Read the Docs build information Build id: 48758 Project: cyverse-discovery-environment-guide Version: latest Commit: c97f398bfe245b82ae242c00e4ea873685f81197 Date: 2017-06-08T17:53:40.131575Z State: finished Success: True [rtd-command-info] start-time: 2017-06-08T22:53:02.876150Z, end-time: 2017-06-08T22:53:06.188280Z, duration: 3, exit-code: 0 python2.7 -mvirtualenv --no-site-packages --no-download New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/bin/python2.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/bin/python2.7) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2017-06-08T22:53:06.374460Z, end-time: 2017-06-08T22:53:08.840036Z, duration: 2, exit-code: 0 python pip install --use-wheel -U --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/.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 Requirement already up-to-date: sphinx==1.5.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: setuptools==28.8.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: docutils==0.13.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: mkdocs==0.15.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: pillow==2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: sphinx-rtd-theme<0.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: commonmark==0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: recommonmark==0.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from sphinx==1.5.3) Requirement already up-to-date: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from sphinx==1.5.3) Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from sphinx==1.5.3) Requirement already up-to-date: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from sphinx==1.5.3) Requirement already up-to-date: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from sphinx==1.5.3) Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from sphinx==1.5.3) Requirement already up-to-date: tornado>=4.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: click>=4.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: livereload>=2.3.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: mkdocs-bootstrap>=0.1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: mkdocs-bootswatch>=0.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: PyYAML>=3.10 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: Markdown>=2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: nilsimsa>=0.3.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from readthedocs-sphinx-ext<0.6) Requirement already up-to-date: idna<2.6,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.5.3) Requirement already up-to-date: urllib3<1.22,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.5.3) Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.5.3) Requirement already up-to-date: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.5.3) Requirement already up-to-date: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx==1.5.3) Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx==1.5.3) Requirement already up-to-date: singledispatch in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from tornado>=4.1->mkdocs==0.15.0) Requirement already up-to-date: backports-abc>=0.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/envs/latest/lib/python2.7/site-packages (from tornado>=4.1->mkdocs==0.15.0) [rtd-command-info] start-time: 2017-06-08T22:53:09.650177Z, end-time: 2017-06-08T22:53:09.704851Z, 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 = 'Discovery Environment Guide' 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': [ ("pdf", "//readthedocs.com/projects/cyverse-discovery-environment-guide/downloads/pdf/latest/"), ("htmlzip", "//readthedocs.com/projects/cyverse-discovery-environment-guide/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/cyverse-discovery-environment-guide/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-discovery-environment-guide', 'name': u'discovery_environment_guide', 'rtd_language': u'en', 'canonical_url': 'https://cyverse-discovery-environment-guide.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/./', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'discovery_environment_guide', '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': 'c97f398b', } 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: 2017-06-08T22:53:09.815374Z, end-time: 2017-06-08T22:53:11.191565Z, 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 5 source files that are out of date updating environment: 5 added, 0 changed, 0 removed reading sources... [ 20%] index reading sources... [ 40%] step1 reading sources... [ 60%] step2 reading sources... [ 80%] step3 reading sources... [100%] step4 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step2.rst:23: WARNING: Title underline too short. **Navigating the Data Window:** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:8: WARNING: Duplicate explicit target name: "de_sample_plants.fas". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: self referenced toctree found. Ignored. done writing output... [ 20%] index writing output... [ 40%] step1 writing output... [ 60%] step2 writing output... [ 80%] step3 writing output... [100%] step4 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index generating indices... genindex writing additional pages... search copying images... [ 4%] ./img/de/data_window.png copying images... [ 9%] ./img/de/beta.png copying images... [ 14%] ./img/de/de-icon.png copying images... [ 19%] ./img/de/manage_sharing_menu.png copying images... [ 23%] ./img/de/favorite.png copying images... [ 28%] ./img/de/manage_data_links.png copying images... [ 33%] ./img/de/apps_icon.png copying images... [ 38%] ./img/de/info.png copying images... [ 42%] ./img/de/muscle_app_window.png copying images... [ 47%] ./img/de/person_icon.png copying images... [ 52%] ./img/de/data_icon.png copying images... [ 57%] ./img/de/comment.png copying images... [ 61%] ./img/de/viewing_window.png copying images... [ 66%] ./img/de/unavailable.png copying images... [ 71%] ./img/de/de_app_icon.png copying images... [ 76%] ./img/cyverse_rgb.png copying images... [ 80%] ./img/de/rating.png copying images... [ 85%] ./img/de/link_icon.png copying images... [ 90%] ./img/de/delete_icon.png copying images... [ 95%] ./img/homeicon.png copying images... [100%] ./img/de/private.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-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, 11 warnings. [rtd-command-info] start-time: 2017-06-08T22:53:11.322601Z, end-time: 2017-06-08T22:53:12.472941Z, duration: 1, 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 5 source files that are out of date updating environment: 5 added, 0 changed, 0 removed reading sources... [ 20%] index reading sources... [ 40%] step1 reading sources... [ 60%] step2 reading sources... [ 80%] step3 reading sources... [100%] step4 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step2.rst:23: WARNING: Title underline too short. **Navigating the Data Window:** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:8: WARNING: Duplicate explicit target name: "de_sample_plants.fas". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: self referenced toctree found. Ignored. done writing output... [ 20%] index writing output... [ 40%] step1 writing output... [ 60%] step2 writing output... [ 80%] step3 writing output... [100%] step4 generating indices... genindex/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index writing additional pages... search copying images... [ 4%] ./img/de/data_window.png copying images... [ 9%] ./img/de/beta.png copying images... [ 14%] ./img/de/de-icon.png copying images... [ 19%] ./img/de/manage_sharing_menu.png copying images... [ 23%] ./img/de/favorite.png copying images... [ 28%] ./img/de/manage_data_links.png copying images... [ 33%] ./img/de/apps_icon.png copying images... [ 38%] ./img/de/info.png copying images... [ 42%] ./img/de/muscle_app_window.png copying images... [ 47%] ./img/de/person_icon.png copying images... [ 52%] ./img/de/data_icon.png copying images... [ 57%] ./img/de/comment.png copying images... [ 61%] ./img/de/viewing_window.png copying images... [ 66%] ./img/de/unavailable.png copying images... [ 71%] ./img/de/de_app_icon.png copying images... [ 76%] ./img/cyverse_rgb.png copying images... [ 80%] ./img/de/rating.png copying images... [ 85%] ./img/de/link_icon.png copying images... [ 90%] ./img/de/delete_icon.png copying images... [ 95%] ./img/homeicon.png copying images... [100%] ./img/de/private.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-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: 2017-06-08T22:53:12.598100Z, end-time: 2017-06-08T22:53:13.831139Z, duration: 1, 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: 5 added, 0 changed, 0 removed reading sources... [ 20%] index reading sources... [ 40%] step1 reading sources... [ 60%] step2 reading sources... [ 80%] step3 reading sources... [100%] step4 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step2.rst:23: WARNING: Title underline too short. **Navigating the Data Window:** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:8: WARNING: Duplicate explicit target name: "de_sample_plants.fas". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: self referenced toctree found. Ignored. done assembling single document... step1 step2 step3 step4 writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index done writing additional files... copying images... [ 4%] ./img/de/data_window.png copying images... [ 9%] ./img/de/beta.png copying images... [ 14%] ./img/de/de-icon.png copying images... [ 19%] ./img/de/manage_sharing_menu.png copying images... [ 23%] ./img/de/favorite.png copying images... [ 28%] ./img/de/manage_data_links.png copying images... [ 33%] ./img/de/apps_icon.png copying images... [ 38%] ./img/de/info.png copying images... [ 42%] ./img/de/muscle_app_window.png copying images... [ 47%] ./img/de/person_icon.png copying images... [ 52%] ./img/de/data_icon.png copying images... [ 57%] ./img/de/comment.png copying images... [ 61%] ./img/de/viewing_window.png copying images... 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[rtd-command-info] start-time: 2017-06-08T22:53:13.981888Z, end-time: 2017-06-08T22:53:14.994473Z, duration: 1, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex 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 [latex]: all documents updating environment: 5 added, 0 changed, 0 removed reading sources... [ 20%] index reading sources... [ 40%] step1 reading sources... [ 60%] step2 reading sources... [ 80%] step3 reading sources... 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3 <./de-icon.png>] [4 <./person_icon.png>] [5 <./data_icon.png> <./data_window.png>] [6 <./viewing_window.png>] [7 <./manage_data_links.png> <./delete_icon.png> <./link_icon.png>] [8 <./manage_sharin g_menu.png>] Underfull \hbox (badness 10000) in paragraph at lines 487--490 \T1/ptm/b/n/10 Tip: \T1/ptm/m/n/10 Ap-pli-ca-tions in the Dis-cov-ery En-v-ior -ment \T1/ptm/b/n/10 Apps \T1/ptm/m/n/10 menu have sev-eral fea-tures: Underfull \hbox (badness 10000) in paragraph at lines 530--532 []\T1/ptm/m/n/10 Under ^^PAnal-y-sis Name^^Q leave the de-faults or make any de -sired notes. [9 <./de_app_icon.png> <./info.png> <./comment.png> <./favorite.png> <./rating. png> <./unavailable.png> <./beta.png> <./private.png> <./apps_icon.png>] [10 <./muscle_app_window.png>] [11] [12] Chapter 2. (./CyVerseDocumentation.ind) Package sphinx Warning: ******** ERROR !! PLEASE UPDATE titlesec.sty !!******** ******** THIS VERSION SWALLOWS SECTION NUMBERS.********. [13] (./CyVerseDocumentation.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on CyVerseDocumentation.pdf (17 pages, 698029 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2017-06-08T22:53:18.442857Z, end-time: 2017-06-08T22:53:18.497286Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/_build/latex/CyVerseDocumentation.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/artifacts/latest/sphinx_pdf/cyverse-discovery-environment-guide.pdf [rtd-command-info] start-time: 2017-06-08T22:53:18.615152Z, end-time: 2017-06-08T22:53:19.828347Z, duration: 1, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub 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 [epub]: targets for 5 source files that are out of date updating environment: 5 added, 0 changed, 0 removed reading sources... [ 20%] index reading sources... [ 40%] step1 reading sources... [ 60%] step2 reading sources... [ 80%] step3 reading sources... [100%] step4 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step2.rst:23: WARNING: Title underline too short. **Navigating the Data Window:** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/step3.rst:8: WARNING: Duplicate explicit target name: "de_sample_plants.fas". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: self referenced toctree found. Ignored. done writing output... [ 20%] index writing output... [ 40%] step1 writing output... [ 60%] step2 writing output... [ 80%] step3 writing output... 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WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-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 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index writing mimetype file... writing META-INF/container.xml file... writing content.opf file... writing nav.xhtml file... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index writing toc.ncx file... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index writing DiscoveryEnvironmentGuide.epub file... build succeeded, 9 warnings. [rtd-command-info] start-time: 2017-06-08T22:53:19.947892Z, end-time: 2017-06-08T22:53:20.002668Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/checkouts/latest/_build/epub/DiscoveryEnvironmentGuide.epub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-discovery-environment-guide/artifacts/latest/sphinx_epub/cyverse-discovery-environment-guide.epub