Read the Docs build information Build id: 1005116 Project: life-epigenetics-methylprep Version: latest Commit: 9828e71977355239a557283f03d9a4657be7b074 Date: 2022-07-07T17:10:02.175125Z State: finished Success: True [rtd-command-info] start-time: 2022-07-07T17:11:09.565101Z, end-time: 2022-07-07T17:11:23.364106Z, duration: 13, 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: 2022-07-07T17:11:23.556894Z, end-time: 2022-07-07T17:11:24.165108Z, duration: 0, 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 9828e71 Bump lxml from 4.7.1 to 4.9.1 (#113) [rtd-command-info] start-time: 2022-07-07T17:11:24.388831Z, end-time: 2022-07-07T17:11:24.448581Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-07-07T17:11:27.905157Z, end-time: 2022-07-07T17:11:33.774545Z, duration: 5, exit-code: 0 python3.8 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.8.6' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python3.8 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: 2022-07-07T17:11:33.984814Z, end-time: 2022-07-07T17:11:35.781111Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.8/site-packages (22.1.2) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 34.0 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 63.1.0 Uninstalling setuptools-63.1.0: Successfully uninstalled setuptools-63.1.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-07-07T17:11:35.982388Z, end-time: 2022-07-07T17:12:02.489263Z, duration: 26, 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 jinja2<3.1.0 setuptools<58.3.0 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 25.0 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1.tar.gz (16.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.0/16.0 MB 204.6 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 kB 204.8 MB/s eta 0:00:00 Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 206.3 MB/s eta 0:00:00 Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 209.6 MB/s eta 0:00:00 Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.8-py2.py3-none-any.whl (11 kB) Collecting jinja2<3.1.0 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.6/133.6 kB 257.4 MB/s eta 0:00:00 Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 284.6 MB/s eta 0:00:00 Collecting future Downloading future-0.18.2.tar.gz (829 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 kB 287.8 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting docutils>=0.11 Downloading docutils-0.19-py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 281.1 MB/s eta 0:00:00 Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting requests>=2.0.0 Downloading requests-2.28.1-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 230.1 MB/s eta 0:00:00 Collecting babel!=2.0,>=1.3 Downloading Babel-2.10.3-py3-none-any.whl (9.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 188.1 MB/s eta 0:00:00 Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 246.9 MB/s eta 0:00:00 Collecting imagesize Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 287.0 MB/s eta 0:00:00 Collecting Pygments>=2.0 Downloading Pygments-2.12.0-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 284.9 MB/s eta 0:00:00 Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 203.4 MB/s eta 0:00:00 Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting pytz>=2015.7 Downloading pytz-2022.1-py2.py3-none-any.whl (503 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 503.5/503.5 kB 287.5 MB/s eta 0:00:00 Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 236.6 MB/s eta 0:00:00 Collecting certifi>=2017.4.17 Downloading certifi-2022.6.15-py3-none-any.whl (160 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 160.2/160.2 kB 264.3 MB/s eta 0:00:00 Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.10-py2.py3-none-any.whl (139 kB) 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(setup.py): started Building wheel for pillow (setup.py): finished with status 'done' Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1260086 sha256=9ac0c6262a303bc93e01c45fc8cf9e2ec70f084d12f97eafea79719515bbfc8b Stored in directory: /tmp/pip-ephem-wheel-cache-kfbrsjga/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d 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=595f3d36414e34ee046531312afd0d554dccfc6aa1bc67faa3e4028ab2935dca Stored in directory: /tmp/pip-ephem-wheel-cache-kfbrsjga/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4 Successfully built mock pillow future Installing collected packages: snowballstemmer, pytz, mock, alabaster, urllib3, sphinxcontrib-serializinghtml, six, setuptools, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, sphinxcontrib-websupport, requests, packaging, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark 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 MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.6.15 charset-normalizer-2.1.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.8 recommonmark-0.5.0 requests-2.28.1 setuptools-58.2.0 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 urllib3-1.26.10 [rtd-command-info] start-time: 2022-07-07T17:12:02.722519Z, end-time: 2022-07-07T17:12:21.173115Z, duration: 18, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting pyparsing<3 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 67.8/67.8 kB 6.4 MB/s eta 0:00:00 Collecting snumpy Downloading snumpy-0.1-py3-none-any.whl (6.4 kB) Collecting pandas>=1.3.0 Downloading pandas-1.4.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 182.2 MB/s eta 0:00:00 Collecting scipy Downloading scipy-1.8.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (41.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 41.6/41.6 MB 185.4 MB/s eta 0:00:00 Collecting statsmodels Downloading statsmodels-0.13.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.9/9.9 MB 191.7 MB/s eta 0:00:00 Collecting pytest Downloading pytest-7.1.2-py3-none-any.whl (297 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 297.0/297.0 kB 274.9 MB/s eta 0:00:00 Collecting coverage Downloading coverage-6.4.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (213 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 213.3/213.3 kB 266.5 MB/s eta 0:00:00 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) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting nbsphinx Downloading nbsphinx-0.8.9-py3-none-any.whl (25 kB) Collecting tqdm Downloading tqdm-4.64.0-py2.py3-none-any.whl (78 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.4/78.4 kB 214.2 MB/s eta 0:00:00 Collecting beautifulsoup4 Downloading beautifulsoup4-4.11.1-py3-none-any.whl (128 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 128.2/128.2 kB 252.9 MB/s eta 0:00:00 Collecting lxml Downloading lxml-4.9.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (6.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.9/6.9 MB 133.1 MB/s eta 0:00:00 Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.8/site-packages (from -r 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patsy, pandocfilters, nest-asyncio, m2r, lxml, jupyterlab-pygments, entrypoints, defusedxml, coverage, bleach, attrs, python-coveralls, pandas, jupyter-core, importlib-resources, beautifulsoup4, statsmodels, pytest, jupyter-client, jsonschema, sphinxcontrib-apidoc, nbformat, nbclient, nbconvert, nbsphinx Attempting uninstall: python-dateutil Found existing installation: python-dateutil 2.8.1 Not uninstalling python-dateutil at /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest Can't uninstall 'python-dateutil'. No files were found to uninstall. Attempting uninstall: pyparsing Found existing installation: pyparsing 3.0.9 Uninstalling pyparsing-3.0.9: Successfully uninstalled pyparsing-3.0.9 Attempting uninstall: pandas Found existing installation: pandas 1.1.3 Not uninstalling pandas at /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest Can't uninstall 'pandas'. No files were found to uninstall. 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 PyYAML-6.0 attrs-21.4.0 beautifulsoup4-4.11.1 bleach-5.0.1 coverage-6.4.1 defusedxml-0.7.1 entrypoints-0.4 fastjsonschema-2.15.3 importlib-resources-5.8.0 iniconfig-1.1.1 jsonschema-4.6.2 jupyter-client-7.3.4 jupyter-core-4.11.0 jupyterlab-pygments-0.2.2 lxml-4.9.1 m2r-0.2.1 mistune-0.8.4 nbclient-0.6.6 nbconvert-6.5.0 nbformat-5.4.0 nbsphinx-0.8.9 nest-asyncio-1.5.5 pandas-1.4.3 pandocfilters-1.5.0 patsy-0.5.2 pbr-5.9.0 pluggy-1.0.0 py-1.11.0 pyparsing-2.4.7 pyrsistent-0.18.1 pytest-7.1.2 python-coveralls-2.9.3 python-dateutil-2.8.2 pyzmq-23.2.0 scipy-1.8.1 snumpy-0.1 soupsieve-2.3.2.post1 sphinxcontrib-apidoc-0.3.0 statsmodels-0.13.2 tinycss2-1.1.1 tomli-2.0.1 tornado-6.2 tqdm-4.64.0 traitlets-5.3.0 webencodings-0.5.1 zipp-3.8.0 [rtd-command-info] start-time: 2022-07-07T17:12:22.756439Z, end-time: 2022-07-07T17:12:22.829231Z, 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 = '2022, FOXO Technologies, inc.' author = 'FOXO Technologies, inc.' # The short X.Y version version = '1.6' # The full version, including alpha/beta/rc tags release = '1.6.5' # -- 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', '**.ipynb_checkpoints'] # 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' html_logo = 'docs/source/foxo_logo_orange_black.png' # 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/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: 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", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("feature-v1.6.1", "/en/feature-v1.6.1/"), ], 'downloads': [ ("pdf", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("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': '9828e719', } # 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/1005116/' 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: 2022-07-07T17:12:23.054742Z, end-time: 2022-07-07T17:12:46.852630Z, duration: 23, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v1.8.6 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. 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1266--1266 []\T1/pcr/m/n/10 bool| Overfull \hbox (8.05069pt too wide) in paragraph at lines 1266--1266 []\T1/pcr/m/n/10 True| [20] Overfull \hbox (6.03357pt too wide) in paragraph at lines 1348--1348 []\T1/phv/m/n/10 Type| Overfull \hbox (3.00366pt too wide) in paragraph at lines 1348--1348 []\T1/pcr/m/n/10 str| Overfull \hbox (9.00366pt too wide) in paragraph at lines 1348--1348 []\T1/pcr/m/n/10 bool| Overfull \hbox (3.00366pt too wide) in paragraph at lines 1348--1348 []\T1/pcr/m/n/10 str| Underfull \hbox (badness 10000) in paragraph at lines 1421--1422 []|\T1/ptm/m/n/10 -b BATCH_SIZE, Underfull \hbox (badness 10000) in paragraph at lines 1421--1422 \T1/ptm/m/n/10 ^^Ubatch_size [21] Overfull \hbox (6.03357pt too wide) in paragraph at lines 1515--1515 []\T1/phv/m/n/10 Type| Overfull \hbox (1.11353pt too wide) in paragraph at lines 1515--1515 []\T1/phv/m/n/10 De- Overfull \hbox (3.60335pt too wide) in paragraph at lines 1515--1515 \T1/phv/m/n/10 fault| Overfull \hbox (3.00366pt too wide) in paragraph at lines 1515--1515 []\T1/pcr/m/n/10 str| Underfull \hbox (badness 10000) in paragraph at lines 1515--1515 []\T1/ptm/m/n/10 -d DATA_DIR, ^^Udata_dir Overfull \hbox (3.00366pt too wide) in paragraph at lines 1515--1515 []\T1/pcr/m/n/10 str| Underfull \hbox (badness 10000) in paragraph at lines 1515--1515 []\T1/ptm/m/n/10 -b BUCKET, ^^Ubucket Overfull \hbox (3.00366pt too wide) in paragraph at lines 1515--1515 []\T1/pcr/m/n/10 str| Overfull \hbox (3.00366pt too wide) in paragraph at lines 1515--1515 []\T1/pcr/m/n/10 str| Underfull \hbox (badness 7012) in paragraph at lines 1515--1515 []\T1/ptm/m/n/10 -p PRO-CESSED_BUCKET, Underfull \hbox (badness 10000) in paragraph at lines 1515--1515 \T1/ptm/m/n/10 ^^Upro-cessed_bucket PRO- Overfull \hbox (3.00366pt too wide) in paragraph at lines 1515--1515 []\T1/pcr/m/n/10 str| [22] Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\T1/pcr/m/n/10 str\T1/ptm/m/n/10 , Overfull \hbox (3.16339pt too wide) in paragraph at lines 1604--1604 \T1/ptm/m/n/10 filepath| Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 -d DATA_DIR, Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 \T1/ptm/m/n/10 ^^Udata_dir Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\T1/pcr/m/n/10 str\T1/ptm/m/n/10 , Overfull \hbox (3.16339pt too wide) in paragraph at lines 1604--1604 \T1/ptm/m/n/10 filepath| Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 -k KEY-WORD Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 \T1/ptm/m/n/10 ^^Ukey-word KEY- [23] Overfull \hbox (2.91867pt too wide) in paragraph at lines 1707--1707 []\T1/phv/m/n/10 Type| Underfull \hbox (badness 10000) in paragraph at lines 1707--1707 []\T1/ptm/m/n/10 -d Underfull \hbox (badness 10000) in paragraph at lines 1707--1707 \T1/ptm/m/n/10 DATA_DIR, Underfull \hbox (badness 10000) in paragraph at lines 1707--1707 \T1/ptm/m/n/10 ^^Udata_dir Underfull \hbox (badness 10000) in paragraph at lines 1707--1707 []\T1/pcr/m/n/10 str Underfull \hbox (badness 10000) in paragraph at lines 1707--1707 \T1/ptm/m/n/10 or Overfull \hbox (5.88876pt too wide) in paragraph at lines 1707--1707 \T1/pcr/m/n/10 path| Underfull \hbox (badness 10000) in paragraph at lines 1707--1707 []\T1/ptm/m/n/10 -k KEY- Underfull \hbox (badness 10000) in paragraph at lines 1707--1707 \T1/ptm/m/n/10 WORD, Underfull \hbox (badness 10000) in paragraph at lines 1707--1707 \T1/ptm/m/n/10 ^^Ukey-word Underfull \hbox (badness 10000) in paragraph at lines 1707--1707 []\T1/ptm/m/n/10 -s, Overfull \hbox (5.88876pt too wide) in paragraph at lines 1707--1707 []\T1/pcr/m/n/10 bool| Underfull \hbox (badness 10000) in paragraph at lines 1707--1707 []\T1/ptm/m/n/10 -o, Overfull \hbox (14.47574pt too wide) in paragraph at lines 1707--1707 \T1/ptm/m/n/10 ^^Udont_download| Overfull \hbox (5.88876pt too wide) in paragraph at lines 1707--1707 []\T1/pcr/m/n/10 bool| [24] Underfull \hbox (badness 10000) in paragraph at lines 1760--1762 \T1/ptm/m/n/10 val-ues are \T1/pcr/m/n/10 custom\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1760--1762 \T1/pcr/m/n/10 450k\T1/ptm/m/n/10 , \T1/pcr/m/n/10 epic\T1/ptm/m/n/10 , and Underfull \hbox (badness 5302) in paragraph at lines 1760--1762 \T1/ptm/m/n/10 to de-ter-mine the ar-ray Overfull \hbox (21.06123pt too wide) in paragraph at lines 1781--1782 []|\T1/pcr/m/n/10 sample_sheet_filepath| [25] Underfull \hbox (badness 10000) in paragraph at lines 1839--1841 []|\T1/ptm/m/n/10 List of pro-cess-ing Underfull \hbox (badness 10000) in paragraph at lines 1839--1841 \T1/ptm/m/n/10 steps: [`all', `in- Underfull \hbox (badness 10000) in paragraph at lines 1839--1841 \T1/ptm/m/n/10 fer_channel_switch', Underfull \hbox (badness 10000) in paragraph at lines 1848--1850 \T1/ptm/m/n/10 Any-thing not spec-i-fied Underfull \hbox (badness 6380) in paragraph at lines 1848--1850 \T1/ptm/m/n/10 is not saved. [`all', Underfull \hbox (badness 10000) in paragraph at lines 1848--1850 \T1/ptm/m/n/10 `un-meth', `noob_meth', Underfull \hbox (badness 10000) in paragraph at lines 1848--1850 \T1/ptm/m/n/10 `noob_unmeth', `sam- Underfull \hbox (badness 10000) in paragraph at lines 1848--1850 \T1/ptm/m/n/10 ple_sheet_meta_data', Underfull \hbox (badness 10000) in paragraph at lines 1857--1859 \T1/ptm/m/n/10 re-turn [beta, m_value, Underfull \hbox (badness 10000) in paragraph at lines 1857--1859 \T1/ptm/m/n/10 copy_number, None] Underfull \hbox (badness 5022) in paragraph at lines 1857--1859 \T1/ptm/m/n/10 (re-turns data con-tain-ers [26] Overfull \hbox (978.80003pt too wide) in paragraph at lines 2--1867 [][][][][][] [27] Overfull \vbox (164.14424pt too high) has occurred while \output is active [28 <./processing_pipeline.png>] Overfull \hbox (21.06123pt too wide) in paragraph at lines 1906--1907 []|\T1/pcr/m/n/10 sample_sheet_filepath| [29] Underfull \hbox (badness 10000) in paragraph at lines 1989--1991 []\T1/ptm/m/n/10 methylprep does not rec-og-nize the older 27k ar-ray file-name for-mat: [30] Overfull \hbox (23.34323pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 GSM_ID| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 Sam- Overfull \hbox (16.54153pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 ple_Name| Overfull \hbox (6.12341pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 Sen- Overfull \hbox (14.04317pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 trix_ID| Overfull \hbox (4.55806pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 Sen- Overfull \hbox (37.5475pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 trix_Position| Overfull \hbox (10.87962pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 source| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 di- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/phv/m/n/10 ag- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/phv/m/n/10 no- Overfull \hbox (1.68347pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 age| Overfull \hbox (1.93358pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 Sex| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 tis- Overfull \hbox (1.12354pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 sue| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 cd8t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 cd4t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (27.7932pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (5.56348pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 bcell| Overfull \hbox (27.1722pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (9.39243pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 mono| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (4.81345pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 gran| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 de- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/phv/m/n/10 scrip- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 GSM3562834| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 R01C01| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.09099| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.06041| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.08542| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.09072| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.62266| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 GSM3562835| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 R01C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.05544| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07946| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.0159| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.09557| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.05515| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.72663| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 GSM3562836| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 R02C01| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.08279| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.22216| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.03107| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.0769| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07915| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.54165| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 GSM3562837| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 R02C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.03779| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07368| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.00385| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07548| Overfull \hbox (11.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.0891| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.74809| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- [31] [32] Overfull \hbox (23.34323pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 GSM_ID| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sam- Overfull \hbox (16.54153pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 ple_Name| Overfull \hbox (6.12341pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sen- Overfull \hbox (14.04317pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 trix_ID| Overfull \hbox (4.55806pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sen- Overfull \hbox (37.5475pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 trix_Position| Overfull \hbox (10.87962pt too wide) in 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[59] [60] LaTeX Warning: Reference `docs/source/modules:module-methylprep' on page 61 und efined on input line 5052. LaTeX Warning: Reference `docs/source/modules:module-methylprep.download' on pa ge 61 undefined on input line 5053. LaTeX Warning: Reference `docs/source/modules:module-methylprep.files' on page 61 undefined on input line 5054. LaTeX Warning: Reference `docs/source/modules:module-methylprep.models' on page 61 undefined on input line 5055. LaTeX Warning: Reference `docs/source/modules:module-methylprep.processing' on page 61 undefined on input line 5056. [61] No file life-epigenetics-methylprep.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. (./life-epigenetics-methylprep.aux) Package rerunfilecheck Warning: File `life-epigenetics-methylprep.out' has chan ged. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. 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 life-epigenetics-methylprep.pdf (65 pages, 943668 bytes). Transcript written on life-epigenetics-methylprep.log. Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Latexmk: Missing input file: 'life-epigenetics-methylprep.ind' from line 'No file life-epigenetics-methylprep.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylprep.pdf' Latexmk: List of undefined refs and citations: Reference `docs/source/modules:module-methylprep' on page 61 undefined on input line 5052 Reference `docs/source/modules:module-methylprep.download' on page 61 undefined on input line 5053 Reference `docs/source/modules:module-methylprep.files' on page 61 undefined on input line 5054 Reference `docs/source/modules:module-methylprep.models' on page 61 undefined on input line 5055 Reference `docs/source/modules:module-methylprep.processing' on page 61 undefined on input line 5056 Latexmk: Summary of warnings: Latex failed to resolve 5 reference(s) 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' ------------ ------------ Running 'makeindex -s python.ist -o "life-epigenetics-methylprep.ind" "life-epigenetics-methylprep.idx"' ------------ Latexmk: applying rule 'makeindex 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 (94 entries accepted, 0 rejected). Sorting entries....done (637 comparisons). Generating output file life-epigenetics-methylprep.ind....done (160 lines written, 0 warnings). Output 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' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylprep" "methylprep.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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paragraph at lines 2252--2252 []\T1/ptm/m/n/10 GSM3562835| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 R01C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.05544| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07946| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.0159| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.09557| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.05515| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.72663| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 GSM3562836| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 R02C01| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.08279| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.22216| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.03107| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.0769| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07915| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.54165| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 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case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.03779| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07368| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.00385| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07548| Overfull \hbox (11.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.0891| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.74809| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- [31] [32] Overfull \hbox (23.34323pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 GSM_ID| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sam- Overfull \hbox (16.54153pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 ple_Name| Overfull \hbox (6.12341pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sen- Overfull \hbox (14.04317pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 trix_ID| Overfull \hbox (4.55806pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sen- Overfull \hbox (37.5475pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 trix_Position| Overfull \hbox (10.87962pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 source| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 di- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/phv/m/n/10 ag- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/phv/m/n/10 no- Overfull \hbox (1.68347pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 age| Overfull \hbox (1.93358pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sex| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 tis- Overfull \hbox (1.12354pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 sue| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 cd8t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 cd4t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (27.7932pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (5.56348pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 bcell| Overfull \hbox (27.1722pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (9.39243pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 mono| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (4.81345pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 gran| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 de- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/phv/m/n/10 scrip- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 GSM3562834| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 R01C01| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.07679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.09099| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.06041| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.08542| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.09072| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.62266| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 GSM3562839| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 R03C02| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.06946| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.12989| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.04703| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.09808| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.14105| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.54662| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 GSM3562842| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 R05C01| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.10986| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.13565| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.07657| Overfull 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\hbox (41.67346pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 GSM3562855| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 3999840037| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 R06C01| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.01668| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.14318| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.1096| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.05545| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.09695| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.60283| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 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e_keyword=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3172--3172 \T1/ptm/m/it/10 sync_idats=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- [38] Underfull \hbox (badness 10000) in paragraph at lines 3230--3230 []\T1/ptm/m/it/10 data_dir\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 ex-port=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 man- i-fest_filepath=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3230--3230 \T1/ptm/m/it/10 sam-ple_sheet_filepath=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam -ple_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3230--3230 \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 make_sample_sheet =False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3230--3230 \T1/ptm/m/it/10 save_uncorrected=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save_con trol=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 meta_data_frame=True\T1/ptm/m/n/10 , [39] [40] Underfull \hbox (badness 10000) in paragraph at lines 3413--3420 []\T1/ptm/m/n/10 export=False, make_sample_sheet=False, ex-port_poobah=False, s ave_uncorrected=False, Underfull \hbox (badness 10000) in paragraph at lines 3421--3426 []\T1/ptm/m/n/10 betas=False, m_value=False, - Underfull \hbox (badness 10000) in paragraph at lines 3437--3443 []\T1/ptm/m/n/10 data_dir, ar-ray_type=None, Underfull \hbox (badness 10000) in paragraph at lines 3451--3454 [] Overfull \hbox (15.91293pt too wide) in paragraph at lines 3465--3465 \T1/ptm/m/it/10 tain_uncorrected_probe_intensities=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3465--3465 \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pval=False\T1/ptm /m/n/10 , Underfull \hbox (badness 10000) in paragraph 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(badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 fest_filepath=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam-ple_shee t_filepath=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 sam-ple_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 make_sample_sheet=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_s ize=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 save_uncorrected=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save_con trol=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 meta_data_frame=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bit='float 32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 ex-port_poobah=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah_dec imals=3\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 low_memory=True \T1/ptm/m/n/10 , \T1/ptm/m/it/10 sesame=True\T1/ptm/m/n/10 , [43] [44] Underfull \hbox (badness 10000) in paragraph at lines 3734--3734 []\T1/ptm/m/it/10 data_containers\T1/ptm/m/n/10 , \T1/ptm/m/it/10 post-pro- Underfull \hbox (badness 10000) in paragraph at lines 3734--3734 \T1/ptm/m/it/10 cess_func_colname='beta_value'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3734--3734 \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=True\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3734--3734 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 3821--3821 []\T1/ptm/m/it/10 sample_sheet\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- 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ple_type=''\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- [49] Underfull \hbox (badness 10000) in paragraph at lines 4353--4353 []\T1/ptm/m/it/10 id\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/p tm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=100\T1/pt m/m/n/10 , \T1/ptm/m/it/10 clean=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4383--4383 []\T1/ptm/m/it/10 list_file\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=10 0\T1/ptm/m/n/10 , [50] Underfull \hbox (badness 10000) in paragraph at lines 4412--4412 \T1/ptm/m/it/10 ex-tract_controls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-quir e_keyword=None\T1/ptm/m/n/10 , [51] Underfull \hbox (badness 10000) in paragraph at lines 4558--4562 []\T1/ptm/m/n/10 to ini-tial-ize, [52] Overfull \hbox (75.29005pt too wide) in paragraph at lines 4593--4593 [] Underfull \hbox (badness 10000) in paragraph at lines 4593--4593 Overfull \hbox (160.70894pt too wide) in paragraph at lines 4611--4611 [] Underfull \hbox (badness 10000) in paragraph at lines 4611--4611 Underfull \hbox (badness 10000) in paragraph at lines 4640--4645 [] [53] Underfull \hbox (badness 10000) in paragraph at lines 4716--4718 [] Overfull \hbox (15.5806pt too wide) in paragraph at lines 4744--4747 [] Overfull \hbox (65.49059pt too wide) in paragraph at lines 4751--4753 [] Overfull \hbox (60.42044pt too wide) in paragraph at lines 4757--4759 [] [54] [55] Overfull \hbox (30.86986pt too wide) in paragraph at lines 4878--4881 [] Underfull \hbox (badness 10000) in paragraph at lines 4921--4923 [] [56] Underfull \hbox (badness 10000) in paragraph at lines 5019--5022 []\T1/ptm/m/n/10 batch_size will split Underfull \hbox (badness 10000) in paragraph at lines 5029--5031 [] [57] [58] Chapter 2. [59] [60] [61] (./life-epigenetics-methylprep.ind [62] Underfull \hbox (badness 10000) in paragraph at lines 9--11 []\T1/pcr/m/n/10 alternate_base_filename \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl - Underfull \hbox (badness 10000) in paragraph at lines 21--22 []\T1/pcr/m/n/10 build_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.fi les.SampleSheet Underfull \hbox (badness 10000) in paragraph at lines 26--28 []\T1/pcr/m/n/10 check_for_probe_loss() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 33--34 []\T1/pcr/m/n/10 control_data_frame \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep .Manifest at- Underfull \hbox (badness 10000) in paragraph at lines 37--38 []\T1/pcr/m/n/10 convert_miniml() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule me thyl- Underfull \hbox (badness 10000) in paragraph at lines 38--39 []\T1/pcr/m/n/10 create_sample_sheet() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le methyl- Underfull \hbox (badness 10000) in paragraph at lines 44--46 []\T1/pcr/m/n/10 detect_and_drop_duplicates() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 m ethyl- Underfull \hbox (badness 10000) in paragraph at lines 46--48 []\T1/pcr/m/n/10 download_default() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep .files.Manifest Overfull \hbox (5.70073pt too wide) in paragraph at lines 52--54 []\T1/pcr/m/n/10 export() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.processin g.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 58--59 []\T1/pcr/m/n/10 from_probe_count \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.A rrayType at- Underfull \hbox (badness 10000) in paragraph at lines 64--66 []\T1/pcr/m/n/10 get_export_filepath() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 67--68 []\T1/pcr/m/n/10 get_filepath() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.mod els.Sample Underfull \hbox (badness 10000) in paragraph at lines 68--69 []\T1/pcr/m/n/10 get_probe_details() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.files.Manifest Underfull \hbox (badness 10000) in paragraph at lines 69--70 []\T1/pcr/m/n/10 get_probe_details() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.Manifest Underfull \hbox (badness 10000) in paragraph at lines 70--71 []\T1/pcr/m/n/10 get_sample() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.files .SampleSheet Underfull \hbox (badness 10000) in paragraph at lines 73--74 []\T1/pcr/m/n/10 get_sample_sheet_s3() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le methyl- [63] Underfull \hbox (badness 10000) in paragraph at lines 74--75 []\T1/pcr/m/n/10 get_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.file s.SampleSheet Underfull \hbox (badness 10000) in paragraph at lines 82--83 []\T1/pcr/m/n/10 ILLUMINA_EPIC_PLUS \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep .ArrayType Overfull \hbox (4.1225pt too wide) in paragraph at lines 107--109 []\T1/pcr/m/n/10 parse_sample_sheet_into_idat_datasets() Overfull \hbox (4.1225pt too wide) in paragraph at lines 109--111 []\T1/pcr/m/n/10 parse_sample_sheet_into_idat_datasets() Underfull \hbox (badness 10000) in paragraph at lines 113--114 []\T1/pcr/m/n/10 preprocess_noob() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule m ethyl- Underfull \hbox (badness 10000) in paragraph at lines 115--117 []\T1/pcr/m/n/10 process_all() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 115--117 \T1/ptm/m/it/10 prep.processing.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 117--119 []\T1/pcr/m/n/10 process_beta_value() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 117--119 \T1/ptm/m/it/10 prep.processing.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 119--121 []\T1/pcr/m/n/10 process_copy_number() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 119--121 \T1/ptm/m/it/10 prep.processing.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 121--123 []\T1/pcr/m/n/10 process_m_value() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 121--123 \T1/ptm/m/it/10 prep.processing.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 128--130 []\T1/pcr/m/n/10 read_control_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 130--131 []\T1/pcr/m/n/10 read_control_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-p rep.Manifest Underfull \hbox (badness 10000) in paragraph at lines 131--132 []\T1/pcr/m/n/10 read_mouse_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.files.Manifest Underfull \hbox (badness 10000) in paragraph at lines 132--133 []\T1/pcr/m/n/10 read_mouse_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.Manifest Underfull \hbox (badness 10000) in paragraph at lines 134--135 []\T1/pcr/m/n/10 read_snp_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep. files.Manifest Underfull \hbox (badness 10000) in paragraph at lines 141--142 []\T1/pcr/m/n/10 run_series_list() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule m ethyl- Underfull \hbox (badness 10000) in paragraph at lines 146--147 []\T1/pcr/m/n/10 SampleDataContainer \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in m ethyl- Underfull \hbox (badness 10000) in paragraph at lines 151--152 []\T1/pcr/m/n/10 seek_to_start() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.Ma nifest static [64]) (./life-epigenetics-methylprep.aux) Package rerunfilecheck Warning: File `life-epigenetics-methylprep.out' has chan ged. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on life-epigenetics-methylprep.pdf (68 pages, 954513 bytes). Transcript written on life-epigenetics-methylprep.log. Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylprep.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylprep.aux' 'life-epigenetics-methylprep.out' 'life-epigenetics-methylprep.toc' ------------ Run number 3 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylprep" "methylprep.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 (./methylprep.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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10000) in paragraph at lines 1760--1762 \T1/ptm/m/n/10 val-ues are \T1/pcr/m/n/10 custom\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1760--1762 \T1/pcr/m/n/10 450k\T1/ptm/m/n/10 , \T1/pcr/m/n/10 epic\T1/ptm/m/n/10 , and Underfull \hbox (badness 5302) in paragraph at lines 1760--1762 \T1/ptm/m/n/10 to de-ter-mine the ar-ray Overfull \hbox (21.06123pt too wide) in paragraph at lines 1781--1782 []|\T1/pcr/m/n/10 sample_sheet_filepath| [25] Underfull \hbox (badness 10000) in paragraph at lines 1839--1841 []|\T1/ptm/m/n/10 List of pro-cess-ing Underfull \hbox (badness 10000) in paragraph at lines 1839--1841 \T1/ptm/m/n/10 steps: [`all', `in- Underfull \hbox (badness 10000) in paragraph at lines 1839--1841 \T1/ptm/m/n/10 fer_channel_switch', Underfull \hbox (badness 10000) in paragraph at lines 1848--1850 \T1/ptm/m/n/10 Any-thing not spec-i-fied Underfull \hbox (badness 6380) in paragraph at lines 1848--1850 \T1/ptm/m/n/10 is not saved. [`all', Underfull \hbox (badness 10000) in paragraph at lines 1848--1850 \T1/ptm/m/n/10 `un-meth', `noob_meth', Underfull \hbox (badness 10000) in paragraph at lines 1848--1850 \T1/ptm/m/n/10 `noob_unmeth', `sam- Underfull \hbox (badness 10000) in paragraph at lines 1848--1850 \T1/ptm/m/n/10 ple_sheet_meta_data', Underfull \hbox (badness 10000) in paragraph at lines 1857--1859 \T1/ptm/m/n/10 re-turn [beta, m_value, Underfull \hbox (badness 10000) in paragraph at lines 1857--1859 \T1/ptm/m/n/10 copy_number, None] Underfull \hbox (badness 5022) in paragraph at lines 1857--1859 \T1/ptm/m/n/10 (re-turns data con-tain-ers [26] Overfull \hbox (978.80003pt too wide) in paragraph at lines 2--1867 [][][][][][] [27] Overfull \vbox (164.14424pt too high) has occurred while \output is active [28 <./processing_pipeline.png>] Overfull \hbox (21.06123pt too wide) in paragraph at lines 1906--1907 []|\T1/pcr/m/n/10 sample_sheet_filepath| [29] Underfull \hbox (badness 10000) in paragraph at lines 1989--1991 []\T1/ptm/m/n/10 methylprep does not rec-og-nize the older 27k ar-ray file-name for-mat: [30] Overfull \hbox (23.34323pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 GSM_ID| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 Sam- Overfull \hbox (16.54153pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 ple_Name| Overfull \hbox (6.12341pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 Sen- Overfull \hbox (14.04317pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 trix_ID| Overfull \hbox (4.55806pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 Sen- Overfull \hbox (37.5475pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 trix_Position| Overfull \hbox (10.87962pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 source| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 di- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/phv/m/n/10 ag- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/phv/m/n/10 no- Overfull \hbox (1.68347pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 age| Overfull \hbox (1.93358pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 Sex| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 tis- Overfull \hbox (1.12354pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 sue| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 cd8t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 cd4t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (27.7932pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (5.56348pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 bcell| Overfull \hbox (27.1722pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (9.39243pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 mono| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 cellcount- Overfull \hbox (4.81345pt too wide) in paragraph at lines 2252--2252 \T1/phv/m/n/10 gran| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/phv/m/n/10 de- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/phv/m/n/10 scrip- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 GSM3562834| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 R01C01| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.09099| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.06041| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.08542| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.09072| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.62266| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 GSM3562835| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 R01C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.05544| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07946| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.0159| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.09557| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.05515| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.72663| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 GSM3562836| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 R02C01| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.08279| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.22216| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.03107| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.0769| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07915| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.54165| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 GSM3562837| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 R02C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.03779| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07368| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.00385| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.07548| Overfull \hbox (11.88266pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.0891| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 0.74809| Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2252--2252 \T1/ptm/m/n/10 sam- [31] [32] Overfull \hbox (23.34323pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 GSM_ID| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sam- Overfull \hbox (16.54153pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 ple_Name| Overfull \hbox (6.12341pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sen- Overfull \hbox (14.04317pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 trix_ID| Overfull \hbox (4.55806pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sen- Overfull \hbox (37.5475pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 trix_Position| Overfull \hbox (10.87962pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 source| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 di- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/phv/m/n/10 ag- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/phv/m/n/10 no- Overfull \hbox (1.68347pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 age| Overfull \hbox (1.93358pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 Sex| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 tis- Overfull \hbox (1.12354pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 sue| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 cd8t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 cd4t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (27.7932pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (5.56348pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 bcell| Overfull \hbox (27.1722pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (9.39243pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 mono| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 cellcount- Overfull \hbox (4.81345pt too wide) in paragraph at lines 2648--2648 \T1/phv/m/n/10 gran| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/phv/m/n/10 de- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/phv/m/n/10 scrip- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 GSM3562834| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 R01C01| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.07679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.09099| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.06041| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.08542| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.09072| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.62266| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 GSM3562839| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 R03C02| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.06946| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.12989| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.04703| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.09808| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.14105| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.54662| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 GSM3562842| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in 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(17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.11508| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.14116| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.0679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.09415| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.15311| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.47829| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- Overfull 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(2.77356pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.01668| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.14318| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.1096| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.05545| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.09695| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 0.60283| Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2648--2648 \T1/ptm/m/n/10 sam- [33] Underfull \hbox (badness 10000) in paragraph at lines 2748--2749 []|[][]\T1/pcr/m/sl/10 methylprep.files. Underfull \hbox (badness 6380) in paragraph at lines 2758--2759 []|[][]\T1/pcr/m/sl/10 methylprep.run_series[][]\T1/ptm/m/n/10 (id, path[, dict _only, Overfull \hbox (2.88234pt too wide) in paragraph at lines 2768--2769 []|[][]\T1/pcr/m/sl/10 methylprep.build_composite_dataset[][]\T1/ptm/m/n/10 (.. .[, [34] Underfull \hbox (badness 10000) in paragraph at lines 2859--2859 []\T1/ptm/m/it/10 array_type\T1/ptm/m/n/10 , \T1/ptm/m/it/10 filepath_or_buffer =None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 on_lambda=False\T1/ptm/m/n/10 , \T1/ptm/m /it/10 ver- [35] Underfull \hbox (badness 10000) in paragraph at lines 3030--3030 []\T1/ptm/m/it/10 data_containers\T1/ptm/m/n/10 , \T1/ptm/m/it/10 post-pro- Underfull \hbox (badness 10000) in paragraph at lines 3030--3030 \T1/ptm/m/it/10 cess_func_colname='beta_value'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3030--3030 \T1/ptm/m/it/10 poobah=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah_sig=0.05\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 ex- [36] Underfull \hbox (badness 10000) in paragraph at lines 3073--3073 []\T1/ptm/m/it/10 id\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/p tm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=100\T1/pt m/m/n/10 , \T1/ptm/m/it/10 clean=True\T1/ptm/m/n/10 , [37] Underfull \hbox (badness 10000) in paragraph at lines 3132--3132 []\T1/ptm/m/it/10 geo_id\T1/ptm/m/n/10 , \T1/ptm/m/it/10 data_dir='.'\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 merge=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 down-load_it= True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 3132--3132 \T1/ptm/m/it/10 tract_controls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-quire_k eyword=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sync_idats=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3172--3172 \T1/ptm/m/it/10 ex-tract_controls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-quir e_keyword=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3172--3172 \T1/ptm/m/it/10 sync_idats=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- [38] Underfull \hbox (badness 10000) in paragraph at lines 3230--3230 []\T1/ptm/m/it/10 data_dir\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 ex-port=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 man- i-fest_filepath=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3230--3230 \T1/ptm/m/it/10 sam-ple_sheet_filepath=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam -ple_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3230--3230 \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 make_sample_sheet =False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3230--3230 \T1/ptm/m/it/10 save_uncorrected=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save_con trol=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 meta_data_frame=True\T1/ptm/m/n/10 , [39] [40] Underfull \hbox (badness 10000) in paragraph at lines 3413--3420 []\T1/ptm/m/n/10 export=False, make_sample_sheet=False, ex-port_poobah=False, s ave_uncorrected=False, Underfull \hbox (badness 10000) in paragraph at lines 3421--3426 []\T1/ptm/m/n/10 betas=False, m_value=False, - Underfull \hbox (badness 10000) in paragraph at lines 3437--3443 []\T1/ptm/m/n/10 data_dir, ar-ray_type=None, Underfull \hbox (badness 10000) in paragraph at lines 3451--3454 [] Overfull \hbox (15.91293pt too wide) in paragraph at lines 3465--3465 \T1/ptm/m/it/10 tain_uncorrected_probe_intensities=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3465--3465 \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pval=False\T1/ptm /m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3465--3465 \T1/ptm/m/it/10 poobah_decimals=3\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3465--3465 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 do_noob=True\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3465--3465 \T1/ptm/m/it/10 qual-ity_mask=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3465--3465 \T1/ptm/m/it/10 switch_probes=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3465--3465 \T1/ptm/m/it/10 do_nonlinear_dye_bias=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3465--3465 \T1/ptm/m/it/10 de-bug=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sesame=True\T1/ptm /m/n/10 , [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 []\T1/ptm/m/it/10 data_dir\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 ex-port=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 man- i- Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 fest_filepath=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam-ple_shee t_filepath=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 sam-ple_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 make_sample_sheet=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_s ize=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 save_uncorrected=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save_con trol=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 meta_data_frame=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bit='float 32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 ex-port_poobah=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah_dec imals=3\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3581--3581 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 low_memory=True \T1/ptm/m/n/10 , \T1/ptm/m/it/10 sesame=True\T1/ptm/m/n/10 , [43] [44] Underfull \hbox (badness 10000) in paragraph at lines 3734--3734 []\T1/ptm/m/it/10 data_containers\T1/ptm/m/n/10 , \T1/ptm/m/it/10 post-pro- Underfull \hbox (badness 10000) in paragraph at lines 3734--3734 \T1/ptm/m/it/10 cess_func_colname='beta_value'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3734--3734 \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=True\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3734--3734 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 3821--3821 []\T1/ptm/m/it/10 sample_sheet\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- Underfull \hbox (badness 10000) in paragraph at lines 3821--3821 \T1/ptm/m/it/10 ple_name=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3821--3821 \T1/ptm/m/it/10 from_s3=None\T1/ptm/m/n/10 , [45] [46] [47] Underfull \hbox (badness 10000) in paragraph at lines 4064--4064 []\T1/ptm/m/it/10 filepath_or_buffer\T1/ptm/m/n/10 , \T1/ptm/m/it/10 chan-nel\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 idat_id='IDAT'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4064--4064 \T1/ptm/m/it/10 idat_version=3\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 std_dev=False\T1/ptm/m/n/10 , [48] Underfull \hbox (badness 10000) in paragraph at lines 4290--4290 []\T1/ptm/m/it/10 dir_path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ma-trix_file=False\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 out- Underfull \hbox (badness 10000) in paragraph at lines 4290--4290 \T1/ptm/m/it/10 put_file='samplesheet.csv'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- ple_type=''\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- [49] Underfull \hbox (badness 10000) in paragraph at lines 4353--4353 []\T1/ptm/m/it/10 id\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/p tm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=100\T1/pt m/m/n/10 , \T1/ptm/m/it/10 clean=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4383--4383 []\T1/ptm/m/it/10 list_file\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=10 0\T1/ptm/m/n/10 , [50] Underfull \hbox (badness 10000) in paragraph at lines 4412--4412 \T1/ptm/m/it/10 ex-tract_controls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-quir e_keyword=None\T1/ptm/m/n/10 , [51] Underfull \hbox (badness 10000) in paragraph at lines 4558--4562 []\T1/ptm/m/n/10 to ini-tial-ize, [52] Overfull \hbox (75.29005pt too wide) in paragraph at lines 4593--4593 [] Underfull \hbox (badness 10000) in paragraph at lines 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