Read the Docs build information Build id: 271135 Project: ucsd-center-for-functional-mri-cfmri-web-rtd Version: latest Commit: f1997611844fb4207302968c4466559d7c460f46 Date: 2019-12-20T17:02:53.579991Z State: finished Success: True [rtd-command-info] start-time: 2019-12-20T17:02:54.080797Z, end-time: 2019-12-20T17:03:07.471975Z, duration: 13, exit-code: 0 git clone --no-single-branch --depth 50 https://bitbucket.org/ucsdcfmri/cfmri_web_rtd.git . Cloning into '.'... [rtd-command-info] start-time: 2019-12-20T17:03:07.751255Z, end-time: 2019-12-20T17:03:08.136893Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at f199761 added a data analysis section with helpful tips [rtd-command-info] start-time: 2019-12-20T17:03:08.215495Z, end-time: 2019-12-20T17:03:08.235512Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-12-20T17:03:09.318476Z, end-time: 2019-12-20T17:03:13.873794Z, 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 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-12-20T17:03:13.969728Z, end-time: 2019-12-20T17:03:16.654317Z, 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 pip Collecting pip Downloading https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl (1.4MB) Installing collected packages: pip Found existing installation: pip 19.1.1 Uninstalling pip-19.1.1: Successfully uninstalled pip-19.1.1 Successfully installed pip-19.3.1 [rtd-command-info] start-time: 2019-12-20T17:03:16.819627Z, end-time: 2019-12-20T17:03:31.252751Z, duration: 14, 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 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/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-cp37-none-any.whl size=491057 sha256=0389026c9b4d9020808af94d99a0aadce95ec212927413ef49b7b263d50e09a7 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/.cache/pip/wheels/8b/99/a0/81daf51dcd359a9377b110a8a886b3895921802d2fc1b2397e Successfully built mock future Installing collected packages: Pygments, docutils, mock, pillow, alabaster, future, commonmark, snowballstemmer, certifi, urllib3, chardet, idna, requests, sphinxcontrib-websupport, imagesize, MarkupSafe, Jinja2, pytz, babel, pyparsing, six, packaging, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Successfully installed Jinja2-2.10.3 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.7.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.2 pillow-5.4.1 pyparsing-2.4.5 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.22.0 six-1.13.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.7 [rtd-command-info] start-time: 2019-12-20T17:03:31.859631Z, end-time: 2019-12-20T17:03:32.170902Z, 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': 'f1997611', } 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: 2019-12-20T17:03:32.280340Z, end-time: 2019-12-20T17:03:34.396656Z, duration: 2, exit-code: 0 python sphinx-build -T -E -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 12 source files that are out of date updating environment: 12 added, 0 changed, 0 removed reading sources... 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WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/nstatic' 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, 8 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2019-12-20T17:03:34.536314Z, end-time: 2019-12-20T17:03:36.945889Z, duration: 2, 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: 12 added, 0 changed, 0 removed reading sources... 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[100%] troubleshooting /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/imageanalysis.txt:: WARNING: image file not readable: images/analysis/plotmotion1.jpg /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/imageanalysis.txt:: WARNING: image file not readable: images/analysis/plotmotion2.jpg /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/peripheral.txt:29: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/peripheral.txt:32: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/safety.txt:31: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/software.txt:3: WARNING: Duplicate explicit target name: "mac osx". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... getstarted training safety events protocols troubleshooting imageanalysis peripheral software license help writing... /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/index.txt:52: WARNING: Could not lex literal_block as "csh". 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[rtd-command-info] start-time: 2019-12-20T17:03:37.119374Z, end-time: 2019-12-20T17:03:38.829988Z, 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: 12 added, 0 changed, 0 removed reading sources... [ 8%] events reading sources... [ 16%] getstarted reading sources... [ 25%] help reading sources... [ 33%] imageanalysis reading sources... [ 41%] index reading sources... [ 50%] license reading sources... [ 58%] peripheral reading sources... [ 66%] protocols reading sources... [ 75%] safety reading sources... [ 83%] software reading sources... [ 91%] training reading sources... [100%] troubleshooting /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/imageanalysis.txt:: WARNING: image file not readable: images/analysis/plotmotion1.jpg /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/imageanalysis.txt:: WARNING: image file not readable: images/analysis/plotmotion2.jpg /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/peripheral.txt:29: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/peripheral.txt:32: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/safety.txt:31: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/software.txt:3: WARNING: Duplicate explicit target name: "mac osx". looking for now-outdated files... none found pickling environment... done checking consistency... done processing cfmri_web_rtd.tex...index getstarted training safety events protocols troubleshooting imageanalysis peripheral software license help resolving references... writing... /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/imageanalysis.txt:52: WARNING: Could not lex literal_block as "csh". 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[rtd-command-info] start-time: 2019-12-20T17:03:53.384766Z, end-time: 2019-12-20T17:03:53.701645Z, 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: 2019-12-20T17:03:54.401501Z, end-time: 2019-12-20T17:04:13.413566Z, duration: 19, 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' ------------ ------------ 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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[63] [64] Chapter 10. No file ucsd-center-for-functional-mri-cfmri-web-rtd.ind. [65] (./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 (69 pages, 9 994676 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: '{images/analysis/plotmotion1}.jpg' from line 'LaTeX Warning: File `{images/analysis/plotmotion1}.jpg' not found on input line' Latexmk: Missing input file: '{images/analysis/plotmotion1}.jpg' from line 'LaTeX Warning: File `{images/analysis/plotmotion1}.jpg' not found on input line 1509.' Latexmk: Missing input file: '{images/analysis/plotmotion2}.jpg' from line 'LaTeX Warning: File `{images/analysis/plotmotion2}.jpg' not found on input line' Latexmk: Missing input file: '{images/analysis/plotmotion2}.jpg' from line 'LaTeX Warning: File `{images/analysis/plotmotion2}.jpg' not found on input line 1523.' 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). 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[63] [64] Chapter 10. (./ucsd-center-for-functional-mri-cfmri-web-rtd.ind) [65] (./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 (69 pages, 1 0002396 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: '{images/analysis/plotmotion1}.jpg' from line 'LaTeX Warning: File `{images/analysis/plotmotion1}.jpg' not found on input line' Latexmk: Missing input file: '{images/analysis/plotmotion1}.jpg' from line 'LaTeX Warning: File `{images/analysis/plotmotion1}.jpg' not found on input line 1509.' Latexmk: Missing input file: '{images/analysis/plotmotion2}.jpg' from line 'LaTeX Warning: File `{images/analysis/plotmotion2}.jpg' not found on input line' Latexmk: Missing input file: '{images/analysis/plotmotion2}.jpg' from line 'LaTeX Warning: File `{images/analysis/plotmotion2}.jpg' not found on input line 1523.' 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'... 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[51] Overfull \hbox (283.0526pt too wide) in paragraph at lines 1459--1460 [] [52 <./weighterror1.jpg>] Overfull \hbox (283.0526pt too wide) in paragraph at lines 1461--1462 [] [53 <./weighterror2.jpg>] [54 <./weighterror3.jpg>] Chapter 7. [55] LaTeX Warning: File `{images/analysis/plotmotion1}.jpg' not found on input line 1509. ! Package pdftex.def Error: File `images/analysis/plotmotion1.jpg' not found: u sing draft setting. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.1509 ...imen]{{images/analysis/plotmotion1}.jpg} LaTeX Warning: File `{images/analysis/plotmotion2}.jpg' not found on input line 1523. ! Package pdftex.def Error: File `images/analysis/plotmotion2.jpg' not found: u sing draft setting. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.1523 ...imen]{{images/analysis/plotmotion2}.jpg} [56] [57] [58] Chapter 8. [59] [60 <./projector1.png> <./projector2.png>] [61] [62] Chapter 9. [63] [64] Chapter 10. (./ucsd-center-for-functional-mri-cfmri-web-rtd.ind) [65] (./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 (69 pages, 1 0002396 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: '{images/analysis/plotmotion1}.jpg' from line 'LaTeX Warning: File `{images/analysis/plotmotion1}.jpg' not found on input line' Latexmk: Missing input file: '{images/analysis/plotmotion1}.jpg' from line 'LaTeX Warning: File `{images/analysis/plotmotion1}.jpg' not found on input line 1509.' 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[rtd-command-info] start-time: 2019-12-20T17:04:16.369500Z, end-time: 2019-12-20T17:04:16.690724Z, 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/epub/UCSDCenterforfMRI.epub /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/artifacts/latest/sphinx_epub/ucsd-center-for-functional-mri-cfmri-web-rtd.epub