Read the Docs build information Build id: 641839 Project: life-epigenetics-methylprep Version: latest Commit: 0dac42f6c3d411583984a8015890168025a24159 Date: 2021-05-26T19:57:18.883777Z State: finished Success: False [rtd-command-info] start-time: 2021-05-26T19:57:20.398499Z, end-time: 2021-05-26T19:57:29.503420Z, duration: 9, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylprep.git . Cloning into '.'... 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[rtd-command-info] start-time: 2021-05-26T19:57:29.629599Z, end-time: 2021-05-26T19:57:30.263155Z, 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 0dac42f Feature/v1.4.6 (#84) [rtd-command-info] start-time: 2021-05-26T19:57:30.370527Z, end-time: 2021-05-26T19:57:30.435796Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-05-26T19:57:33.013924Z, end-time: 2021-05-26T19:57:37.161989Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-05-26T19:57:37.273347Z, end-time: 2021-05-26T19:57:38.419280Z, 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/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (21.1.2) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (57.0.0) [rtd-command-info] start-time: 2021-05-26T19:57:38.545003Z, end-time: 2021-05-26T19:57:47.523264Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I 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) 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-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting setuptools Downloading setuptools-57.0.0-py3-none-any.whl (821 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.1-py3-none-any.whl (133 kB) Collecting Pygments>=2.0 Downloading Pygments-2.9.0-py3-none-any.whl (1.0 MB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting requests>=2.0.0 Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux2010_x86_64.whl (31 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.5-py2.py3-none-any.whl (138 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 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=23772 sha256=6f416d68cc77e0e363968e2ca84334138de930ebbbd6c9ccde6366557c860a6c Stored in directory: /tmp/pip-ephem-wheel-cache-1wy39ms6/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=491070 sha256=884e4f96acd203cf6d7d9678dd2b83ee0aeaf659daf07816cfb78043370b5760 Stored in directory: /tmp/pip-ephem-wheel-cache-1wy39ms6/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, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-3.0.1 MarkupSafe-2.0.1 Pygments-2.9.0 alabaster-0.7.12 babel-2.9.1 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 setuptools-57.0.0 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.5 [rtd-command-info] start-time: 2021-05-26T19:57:47.625513Z, end-time: 2021-05-26T19:58:00.734927Z, duration: 13, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: numpy>=1.18.5 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (1.19.2) Requirement already satisfied: pandas>=1.0 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 2)) (1.1.3) Requirement already satisfied: scipy>=1.2.3 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 3)) (1.5.3) Collecting statsmodels Downloading statsmodels-0.12.2-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB) Collecting pytest Downloading pytest-6.2.4-py3-none-any.whl (280 kB) Collecting coverage Downloading coverage-5.5-cp37-cp37m-manylinux2010_x86_64.whl (242 kB) Collecting python-coveralls Downloading python_coveralls-2.9.3-py2.py3-none-any.whl (9.9 kB) Collecting sphinxcontrib-apidoc Downloading sphinxcontrib_apidoc-0.3.0-py2.py3-none-any.whl (8.5 kB) Collecting m2r Downloading m2r-0.2.1.tar.gz (16 kB) Collecting nbsphinx Downloading nbsphinx-0.8.5-py3-none-any.whl (24 kB) Collecting tqdm Downloading tqdm-4.61.0-py2.py3-none-any.whl (75 kB) Collecting bs4 Downloading bs4-0.0.1.tar.gz (1.1 kB) Collecting lxml Downloading lxml-4.6.3-cp37-cp37m-manylinux2014_x86_64.whl (6.3 MB) Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 14)) (2.25.1) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from pandas>=1.0->-r requirements.txt (line 2)) (2021.1) Requirement already satisfied: python-dateutil>=2.7.3 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from pandas>=1.0->-r requirements.txt (line 2)) (2.8.1) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from python-dateutil>=2.7.3->pandas>=1.0->-r requirements.txt (line 2)) (1.16.0) Collecting patsy>=0.5 Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting iniconfig Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting importlib-metadata>=0.12 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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.8.5) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (3.0.1) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (0.17.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (57.0.0) Requirement already satisfied: sphinxcontrib-websupport in 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pyzmq-22.1.0-cp37-cp37m-manylinux1_x86_64.whl (1.1 MB) Collecting tornado>=4.1 Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.17.3.tar.gz (106 kB) Collecting beautifulsoup4 Downloading beautifulsoup4-4.9.3-py3-none-any.whl (115 kB) Collecting soupsieve>1.2 Downloading soupsieve-2.2.1-py3-none-any.whl (33 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from packaging->pytest->-r requirements.txt (line 5)) (2.4.7) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.1.5) Building wheels for collected packages: m2r, pandocfilters, pyrsistent, bs4 Building wheel for m2r (setup.py): started Building wheel for m2r (setup.py): finished with status 'done' Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10475 sha256=b7565ba0a31aea1bfcf334fe689c5af427639106ed9982e2351c72a4a5e714a4 Stored in directory: /tmp/pip-ephem-wheel-cache-jm06657x/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=8006 sha256=fa0397afc63e1a788aae8bf7b1c3f51db4490f034909a1da25d3aee410e0eff3 Stored in directory: /tmp/pip-ephem-wheel-cache-jm06657x/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp37-cp37m-linux_x86_64.whl size=115348 sha256=a1b22f553c5a14c4c0db912d75ea4c5b8ebd1311009f8841886410ad55524b26 Stored in directory: /tmp/pip-ephem-wheel-cache-jm06657x/wheels/a5/52/bf/71258a1d7b3c8cbe1ee53f9314c6f65f20385481eaee573cc5 Building wheel for bs4 (setup.py): started Building wheel for bs4 (setup.py): finished with status 'done' Created wheel for bs4: filename=bs4-0.0.1-py3-none-any.whl size=1271 sha256=68c54a5facc0b6a45c4046581d1baba72a01b3c664941a1c8a75888f5e22c8c7 Stored in directory: /tmp/pip-ephem-wheel-cache-jm06657x/wheels/0a/9e/ba/20e5bbc1afef3a491f0b3bb74d508f99403aabe76eda2167ca Successfully built m2r pandocfilters pyrsistent bs4 Installing collected packages: zipp, typing-extensions, ipython-genutils, traitlets, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, jupyter-core, jsonschema, webencodings, nest-asyncio, nbformat, jupyter-client, async-generator, testpath, soupsieve, pandocfilters, nbclient, mistune, jupyterlab-pygments, Jinja2, entrypoints, defusedxml, bleach, toml, PyYAML, py, pluggy, pbr, patsy, nbconvert, iniconfig, coverage, beautifulsoup4, tqdm, statsmodels, sphinxcontrib-apidoc, python-coveralls, pytest, nbsphinx, m2r, lxml, bs4 Attempting uninstall: Jinja2 Found existing installation: Jinja2 3.0.1 Uninstalling Jinja2-3.0.1: Successfully uninstalled Jinja2-3.0.1 Successfully installed Jinja2-2.11.3 PyYAML-5.4.1 async-generator-1.10 attrs-21.2.0 beautifulsoup4-4.9.3 bleach-3.3.0 bs4-0.0.1 coverage-5.5 defusedxml-0.7.1 entrypoints-0.3 importlib-metadata-4.2.0 iniconfig-1.1.1 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-client-6.1.12 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 lxml-4.6.3 m2r-0.2.1 mistune-0.8.4 nbclient-0.5.3 nbconvert-6.0.7 nbformat-5.1.3 nbsphinx-0.8.5 nest-asyncio-1.5.1 pandocfilters-1.4.3 patsy-0.5.1 pbr-5.6.0 pluggy-0.13.1 py-1.10.0 pyrsistent-0.17.3 pytest-6.2.4 python-coveralls-2.9.3 pyzmq-22.1.0 soupsieve-2.2.1 sphinxcontrib-apidoc-0.3.0 statsmodels-0.12.2 testpath-0.5.0 toml-0.10.2 tornado-6.1 tqdm-4.61.0 traitlets-5.0.5 typing-extensions-3.10.0.0 webencodings-0.5.1 zipp-3.4.1 [rtd-command-info] start-time: 2021-05-26T19:58:01.604068Z, end-time: 2021-05-26T19:58:01.677313Z, duration: 0, exit-code: 0 cat 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('.')) # -- Project information ----------------------------------------------------- project = 'methylprep' copyright = '2021, FOXO Technologies, inc.' author = 'FOXO Technologies, inc.' # The short X.Y version version = '1.4' # The full version, including alpha/beta/rc tags release = '1.4.2' # -- 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', 'sphinxcontrib.apidoc', 'm2r', 'nbsphinx', 'sphinx.ext.autosummary', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinx.ext.githubpages', ] # instead of CLI "sphinx-autodoc . _build/html" you write this apidoc_module_dir = '.' apidoc_output_dir = '_sphinx_build' apidoc_excluded_paths = ['tests'] apidoc_separate_modules = False # Add any paths that contain templates here, relative to this directory. templates_path = ['_sphinx_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] # source_suffix = '.rst' # 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 = ['_sphinx_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' todo_include_todos = True # -- 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 = 'sphinx_rtd_theme' #'alabaster', 'nature' # 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 = ['_sphinx_static'] # 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 = 'methylpredoc' # -- Options for LaTeX output ------------------------------------------------ latex_engine = 'xelatex' #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, 'methylprep.tex', 'methylprep Documentation', 'Life Epigenetics', '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, 'methylprep', 'methylprep 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, 'methylprep', 'methylprep Documentation', author, 'methylprep', 'One line description of project.', 'Miscellaneous'), ] # -- 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': [ ("html", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylprep', 'name': u'methylprep', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://life-epigenetics-methylprep.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'FOXOBioScience', 'proxied_api_host': '/_', 'github_repo': 'methylprep', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, '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': '0dac42f6', } # 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/life-epigenetics-methylprep/builds/641839/' 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: 2021-05-26T19:58:01.825347Z, end-time: 2021-05-26T19:58:21.137514Z, duration: 19, 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... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.download.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/modules.rst. building [mo]: targets for 0 po files that are out of date building [html]: targets for 14 source files that are out of date updating environment: 14 added, 0 changed, 0 removed reading sources... [ 7%] README reading sources... [ 14%] docs/README reading sources... [ 21%] docs/cli reading sources... [ 28%] docs/debug_notebooks/float16_error reading sources... [ 35%] docs/debug_notebooks/improving idat.py reading sources... [ 42%] docs/example_download reading sources... [ 50%] docs/faq reading sources... [ 57%] docs/how_to_add_new_array_type reading sources... [ 64%] docs/installation reading sources... [ 71%] docs/methylprep_tutorial reading sources... [ 78%] docs/package reading sources... 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/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/life-epigenetics-methylprep/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/life-epigenetics-methylprep/checkouts/latest/README.md:302: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 2 does not contain the same number of items as row 1 (3 vs 4). .. list-table:: :header-rows: 1 * - Argument - Type - Default - Description * - -h, --help - - show this help message and exit * - -d , --data_dir - ``str`` - [required path] - path to where the data series will be saved. Folder must exist already. * - -i ID, --id ID - ``str`` - [required ID] - The dataset's reference ID (Starts with ``GSE`` for GEO or ``E-MTAB-`` for ArrayExpress) * - -l LIST, --list LIST - ``multiple strings`` - optional - List of series IDs (can be either GEO or ArrayExpress), for partial downloading * - -o, --dict_only - ``True`` - pass flag only - If passed, will only create dictionaries and not process any samples * - -b BATCH_SIZE, --batch_size BATCH_SIZE - ``int`` - optional - Number of samples to process at a time, 100 by default. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/debug_notebooks/float16_error.ipynb:1: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/debug_notebooks/improving idat.py.ipynb:1: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:203: WARNING: Title level inconsistent: list of code edits by file in methylprep for mouse support ---------------------------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:266: WARNING: Title level inconsistent: testing ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:278: WARNING: Title level inconsistent: other bugs discovered: ~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:285: WARNING: Title level inconsistent: data flow through methylprep ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:124: WARNING: Unknown target name: "ctl". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylcheck". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:370: WARNING: Title level inconsistent: Visual Filtering Functions ~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md:161: WARNING: Title level inconsistent: ``get_sample_sheet`` ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md:191: WARNING: Title level inconsistent: ``get_manifest`` ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md:225: WARNING: Title level inconsistent: ``get_raw_datasets`` ~~~~~~~~~~~~~~~~~~~~~~~~ WARNING: missing attribute mentioned in :members: or __all__: module methylprep, attribute make_pipeline /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:92: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:105: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:106: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:27: WARNING: Unexpected indentation. 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' %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: 2021-05-26T19:58:30.551454Z, end-time: 2021-05-26T19:58:42.447278Z, duration: 11, exit-code: 12 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=life-epigenetics-methylprep -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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--dict:977/1684(ro)(G)-- --dict:0/20(G)-- --dict:77/200(L)-- Current allocation mode is local GPL Ghostscript 9.26: Unrecoverable error, exit code 1 xdvipdfmx:fatal: pdf_ref_obj(): passed invalid object. Output file removed. Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Latexmk: References changed. Rule 'makeindex life-epigenetics-methylprep.idx': File changes, etc: Non-existent destination files: 'life-epigenetics-methylprep.ind' ------------ Run number 1 of rule 'makeindex life-epigenetics-methylprep.idx' ------------ Latexmk: applying rule 'makeindex life-epigenetics-methylprep.idx'... ------------ Running 'makeindex -s python.ist -o "life-epigenetics-methylprep.ind" "life-epigenetics-methylprep.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 life-epigenetics-methylprep.idx...done (0 entries accepted, 0 rejected). Nothing written in life-epigenetics-methylprep.ind. Transcript written in life-epigenetics-methylprep.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylprep.aux' 'life-epigenetics-methylprep.ind' ------------ Run number 2 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'xelatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylprep" "methylprep.tex"' ------------ This is XeTeX, Version 3.14159265-2.6-0.99998 (TeX Live 2017/Debian) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode (./methylprep.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1] [2] Package hyperref Warning: old toc file detected, not used; run LaTeX again. [1] [2] Chapter 1. ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.219 ...f4fb1ab4bd65d97fd6c710f9f2b4821011}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/831cdbbb218a9e5c043d87d8dd04cc731d5165b4/0bf507f4fb1ab4bd65d97fd6c710 f9f2b4821011.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.219 ...f4fb1ab4bd65d97fd6c710f9f2b4821011}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.219 ...f4fb1ab4bd65d97fd6c710f9f2b4821011}.svg}} ^^M ! 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Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.221 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/520f473109738a62720092529c38de6bb2bf7b78/License-MIT-yellow.svg (no B oundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.221 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.223 ...2d50c48b22d9a371faafd4f/methylprep}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/ce065e466ca3a2e102d50c48b22d9a371faafd4f/methylprep.svg (no BoundingB ox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.223 ...2d50c48b22d9a371faafd4f/methylprep}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.223 ...2d50c48b22d9a371faafd4f/methylprep}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/ce065e466ca3a2e102d50c48b22d9a371faafd4f/methylprep.svg (no BoundingB ox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.223 ...2d50c48b22d9a371faafd4f/methylprep}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.225 ...9/e7228cfdfd714411bda7d6f8d6656630}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/6afe27f6c8e94648b14410dc5ed665603a4ca879/e7228cfdfd714411bda7d6f8d665 6630.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.225 ...9/e7228cfdfd714411bda7d6f8d6656630}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.225 ...9/e7228cfdfd714411bda7d6f8d6656630}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/6afe27f6c8e94648b14410dc5ed665603a4ca879/e7228cfdfd714411bda7d6f8d665 6630.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.225 ...9/e7228cfdfd714411bda7d6f8d6656630}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.227 ...160efd19f188b899042a5bb90393/badge}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/ca417d82df7c160efd19f188b899042a5bb90393/badge.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.227 ...160efd19f188b899042a5bb90393/badge}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.227 ...160efd19f188b899042a5bb90393/badge}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/ca417d82df7c160efd19f188b899042a5bb90393/badge.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.227 ...160efd19f188b899042a5bb90393/badge}.svg}} ^^M [1] ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.229 ...a80f68ea70f095757f7e98f/methylprep}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/b8f4bc0d89e561a97a80f68ea70f095757f7e98f/methylprep.svg (no BoundingB ox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.229 ...a80f68ea70f095757f7e98f/methylprep}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.229 ...a80f68ea70f095757f7e98f/methylprep}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/b8f4bc0d89e561a97a80f68ea70f095757f7e98f/methylprep.svg (no BoundingB ox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.229 ...a80f68ea70f095757f7e98f/methylprep}.svg}} ^^M Overfull \hbox (493.86227pt too wide) in paragraph at lines 2--235 [][][][][] [2] ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.314 ...33f7e935844ac3b8c6208f2ff}.png?raw=true}} ^^M ! LaTeX Error: Cannot determine size of graphic in ad421a0abd2cf7333f7e935844ac 3b8c6208f2ff.png?raw=true (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. 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(21.25262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 no_export| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull \hbox (47.50262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 no_meta_export| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull \hbox (10.75262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 m_value| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull 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Overfull \hbox (26.50262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 batch_size| Overfull \hbox (0.75pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 int| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 None| Overfull \hbox (5.50262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 poobah| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 True| [5] [6Error: /syntaxerror in /----nostringval---- Operand stack: Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 2045 1 3 %oparray_pop 2044 1 3 %oparray_pop 2025 1 3 %oparray_pop 1884 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push Dictionary stack: --dict:977/1684(ro)(G)-- --dict:0/20(G)-- --dict:77/200(L)-- Current allocation mode is local GPL Ghostscript 9.26: Unrecoverable error, exit code 1 xdvipdfmx:fatal: pdf_ref_obj(): passed invalid object. Output file removed. Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Latexmk: References changed. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylprep.out' 'life-epigenetics-methylprep.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'xelatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylprep" "methylprep.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is XeTeX, Version 3.14159265-2.6-0.99998 (TeX Live 2017/Debian) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode (./methylprep.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1] [2] Package hyperref Warning: old toc file detected, not used; run LaTeX again. [1] [2] Chapter 1. ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.219 ...f4fb1ab4bd65d97fd6c710f9f2b4821011}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/831cdbbb218a9e5c043d87d8dd04cc731d5165b4/0bf507f4fb1ab4bd65d97fd6c710 f9f2b4821011.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.219 ...f4fb1ab4bd65d97fd6c710f9f2b4821011}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.219 ...f4fb1ab4bd65d97fd6c710f9f2b4821011}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/831cdbbb218a9e5c043d87d8dd04cc731d5165b4/0bf507f4fb1ab4bd65d97fd6c710 f9f2b4821011.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.219 ...f4fb1ab4bd65d97fd6c710f9f2b4821011}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.221 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/520f473109738a62720092529c38de6bb2bf7b78/License-MIT-yellow.svg (no B oundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.221 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.221 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/520f473109738a62720092529c38de6bb2bf7b78/License-MIT-yellow.svg (no B oundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.221 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.223 ...2d50c48b22d9a371faafd4f/methylprep}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/ce065e466ca3a2e102d50c48b22d9a371faafd4f/methylprep.svg (no BoundingB ox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.223 ...2d50c48b22d9a371faafd4f/methylprep}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.223 ...2d50c48b22d9a371faafd4f/methylprep}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/ce065e466ca3a2e102d50c48b22d9a371faafd4f/methylprep.svg (no BoundingB ox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.223 ...2d50c48b22d9a371faafd4f/methylprep}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.225 ...9/e7228cfdfd714411bda7d6f8d6656630}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/6afe27f6c8e94648b14410dc5ed665603a4ca879/e7228cfdfd714411bda7d6f8d665 6630.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.225 ...9/e7228cfdfd714411bda7d6f8d6656630}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.225 ...9/e7228cfdfd714411bda7d6f8d6656630}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/6afe27f6c8e94648b14410dc5ed665603a4ca879/e7228cfdfd714411bda7d6f8d665 6630.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.225 ...9/e7228cfdfd714411bda7d6f8d6656630}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.227 ...160efd19f188b899042a5bb90393/badge}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/ca417d82df7c160efd19f188b899042a5bb90393/badge.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.227 ...160efd19f188b899042a5bb90393/badge}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.227 ...160efd19f188b899042a5bb90393/badge}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/ca417d82df7c160efd19f188b899042a5bb90393/badge.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.227 ...160efd19f188b899042a5bb90393/badge}.svg}} ^^M [1] ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.229 ...a80f68ea70f095757f7e98f/methylprep}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/b8f4bc0d89e561a97a80f68ea70f095757f7e98f/methylprep.svg (no BoundingB ox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.229 ...a80f68ea70f095757f7e98f/methylprep}.svg}} ^^M ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.229 ...a80f68ea70f095757f7e98f/methylprep}.svg}} ^^M ! LaTeX Error: Cannot determine size of graphic in /home/docs/checkouts/readthe docs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/doctre es/images/b8f4bc0d89e561a97a80f68ea70f095757f7e98f/methylprep.svg (no BoundingB ox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.229 ...a80f68ea70f095757f7e98f/methylprep}.svg}} ^^M Overfull \hbox (493.86227pt too wide) in paragraph at lines 2--235 [][][][][] [2] ! Bad character code (-1). \Gread@generic@aux ...^^I10 \catcode \endlinechar 5 \@makeother \:\@makeothe... l.314 ...33f7e935844ac3b8c6208f2ff}.png?raw=true}} ^^M ! LaTeX Error: Cannot determine size of graphic in ad421a0abd2cf7333f7e935844ac 3b8c6208f2ff.png?raw=true (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.314 ...33f7e935844ac3b8c6208f2ff}.png?raw=true}} ^^M Overfull \hbox (524.97847pt too wide) in paragraph at lines 2--315 [][][][][][] [3] Underfull \hbox (badness 10000) in paragraph at lines 362--362 []\TU/lmss/m/n/10 Argu- Overfull \hbox (1.65414pt too wide) in paragraph at lines 362--362 []\TU/lmtt/m/n/10 data_dir| Underfull \hbox (badness 10000) in paragraph at lines 362--362 []\TU/lmtt/m/n/10 str\TU/lmr/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 362--362 []\TU/lmr/bx/n/10 RE- Underfull \hbox (badness 10000) in paragraph at lines 428--428 []\TU/lmss/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 428--428 \TU/lmss/m/n/10 gu- Overfull \hbox (5.48pt too wide) in paragraph at lines 428--428 []\TU/lmss/m/n/10 Type| Underfull \hbox (badness 10000) in paragraph at lines 428--428 []\TU/lmss/m/n/10 De- Overfull \hbox (4.04001pt too wide) in paragraph at lines 428--428 \TU/lmss/m/n/10 fault| Overfull \hbox (30.1289pt too 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wide) in paragraph at lines 428--428 []\TU/lmtt/m/n/10 no_sample_sheet| Overfull \hbox (6.0pt too wide) in paragraph at lines 428--428 []\TU/lmtt/m/n/10 bool| Overfull \hbox (6.0pt too wide) in paragraph at lines 428--428 []\TU/lmtt/m/n/10 None| Overfull \hbox (87.8789pt too wide) in paragraph at lines 428--428 []\TU/lmtt/m/n/10 sample_sheet_filepath| Overfull \hbox (3.53pt too wide) in paragraph at lines 428--428 []\TU/lmtt/m/n/10 str\TU/lmr/m/n/10 , Overfull \hbox (6.0pt too wide) in paragraph at lines 428--428 \TU/lmtt/m/n/10 Path| Overfull \hbox (6.0pt too wide) in paragraph at lines 428--428 []\TU/lmtt/m/n/10 None| [4] Underfull \hbox (badness 10000) in paragraph at lines 539--539 []\TU/lmss/m/n/10 Argu- Overfull \hbox (5.48pt too wide) in paragraph at lines 539--539 []\TU/lmss/m/n/10 Type| Underfull \hbox (badness 10000) in paragraph at lines 539--539 []\TU/lmss/m/n/10 De- Overfull \hbox (4.04001pt too wide) in paragraph at lines 539--539 \TU/lmss/m/n/10 fault| Overfull \hbox (21.25262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 no_export| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull \hbox (47.50262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 no_meta_export| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull \hbox (10.75262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 m_value| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull \hbox (31.75262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 uncorrected| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull \hbox (37.00262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 save_control| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull \hbox (42.25262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 export_poobah| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (11.25pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 False| Overfull \hbox (0.75pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 str| Overfull \hbox (21.75pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 float32| Overfull \hbox (26.50262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 batch_size| Overfull \hbox (0.75pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 int| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 None| Overfull \hbox (5.50262pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 poobah| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 bool| Overfull \hbox (6.0pt too wide) in paragraph at lines 539--539 []\TU/lmtt/m/n/10 True| [5] [6Error: /syntaxerror in /----nostringval---- Operand stack: Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 2045 1 3 %oparray_pop 2044 1 3 %oparray_pop 2025 1 3 %oparray_pop 1884 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2GPL Ghostscript 9.26: Unrecoverable error, exit code 1 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push Dictionary stack: --dict:977/1684(ro)(G)-- --dict:0/20(G)-- --dict:77/200(L)-- Current allocation mode is local xdvipdfmx:fatal: pdf_ref_obj(): passed invalid object. Output file removed. Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Latexmk: References changed. Failure to make 'life-epigenetics-methylprep.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 36096 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2021-05-26T19:58:42.559947Z, end-time: 2021-05-26T19:58:55.973257Z, duration: 13, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading pickled environment... done Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst. 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