Read the Docs build information
Build id: 619222
Project: ucsd-center-for-functional-mri-cfmri-web-rtd
Version: latest
Commit: 482a5fe05491ce096aa96f7b282d0bb7ee0f939a
Date: 2021-04-23T19:35:07.899188Z
State: finished
Success: True


[rtd-command-info] start-time: 2021-04-23T19:35:09.322994Z, end-time: 2021-04-23T19:35:26.236531Z, duration: 16, exit-code: 0
git clone --no-single-branch --depth 50 https://bitbucket.org/ucsdcfmri/cfmri_web_rtd.git .
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[rtd-command-info] start-time: 2021-04-23T19:35:26.378160Z, end-time: 2021-04-23T19:35:27.991694Z, 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 <new-branch-name>

HEAD is now at 482a5fe added info on where the coil images came from

[rtd-command-info] start-time: 2021-04-23T19:35:28.117847Z, end-time: 2021-04-23T19:35:28.187954Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-04-23T19:35:32.511786Z, end-time: 2021-04-23T19:35:36.596844Z, 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: 2021-04-23T19:35:36.724017Z, end-time: 2021-04-23T19:35:38.355432Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (21.0.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (56.0.0)

[rtd-command-info] start-time: 2021-04-23T19:35:38.457530Z, end-time: 2021-04-23T19:35:47.287639Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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 mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
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Collecting packaging
  Downloading packaging-20.9-py2.py3-none-any.whl (40 kB)
Requirement already satisfied: setuptools 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) (56.0.0)
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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=23755 sha256=d8f988eb4ef6f3e376bf54341781f2ab7c560ae6306b77c1c4df99ac73e1f0bc
  Stored in directory: /tmp/pip-ephem-wheel-cache-d9mvqvi6/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
  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=855d47f2b09331394c8915f3dcd3de88633020fb2b27acd8161da781dba8e967
  Stored in directory: /tmp/pip-ephem-wheel-cache-d9mvqvi6/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.8.1 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 six-1.15.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.4

[rtd-command-info] start-time: 2021-04-23T19:35:48.092381Z, end-time: 2021-04-23T19:35:48.156239Z, 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
#
# Note: this file should't rely on extra depencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

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': '482a5fe0',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





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")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/ucsd-center-for-functional-mri-cfmri-web-rtd/builds/619222/'

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: 2021-04-23T19:35:48.298986Z, end-time: 2021-04-23T19:35:51.059747Z, duration: 2, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
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updating environment: 24 added, 0 changed, 0 removed
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   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
/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".
none found
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writing output... [ 79%] prisma_toc
writing output... [ 83%] protocols
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writing output... [ 95%] training
writing output... [100%] troubleshooting

generating indices.../home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/motion_plot.txt:49: WARNING: Could not lex literal_block as "csh". Highlighting skipped.
 genindex
writing additional pages... search
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copying static files... done
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dumping object inventory... done
build succeeded, 2 warnings.

The HTML pages are in _build/html.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2021-04-23T19:35:51.297468Z, end-time: 2021-04-23T19:35:52.685404Z, duration: 1, exit-code: 0
python -m sphinx -T -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
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preparing documents... done
assembling single document... prisma_toc prisma/timeline_announcement prisma/coil_info coronavirus getstarted training safety events protocols mb_recon_rtd troubleshooting audio_system copying_scan_data imageanalysis motion_plot multiband_expl fmri_topup dicom_strip_vast_instructions cbfbirn 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:49: WARNING: Could not lex literal_block as "csh". Highlighting skipped.
done
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build succeeded, 1 warning.

The HTML page is in _build/localmedia.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2021-04-23T19:35:53.027049Z, end-time: 2021-04-23T19:35:54.150684Z, duration: 1, exit-code: 0
python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.8.5
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making output directory...
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
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updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
processing cfmri_web_rtd.tex...index prisma_toc prisma/timeline_announcement prisma/coil_info coronavirus getstarted training safety events protocols mb_recon_rtd troubleshooting audio_system copying_scan_data imageanalysis motion_plot multiband_expl fmri_topup dicom_strip_vast_instructions cbfbirn peripheral software license help 
resolving references...
writing... /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages/sphinx/builders/latex/__init__.py:201: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  if toctrees[0].get('maxdepth') > 0:
/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/motion_plot.txt:49: WARNING: Could not lex literal_block as "csh". Highlighting skipped.
done
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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).
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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: 2021-04-23T19:36:07.076372Z, end-time: 2021-04-23T19:36:46.641260Z, duration: 39, exit-code: 0
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Chapter 1.

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l.106 ...estions or concerns about the upcoming 
                                                  installation, please do no...


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l.106 ...lease do not hesitate to contact us at 
                                                  \sphinxhref{mailto:cfmri@u...

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Chapter 2.
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Chapter 3.
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Chapter 4.
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Chapter 7.
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Chapter 8.

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Chapter 1.

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Chapter 17.
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Chapter 1.

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l.106 ...estions or concerns about the upcoming 
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l.106 ...lease do not hesitate to contact us at 
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Chapter 2.
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Chapter 3.
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Chapter 4.
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Chapter 8.

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Chapter 9.
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Chapter 10.

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Chapter 11.
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Chapter 12.
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Chapter 13.
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Chapter 14.

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Chapter 15.

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Chapter 16.
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Chapter 17.
(./ucsd-center-for-functional-mri-cfmri-web-rtd.ind) [141]
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copying static files... done
copying extra files... done
WARNING: conf value "version" should not be empty for EPUB3
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build succeeded, 2 warnings.

The ePub file is in _build/epub.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2021-04-23T19:36:49.721169Z, end-time: 2021-04-23T19:36:49.791580Z, 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