Read the Docs build information Build id: 1328034 Project: ucsd-center-for-functional-mri-cfmri-web-rtd Version: latest Commit: 404ee1614e6bbf27a97924c359f712c7747f3463 Date: 2023-03-02T23:39:55.592513Z State: finished Success: True [rtd-command-info] start-time: 2023-03-02T23:39:57.961035Z, end-time: 2023-03-02T23:40:17.677361Z, duration: 19, 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: 2023-03-02T23:40:17.892264Z, end-time: 2023-03-02T23:40:19.483290Z, duration: 1, exit-code: 0 git checkout --force origin/master Note: switching to '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 switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 404ee16 updated cfmri contact and maps [rtd-command-info] start-time: 2023-03-02T23:40:19.671695Z, end-time: 2023-03-02T23:40:19.762257Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-03-02T23:40:24.283135Z, end-time: 2023-03-02T23:40:28.909031Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH 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. 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sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting Pygments>=2.0 Downloading Pygments-2.14.0-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 227.5 MB/s eta 0:00:00 Collecting packaging Downloading packaging-23.0-py3-none-any.whl (42 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.7/42.7 kB 162.8 MB/s eta 0:00:00 Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 238.6 MB/s eta 0:00:00 Collecting babel!=2.0,>=1.3 Downloading Babel-2.12.1-py3-none-any.whl (10.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.1/10.1 MB 205.3 MB/s eta 0:00:00 Collecting requests>=2.0.0 Downloading requests-2.28.2-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 173.3 MB/s eta 0:00:00 Collecting imagesize Downloading 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Successfully installed MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.12.1 certifi-2022.12.7 charset-normalizer-3.0.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.0 pillow-9.4.0 pytz-2022.7.1 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.14 [rtd-command-info] start-time: 2023-03-02T23:40:39.059154Z, end-time: 2023-03-02T23:40:39.126243Z, 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/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. 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: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url 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", 'proxied_static_path': "/_/static/", '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': '404ee161', } # 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/1328034/' 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: 2023-03-02T23:40:39.318042Z, end-time: 2023-03-02T23:40:42.047412Z, duration: 2, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v1.8.6 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [html]: targets for 24 source files that are out of date updating environment: 24 added, 0 changed, 0 removed reading sources... [ 4%] alt_parking reading sources... [ 8%] audio_system reading sources... [ 12%] cbfbirn reading sources... [ 16%] cfmridcm2bids reading sources... [ 20%] contact reading sources... [ 25%] copying_scan_data reading sources... [ 29%] coronavirus reading sources... [ 33%] dicom_strip_vast_instructions reading sources... [ 37%] events reading sources... [ 41%] fmri_topup reading sources... [ 45%] getstarted reading sources... [ 50%] help reading sources... [ 54%] imageanalysis reading sources... [ 58%] index reading sources... [ 62%] mb_recon_rtd reading sources... [ 66%] motion_plot reading sources... [ 70%] multiband_expl reading sources... [ 75%] peripheral reading sources... [ 79%] prisma_external_link reading sources... [ 83%] protocols reading sources... [ 87%] safety reading sources... [ 91%] software reading sources... [ 95%] training reading sources... [100%] troubleshooting /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 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/cfmridcm2bids.txt:119: WARNING: Title underline too short. Step 4.1 - exclude scans ^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/index.txt:102: WARNING: Title underline too short. CFMRI BIDS conversion script cfmridcm2bids =========================== /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/index.txt:102: WARNING: Title underline too short. CFMRI BIDS conversion script cfmridcm2bids =========================== /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 writing output... [ 4%] alt_parking writing output... [ 8%] audio_system writing output... [ 12%] cbfbirn writing output... [ 16%] cfmridcm2bids writing output... [ 20%] contact writing output... [ 25%] copying_scan_data writing output... [ 29%] coronavirus writing output... [ 33%] dicom_strip_vast_instructions writing output... [ 37%] events writing output... [ 41%] fmri_topup writing output... [ 45%] getstarted writing output... [ 50%] help writing output... [ 54%] imageanalysis writing output... [ 58%] index writing output... [ 62%] mb_recon_rtd writing output... [ 66%] motion_plot writing output... [ 70%] multiband_expl writing output... [ 75%] peripheral writing output... [ 79%] prisma_external_link writing output... [ 83%] protocols writing output... [ 87%] safety writing output... [ 91%] software writing output... [ 95%] training writing output... [100%] troubleshooting /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. generating indices... genindex writing additional pages... search copying images... [ 1%] images/audio_system/CFMRI_MrConfon_User_Manual_20171228_v3.png copying images... [ 2%] images/audio_system/pen_console.jpg copying images... [ 3%] images/audio_system/stim_cable.jpg copying images... [ 4%] images/audio_system/mag_cable.jpg copying images... [ 5%] images/audio_system/pen_mag.jpg copying images... [ 6%] images/cbfbirn/cfmricp_log.png copying images... [ 7%] images/cbfbirn/beforefmap.png copying images... [ 8%] images/cbfbirn/afterfmap.png copying images... [ 9%] images/cbfbirn/cbf1.png copying images... [ 10%] images/cfmridcm2bids/bids_protocol_v1_20220517.jpg copying images... [ 11%] images/cfmridcm2bids/exist_dataset_example.png copying images... [ 12%] images/cfmridcm2bids/dataset_add_scan_codes.png copying images... [ 13%] images/cfmridcm2bids/startbids.png copying images... [ 15%] images/cfmridcm2bids/select_data_folder.png copying images... [ 16%] images/cfmridcm2bids/give_output_folder_name.png copying images... [ 17%] images/cfmridcm2bids/check_input_output_dir.png copying images... [ 18%] images/cfmridcm2bids/subject_code.png copying images... [ 19%] images/cfmridcm2bids/session_code.png copying images... [ 20%] images/cfmridcm2bids/ask_for_BIDS_config_file.png copying images... [ 21%] images/cfmridcm2bids/ask_exclude_scans.png copying images... [ 22%] images/cfmridcm2bids/exclude_scans.png copying images... [ 23%] images/cfmridcm2bids/scans_after_exclude.png copying images... [ 24%] images/cfmridcm2bids/ask_func_fmap_scans.png copying images... [ 25%] images/cfmridcm2bids/func_task_name.png copying images... [ 26%] images/cfmridcm2bids/func_taskname_enter.png copying images... [ 27%] images/cfmridcm2bids/check_func_task_name.png copying images... [ 29%] images/cfmridcm2bids/ask_fmap_info.png copying images... [ 30%] images/cfmridcm2bids/enter_fmap_intendfor.png copying images... [ 31%] images/cfmridcm2bids/check_fmap_intendfor.png copying images... [ 32%] images/cfmridcm2bids/check_scan_info.png copying images... 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[ 80%] pdf/3T_UCSD_recruit_screen_rev08-2006.pdf copying downloadable files... [ 90%] pdf/3T_UCSD_pre-entry_Screen_rev08-2006.pdf copying downloadable files... [100%] pdf/3T_UCSD_operator_checklist_rev08-2006.pdf copying static files... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 5 warnings. The HTML pages are in ../../_readthedocs/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2023-03-02T23:40:42.232078Z, end-time: 2023-03-02T23:40:44.305458Z, duration: 2, exit-code: 0 python -m sphinx -T -E -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v1.8.6 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: 24 added, 0 changed, 0 removed reading sources... [ 4%] alt_parking reading sources... [ 8%] audio_system reading sources... [ 12%] cbfbirn reading sources... [ 16%] cfmridcm2bids reading sources... [ 20%] contact reading sources... [ 25%] copying_scan_data reading sources... [ 29%] coronavirus reading sources... [ 33%] dicom_strip_vast_instructions reading sources... [ 37%] events reading sources... [ 41%] fmri_topup reading sources... [ 45%] getstarted reading sources... [ 50%] help reading sources... [ 54%] imageanalysis reading sources... [ 58%] index reading sources... [ 62%] mb_recon_rtd reading sources... [ 66%] motion_plot reading sources... [ 70%] multiband_expl reading sources... [ 75%] peripheral reading sources... [ 79%] prisma_external_link reading sources... [ 83%] protocols reading sources... [ 87%] safety reading sources... [ 91%] software reading sources... [ 95%] training reading sources... [100%] troubleshooting /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 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/cfmridcm2bids.txt:119: WARNING: Title underline too short. Step 4.1 - exclude scans ^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/index.txt:102: WARNING: Title underline too short. CFMRI BIDS conversion script cfmridcm2bids =========================== /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/index.txt:102: WARNING: Title underline too short. CFMRI BIDS conversion script cfmridcm2bids =========================== /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 prisma_external_link training safety coronavirus events protocols mb_recon_rtd troubleshooting audio_system copying_scan_data imageanalysis motion_plot multiband_expl fmri_topup cfmridcm2bids dicom_strip_vast_instructions cbfbirn peripheral software alt_parking contact 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 writing additional files... copying images... 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' %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: 2023-03-02T23:41:01.542807Z, end-time: 2023-03-02T23:41:43.950054Z, duration: 42, 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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[109] [110] [111] [112] Chapter 15. 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Underfull \hbox (badness 10000) in paragraph at lines 3273--3275 []|\T1/ptm/m/n/10 Custom MAT-LAB code. Equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 3273--3275 \T1/ptm/m/n/10 lent to CBF+nomask+orig masked by Underfull \hbox (badness 10000) in paragraph at lines 3302--3303 \T1/ptm/m/n/10 via par-tial vol-ume cor-rec-tion Underfull \hbox (badness 5260) in paragraph at lines 3309--3310 []|\T1/ptm/m/n/10 White mat-ter CBF im-age pro- [117] [118] [119] [120] Chapter 16. Overfull \hbox (308.05263pt too wide) in paragraph at lines 3369--3370 [] [121] Overfull \hbox (308.05263pt too wide) in paragraph at lines 3371--3372 [] [122 <./projector1.png>] Overfull \vbox (1130.98615pt too high) has occurred while \output is active [123 <./projector2.png>] [124] Chapter 17. [125] [126 <./mat1.png> <./mat2.png>] [127 <./mat3.png> <./mat4.png>] [128 <./m at5.png> <./mat6.png>] [129 <./mat7.png> <./mat8.png>] [130 <./mat9.png> <./mat 10.png>] [131 <./mat11.png> <./mat12.png>] [132 <./mat13.png>] [133 <./mat14.pn g>] [134 <./mat15.png> <./mat16.png>] Chapter 18. [135] [136] [137] [138] Chapter 19. No file ucsd-center-for-functional-mri-cfmri-web-rtd.ind. [139] (./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 (143 pages, 25906404 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. 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[125] [126 <./mat1.png> <./mat2.png>] [127 <./mat3.png> <./mat4.png>] [128 <./m at5.png> <./mat6.png>] [129 <./mat7.png> <./mat8.png>] [130 <./mat9.png> <./mat 10.png>] [131 <./mat11.png> <./mat12.png>] [132 <./mat13.png>] [133 <./mat14.pn g>] [134 <./mat15.png> <./mat16.png>] Chapter 18. [135] [136] [137] [138] Chapter 19. (./ucsd-center-for-functional-mri-cfmri-web-rtd.ind) [139] (./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 (145 pages, 25922707 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' ------------ 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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[125] [126 <./mat1.png> <./mat2.png>] [127 <./mat3.png> <./mat4.png>] [128 <./m at5.png> <./mat6.png>] [129 <./mat7.png> <./mat8.png>] [130 <./mat9.png> <./mat 10.png>] [131 <./mat11.png> <./mat12.png>] [132 <./mat13.png>] [133 <./mat14.pn g>] [134 <./mat15.png> <./mat16.png>] Chapter 18. [135] [136] [137] [138] Chapter 19. (./ucsd-center-for-functional-mri-cfmri-web-rtd.ind) [139] (./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 (145 pages, 25922707 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: 2023-03-02T23:41:44.548327Z, end-time: 2023-03-02T23:41:47.649974Z, duration: 3, exit-code: 0 python -m sphinx -T -E -b epub -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/epub Running Sphinx v1.8.6 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [epub]: targets for 24 source files that are out of date updating environment: 24 added, 0 changed, 0 removed reading sources... [ 4%] alt_parking reading sources... [ 8%] audio_system reading sources... [ 12%] cbfbirn reading sources... [ 16%] cfmridcm2bids reading sources... [ 20%] contact reading sources... [ 25%] copying_scan_data reading sources... [ 29%] coronavirus reading sources... [ 33%] dicom_strip_vast_instructions reading sources... [ 37%] events reading sources... [ 41%] fmri_topup reading sources... [ 45%] getstarted reading sources... [ 50%] help reading sources... [ 54%] imageanalysis reading sources... [ 58%] index reading sources... [ 62%] mb_recon_rtd reading sources... [ 66%] motion_plot reading sources... [ 70%] multiband_expl reading sources... [ 75%] peripheral reading sources... [ 79%] prisma_external_link reading sources... [ 83%] protocols reading sources... [ 87%] safety reading sources... [ 91%] software reading sources... [ 95%] training reading sources... [100%] troubleshooting /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 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/cfmridcm2bids.txt:119: WARNING: Title underline too short. Step 4.1 - exclude scans ^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/index.txt:102: WARNING: Title underline too short. CFMRI BIDS conversion script cfmridcm2bids =========================== /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/index.txt:102: WARNING: Title underline too short. CFMRI BIDS conversion script cfmridcm2bids =========================== /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 writing output... [ 4%] alt_parking writing output... [ 8%] audio_system writing output... [ 12%] cbfbirn writing output... [ 16%] cfmridcm2bids writing output... [ 20%] contact writing output... [ 25%] copying_scan_data writing output... [ 29%] coronavirus writing output... [ 33%] dicom_strip_vast_instructions writing output... 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