootstrap, mkdocs-bootswatch, PyYAML, Markdown, mkdocs, mock, pillow, nilsimsa, readthedocs-sphinx-ext, sphinx-rtd-theme, commonmark, recommonmark Successfully installed Jinja2-2.9.6 Markdown-2.6.8 MarkupSafe-1.0 PyYAML-3.12 Pygments-2.2.0 alabaster-0.7.10 babel-2.4.0 backports-abc-0.5 certifi-2017.7.27.1 chardet-3.0.4 click-6.7 commonmark-0.5.4 docutils-0.13.1 idna-2.5 imagesize-0.7.1 livereload-2.5.1 mkdocs-0.15.0 mkdocs-bootstrap-0.1.1 mkdocs-bootswatch-0.4.0 mock-1.0.1 nilsimsa-0.3.8 pillow-2.6.1 pytz-2017.2 readthedocs-sphinx-ext-0.5.5 recommonmark-0.4.0 requests-2.18.2 singledispatch-3.4.0.3 six-1.10.0 snowballstemmer-1.2.1 sphinx-1.5.3 sphinx-rtd-theme-0.2.4 tornado-4.5.1 urllib3-1.22 [rtd-command-info] start-time: 2017-08-01T21:41:34.968497Z, end-time: 2017-08-01T21:41:35.023471Z, 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 = 'Evaluate High-throughput Sequencing Reads with FastQC Quickstart' copyright = '2017, 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", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("htmlzip", "//readthedocs.com/projects/cyverse-fastqc-quickstart/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-fastqc-quickstart', 'name': u'fastqc_quickstart', 'rtd_language': u'en', 'canonical_url': 'https://learning.cyverse.org/projects/fastqc_quickstart/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/./', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'fastqc_quickstart', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': 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': '531ca9a7', } 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: 2017-08-01T21:41:35.150309Z, end-time: 2017-08-01T21:41:36.166906Z, duration: 1, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.5.3 making output directory... loading translations [en]... done building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 1 source files that are out of date updating environment: 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [100%] index generating indices... genindex writing additional pages... search copying images... [ 20%] ./img/adapter_good.png copying images... [ 40%] ./img/perbase_good.png copying images... [ 60%] ./img/homeicon.png copying images... [ 80%] ./img/cyverse_rgb.png copying images... [100%] ./img/persequence_good.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/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, 2 warnings. [rtd-command-info] start-time: 2017-08-01T21:41:36.328761Z, end-time: 2017-08-01T21:41:37.193261Z, duration: 0, exit-code: 0 python sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json Running Sphinx v1.5.3 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 1 source files that are out of date updating environment: 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [100%] index generating indices... genindex writing additional pages... search copying images... [ 20%] ./img/adapter_good.png copying images... [ 40%] ./img/perbase_good.png copying images... [ 60%] ./img/homeicon.png copying images... [ 80%] ./img/cyverse_rgb.png copying images... [100%] ./img/persequence_good.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/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, 2 warnings. [rtd-command-info] start-time: 2017-08-01T21:41:37.332545Z, end-time: 2017-08-01T21:41:38.283555Z, duration: 0, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.5.3 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: 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... writing... done writing additional files... copying images... [ 20%] ./img/adapter_good.png copying images... [ 40%] ./img/perbase_good.png copying images... [ 60%] ./img/homeicon.png copying images... [ 80%] ./img/cyverse_rgb.png copying images... [100%] ./img/persequence_good.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-fastqc-quickstart/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, 2 warnings.