Read the Docs build information Build id: 487995 Project: ucsd-center-for-functional-mri-cfmri-web-rtd Version: latest Commit: 32acf1973f3ac91eec54b5e4bddcbf534b50465d Date: 2020-11-24T00:59:13.451960Z State: finished Success: True [rtd-command-info] start-time: 2020-11-24T00:59:14.738278Z, end-time: 2020-11-24T00:59:41.593788Z, duration: 26, exit-code: 0 git clone --no-single-branch --depth 50 https://bitbucket.org/ucsdcfmri/cfmri_web_rtd.git . Cloning into '.'... 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[rtd-command-info] start-time: 2020-11-24T00:59:42.026563Z, end-time: 2020-11-24T00:59:43.571807Z, duration: 1, 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 32acf19 added dicomDate instructions [rtd-command-info] start-time: 2020-11-24T00:59:43.745769Z, end-time: 2020-11-24T00:59:43.801899Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-11-24T01:00:00.136044Z, end-time: 2020-11-24T01:00:04.288024Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' 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: 2020-11-24T01:00:04.474061Z, end-time: 2020-11-24T01:00:05.152970Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 (20.2.4) [rtd-command-info] start-time: 2020-11-24T01:00:05.434436Z, end-time: 2020-11-24T01:00:13.810458Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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<2.2 Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.1-py2.py3-none-any.whl (13 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting Pygments>=2.0 Downloading Pygments-2.7.2-py3-none-any.whl (948 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting requests>=2.0.0 Downloading requests-2.25.0-py2.py3-none-any.whl (61 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting pytz>=2015.7 Downloading pytz-2020.4-py2.py3-none-any.whl (509 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.2-py2.py3-none-any.whl (136 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.11.8-py2.py3-none-any.whl (155 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=31c3f17accc46c2f6a93067df9ee43d60d8cb3c21a3565e09c6a1c35735c425a Stored in directory: /tmp/pip-ephem-wheel-cache-caj0hoxr/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b 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-py3-none-any.whl size=491059 sha256=c22d63305a922a3eda66d83a5b5e88388bdd78cd54f41d760a0a7607057f4990 Stored in directory: /tmp/pip-ephem-wheel-cache-caj0hoxr/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, Pygments, snowballstemmer, imagesize, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, MarkupSafe, Jinja2, pytz, babel, urllib3, idna, certifi, chardet, requests, six, pyparsing, packaging, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 50.3.2 Uninstalling setuptools-50.3.2: Successfully uninstalled setuptools-50.3.2 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.2 alabaster-0.7.12 babel-2.9.0 certifi-2020.11.8 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.25.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2 [rtd-command-info] start-time: 2020-11-24T01:00:15.250097Z, end-time: 2020-11-24T01:00:15.318104Z, 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 = {} # # Adding word wrapping into tables # https://rackerlabs.github.io/docs-rackspace/tools/rtd-tables.html #html_context = { # 'css_files': [ # '_static/theme_overrides.css', # override wide tables in RTD theme # ], # } # -- 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://assets.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://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//ucsd-center-for-functional-mri-cfmri-web-rtd.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//ucsd-center-for-functional-mri-cfmri-web-rtd.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//ucsd-center-for-functional-mri-cfmri-web-rtd.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], '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', 'github_user': 'None', 'proxied_api_host': '/_', '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, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '32acf197', } 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' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2020-11-24T01:00:15.458262Z, end-time: 2020-11-24T01:00:17.710174Z, 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 20 source files that are out of date updating environment: 20 added, 0 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2020-11-24T01:00:17.939227Z, end-time: 2020-11-24T01:00:19.731857Z, 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: 20 added, 0 changed, 0 removed reading sources... [ 5%] audio_system reading sources... [ 10%] cbfbirn reading sources... [ 15%] coronavirus reading sources... [ 20%] dicom_strip_vast_instructions reading sources... [ 25%] events reading sources... [ 30%] fmri_topup reading sources... [ 35%] getstarted reading sources... [ 40%] help reading sources... [ 45%] imageanalysis reading sources... [ 50%] index reading sources... [ 55%] license reading sources... [ 60%] mb_recon_rtd reading sources... 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[ 97%] images/matlab_install/mat14.png copying images... [ 98%] images/matlab_install/mat15.png copying images... [100%] images/matlab_install/mat16.png copying TeX support files... done build succeeded, 6 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2020-11-24T01:00:30.650929Z, end-time: 2020-11-24T01:00:30.716812Z, 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: 2020-11-24T01:00:30.831171Z, end-time: 2020-11-24T01:01:08.113094Z, duration: 37, 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. 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[115] (./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 (119 pages, 27144969 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. 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(./ucsd-center-for-functional-mri-cfmri-web-rtd.ind) [115] (./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 (121 pages, 27160784 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' 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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Underfull \hbox (badness 10000) in paragraph at lines 2997--2999 []|\T1/ptm/m/n/10 Custom MAT-LAB code. Equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 2997--2999 \T1/ptm/m/n/10 lent to CBF+nomask+orig masked by Underfull \hbox (badness 10000) in paragraph at lines 3026--3027 \T1/ptm/m/n/10 via par-tial vol-ume cor-rec-tion Underfull \hbox (badness 5260) in paragraph at lines 3033--3034 []|\T1/ptm/m/n/10 White mat-ter CBF im-age pro- [95] [96] [97] [98] Chapter 13. [99] [100 <./projector1.png> <./projector2.png>] [101] [102] Chapter 14. [103] [104 <./mat1.png> <./mat2.png>] [105 <./mat3.png> <./mat4.png>] [106 <./m at5.png> <./mat6.png>] [107 <./mat7.png> <./mat8.png>] [108 <./mat9.png> <./mat 10.png>] [109 <./mat11.png> <./mat12.png>] [110 <./mat13.png>] [111 <./mat14.pn g>] [112 <./mat15.png> <./mat16.png>] [113] [114] Chapter 15. (./ucsd-center-for-functional-mri-cfmri-web-rtd.ind) [115] (./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 (121 pages, 27160784 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: 2020-11-24T01:01:08.300415Z, end-time: 2020-11-24T01:01:08.362308Z, 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: 2020-11-24T01:01:08.493427Z, end-time: 2020-11-24T01:01:11.315872Z, 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 20 source files that are out of date updating environment: 20 added, 0 changed, 0 removed reading sources... 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