Read the Docs build information Build id: 847681 Project: life-epigenetics-methylcheck Version: feature-v0.8.4 Commit: d29e30e6a1607fda28077495c0228ae0b442bfaa Date: 2022-02-08T19:32:12.697264Z State: finished Success: True [rtd-command-info] start-time: 2022-02-08T19:32:14.579429Z, end-time: 2022-02-08T19:32:44.661821Z, duration: 30, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylcheck.git . Cloning into '.'... 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[rtd-command-info] start-time: 2022-02-08T19:32:44.854146Z, end-time: 2022-02-08T19:32:45.925381Z, duration: 1, exit-code: 0 git checkout --force origin/feature/v0.8.4 Note: checking out 'origin/feature/v0.8.4'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at d29e30e docs bug [rtd-command-info] start-time: 2022-02-08T19:32:46.106546Z, end-time: 2022-02-08T19:32:46.189400Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-02-08T19:32:55.342300Z, end-time: 2022-02-08T19:33:00.925501Z, 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-methylcheck/envs/feature-v0.8.4/bin/python3.8 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2022-02-08T19:33:01.098409Z, end-time: 2022-02-08T19:33:04.274882Z, duration: 3, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip<=21.3.1 setuptools<58.3.0 Collecting pip<=21.3.1 Downloading pip-21.3.1-py3-none-any.whl (1.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 44.5 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 282.1 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 60.8.1 Uninstalling setuptools-60.8.1: Successfully uninstalled setuptools-60.8.1 Attempting uninstall: pip Found existing installation: pip 22.0.3 Uninstalling pip-22.0.3: Successfully uninstalled pip-22.0.3 Successfully installed pip-21.3.1 setuptools-58.2.0 [rtd-command-info] start-time: 2022-02-08T19:33:04.458409Z, end-time: 2022-02-08T19:33:32.193003Z, duration: 27, 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 setuptools<58.3.0 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) 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) 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) 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) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting docutils>=0.11 Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) Collecting imagesize Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting requests>=2.0.0 Downloading requests-2.27.1-py2.py3-none-any.whl (63 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting Pygments>=2.0 Downloading Pygments-2.11.2-py3-none-any.whl (1.1 MB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting pytz>=2015.7 Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (30 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.11-py3-none-any.whl (39 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.8-py2.py3-none-any.whl (138 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) Collecting pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.7-py3-none-any.whl (98 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Building wheels for collected packages: mock, pillow, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23773 sha256=a85667b671b275559805ea99b05ce5210ae4fa5fef2c8495ef130ccc23f4cb4f Stored in directory: /tmp/pip-ephem-wheel-cache-meqg6zy1/wheels/41/7c/21/90057f91c6ead7c77a90c52d6e85ca48bf82d8b0d3f8dfbb65 Building wheel for pillow (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=1260055 sha256=a2293ac1025a2374afdab32300aafac5286b5addd71ba8b33d060717cffd4468 Stored in directory: /tmp/pip-ephem-wheel-cache-meqg6zy1/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=24e31d95d0bcb123346e05671d1e1b260b0450d55a2b0f63bbd99f58c31ef46f Stored in directory: /tmp/pip-ephem-wheel-cache-meqg6zy1/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4 Successfully built mock pillow future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.11 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.7 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.27.1 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 urllib3-1.26.8 WARNING: You are using pip version 21.3.1; however, version 22.0.3 is available. You should consider upgrading via the '/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/bin/python -m pip install --upgrade pip' command. [rtd-command-info] start-time: 2022-02-08T19:33:32.370502Z, end-time: 2022-02-08T19:33:52.402533Z, duration: 20, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: numpy in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from -r requirements.txt (line 1)) (1.19.2) Collecting pandas>=1.3.0 Downloading pandas-1.4.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB) Collecting scipy Downloading scipy-1.8.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (41.6 MB) Requirement already satisfied: matplotlib in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from -r requirements.txt (line 4)) (3.3.2) Collecting seaborn Downloading seaborn-0.11.2-py3-none-any.whl (292 kB) Collecting tqdm>=4.61.2 Downloading tqdm-4.62.3-py2.py3-none-any.whl (76 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-0.8.8-py3-none-any.whl (25 kB) Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages (from -r requirements.txt (line 11)) (1.8.6) Collecting ipykernel Downloading ipykernel-6.9.0-py3-none-any.whl (128 kB) Collecting joblib Downloading joblib-1.1.0-py2.py3-none-any.whl (306 kB) Collecting xlsxwriter Downloading XlsxWriter-3.0.2-py3-none-any.whl (149 kB) Collecting openpyxl Downloading openpyxl-3.0.9-py2.py3-none-any.whl (242 kB) Requirement already satisfied: pytz>=2020.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages (from pandas>=1.3.0->-r requirements.txt (line 2)) (2021.3) Requirement already satisfied: python-dateutil>=2.8.1 in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from pandas>=1.3.0->-r requirements.txt (line 2)) (2.8.1) Requirement already satisfied: kiwisolver>=1.0.1 in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from matplotlib->-r requirements.txt (line 4)) (1.2.0) Collecting pillow>=6.2.0 Downloading Pillow-9.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages (from matplotlib->-r requirements.txt (line 4)) (3.0.7) Requirement already satisfied: cycler>=0.10 in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from matplotlib->-r requirements.txt (line 4)) (0.10.0) Requirement already satisfied: certifi>=2020.06.20 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages (from matplotlib->-r requirements.txt (line 4)) (2021.10.8) Collecting pbr Downloading pbr-5.8.1-py2.py3-none-any.whl (113 kB) Collecting mistune Downloading mistune-2.0.2-py2.py3-none-any.whl (24 kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages (from m2r->-r requirements.txt (line 9)) (0.17.1) Collecting nbconvert!=5.4 Downloading nbconvert-6.4.1-py3-none-any.whl (557 kB) Collecting traitlets Downloading traitlets-5.1.1-py3-none-any.whl (102 kB) Collecting nbformat Downloading nbformat-5.1.3-py3-none-any.whl (178 kB) Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages (from nbsphinx->-r requirements.txt (line 10)) (3.0.3) 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Stored in directory: /tmp/pip-ephem-wheel-cache-zxbqkvcs/wheels/f0/0d/a1/905017ebb11fce6b0316028bf05fc5c4229fbadff0db60182d Successfully built m2r Installing collected packages: zipp, traitlets, pyrsistent, importlib-resources, attrs, tornado, pyzmq, nest-asyncio, jupyter-core, jsonschema, ipython-genutils, entrypoints, webencodings, wcwidth, typing-extensions, tomli, pure-eval, ptyprocess, platformdirs, pathspec, parso, nbformat, mypy-extensions, jupyter-client, executing, click, asttokens, testpath, stack-data, prompt-toolkit, pillow, pickleshare, pexpect, pandocfilters, nbclient, mistune, matplotlib-inline, jupyterlab-pygments, jedi, defusedxml, decorator, bleach, black, backcall, scipy, pbr, pandas, nbconvert, ipython, et-xmlfile, debugpy, xlsxwriter, tqdm, sphinxcontrib-apidoc, seaborn, openpyxl, nbsphinx, m2r, joblib, ipykernel Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 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-methylcheck/envs/feature-v0.8.4 Can't uninstall 'pandas'. No files were found to uninstall. Successfully installed asttokens-2.0.5 attrs-21.4.0 backcall-0.2.0 black-22.1.0 bleach-4.1.0 click-8.0.3 debugpy-1.5.1 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 et-xmlfile-1.1.0 executing-0.8.2 importlib-resources-5.4.0 ipykernel-6.9.0 ipython-8.0.1 ipython-genutils-0.2.0 jedi-0.18.1 joblib-1.1.0 jsonschema-4.4.0 jupyter-client-7.1.2 jupyter-core-4.9.1 jupyterlab-pygments-0.1.2 m2r-0.2.1 matplotlib-inline-0.1.3 mistune-0.8.4 mypy-extensions-0.4.3 nbclient-0.5.10 nbconvert-6.4.1 nbformat-5.1.3 nbsphinx-0.8.8 nest-asyncio-1.5.4 openpyxl-3.0.9 pandas-1.4.0 pandocfilters-1.5.0 parso-0.8.3 pathspec-0.9.0 pbr-5.8.1 pexpect-4.8.0 pickleshare-0.7.5 pillow-9.0.1 platformdirs-2.4.1 prompt-toolkit-3.0.27 ptyprocess-0.7.0 pure-eval-0.2.2 pyrsistent-0.18.1 pyzmq-22.3.0 scipy-1.8.0 seaborn-0.11.2 sphinxcontrib-apidoc-0.3.0 stack-data-0.1.4 testpath-0.5.0 tomli-2.0.1 tornado-6.1 tqdm-4.62.3 traitlets-5.1.1 typing-extensions-4.0.1 wcwidth-0.2.5 webencodings-0.5.1 xlsxwriter-3.0.2 zipp-3.7.0 WARNING: You are using pip version 21.3.1; however, version 22.0.3 is available. You should consider upgrading via the '/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/bin/python -m pip install --upgrade pip' command. [rtd-command-info] start-time: 2022-02-08T19:33:52.590308Z, end-time: 2022-02-08T19:33:53.608412Z, duration: 1, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Requirement already satisfied: docutils<0.18 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages (from -r docs/requirements.txt (line 1)) (0.17.1) WARNING: You are using pip version 21.3.1; however, version 22.0.3 is available. You should consider upgrading via the '/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/bin/python -m pip install --upgrade pip' command. [rtd-command-info] start-time: 2022-02-08T19:33:55.037655Z, end-time: 2022-02-08T19:33:55.100704Z, 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 = 'methylcheck' copyright = '2022, FOXO Technologies, inc.' author = 'FOXO Technologies, inc.' # The short X.Y version version = '0.8' # The full version, including alpha/beta/rc tags release = '0.8.4' # -- 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' ] autosummary_generate = True # new in sphinx 3.1 2020 # instead of CLI "sphinx-autodoc . _build/html" you write this apidoc_module_dir = '.' apidoc_output_dir = '_sphinx_build' apidoc_excluded_paths = ['tests'] apidoc_separate_modules = False # Add any paths that contain templates here, relative to this directory. templates_path = ['_sphinx_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] # source_suffix = '.rst' # The master toctree document. master_doc = 'index' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path . exclude_patterns = ['_sphinx_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # -- 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' # 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 = 'methylcheckdoc' # -- Options for LaTeX output ------------------------------------------------ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'methylcheck.tex', 'methylcheck Documentation', 'FOXO Technologies, inc', '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, 'methylcheck', 'methylcheck 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, 'methylcheck', 'methylcheck Documentation', author, 'methylcheck', 'Methylation array quality control and filtering.', 'Miscellaneous'), ] # -- Extension configuration ------------------------------------------------- # numpydoc_show_class_members = False ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file 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': "feature/v0.8.4", 'version_slug': "feature-v0.8.4", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("feature-v0.8.4", "/en/feature-v0.8.4/"), ], 'downloads': [ ("pdf", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/feature-v0.8.4/pdf/"), ("html", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/feature-v0.8.4/htmlzip/"), ("epub", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/feature-v0.8.4/epub/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylcheck', 'name': u'methylcheck', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://life-epigenetics-methylcheck.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': 'methylcheck', 'github_version': 'feature/v0.8.4', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'feature/v0.8.4', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'feature/v0.8.4', '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': 'd29e30e6', } # 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-methylcheck/builds/847681/' 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: 2022-02-08T19:33:55.295360Z, end-time: 2022-02-08T19:34:57.553958Z, duration: 62, 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-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.data_files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.predict.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.probes.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.reports.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.samples.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/modules.rst. [autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.ipynb, docs/poobah_filtering_tutorial.ipynb, docs/quality-control-example.ipynb, docs/release-history.md, docs/research_notebooks/postprocessQC_example.ipynb, docs/research_notebooks/pval.ipynb, docs/research_notebooks/rawQC_example.ipynb, docs/source/modules.rst, index.rst Matplotlib is building the font cache; this may take a moment. [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.assign.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.beta_density_plot.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.beta_mds_plot.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.cli.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.combine_mds.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.drop_nan_probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.exclude_probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.exclude_sex_control_probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.get_sex.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.plot_beta_by_type.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.plot_controls.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.predict.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.qc_signal_intensity.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.read_geo.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.run_pipeline.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.run_qc.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.sample_plot.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/source/_autosummary/methylcheck.samples.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 12 source files that are out of date updating environment: 38 added, 0 changed, 0 removed reading sources... 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in 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0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/poobah_filtering_tutorial.ipynb:3381: WARNING: File not found: 'docs/quality-control-example.html#Predicting-Sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/poobah_filtering_tutorial.ipynb:3392: WARNING: File not found: 'docs/filtering-probes.html#Filtering-sex-linked-probes-and-control-probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/postprocessQC_example.ipynb:1: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/rawQC_example.ipynb:1: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.beta_mds_plot:65: WARNING: Unknown directive type "todo". .. todo:: - Reads the manifest file for the array, or at least a list of probe names to exclude/include. - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']] - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values df_no_sex_probes = df[probe_names_no_sex_probes] df_no_sex_probes.head() /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:3: WARNING: Unexpected section title or transition. -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:5: WARNING: Unexpected section title. how it works: -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:18: WARNING: Unexpected section title or transition. ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:20: WARNING: Unexpected section title. inputs: ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:28: WARNING: Unexpected section title. optional keyword arguments: --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:40: WARNING: Unexpected section title. analysis parameters: -------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:47: WARNING: Unexpected section title. returns: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:51: WARNING: Unknown directive type "todo". .. todo:: - TODO: one dataframe of the retained samples, cutoff box is avg of datasets - TODO: each dataset's results as a transformed file - default: list of samples retained or excluded - option: a list of pyplot subplot objects /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:11: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:26: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/predict/sex.py:docstring of methylcheck.get_sex:4: WARNING: Unexpected section title. inputs: ======= /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.list_problem_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.list_problem_probes:50: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.list_problem_probes:47: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load:92: WARNING: Unknown directive type "todo". .. todo:: - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs - DONE: meth_df deal with batches of files /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load:44: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.mean_beta_compare:3: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:4: WARNING: Unexpected section title. input (choose one of these): ============================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:34: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_controls:5: WARNING: Unexpected section title. input: ====== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_controls:11: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:4: WARNING: Unexpected section title. input (one of these): ===================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:23: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:27: WARNING: Unexpected section title. optional params: ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:40: WARNING: Unexpected section title. returns: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:27: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:19: WARNING: Unknown target name: "matrix". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.run_pipeline:25: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.sample_plot:1: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:92: WARNING: Unknown directive type "todo". .. todo:: - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs - DONE: meth_df deal with batches of files /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title. example: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.ReportPDF:44: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.ReportPDF:45: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.ReportPDF.exec_summary:17: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.run_pipeline:25: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:11: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:65: WARNING: Unknown directive type "todo". .. todo:: - Reads the manifest file for the array, or at least a list of probe names to exclude/include. - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']] - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values df_no_sex_probes = df[probe_names_no_sex_probes] df_no_sex_probes.head() /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition. -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title. how it works: -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition. ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title. inputs: ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title. optional keyword arguments: --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title. analysis parameters: -------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title. returns: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo". .. todo:: - TODO: one dataframe of the retained samples, cutoff box is avg of datasets - TODO: each dataset's results as a transformed file - default: list of samples retained or excluded - option: a list of pyplot subplot objects /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title. input (one of these): ===================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title. optional params: ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title. returns: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title. input (choose one of these): ============================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:5: WARNING: Unexpected section title. input: ====== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title. inputs: ======= /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/poobah_filtering_tutorial.ipynb:3381: WARNING: File not found: 'docs/quality-control-example.html#Predicting-Sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/poobah_filtering_tutorial.ipynb:3392: WARNING: File not found: 'docs/filtering-probes.html#Filtering-sex-linked-probes-and-control-probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/postprocessQC_example.ipynb:1: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/rawQC_example.ipynb:1: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.beta_mds_plot:65: WARNING: Unknown directive type "todo". .. todo:: - Reads the manifest file for the array, or at least a list of probe names to exclude/include. - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']] - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values df_no_sex_probes = df[probe_names_no_sex_probes] df_no_sex_probes.head() /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:3: WARNING: Unexpected section title or transition. -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:5: WARNING: Unexpected section title. how it works: -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:18: WARNING: Unexpected section title or transition. ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:20: WARNING: Unexpected section title. inputs: ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:28: WARNING: Unexpected section title. optional keyword arguments: --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:40: WARNING: Unexpected section title. analysis parameters: -------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:47: WARNING: Unexpected section title. returns: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:51: WARNING: Unknown directive type "todo". .. todo:: - TODO: one dataframe of the retained samples, cutoff box is avg of datasets - TODO: each dataset's results as a transformed file - default: list of samples retained or excluded - option: a list of pyplot subplot objects /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:11: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:26: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/predict/sex.py:docstring of methylcheck.get_sex:4: WARNING: Unexpected section title. inputs: ======= /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.list_problem_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.list_problem_probes:50: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.list_problem_probes:47: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load:92: WARNING: Unknown directive type "todo". .. todo:: - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs - DONE: meth_df deal with batches of files /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load:44: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.mean_beta_compare:3: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:4: WARNING: Unexpected section title. input (choose one of these): ============================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:34: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_controls:5: WARNING: Unexpected section title. input: ====== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_controls:11: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:4: WARNING: Unexpected section title. input (one of these): ===================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:23: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:27: WARNING: Unexpected section title. optional params: ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:40: WARNING: Unexpected section title. returns: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:27: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:19: WARNING: Unknown target name: "matrix". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.run_pipeline:25: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.sample_plot:1: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:92: WARNING: Unknown directive type "todo". .. todo:: - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs - DONE: meth_df deal with batches of files /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title. example: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.ReportPDF:44: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.ReportPDF:45: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.ReportPDF.exec_summary:17: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.run_pipeline:25: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:11: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:65: WARNING: Unknown directive type "todo". .. todo:: - Reads the manifest file for the array, or at least a list of probe names to exclude/include. - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']] - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values df_no_sex_probes = df[probe_names_no_sex_probes] df_no_sex_probes.head() /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition. -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title. how it works: -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition. ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title. inputs: ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title. optional keyword arguments: --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title. analysis parameters: -------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title. returns: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo". .. todo:: - TODO: one dataframe of the retained samples, cutoff box is avg of datasets - TODO: each dataset's results as a transformed file - default: list of samples retained or excluded - option: a list of pyplot subplot objects /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title. input (one of these): ===================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title. optional params: ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title. returns: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title. input (choose one of these): ============================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; 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[autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.ipynb, docs/poobah_filtering_tutorial.ipynb, docs/quality-control-example.ipynb, docs/release-history.md, docs/research_notebooks/postprocessQC_example.ipynb, docs/research_notebooks/pval.ipynb, docs/research_notebooks/rawQC_example.ipynb, ..., docs/source/_autosummary/methylcheck.predict.rst, docs/source/_autosummary/methylcheck.probes.rst, docs/source/_autosummary/methylcheck.qc_signal_intensity.rst, docs/source/_autosummary/methylcheck.read_geo.rst, docs/source/_autosummary/methylcheck.run_pipeline.rst, docs/source/_autosummary/methylcheck.run_qc.rst, docs/source/_autosummary/methylcheck.sample_plot.rst, docs/source/_autosummary/methylcheck.samples.rst, docs/source/modules.rst, index.rst building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found processing methylcheck.tex...index docs/loading-data docs/filtering-probes docs/quality-control-example docs/poobah_filtering_tutorial docs/mds-example docs/source/modules docs/source/_autosummary/methylcheck.cli docs/source/_autosummary/methylcheck.run_pipeline docs/source/_autosummary/methylcheck.run_qc docs/source/_autosummary/methylcheck.read_geo docs/source/_autosummary/methylcheck.load docs/source/_autosummary/methylcheck.load_both docs/source/_autosummary/methylcheck.qc_signal_intensity docs/source/_autosummary/methylcheck.plot_M_vs_U docs/source/_autosummary/methylcheck.plot_controls docs/source/_autosummary/methylcheck.plot_beta_by_type docs/source/_autosummary/methylcheck.probes docs/source/_autosummary/methylcheck.list_problem_probes docs/source/_autosummary/methylcheck.exclude_probes docs/source/_autosummary/methylcheck.exclude_sex_control_probes docs/source/_autosummary/methylcheck.drop_nan_probes docs/source/_autosummary/methylcheck.samples docs/source/_autosummary/methylcheck.sample_plot docs/source/_autosummary/methylcheck.beta_density_plot docs/source/_autosummary/methylcheck.mean_beta_plot docs/source/_autosummary/methylcheck.mean_beta_compare docs/source/_autosummary/methylcheck.beta_mds_plot docs/source/_autosummary/methylcheck.combine_mds docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution docs/source/_autosummary/methylcheck.predict docs/source/_autosummary/methylcheck.get_sex docs/source/_autosummary/methylcheck.assign docs/release-history resolving references... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/builders/latex/__init__.py:201: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. if toctrees[0].get('maxdepth') > 0: README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://github.com/FoxoTech/methylcheck/workflows/tests/badge.svg) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://readthedocs.com/projects/life-epigenetics-methylcheck/badge/?version=latest) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/badge/License-MIT-yellow.svg) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://circleci.com/gh/FoxoTech/methylcheck.svg?style=shield) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://app.codacy.com/project/badge/Grade/6fdca9f2600342839379a0dd22bebad5) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://coveralls.io/repos/github/FoxoTech/methylcheck/badge.svg?t=OVL45Q) README.md:37: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/dm/methylcheck.svg?label=pypi%20downloads&logo=PyPI&logoColor=white:target:https://pypi.org/project/methylcheck/:alt:PyPI-Downloads:raw-html-m2r:``) writing... done copying images... 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Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2022-02-08T19:35:16.474520Z, end-time: 2022-02-08T19:35:16.537405Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2022-02-08T19:35:16.697576Z, end-time: 2022-02-08T19:35:28.703693Z, duration: 12, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=life-epigenetics-methylcheck -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. 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LaTeX Warning: Hyper reference `docs/loading-data::doc' on page 9 undefined on input line 353. LaTeX Warning: Hyper reference `docs/filtering-probes::doc' on page 9 undefined on input line 356. LaTeX Warning: Hyper reference `docs/quality-control-example::doc' on page 9 un defined on input line 359. LaTeX Warning: Hyper reference `docs/mds-example::doc' on page 9 undefined on i nput line 362. LaTeX Warning: Hyper reference `docs/quality-control-example:Predicting-Sex' on page 9 undefined on input line 365. [9] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.436 ...��███| 1/1 [00:00<00:00, 5.92it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. 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Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.593 ...�██| 16/16 [00:00<00:00, 1480.91it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. 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Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.676 ...��██| 16/16 [00:00<00:00, 550.34it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. 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Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s] [13] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. 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Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. 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Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] [15] Underfull \vbox (badness 10000) detected at line 965 Overfull \vbox (2.68169pt too high) detected at line 965 [16] [17 <./docs_loading-data_16_1.png>] [18 <./docs_loading-data_18_0.png>] [19] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. 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Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] [26] Underfull \hbox (badness 10000) in paragraph at lines 1602--1603 []\T1/ptm/m/n/10 The color-coded re-sults are con-tained in an ex-cel file that will be saved in the Underfull \hbox (badness 10000) in paragraph at lines 1602--1603 \T1/ptm/m/n/10 same di-rec-tory that was spec-i-fied as an in-put. It will look sim-i-lar to this: Overfull \hbox (283.13986pt too wide) in paragraph at lines 1602--1603 [] [27 <./bead_array_report.png>] Underfull \vbox (badness 10000) detected at line 1642 [28] Underfull \vbox (badness 10000) detected at line 1653 [29 <./docs_quality-control-example_9_0.png>] Underfull \vbox (badness 10000) detected at line 1678 [30 <./docs_quality-control-example_9_1.png>] Underfull \vbox (badness 10000) detected at line 1689 [31 <./docs_quality-control-example_9_3.png>] Underfull \vbox (badness 10000) detected at line 1700 [32 <./docs_quality-control-example_9_4.png>] Underfull \vbox (badness 10000) detected at line 1711 [33 <./docs_quality-control-example_9_5.png>] Underfull \vbox (badness 10000) detected at line 1722 [34 <./docs_quality-control-example_9_6.png>] Underfull \vbox (badness 10000) detected at line 1733 [35 <./docs_quality-control-example_9_7.png>] Underfull \vbox (badness 10000) detected at line 1744 [36 <./docs_quality-control-example_9_8.png>] Underfull \vbox (badness 10000) detected at line 1755 [37 <./docs_quality-control-example_9_9.png>] Underfull \vbox (badness 10000) detected at line 1793 [38 <./docs_quality-control-example_9_10.png>] Underfull \vbox (badness 10000) detected at line 1830 [39 <./docs_quality-control-example_9_13.png>] Underfull \vbox (badness 10000) detected at line 1867 [40 <./docs_quality-control-example_9_16.png>] Underfull \vbox (badness 10000) detected at line 1904 [41 <./docs_quality-control-example_9_19.png>] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. 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Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] [42 <./docs_quality-control-example_9_22.png>] Underfull \hbox (badness 10000) in paragraph at lines 1989--1990 []\T1/ptm/m/n/10 kwargs: \T1/pcr/m/n/10 filename, poobah_max_percent, pval_cuto ff, title, author, subject, [43 <./docs_quality-control-example_12_1.png>] Underfull \hbox (badness 10000) in paragraph at lines 1993--1994 []\T1/ptm/m/n/10 If you want a quick one-line ver-sion with no fur-ther re-port edit-ing, try \T1/pcr/m/n/10 methylcheck. [44] [45] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! 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Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! 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[73] Underfull \hbox (badness 10000) in paragraph at lines 4116--4122 []\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Chen2013\TS1/pcr/m/n/10 ' '\T1/pcr/m/n/10 Pri ce2013\TS1/pcr/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 4127--4132 []\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Polymorphism\TS1/pcr/m/n/10 ' '\T1/pcr/m/n/10 CrossHybridization\TS1/pcr/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 4139--4142 []\T1/ptm/m/n/10 [`mean_beta_plot', `beta_density_plot', `cu-mu-la-tive_sum_bet a_distribution', [74] [75] [76] Underfull \hbox (badness 10000) in paragraph at lines 4399--4399 []\T1/ptm/m/it/10 filepath='.'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 for-mat='beta_va lue'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_stem=''\T1/ptm/m/n/10 , \T1/ptm/m/it/ 10 ver-bose=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4399--4399 \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 col-umn_names=None \T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-name_samples=False\T1/ptm/m/n/10 , \T1/ptm/ m/it/10 sam- [77] Underfull \hbox (badness 10000) in paragraph at lines 4452--4452 []\T1/ptm/m/it/10 data_containers=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path=Non e\T1/ptm/m/n/10 , \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 un- Underfull \hbox (badness 10000) in paragraph at lines 4452--4452 \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=None\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 palette=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 noob=True\T 1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 4465--4470 []\T1/ptm/m/n/10 if you chose \T1/ptm/m/it/10 pro-cess ^^Uall \T1/ptm/m/n/10 yo u can load the raw in-ten-si-ties like Underfull \hbox (badness 10000) in paragraph at lines 4465--4470 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = [78] Underfull \hbox (badness 10000) in paragraph at lines 4516--4516 []\T1/ptm/m/it/10 data_containers_or_path=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 un-meth=None\T1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 4533--4538 []\T1/ptm/m/n/10 if you chose \T1/ptm/m/it/10 pro-cess ^^Uall \T1/ptm/m/n/10 yo u can load the raw in-ten-si-ties like Underfull \hbox (badness 10000) in paragraph at lines 4533--4538 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = Underfull \hbox (badness 10000) in paragraph at lines 4591--4593 []\T1/ptm/m/n/10 `non-polymorphic' | [79] Underfull \hbox (badness 10000) in paragraph at lines 4614--4614 []\T1/ptm/m/it/10 beta_df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 probe_type='all'\T1/p tm/m/n/10 , \T1/ptm/m/it/10 re-turn_fig=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 s ilent=False\T1/ptm/m/n/10 , [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 4812--4813 []\T1/ptm/m/n/10 Index([`cg00000029_II_F_C_rep1_EPIC', `cg00000103_II_F_C_rep1_ EPIC', Underfull \hbox (badness 10000) in paragraph at lines 4815--4818 []\T1/ptm/m/n/10 `cg00000158_II_F_C_rep1_EPIC', `cg00000165_II_R_C_rep1_EPIC', Underfull \hbox (badness 10000) in paragraph at lines 4815--4818 \T1/ptm/m/n/10 `cg00000221_II_R_C_rep1_EPIC', `cg00000236_II_R_C_rep1_EPIC', .. . 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It cannot appear first in list.", \TS1/pcr/m/n/10 '\ T1/pcr/m/n/10 font_size\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : Output written on life-epigenetics-methylcheck.pdf (115 pages, 2244481 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.pngheight=40">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.png"height="40">`' not found on input' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.pngheight=40">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.png"height="40">`' not found on input line 240.' Latexmk: Missing input file: 'life-epigenetics-methylcheck.ind' from line 'No file life-epigenetics-methylcheck.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Latexmk: List of undefined refs and citations: Reference `docs/source/_autosummary/methylcheck.cli:module-methylcheck.cli' on page 111 undefined on input line 7378 Reference `docs/source/modules:module-methylcheck.load_processed' on page 111 undefined on input line 7379 Reference `docs/source/modules:module-methylcheck.predict' on page 111 undefined on input line 7380 Reference `docs/source/modules:module-methylcheck.probes' on page 111 undefined on input line 7381 Reference `docs/source/modules:module-methylcheck.qc_plot' on page 111 undefined on input line 7382 Reference `docs/source/modules:module-methylcheck.read_geo_processed' on page 111 undefined on input line 7383 Reference `docs/source/modules:module-methylcheck.reports.qc_report.run_pipeline' on page 111 undefined on input line 7384 Reference `docs/source/modules:module-methylcheck.samples' on page 111 undefined on input line 7385 Latexmk: Summary of warnings: Latex failed to resolve 8 reference(s) Rule 'makeindex life-epigenetics-methylcheck.idx': File changes, etc: Non-existent destination files: 'life-epigenetics-methylcheck.ind' ------------ Run number 1 of rule 'makeindex life-epigenetics-methylcheck.idx' ------------ Latexmk: applying rule 'makeindex life-epigenetics-methylcheck.idx'... ------------ Running 'makeindex -s python.ist -o "life-epigenetics-methylcheck.ind" "life-epigenetics-methylcheck.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-methylcheck.idx....done (68 entries accepted, 0 rejected). Sorting entries....done (438 comparisons). Generating output file life-epigenetics-methylcheck.ind....done (133 lines written, 0 warnings). Output written in life-epigenetics-methylcheck.ind. Transcript written in life-epigenetics-methylcheck.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylcheck.aux' 'life-epigenetics-methylcheck.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylcheck" "methylcheck.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.677 ...�██| 16/16 [00:00<00:00, 1499.81it/s] [13] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] Overfull \vbox (13.12581pt too high) detected at line 829 [14] Underfull \hbox (badness 10000) in paragraph at lines 835--836 []\T1/pcr/m/n/10 sdc[0]._SampleDataContainer__data_frame \T1/ptm/m/n/10 will gi ve you a dataframe of the first ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] [15] Underfull \vbox (badness 10000) detected at line 965 Overfull \vbox (2.68169pt too high) detected at line 965 [16] [17 <./docs_loading-data_16_1.png>] [18 <./docs_loading-data_18_0.png>] [19] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] [20] Underfull \vbox (badness 10000) detected at line 1295 [21 <./docs_filtering-probes_9_1.png>] [22 <./docs_filtering-probes_11_0.png>] Underfull \vbox (badness 10000) detected at line 1420 [23] Underfull \vbox (badness 10000) detected at line 1439 [24 <./docs_filtering-probes_16_1.png>] [25 <./docs_filtering-probes_17_0.png>] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] [26] Underfull \hbox (badness 10000) in paragraph at lines 1602--1603 []\T1/ptm/m/n/10 The color-coded re-sults are con-tained in an ex-cel file that will be saved in the Underfull \hbox (badness 10000) in paragraph at lines 1602--1603 \T1/ptm/m/n/10 same di-rec-tory that was spec-i-fied as an in-put. It will look sim-i-lar to this: Overfull \hbox (283.13986pt too wide) in paragraph at lines 1602--1603 [] [27 <./bead_array_report.png>] Underfull \vbox (badness 10000) detected at line 1642 [28] Underfull \vbox (badness 10000) detected at line 1653 [29 <./docs_quality-control-example_9_0.png>] Underfull \vbox (badness 10000) detected at line 1678 [30 <./docs_quality-control-example_9_1.png>] Underfull \vbox (badness 10000) detected at line 1689 [31 <./docs_quality-control-example_9_3.png>] Underfull \vbox (badness 10000) detected at line 1700 [32 <./docs_quality-control-example_9_4.png>] Underfull \vbox (badness 10000) detected at line 1711 [33 <./docs_quality-control-example_9_5.png>] Underfull \vbox (badness 10000) detected at line 1722 [34 <./docs_quality-control-example_9_6.png>] Underfull \vbox (badness 10000) detected at line 1733 [35 <./docs_quality-control-example_9_7.png>] Underfull \vbox (badness 10000) detected at line 1744 [36 <./docs_quality-control-example_9_8.png>] Underfull \vbox (badness 10000) detected at line 1755 [37 <./docs_quality-control-example_9_9.png>] Underfull \vbox (badness 10000) detected at line 1793 [38 <./docs_quality-control-example_9_10.png>] Underfull \vbox (badness 10000) detected at line 1830 [39 <./docs_quality-control-example_9_13.png>] Underfull \vbox (badness 10000) detected at line 1867 [40 <./docs_quality-control-example_9_16.png>] Underfull \vbox (badness 10000) detected at line 1904 [41 <./docs_quality-control-example_9_19.png>] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] [42 <./docs_quality-control-example_9_22.png>] Underfull \hbox (badness 10000) in paragraph at lines 1989--1990 []\T1/ptm/m/n/10 kwargs: \T1/pcr/m/n/10 filename, poobah_max_percent, pval_cuto ff, title, author, subject, [43 <./docs_quality-control-example_12_1.png>] Underfull \hbox (badness 10000) in paragraph at lines 1993--1994 []\T1/ptm/m/n/10 If you want a quick one-line ver-sion with no fur-ther re-port edit-ing, try \T1/pcr/m/n/10 methylcheck. [44] [45] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! 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Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] [46] Underfull \vbox (badness 10000) detected at line 2348 Overfull \vbox (2.68169pt too high) detected at line 2348 [47] Overfull \vbox (1.63934pt too high) detected at line 2436 [48] Overfull \vbox (0.63934pt too high) detected at line 2559 [49] [50] [51] Overfull \vbox (10.43936pt too high) detected at line 2706 [52] Overfull \vbox (2.88167pt too high) detected at line 2810 [53] [54] Underfull \vbox (badness 10000) detected at line 2928 [55] Underfull \vbox (badness 7116) detected at line 3052 [56 <./docs_mds-example_4_1.png>] Underfull \vbox (badness 10000) detected at line 3052 Overfull \vbox (2.68169pt too high) detected at line 3052 [57] [58] [59 <./docs_mds-example_12_1.png>] Underfull \vbox (badness 10000) detected at line 3278 Overfull \vbox (2.68169pt too high) detected at line 3278 [60] Underfull \vbox (badness 10000) detected at line 3317 [61] Underfull \vbox (badness 7116) detected at line 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(df[, ver-b ose, Underfull \hbox (badness 6284) in paragraph at lines 3953--3954 []|[][]\T1/pcr/m/sl/10 methylcheck.mean_beta_compare[][]\T1/ptm/m/n/10 (df1, df 2[, Overfull \hbox (56.71234pt too wide) in paragraph at lines 3968--3969 []|[][]\T1/pcr/m/sl/10 methylcheck.cumulative_sum_beta_distribution[][]\T1/ptm/ m/n/10 (df)| [72 <./docs_mds-example_21_0.png>] [73] Underfull \hbox (badness 10000) in paragraph at lines 4116--4122 []\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Chen2013\TS1/pcr/m/n/10 ' '\T1/pcr/m/n/10 Pri ce2013\TS1/pcr/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 4127--4132 []\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Polymorphism\TS1/pcr/m/n/10 ' '\T1/pcr/m/n/10 CrossHybridization\TS1/pcr/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 4139--4142 []\T1/ptm/m/n/10 [`mean_beta_plot', `beta_density_plot', `cu-mu-la-tive_sum_bet a_distribution', [74] [75] [76] Underfull \hbox (badness 10000) in paragraph at lines 4399--4399 []\T1/ptm/m/it/10 filepath='.'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 for-mat='beta_va lue'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_stem=''\T1/ptm/m/n/10 , \T1/ptm/m/it/ 10 ver-bose=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4399--4399 \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 col-umn_names=None \T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-name_samples=False\T1/ptm/m/n/10 , \T1/ptm/ m/it/10 sam- [77] Underfull \hbox (badness 10000) in paragraph at lines 4452--4452 []\T1/ptm/m/it/10 data_containers=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path=Non e\T1/ptm/m/n/10 , \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 un- Underfull \hbox (badness 10000) in paragraph at lines 4452--4452 \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=None\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 palette=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 noob=True\T 1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 4465--4470 []\T1/ptm/m/n/10 if you chose \T1/ptm/m/it/10 pro-cess ^^Uall \T1/ptm/m/n/10 yo u can load the raw in-ten-si-ties like Underfull \hbox (badness 10000) in paragraph at lines 4465--4470 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = [78] Underfull \hbox (badness 10000) in paragraph at lines 4516--4516 []\T1/ptm/m/it/10 data_containers_or_path=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 un-meth=None\T1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 4533--4538 []\T1/ptm/m/n/10 if you chose \T1/ptm/m/it/10 pro-cess ^^Uall \T1/ptm/m/n/10 yo u can load the raw in-ten-si-ties like Underfull \hbox (badness 10000) in paragraph at lines 4533--4538 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = Underfull \hbox (badness 10000) in paragraph at lines 4591--4593 []\T1/ptm/m/n/10 `non-polymorphic' | [79] Underfull \hbox (badness 10000) in paragraph at lines 4614--4614 []\T1/ptm/m/it/10 beta_df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 probe_type='all'\T1/p tm/m/n/10 , \T1/ptm/m/it/10 re-turn_fig=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 s ilent=False\T1/ptm/m/n/10 , [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 4812--4813 []\T1/ptm/m/n/10 Index([`cg00000029_II_F_C_rep1_EPIC', `cg00000103_II_F_C_rep1_ EPIC', Underfull \hbox (badness 10000) in paragraph at lines 4815--4818 []\T1/ptm/m/n/10 `cg00000158_II_F_C_rep1_EPIC', `cg00000165_II_R_C_rep1_EPIC', Underfull \hbox (badness 10000) in paragraph at lines 4815--4818 \T1/ptm/m/n/10 `cg00000221_II_R_C_rep1_EPIC', `cg00000236_II_R_C_rep1_EPIC', .. . Underfull \hbox (badness 10000) in paragraph at lines 4815--4818 \T1/ptm/m/n/10 `ch.9.98957343R_II_R_O_rep1_EPIC', `ch.9.98959675F_II_F_O_rep1_E PIC', Underfull \hbox (badness 10000) in paragraph at lines 4827--4829 []\T1/ptm/m/n/10 ref: [][]$https : / / bioconductor . org / packages / devel / bioc / vignettes / sesame / inst / doc / sesame . html # Underfull \hbox (badness 10000) in paragraph at lines 4850--4852 []\T1/ptm/m/n/10 {`27k', `450k', `EPIC', `EPIC-PLUS', `MOUSE'} or {`Il-lu-mi-na Hu-man-Methy-la- Underfull \hbox (badness 10000) in paragraph at lines 4850--4852 \T1/ptm/m/n/10 tion27k','IlluminaHumanMethylation450k','IlluminaHumanMethylatio nEPIC', `mouse'} or [82] Underfull \hbox (badness 10000) in paragraph at lines 4909--4909 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 save=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 silent=False\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 10000) in paragraph at lines 4909--4909 \T1/ptm/m/it/10 duce=0.1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot_title=None\T1/ptm /m/n/10 , \T1/ptm/m/it/10 ymax=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-turn_fig =False\T1/ptm/m/n/10 , Underfull \hbox (badness 6825) in paragraph at lines 4909--4909 \T1/ptm/m/it/10 full_range=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 high-light_sam ples=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fig-size=(12\T1/ptm/m/n/10 , \T1/ptm/ m/it/10 9)\T1/ptm/m/n/10 , [83] Underfull \hbox (badness 10000) in paragraph at lines 5023--5023 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fil-ter_stdev=1.5\T1/ptm/m /n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save=Fal se\T1/ptm/m/n/10 , \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5023--5023 \T1/ptm/m/it/10 multi_params={'draw_box': True}\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot_removed=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5023--5023 \T1/ptm/m/it/10 nafill='quick'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=None\T1/p tm/m/n/10 , \T1/ptm/m/it/10 palette=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 la-bel s=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- [84] [85] Underfull \hbox (badness 8132) in paragraph at lines 5241--5241 []\T1/ptm/m/it/10 data_source\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5241--5241 \T1/ptm/m/it/10 on_lambda=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 median_cutoff=- 2\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-clude_probe_failure_percent=True\T1/ptm/m/ n/10 , [86] Underfull \hbox (badness 10000) in paragraph at lines 5310--5312 []\T1/ptm/m/n/10 This Underfull \hbox (badness 10000) in paragraph at lines 5332--5332 \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 col-umn_names=None \T1/ptm/m/n/10 , \T1/ptm/m/it/10 no_poobah=False\T1/ptm/m/n/10 , [87] [88] Underfull \hbox (badness 10000) in paragraph at lines 5456--5456 []\T1/ptm/m/it/10 filepath='.'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 for-mat='beta_va lue'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_stem=''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5456--5456 \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 silent=False\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 col- Underfull \hbox (badness 10000) in paragraph at lines 5456--5456 \T1/ptm/m/it/10 umn_names=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-name_samples= False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- [89] Underfull \hbox (badness 7907) in paragraph at lines 5526--5533 []\T1/ptm/m/n/10 this is for load-ing a bunch of pro-cessed csv files into con- tain-ers, then into be- Underfull \hbox (badness 10000) in paragraph at lines 5526--5533 \T1/ptm/m/n/10 tas \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 import methylcheck as m fil es = \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 /Volumes/202761400007\TS1/pcr/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 5526--5533 \T1/pcr/m/n/10 containers = m.load(files, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 meth\ TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ) df = m.load_processed. Underfull \hbox (badness 10000) in paragraph at lines 5540--5540 []\T1/ptm/m/it/10 filepath\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/pt m/m/n/10 , \T1/ptm/m/it/10 de-bug=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5540--5540 \T1/ptm/m/it/10 as_beta=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 col-umn_pattern=No ne\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5540--5540 \T1/ptm/m/it/10 test_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-name_probe_c olumn=True\T1/ptm/m/n/10 , [90] Underfull \hbox (badness 10000) in paragraph at lines 5608--5608 []\T1/ptm/m/it/10 test\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Overfull \hbox (22.45381pt too wide) in paragraph at lines 5608--5608 \T1/ptm/m/it/10 turn_sample_column_names=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 5612--5619 []\T1/ptm/m/n/10 betas non-normalized ma-trix_processed ma-trix_signal se-ries_ matrix ^^U read_series_matrix(file, de- [91] Underfull \hbox (badness 10000) in paragraph at lines 5741--5742 []\TS1/pcr/m/n/10 `\T1/pcr/m/n/10 python custom_tables=[ { \TS1/pcr/m/n/10 '\T1 /pcr/m/n/10 title\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : "some title, optional", # NO TE: chart Underfull \hbox (badness 10000) in paragraph at lines 5741--5742 \T1/pcr/m/n/10 titles must be unique! \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 col_names \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : [""], \TS1/pcr/m/n/10 '\T1/p cr/m/n/10 row_names\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : Underfull \hbox (badness 10000) in paragraph at lines 5741--5742 \T1/pcr/m/n/10 [""], \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : [""], \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 order_aft er\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : "string name of the plot this should Underfull \hbox (badness 10000) in paragraph at lines 5741--5742 \T1/pcr/m/n/10 come after. It cannot appear first in list.", \TS1/pcr/m/n/10 '\ T1/pcr/m/n/10 font_size\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : Output written on life-epigenetics-methylcheck.pdf (118 pages, 2263378 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.pngheight=40">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.png"height="40">`' not found on input' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.pngheight=40">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.png"height="40">`' not found on input line 240.' Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylcheck.aux' 'life-epigenetics-methylcheck.out' 'life-epigenetics-methylcheck.toc' ------------ Run number 3 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylcheck" "methylcheck.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 (./methylcheck.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.760 ...��███| 1/1 [00:00<00:00, 5.41it/s] Overfull \vbox (13.12581pt too high) detected at line 829 [14] Underfull \hbox (badness 10000) in paragraph at lines 835--836 []\T1/pcr/m/n/10 sdc[0]._SampleDataContainer__data_frame \T1/ptm/m/n/10 will gi ve you a dataframe of the first ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.865 ...███| 16/16 [00:20<00:00, 1.29s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.867 ...��██| 16/16 [00:00<00:00, 524.09it/s] [15] Underfull \vbox (badness 10000) detected at line 965 Overfull \vbox (2.68169pt too high) detected at line 965 [16] [17 <./docs_loading-data_16_1.png>] [18 <./docs_loading-data_18_0.png>] [19] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1166 ...�███| 1/1 [00:00<00:00, 4.75it/s] [20] Underfull \vbox (badness 10000) detected at line 1295 [21 <./docs_filtering-probes_9_1.png>] [22 <./docs_filtering-probes_11_0.png>] Underfull \vbox (badness 10000) detected at line 1420 [23] Underfull \vbox (badness 10000) detected at line 1439 [24 <./docs_filtering-probes_16_1.png>] [25 <./docs_filtering-probes_17_0.png>] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1488 ...�███| 1/1 [00:00<00:00, 5.07it/s] [26] Underfull \hbox (badness 10000) in paragraph at lines 1602--1603 []\T1/ptm/m/n/10 The color-coded re-sults are con-tained in an ex-cel file that will be saved in the Underfull \hbox (badness 10000) in paragraph at lines 1602--1603 \T1/ptm/m/n/10 same di-rec-tory that was spec-i-fied as an in-put. It will look sim-i-lar to this: Overfull \hbox (283.13986pt too wide) in paragraph at lines 1602--1603 [] [27 <./bead_array_report.png>] Underfull \vbox (badness 10000) detected at line 1642 [28] Underfull \vbox (badness 10000) detected at line 1653 [29 <./docs_quality-control-example_9_0.png>] Underfull \vbox (badness 10000) detected at line 1678 [30 <./docs_quality-control-example_9_1.png>] Underfull \vbox (badness 10000) detected at line 1689 [31 <./docs_quality-control-example_9_3.png>] Underfull \vbox (badness 10000) detected at line 1700 [32 <./docs_quality-control-example_9_4.png>] Underfull \vbox (badness 10000) detected at line 1711 [33 <./docs_quality-control-example_9_5.png>] Underfull \vbox (badness 10000) detected at line 1722 [34 <./docs_quality-control-example_9_6.png>] Underfull \vbox (badness 10000) detected at line 1733 [35 <./docs_quality-control-example_9_7.png>] Underfull \vbox (badness 10000) detected at line 1744 [36 <./docs_quality-control-example_9_8.png>] Underfull \vbox (badness 10000) detected at line 1755 [37 <./docs_quality-control-example_9_9.png>] Underfull \vbox (badness 10000) detected at line 1793 [38 <./docs_quality-control-example_9_10.png>] Underfull \vbox (badness 10000) detected at line 1830 [39 <./docs_quality-control-example_9_13.png>] Underfull \vbox (badness 10000) detected at line 1867 [40 <./docs_quality-control-example_9_16.png>] Underfull \vbox (badness 10000) detected at line 1904 [41 <./docs_quality-control-example_9_19.png>] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1933 ...�██| 16/16 [00:00<00:00, 491.79it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1934 ...██| 16/16 [00:00<00:00, 1415.80it/s] [42 <./docs_quality-control-example_9_22.png>] Underfull \hbox (badness 10000) in paragraph at lines 1989--1990 []\T1/ptm/m/n/10 kwargs: \T1/pcr/m/n/10 filename, poobah_max_percent, pval_cuto ff, title, author, subject, [43 <./docs_quality-control-example_12_1.png>] Underfull \hbox (badness 10000) in paragraph at lines 1993--1994 []\T1/ptm/m/n/10 If you want a quick one-line ver-sion with no fur-ther re-port edit-ing, try \T1/pcr/m/n/10 methylcheck. [44] [45] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2173 ...██| 121/121 [00:52<00:00, 2.30it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2175 ...��█| 121/121 [00:00<00:00, 692.51it/s] [46] Underfull \vbox (badness 10000) detected at line 2348 Overfull \vbox (2.68169pt too high) detected at line 2348 [47] Overfull \vbox (1.63934pt too high) detected at line 2436 [48] Overfull \vbox (0.63934pt too high) detected at line 2559 [49] [50] [51] Overfull \vbox (10.43936pt too high) detected at line 2706 [52] Overfull \vbox (2.88167pt too high) detected at line 2810 [53] [54] Underfull \vbox (badness 10000) detected at line 2928 [55] Underfull \vbox (badness 7116) detected at line 3052 [56 <./docs_mds-example_4_1.png>] Underfull \vbox (badness 10000) detected at line 3052 Overfull \vbox (2.68169pt too high) detected at line 3052 [57] [58] [59 <./docs_mds-example_12_1.png>] Underfull \vbox (badness 10000) detected at line 3278 Overfull \vbox (2.68169pt too high) detected at line 3278 [60] Underfull \vbox (badness 10000) detected at line 3317 [61] Underfull \vbox (badness 7116) detected at line 3441 [62 <./docs_mds-example_14_1.png>] Underfull \vbox (badness 10000) detected at line 3441 Overfull \vbox (2.68169pt too high) detected at line 3441 [63] Underfull \vbox (badness 10000) detected at line 3480 [64] Underfull \vbox (badness 7116) detected at line 3604 [65 <./docs_mds-example_16_1.png>] Underfull \vbox (badness 10000) detected at line 3604 Overfull \vbox (2.68169pt too high) detected at line 3604 [66] Underfull \vbox (badness 10000) detected at line 3639 [67] Underfull \vbox (badness 7116) detected at line 3763 [68 <./docs_mds-example_18_1.png>] Underfull \vbox (badness 10000) detected at line 3763 Overfull \vbox (2.68169pt too high) detected at line 3763 [69] Underfull \vbox (badness 10000) detected at line 3800 [70] Underfull \vbox (badness 10000) detected at line 3833 [71 <./docs_mds-example_20_1.png>] Underfull \hbox (badness 10000) in paragraph at lines 3898--3899 []|[][]\T1/pcr/m/sl/10 methylcheck.plot_controls[][]\T1/ptm/m/n/10 ([path, sub- set, Underfull \hbox (badness 10000) in paragraph at lines 3900--3902 []|\T1/ptm/m/n/10 internal ar-ray QC con-trols (avail-able with the Underfull \hbox (badness 10000) in paragraph at lines 3903--3904 []|[][]\T1/pcr/m/sl/10 methylcheck.plot_beta_by_type[][]\T1/ptm/m/n/10 (beta_df [, Underfull \hbox (badness 10000) in paragraph at lines 3913--3914 []|[][]\T1/pcr/m/sl/10 methylcheck.list_problem_probes[][]\T1/ptm/m/n/10 (array [, Overfull \hbox (19.88239pt too wide) in paragraph at lines 3923--3924 []|[][]\T1/pcr/m/sl/10 methylcheck.exclude_sex_control_probes[][]\T1/ptm/m/n/10 (df, Underfull \hbox (badness 10000) in paragraph at lines 3928--3929 []|[][]\T1/pcr/m/sl/10 methylcheck.drop_nan_probes[][]\T1/ptm/m/n/10 (df[, sile nt, Underfull \hbox (badness 10000) in paragraph at lines 3943--3944 []|[][]\T1/pcr/m/sl/10 methylcheck.beta_density_plot[][]\T1/ptm/m/n/10 (df[, ve r- Underfull \hbox (badness 10000) in paragraph at lines 3948--3949 []|[][]\T1/pcr/m/sl/10 methylcheck.mean_beta_plot[][]\T1/ptm/m/n/10 (df[, ver-b ose, Underfull \hbox (badness 6284) in paragraph at lines 3953--3954 []|[][]\T1/pcr/m/sl/10 methylcheck.mean_beta_compare[][]\T1/ptm/m/n/10 (df1, df 2[, Overfull \hbox (56.71234pt too wide) in paragraph at lines 3968--3969 []|[][]\T1/pcr/m/sl/10 methylcheck.cumulative_sum_beta_distribution[][]\T1/ptm/ m/n/10 (df)| [72 <./docs_mds-example_21_0.png>] [73] Underfull \hbox (badness 10000) in paragraph at lines 4116--4122 []\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Chen2013\TS1/pcr/m/n/10 ' '\T1/pcr/m/n/10 Pri ce2013\TS1/pcr/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 4127--4132 []\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Polymorphism\TS1/pcr/m/n/10 ' '\T1/pcr/m/n/10 CrossHybridization\TS1/pcr/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 4139--4142 []\T1/ptm/m/n/10 [`mean_beta_plot', `beta_density_plot', `cu-mu-la-tive_sum_bet a_distribution', [74] [75] [76] Underfull \hbox (badness 10000) in paragraph at lines 4399--4399 []\T1/ptm/m/it/10 filepath='.'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 for-mat='beta_va lue'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_stem=''\T1/ptm/m/n/10 , \T1/ptm/m/it/ 10 ver-bose=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4399--4399 \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 col-umn_names=None \T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-name_samples=False\T1/ptm/m/n/10 , \T1/ptm/ m/it/10 sam- [77] Underfull \hbox (badness 10000) in paragraph at lines 4452--4452 []\T1/ptm/m/it/10 data_containers=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path=Non e\T1/ptm/m/n/10 , \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 un- Underfull \hbox (badness 10000) in paragraph at lines 4452--4452 \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=None\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 palette=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 noob=True\T 1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 4465--4470 []\T1/ptm/m/n/10 if you chose \T1/ptm/m/it/10 pro-cess ^^Uall \T1/ptm/m/n/10 yo u can load the raw in-ten-si-ties like Underfull \hbox (badness 10000) in paragraph at lines 4465--4470 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = [78] Underfull \hbox (badness 10000) in paragraph at lines 4516--4516 []\T1/ptm/m/it/10 data_containers_or_path=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 un-meth=None\T1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 4533--4538 []\T1/ptm/m/n/10 if you chose \T1/ptm/m/it/10 pro-cess ^^Uall \T1/ptm/m/n/10 yo u can load the raw in-ten-si-ties like Underfull \hbox (badness 10000) in paragraph at lines 4533--4538 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = Underfull \hbox (badness 10000) in paragraph at lines 4591--4593 []\T1/ptm/m/n/10 `non-polymorphic' | [79] Underfull \hbox (badness 10000) in paragraph at lines 4614--4614 []\T1/ptm/m/it/10 beta_df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 probe_type='all'\T1/p tm/m/n/10 , \T1/ptm/m/it/10 re-turn_fig=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 s ilent=False\T1/ptm/m/n/10 , [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 4812--4813 []\T1/ptm/m/n/10 Index([`cg00000029_II_F_C_rep1_EPIC', `cg00000103_II_F_C_rep1_ EPIC', Underfull \hbox (badness 10000) in paragraph at lines 4815--4818 []\T1/ptm/m/n/10 `cg00000158_II_F_C_rep1_EPIC', `cg00000165_II_R_C_rep1_EPIC', Underfull \hbox (badness 10000) in paragraph at lines 4815--4818 \T1/ptm/m/n/10 `cg00000221_II_R_C_rep1_EPIC', `cg00000236_II_R_C_rep1_EPIC', .. . Underfull \hbox (badness 10000) in paragraph at lines 4815--4818 \T1/ptm/m/n/10 `ch.9.98957343R_II_R_O_rep1_EPIC', `ch.9.98959675F_II_F_O_rep1_E PIC', Underfull \hbox (badness 10000) in paragraph at lines 4827--4829 []\T1/ptm/m/n/10 ref: [][]$https : / / bioconductor . org / packages / devel / bioc / vignettes / sesame / inst / doc / sesame . html # Underfull \hbox (badness 10000) in paragraph at lines 4850--4852 []\T1/ptm/m/n/10 {`27k', `450k', `EPIC', `EPIC-PLUS', `MOUSE'} or {`Il-lu-mi-na Hu-man-Methy-la- Underfull \hbox (badness 10000) in paragraph at lines 4850--4852 \T1/ptm/m/n/10 tion27k','IlluminaHumanMethylation450k','IlluminaHumanMethylatio nEPIC', `mouse'} or [82] Underfull \hbox (badness 10000) in paragraph at lines 4909--4909 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 save=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 silent=False\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 10000) in paragraph at lines 4909--4909 \T1/ptm/m/it/10 duce=0.1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot_title=None\T1/ptm /m/n/10 , \T1/ptm/m/it/10 ymax=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-turn_fig =False\T1/ptm/m/n/10 , Underfull \hbox (badness 6825) in paragraph at lines 4909--4909 \T1/ptm/m/it/10 full_range=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 high-light_sam ples=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fig-size=(12\T1/ptm/m/n/10 , \T1/ptm/ m/it/10 9)\T1/ptm/m/n/10 , [83] Underfull \hbox (badness 10000) in paragraph at lines 5023--5023 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fil-ter_stdev=1.5\T1/ptm/m /n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save=Fal se\T1/ptm/m/n/10 , \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5023--5023 \T1/ptm/m/it/10 multi_params={'draw_box': True}\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot_removed=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5023--5023 \T1/ptm/m/it/10 nafill='quick'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=None\T1/p tm/m/n/10 , \T1/ptm/m/it/10 palette=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 la-bel s=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- [84] [85] Underfull \hbox (badness 8132) in paragraph at lines 5241--5241 []\T1/ptm/m/it/10 data_source\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5241--5241 \T1/ptm/m/it/10 on_lambda=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 median_cutoff=- 2\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-clude_probe_failure_percent=True\T1/ptm/m/ n/10 , [86] Underfull \hbox (badness 10000) in paragraph at lines 5310--5312 []\T1/ptm/m/n/10 This Underfull \hbox (badness 10000) in paragraph at lines 5332--5332 \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 col-umn_names=None \T1/ptm/m/n/10 , \T1/ptm/m/it/10 no_poobah=False\T1/ptm/m/n/10 , [87] [88] Underfull \hbox (badness 10000) in paragraph at lines 5456--5456 []\T1/ptm/m/it/10 filepath='.'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 for-mat='beta_va lue'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_stem=''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5456--5456 \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 silent=False\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 col- Underfull \hbox (badness 10000) in paragraph at lines 5456--5456 \T1/ptm/m/it/10 umn_names=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-name_samples= False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- [89] Underfull \hbox (badness 7907) in paragraph at lines 5526--5533 []\T1/ptm/m/n/10 this is for load-ing a bunch of pro-cessed csv files into con- tain-ers, then into be- Underfull \hbox (badness 10000) in paragraph at lines 5526--5533 \T1/ptm/m/n/10 tas \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 import methylcheck as m fil es = \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 /Volumes/202761400007\TS1/pcr/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 5526--5533 \T1/pcr/m/n/10 containers = m.load(files, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 meth\ TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ) df = m.load_processed. Underfull \hbox (badness 10000) in paragraph at lines 5540--5540 []\T1/ptm/m/it/10 filepath\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/pt m/m/n/10 , \T1/ptm/m/it/10 de-bug=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5540--5540 \T1/ptm/m/it/10 as_beta=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 col-umn_pattern=No ne\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5540--5540 \T1/ptm/m/it/10 test_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-name_probe_c olumn=True\T1/ptm/m/n/10 , [90] Underfull \hbox (badness 10000) in paragraph at lines 5608--5608 []\T1/ptm/m/it/10 test\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Overfull \hbox (22.45381pt too wide) in paragraph at lines 5608--5608 \T1/ptm/m/it/10 turn_sample_column_names=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 5612--5619 []\T1/ptm/m/n/10 betas non-normalized ma-trix_processed ma-trix_signal se-ries_ matrix ^^U read_series_matrix(file, de- [91] Underfull \hbox (badness 10000) in paragraph at lines 5741--5742 []\TS1/pcr/m/n/10 `\T1/pcr/m/n/10 python custom_tables=[ { \TS1/pcr/m/n/10 '\T1 /pcr/m/n/10 title\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : "some title, optional", # NO TE: chart Underfull \hbox (badness 10000) in paragraph at lines 5741--5742 \T1/pcr/m/n/10 titles must be unique! \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 col_names \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : [""], \TS1/pcr/m/n/10 '\T1/p cr/m/n/10 row_names\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : Underfull \hbox (badness 10000) in paragraph at lines 5741--5742 \T1/pcr/m/n/10 [""], \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : [""], \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 order_aft er\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : "string name of the plot this should Underfull \hbox (badness 10000) in paragraph at lines 5741--5742 \T1/pcr/m/n/10 come after. It cannot appear first in list.", \TS1/pcr/m/n/10 '\ T1/pcr/m/n/10 font_size\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : Output written on life-epigenetics-methylcheck.pdf (118 pages, 2263486 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.pngheight=40">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.png"height="40">`' not found on input' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.pngheight=40">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/doctrees/images/ca988db3c7687f5cd19dd1a26cf750cf4bb45506/python3.6}.png"height="40">`' not found on input line 240.' Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2022-02-08T19:35:28.971240Z, end-time: 2022-02-08T19:35:29.057139Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_build/latex/life-epigenetics-methylcheck.pdf /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/artifacts/feature-v0.8.4/sphinx_pdf/life-epigenetics-methylcheck.pdf [rtd-command-info] start-time: 2022-02-08T19:35:29.265957Z, end-time: 2022-02-08T19:35:47.113181Z, duration: 17, exit-code: 0 python -m sphinx -T -E -b epub -d _build/doctrees -D language=en . _build/epub Running Sphinx v1.8.6 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.data_files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.predict.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.probes.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.reports.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/methylcheck.samples.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/_sphinx_build/modules.rst. [autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.ipynb, docs/poobah_filtering_tutorial.ipynb, docs/quality-control-example.ipynb, docs/release-history.md, docs/research_notebooks/postprocessQC_example.ipynb, docs/research_notebooks/pval.ipynb, docs/research_notebooks/rawQC_example.ipynb, ..., docs/source/_autosummary/methylcheck.predict.rst, docs/source/_autosummary/methylcheck.probes.rst, docs/source/_autosummary/methylcheck.qc_signal_intensity.rst, docs/source/_autosummary/methylcheck.read_geo.rst, docs/source/_autosummary/methylcheck.run_pipeline.rst, docs/source/_autosummary/methylcheck.run_qc.rst, docs/source/_autosummary/methylcheck.sample_plot.rst, docs/source/_autosummary/methylcheck.samples.rst, docs/source/modules.rst, index.rst building [mo]: targets for 0 po files that are out of date building [epub]: targets for 38 source files that are out of date updating environment: 38 added, 0 changed, 0 removed reading sources... 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in 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0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/feature-v0.8.4/lib/python3.8/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/poobah_filtering_tutorial.ipynb:3381: WARNING: File not found: 'docs/quality-control-example.html#Predicting-Sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/poobah_filtering_tutorial.ipynb:3392: WARNING: File not found: 'docs/filtering-probes.html#Filtering-sex-linked-probes-and-control-probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/postprocessQC_example.ipynb:1: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/rawQC_example.ipynb:1: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.beta_mds_plot:65: WARNING: Unknown directive type "todo". .. todo:: - Reads the manifest file for the array, or at least a list of probe names to exclude/include. - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']] - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values df_no_sex_probes = df[probe_names_no_sex_probes] df_no_sex_probes.head() /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:3: WARNING: Unexpected section title or transition. -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:5: WARNING: Unexpected section title. how it works: -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:18: WARNING: Unexpected section title or transition. ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:20: WARNING: Unexpected section title. inputs: ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:28: WARNING: Unexpected section title. optional keyword arguments: --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:40: WARNING: Unexpected section title. analysis parameters: -------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:47: WARNING: Unexpected section title. returns: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.combine_mds:51: WARNING: Unknown directive type "todo". .. todo:: - TODO: one dataframe of the retained samples, cutoff box is avg of datasets - TODO: each dataset's results as a transformed file - default: list of samples retained or excluded - option: a list of pyplot subplot objects /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:11: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.exclude_sex_control_probes:26: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/predict/sex.py:docstring of methylcheck.get_sex:4: WARNING: Unexpected section title. inputs: ======= /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.list_problem_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.list_problem_probes:50: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/filters.py:docstring of methylcheck.list_problem_probes:47: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load:92: WARNING: Unknown directive type "todo". .. todo:: - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs - DONE: meth_df deal with batches of files /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load:44: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.mean_beta_compare:3: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:4: WARNING: Unexpected section title. input (choose one of these): ============================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:34: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_controls:5: WARNING: Unexpected section title. input: ====== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_controls:11: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:4: WARNING: Unexpected section title. input (one of these): ===================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:23: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:27: WARNING: Unexpected section title. optional params: ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_signal_intensity:40: WARNING: Unexpected section title. returns: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:27: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo:19: WARNING: Unknown target name: "matrix". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.run_pipeline:25: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/postprocessQC.py:docstring of methylcheck.sample_plot:1: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:92: WARNING: Unknown directive type "todo". .. todo:: - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs - DONE: meth_df deal with batches of files /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title. example: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.ReportPDF:44: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.ReportPDF:45: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.ReportPDF.exec_summary:17: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/reports/qc_report.py:docstring of methylcheck.reports.qc_report.run_pipeline:25: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:11: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:65: WARNING: Unknown directive type "todo". .. todo:: - Reads the manifest file for the array, or at least a list of probe names to exclude/include. - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']] - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values df_no_sex_probes = df[probe_names_no_sex_probes] df_no_sex_probes.head() /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition. -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title. how it works: -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition. ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title. inputs: ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title. optional keyword arguments: --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title. analysis parameters: -------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title. returns: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo". .. todo:: - TODO: one dataframe of the retained samples, cutoff box is avg of datasets - TODO: each dataset's results as a transformed file - default: list of samples retained or excluded - option: a list of pyplot subplot objects /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title. input (one of these): ===================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title. optional params: ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title. returns: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title. input (choose one of these): ============================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:5: WARNING: Unexpected section title. input: ====== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title. inputs: ======= /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/feature-v0.8.4/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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