Read the Docs build information Build id: 56130 Project: cyverse-ez-quickstart Version: latest Commit: f9c546f7e267c98de16b59b665debe21ae2276b6 Date: 2017-08-04T23:27:19.941630Z State: finished Success: True [rtd-command-info] start-time: 2017-08-05T04:26:27.343089Z, end-time: 2017-08-05T04:26:29.626158Z, 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-ez-quickstart/envs/latest/bin/python2.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/envs/latest/bin/python2.7) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2017-08-05T04:26:29.740249Z, end-time: 2017-08-05T04:26:32.992660Z, duration: 3, exit-code: 0 python pip install --use-wheel -U --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-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 Requirement already up-to-date: sphinx==1.5.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx==1.5.3) Requirement already up-to-date: urllib3<1.23,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/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-ez-quickstart/envs/latest/lib/python2.7/site-packages (from tornado>=4.1->mkdocs==0.15.0) [rtd-command-info] start-time: 2017-08-05T04:26:33.716412Z, end-time: 2017-08-05T04:26:33.770584Z, 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 = 'EZ' copyright = '2017, CyVerse' author = 'Blake Joyce' 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-ez-quickstart/downloads/pdf/latest/"), ("htmlzip", "//readthedocs.com/projects/cyverse-ez-quickstart/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/cyverse-ez-quickstart/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-ez-quickstart', 'name': u'ez_quickstart', 'rtd_language': u'en', 'canonical_url': 'https://cyverse-ez-quickstart.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': 'ez_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': 'f9c546f7', } 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: 2017-08-05T04:26:33.893872Z, end-time: 2017-08-05T04:26:36.867347Z, duration: 2, 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 3 source files that are out of date updating environment: 3 added, 0 changed, 0 removed reading sources... [ 33%] docker reading sources... [ 66%] index reading sources... [100%] rstudio /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/docker.rst:48: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/docker.rst:48: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:27: WARNING: toctree contains reference to nonexisting document u' :maxdepth: 2' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:212: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:212: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:152: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:152: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 33%] docker writing output... [ 66%] index writing output... [100%] rstudio generating indices... genindex writing additional pages... search copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-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, 9 warnings. [rtd-command-info] start-time: 2017-08-05T04:26:37.050224Z, end-time: 2017-08-05T04:26:38.002417Z, 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... done building [mo]: targets for 0 po files that are out of date building [json]: targets for 3 source files that are out of date updating environment: 0 added, 2 changed, 0 removed reading sources... [ 50%] index reading sources... [100%] rstudio /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:27: WARNING: toctree contains reference to nonexisting document u' :maxdepth: 2' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:212: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:212: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:152: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:152: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 33%] docker writing output... [ 66%] index writing output... [100%] rstudio generating indices... genindex writing additional pages... search copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-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, 7 warnings. [rtd-command-info] start-time: 2017-08-05T04:26:38.144210Z, end-time: 2017-08-05T04:26:39.146030Z, 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... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 2 changed, 0 removed reading sources... [ 50%] index reading sources... [100%] rstudio /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:27: WARNING: toctree contains reference to nonexisting document u' :maxdepth: 2' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:212: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:212: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:152: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:152: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... rstudio docker writing... done writing additional files... copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-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, 7 warnings. [rtd-command-info] start-time: 2017-08-05T04:26:39.281814Z, end-time: 2017-08-05T04:26:40.188496Z, duration: 0, 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... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 2 changed, 0 removed reading sources... [ 50%] index reading sources... [100%] rstudio /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:27: WARNING: toctree contains reference to nonexisting document u' :maxdepth: 2' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:212: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:212: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:152: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:152: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". looking for now-outdated files... none found pickling environment... done checking consistency... done processing CyVerseDocumentation.tex... index rstudio docker resolving references... writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:: WARNING: unusable reference target found: rstudio.html /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:: WARNING: unusable reference target found: docker.html done copying images... ./img/homeicon.png ./img/cyverse_rgb.png copying TeX support files... done build succeeded, 7 warnings. [rtd-command-info] start-time: 2017-08-05T04:26:40.298264Z, end-time: 2017-08-05T04:26:41.058482Z, duration: 0, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/_build/latex/CyVerseDocumentation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkou ts/latest/_build/latex/CyVerseDocumentation.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file CyVerseDocumentation.idx No file CyVerseDocumentation.aux. 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Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 63. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 75. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Underfull \hbox (badness 10000) in paragraph at lines 1--111 []\T1/pcr/m/n/10 sudo sh -c \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 echo "export RSTUDI O_WHICH_R="/home/anaconda3/bin/R"" >> Underfull \hbox (badness 10000) in paragraph at lines 1--113 []\T1/pcr/m/n/10 sudo sh -c \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 echo "launchctl set env RSTUDIO_WHICH_R $RSTUDIO_WHICH_R" [3] Underfull \hbox (badness 10000) in paragraph at lines 1--128 []\T1/pcr/m/n/10 sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib / Underfull \hbox (badness 10000) in paragraph at lines 1--138 []\T1/pcr/m/n/10 sudo wget https://download2.rstudio.org/rstudio-server-1.0. Underfull \hbox (badness 10000) in paragraph at lines 1--148 []\T1/pcr/m/n/10 sudo wget https://download2.rstudio.org/rstudio-server-rhel-1. 0. ! Package inputenc Error: Unicode char ● (U+25CF) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.173 ...{}server.service \PYGZhy{} RStudio Server ! Package inputenc Error: Unicode char └ (U+2514) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.183 ...sr/lib/rstudio\PYGZhy{}server/bin/rserver Overfull \vbox (11.56998pt too high) detected at line 192 [4] Underfull \hbox (badness 10000) in paragraph at lines 1--202 []\T1/pcr/m/n/10 sudo sh -c \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 echo "rsession-whic h-r=/home/anaconda3/bin/R" >> /etc/ [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Overfull \hbox (1.78171pt too wide) in paragraph at lines 269--270 []\T1/ptm/m/n/10 On Github: []\T1/ptm/b/n/10 `Repo link `_[] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 289. [6] Overfull \hbox (1.78171pt too wide) in paragraph at lines 355--356 []\T1/ptm/m/n/10 On Github: []\T1/ptm/b/n/10 `Repo link `_[] [7] [8] Chapter 2. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 374. [9] [10] Chapter 3. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 468. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 471. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 542. [11] Underfull \hbox (badness 10000) in paragraph at lines 1--557 []\T1/pcr/m/n/10 * Updating ez singularity and installing singularity (this may take a Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 574. [12] Chapter 4. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 599. Overfull \hbox (1.78171pt too wide) in paragraph at lines 627--628 []\T1/ptm/m/n/10 On Github: []\T1/ptm/b/n/10 `Repo link `_[] No file CyVerseDocumentation.ind. Package sphinx Warning: ******** ERROR !! PLEASE UPDATE titlesec.sty !!******** ******** THIS VERSION SWALLOWS SECTION NUMBERS.********. [13] (./CyVerseDocumentation.aux) Package rerunfilecheck Warning: File `CyVerseDocumentation.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (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, 172770 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2017-08-05T04:26:41.172293Z, end-time: 2017-08-05T04:26:41.285881Z, duration: 0, exit-code: 0 makeindex -s python.ist CyVerseDocumentation.idx This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file CyVerseDocumentation.idx...done (0 entries accepted, 0 rejected). Nothing written in CyVerseDocumentation.ind. Transcript written in CyVerseDocumentation.ilg. [rtd-command-info] start-time: 2017-08-05T04:26:41.464689Z, end-time: 2017-08-05T04:26:42.154478Z, duration: 0, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/_build/latex/CyVerseDocumentation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkou ts/latest/_build/latex/CyVerseDocumentation.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file CyVerseDocumentation.idx (./CyVerseDocumentation.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./CyVerseDocumentation.out) (./CyVerseDocumentation.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./CyVerseDocumentation.toc) [1] [2] [1 <./cyverse_ rgb.png> <./homeicon.png>] [2] Chapter 1. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 63. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 75. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Underfull \hbox (badness 10000) in paragraph at lines 1--111 []\T1/pcr/m/n/10 sudo sh -c \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 echo "export RSTUDI O_WHICH_R="/home/anaconda3/bin/R"" >> Underfull \hbox (badness 10000) in paragraph at lines 1--113 []\T1/pcr/m/n/10 sudo sh -c \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 echo "launchctl set env RSTUDIO_WHICH_R $RSTUDIO_WHICH_R" [3] Underfull \hbox (badness 10000) in paragraph at lines 1--128 []\T1/pcr/m/n/10 sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib / Underfull \hbox (badness 10000) in paragraph at lines 1--138 []\T1/pcr/m/n/10 sudo wget https://download2.rstudio.org/rstudio-server-1.0. Underfull \hbox (badness 10000) in paragraph at lines 1--148 []\T1/pcr/m/n/10 sudo wget https://download2.rstudio.org/rstudio-server-rhel-1. 0. ! Package inputenc Error: Unicode char ● (U+25CF) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.173 ...{}server.service \PYGZhy{} RStudio Server ! Package inputenc Error: Unicode char └ (U+2514) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.183 ...sr/lib/rstudio\PYGZhy{}server/bin/rserver Overfull \vbox (11.56998pt too high) detected at line 192 [4] Underfull \hbox (badness 10000) in paragraph at lines 1--202 []\T1/pcr/m/n/10 sudo sh -c \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 echo "rsession-whic h-r=/home/anaconda3/bin/R" >> /etc/ [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Overfull \hbox (1.78171pt too wide) in paragraph at lines 269--270 []\T1/ptm/m/n/10 On Github: []\T1/ptm/b/n/10 `Repo link `_[] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 289. [6] Overfull \hbox (1.78171pt too wide) in paragraph at lines 355--356 []\T1/ptm/m/n/10 On Github: []\T1/ptm/b/n/10 `Repo link `_[] [7] [8] Chapter 2. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 374. [9] [10] Chapter 3. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 468. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 471. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 542. [11] Underfull \hbox (badness 10000) in paragraph at lines 1--557 []\T1/pcr/m/n/10 * Updating ez singularity and installing singularity (this may take a Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 574. [12] Chapter 4. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstyleemphasis' on input line 599. Overfull \hbox (1.78171pt too wide) in paragraph at lines 627--628 []\T1/ptm/m/n/10 On Github: []\T1/ptm/b/n/10 `Repo link `_[] (./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, 186272 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2017-08-05T04:26:42.351154Z, end-time: 2017-08-05T04:26:42.409671Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/_build/latex/CyVerseDocumentation.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/artifacts/latest/sphinx_pdf/cyverse-ez-quickstart.pdf [rtd-command-info] start-time: 2017-08-05T04:26:42.572942Z, end-time: 2017-08-05T04:26:43.586162Z, 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... done building [mo]: targets for 0 po files that are out of date building [epub]: targets for 3 source files that are out of date updating environment: 0 added, 2 changed, 0 removed reading sources... [ 50%] index reading sources... [100%] rstudio /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:27: WARNING: toctree contains reference to nonexisting document u' :maxdepth: 2' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:212: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/index.rst:212: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:152: ERROR: Indirect hyperlink target "repo link" refers to target "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix", which does not exist. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/rstudio.rst:152: ERROR: Unknown target name: "fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix_fix". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 33%] docker writing output... [ 66%] index writing output... [100%] rstudio generating indices... genindex writing additional pages... copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-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 writing mimetype file... writing META-INF/container.xml file... writing content.opf file... writing nav.xhtml file... writing toc.ncx file... writing EZ.epub file... build succeeded, 7 warnings. [rtd-command-info] start-time: 2017-08-05T04:26:43.738119Z, end-time: 2017-08-05T04:26:43.792249Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/checkouts/latest/_build/epub/EZ.epub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-ez-quickstart/artifacts/latest/sphinx_epub/cyverse-ez-quickstart.epub