Read the Docs build information Build id: 263367 Project: ucsd-center-for-functional-mri-cfmri-web-rtd Version: latest Commit: b1415633128a11878b180e4393b038b8098c4790 Date: 2019-11-25T21:31:11.636189Z State: finished Success: True [rtd-command-info] start-time: 2019-11-25T21:32:44.063862Z, end-time: 2019-11-25T21:32:44.088924Z, duration: 0, exit-code: 0 git remote set-url origin https://bitbucket.org/ucsdcfmri/cfmri_web_rtd.git [rtd-command-info] start-time: 2019-11-25T21:32:44.193114Z, end-time: 2019-11-25T21:32:45.545828Z, duration: 1, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 [rtd-command-info] start-time: 2019-11-25T21:32:45.768162Z, end-time: 2019-11-25T21:32:45.788911Z, duration: 0, exit-code: 0 git checkout --force origin/master HEAD is now at b141563 Updated the events file to include CFN talk details [rtd-command-info] start-time: 2019-11-25T21:32:45.866501Z, end-time: 2019-11-25T21:32:45.912538Z, duration: 0, exit-code: 0 git clean -d -f -f Removing docs/source/_build/ [rtd-command-info] start-time: 2019-11-25T21:32:47.247070Z, end-time: 2019-11-25T21:32:51.926353Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/bin/python3.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/bin/python3.7) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-11-25T21:32:52.020760Z, end-time: 2019-11-25T21:32:53.001803Z, duration: 0, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (19.3.1) [rtd-command-info] start-time: 2019-11-25T21:32:53.104819Z, end-time: 2019-11-25T21:32:55.132303Z, duration: 2, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (2.3.1) Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (41.0.1) Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (0.14) Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (1.0.1) Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (5.4.1) Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (0.7.12) Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (0.8.1) Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (0.5.0) Requirement already up-to-date: sphinx<2 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (1.8.5) Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (0.4.3) Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (1.0.1) Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from commonmark==0.8.1) (0.18.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.0.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.10.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.7.0) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.13.0) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.0) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from sphinx<2) (19.2) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (1.25.7) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2.8) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2019.9.11) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (from packaging->sphinx<2) (2.4.5) [rtd-command-info] start-time: 2019-11-25T21:32:55.721526Z, end-time: 2019-11-25T21:32:56.037564Z, duration: 0, exit-code: 0 cat docs/source/conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. # # This file does only contain a selection of the most common options. For a # full list see the documentation: # http://www.sphinx-doc.org/en/master/config # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # # import os # import sys # sys.path.insert(0, os.path.abspath('.')) RTD_NEW_THEME = True master_doc = 'index' # -- Project information ----------------------------------------------------- project = u'UCSD Center for fMRI' copyright = u'2019, CFMRI' author = u'CFMRI' # The short X.Y version version = u'' # The full version, including alpha/beta/rc tags release = u'0.0.1' # -- General configuration --------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', ] # Add any paths that contain templates here, relative to this directory. templates_path = ['ntemplates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.txt' # The master toctree document. master_doc = 'index' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. exclude_patterns = [] # The name of the Pygments (syntax highlighting) style to use. pygments_style = None # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # #html_theme = 'alabaster' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['nstatic'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # The default sidebars (for documents that don't match any pattern) are # defined by theme itself. Builtin themes are using these templates by # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', # 'searchbox.html']``. # # html_sidebars = {} # -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = 'cfmri_web_rtddoc' # -- Options for LaTeX output ------------------------------------------------ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'cfmri_web_rtd.tex', u'cfmri\\_web\\_rtd Documentation', u'CFMRI', 'manual'), ] # -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'cfmri_web_rtd', u'cfmri_web_rtd Documentation', [author], 1) ] # -- Options for Texinfo output ---------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'cfmri_web_rtd', u'cfmri_web_rtd Documentation', author, 'cfmri_web_rtd', 'One line description of project.', 'Miscellaneous'), ] # -- Options for Epub output ------------------------------------------------- # Bibliographic Dublin Core info. epub_title = project # The unique identifier of the text. This can be a ISBN number # or the project homepage. # # epub_identifier = '' # A unique identification for the text. # # epub_uid = '' # A list of files that should not be packed into the epub file. epub_exclude_files = ['search.html'] # -- Extension configuration ------------------------------------------------- ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//readthedocs.com/projects/ucsd-center-for-functional-mri-cfmri-web-rtd/downloads/pdf/latest/"), ("html", "//readthedocs.com/projects/ucsd-center-for-functional-mri-cfmri-web-rtd/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/ucsd-center-for-functional-mri-cfmri-web-rtd/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'ucsd-center-for-functional-mri-cfmri-web-rtd', 'name': u'cfmri_web_rtd', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://ucsd-center-for-functional-mri-cfmri-web-rtd.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/source/', 'api_host': 'https://readthedocs.com', 'proxied_api_host': 'https://readthedocs.com', 'github_user': 'None', 'github_repo': 'None', 'github_version': 'master', 'display_github': False, 'bitbucket_user': 'ucsdcfmri', 'bitbucket_repo': 'cfmri_web_rtd', 'bitbucket_version': 'master', 'display_bitbucket': True, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'b1415633', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' [rtd-command-info] start-time: 2019-11-25T21:32:56.157183Z, end-time: 2019-11-25T21:32:58.233573Z, duration: 2, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 11 source files that are out of date updating environment: 11 added, 0 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2019-11-25T21:32:58.388604Z, end-time: 2019-11-25T21:33:00.256898Z, duration: 1, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 11 added, 0 changed, 0 removed reading sources... [ 9%] events reading sources... [ 18%] getstarted reading sources... [ 27%] help reading sources... [ 36%] index reading sources... [ 45%] license reading sources... [ 54%] peripheral reading sources... [ 63%] prev_events reading sources... [ 72%] protocols reading sources... [ 81%] safety reading sources... [ 90%] training reading sources... 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[rtd-command-info] start-time: 2019-11-25T21:33:00.441530Z, end-time: 2019-11-25T21:33:02.189006Z, duration: 1, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 11 added, 0 changed, 0 removed reading sources... [ 9%] events reading sources... [ 18%] getstarted reading sources... [ 27%] help reading sources... [ 36%] index reading sources... [ 45%] license reading sources... [ 54%] peripheral reading sources... [ 63%] prev_events reading sources... [ 72%] protocols reading sources... [ 81%] safety reading sources... [ 90%] training reading sources... 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[rtd-command-info] start-time: 2019-11-25T21:33:15.912655Z, end-time: 2019-11-25T21:33:16.235901Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2019-11-25T21:33:16.323094Z, end-time: 2019-11-25T21:33:34.309124Z, duration: 17, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=ucsd-center-for-functional-mri-cfmri-web-rtd -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="ucsd-center-for-functional-mri-cfmri-web-rtd" "cfmri_web_rtd.tex"' ------------ This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./cfmri_web_rtd.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[53] Overfull \hbox (283.0526pt too wide) in paragraph at lines 1465--1466 [] [54 <./weighterror1.jpg>] Overfull \hbox (283.0526pt too wide) in paragraph at lines 1467--1468 [] [55 <./weighterror2.jpg>] [56 <./weighterror3.jpg>] Chapter 8. [57] [58 <./projector1.png> <./projector2.png>] [59] [60] Chapter 9. No file ucsd-center-for-functional-mri-cfmri-web-rtd.ind. [61] (./ucsd-center-for-functional-mri-cfmri-web-rtd.aux) Package rerunfilecheck Warning: File `ucsd-center-for-functional-mri-cfmri-web- rtd.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 ucsd-center-for-functional-mri-cfmri-web-rtd.pdf (65 pages, 9 989565 bytes). Transcript written on ucsd-center-for-functional-mri-cfmri-web-rtd.log. Latexmk: Index file 'ucsd-center-for-functional-mri-cfmri-web-rtd.idx' was written Latexmk: Missing input file: 'ucsd-center-for-functional-mri-cfmri-web-rtd.ind' from line 'No file ucsd-center-for-functional-mri-cfmri-web-rtd.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'ucsd-center-for-functional-mri-cfmri-web-rtd.pdf' Latexmk: Log file says output to 'ucsd-center-for-functional-mri-cfmri-web-rtd.pdf' Rule 'makeindex ucsd-center-for-functional-mri-cfmri-web-rtd.idx': File changes, etc: Non-existent destination files: 'ucsd-center-for-functional-mri-cfmri-web-rtd.ind' ------------ Run number 1 of rule 'makeindex ucsd-center-for-functional-mri-cfmri-web-rtd.idx' ------------ ------------ Running 'makeindex -s python.ist -o "ucsd-center-for-functional-mri-cfmri-web-rtd.ind" "ucsd-center-for-functional-mri-cfmri-web-rtd.idx"' ------------ Latexmk: applying rule 'makeindex ucsd-center-for-functional-mri-cfmri-web-rtd.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file ucsd-center-for-functional-mri-cfmri-web-rtd.idx...done (0 entries accepted, 0 rejected). Nothing written in ucsd-center-for-functional-mri-cfmri-web-rtd.ind. Transcript written in ucsd-center-for-functional-mri-cfmri-web-rtd.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'ucsd-center-for-functional-mri-cfmri-web-rtd.aux' 'ucsd-center-for-functional-mri-cfmri-web-rtd.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="ucsd-center-for-functional-mri-cfmri-web-rtd" "cfmri_web_rtd.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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Latexmk: Index file 'ucsd-center-for-functional-mri-cfmri-web-rtd.idx' was written Latexmk: Log file says output to 'ucsd-center-for-functional-mri-cfmri-web-rtd.pdf' Latexmk: Log file says output to 'ucsd-center-for-functional-mri-cfmri-web-rtd.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'ucsd-center-for-functional-mri-cfmri-web-rtd.out' 'ucsd-center-for-functional-mri-cfmri-web-rtd.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="ucsd-center-for-functional-mri-cfmri-web-rtd" "cfmri_web_rtd.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./cfmri_web_rtd.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[53] Overfull \hbox (283.0526pt too wide) in paragraph at lines 1465--1466 [] [54 <./weighterror1.jpg>] Overfull \hbox (283.0526pt too wide) in paragraph at lines 1467--1468 [] [55 <./weighterror2.jpg>] [56 <./weighterror3.jpg>] Chapter 8. [57] [58 <./projector1.png> <./projector2.png>] [59] [60] Chapter 9. (./ucsd-center-for-functional-mri-cfmri-web-rtd.ind) [61] (./ucsd-center-for-functional-mri-cfmri-web-rtd.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on ucsd-center-for-functional-mri-cfmri-web-rtd.pdf (65 pages, 9 997088 bytes). Transcript written on ucsd-center-for-functional-mri-cfmri-web-rtd.log. Latexmk: Index file 'ucsd-center-for-functional-mri-cfmri-web-rtd.idx' was written Latexmk: Log file says output to 'ucsd-center-for-functional-mri-cfmri-web-rtd.pdf' Latexmk: Log file says output to 'ucsd-center-for-functional-mri-cfmri-web-rtd.pdf' Latexmk: All targets (ucsd-center-for-functional-mri-cfmri-web-rtd.pdf) are up-to-date [rtd-command-info] start-time: 2019-11-25T21:33:34.406014Z, end-time: 2019-11-25T21:33:34.727956Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/_build/latex/ucsd-center-for-functional-mri-cfmri-web-rtd.pdf /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/artifacts/latest/sphinx_pdf/ucsd-center-for-functional-mri-cfmri-web-rtd.pdf [rtd-command-info] start-time: 2019-11-25T21:33:34.803539Z, end-time: 2019-11-25T21:33:37.056391Z, duration: 2, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [epub]: targets for 11 source files that are out of date updating environment: 11 added, 0 changed, 0 removed reading sources... 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