Read the Docs build information Build id: 814858 Project: life-epigenetics-methylcheck Version: latest Commit: 881d14d78e6086aab184716e0b79cdf87e9be8bf Date: 2022-01-05T21:12:13.468349Z State: finished Success: True [rtd-command-info] start-time: 2022-01-05T21:18:45.931570Z, end-time: 2022-01-05T21:19:43.878470Z, duration: 57, 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: 2022-01-05T21:19:44.056689Z, end-time: 2022-01-05T21:19:45.442637Z, duration: 1, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 881d14d Feature/v0.8.1 (#63) [rtd-command-info] start-time: 2022-01-05T21:19:45.567455Z, end-time: 2022-01-05T21:19:45.651914Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-01-05T21:19:57.888403Z, end-time: 2022-01-05T21:20:03.554089Z, 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/latest/bin/python3.8 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2022-01-05T21:20:03.677176Z, end-time: 2022-01-05T21:20:05.472938Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (21.3.1) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 60.2.0 Uninstalling setuptools-60.2.0: Successfully uninstalled setuptools-60.2.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-01-05T21:20:05.590053Z, end-time: 2022-01-05T21:20:34.375612Z, duration: 28, 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) Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) 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 sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting Pygments>=2.0 Downloading Pygments-2.11.1-py3-none-any.whl (1.1 MB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.3-py3-none-any.whl (133 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 certifi>=2017.4.17 Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.10-py3-none-any.whl (39 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB) Collecting pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.6-py3-none-any.whl (97 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=728ce58bc3a655d769494e9d64e617d973c02ab9b67dfb9d5ce2b1fa3bdb542e Stored in directory: /tmp/pip-ephem-wheel-cache-7wq8f1ij/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=1260196 sha256=3a2f83d80b709f6cad26589c4fd99941b97ed6de60e020f9ac77e857d5c44873 Stored in directory: /tmp/pip-ephem-wheel-cache-7wq8f1ij/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=24c715722eeebeb3cec5260723df9b6c03071e779bc20016e0c30c977a06fa0b Stored in directory: /tmp/pip-ephem-wheel-cache-7wq8f1ij/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-2.11.1 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.10 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-3.0.6 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 urllib3-1.26.7 [rtd-command-info] start-time: 2022-01-05T21:20:34.531943Z, end-time: 2022-01-05T21:20:52.996818Z, duration: 18, 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-1.3.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.5 MB) Collecting scipy Downloading scipy-1.7.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.3 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/latest/lib/python3.8/site-packages (from -r requirements.txt (line 11)) (1.8.6) Collecting ipykernel Downloading ipykernel-6.6.1-py3-none-any.whl (126 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>=2017.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from pandas>=1.3.0->-r requirements.txt (line 2)) (2021.3) Requirement already satisfied: python-dateutil>=2.7.3 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: 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: 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-9.0.0-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/latest/lib/python3.8/site-packages (from matplotlib->-r requirements.txt (line 4)) (3.0.6) Requirement already satisfied: certifi>=2020.06.20 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from matplotlib->-r requirements.txt (line 4)) (2021.10.8) Collecting pbr Downloading pbr-5.8.0-py2.py3-none-any.whl (112 kB) Collecting mistune Downloading mistune-2.0.1-py2.py3-none-any.whl (24 kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from m2r->-r requirements.txt (line 9)) (0.17.1) Collecting traitlets Downloading traitlets-5.1.1-py3-none-any.whl (102 kB) Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from nbsphinx->-r requirements.txt (line 10)) (3.0.3) Collecting nbformat Downloading nbformat-5.1.3-py3-none-any.whl (178 kB) Collecting nbconvert!=5.4 Downloading nbconvert-6.4.0-py3-none-any.whl (557 kB) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 11)) (1.16.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 11)) (21.3) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 11)) (2.2.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 11)) (58.2.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 11)) (2.11.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 11)) (0.7.12) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 11)) (1.3.0) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 11)) (2.27.1) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 11)) (2.9.1) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 11)) (1.2.4) Collecting debugpy<2.0,>=1.0.0 Downloading debugpy-1.5.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.9 MB) Collecting tornado<7.0,>=4.2 Downloading tornado-6.1-cp38-cp38-manylinux2010_x86_64.whl (427 kB) Collecting nest-asyncio Downloading nest_asyncio-1.5.4-py3-none-any.whl (5.1 kB) Collecting 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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from jinja2->nbsphinx->-r requirements.txt (line 10)) (2.0.1) Collecting jupyter-core>=4.6.0 Downloading jupyter_core-4.9.1-py3-none-any.whl (86 kB) Collecting pyzmq>=13 Downloading pyzmq-22.3.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.1 MB) Collecting entrypoints Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting defusedxml Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Collecting mistune Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Collecting bleach Downloading bleach-4.1.0-py2.py3-none-any.whl (157 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.5.0-py2.py3-none-any.whl (8.7 kB) Collecting testpath Downloading testpath-0.5.0-py3-none-any.whl (84 kB) Collecting jupyterlab-pygments Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB) Collecting nbclient<0.6.0,>=0.5.0 Downloading nbclient-0.5.9-py3-none-any.whl (69 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-4.3.3-py3-none-any.whl (71 kB) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (2.0.10) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (1.26.7) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (3.3) Requirement already satisfied: 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m2r (setup.py): started Building wheel for m2r (setup.py): finished with status 'done' Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10477 sha256=c21c2f7fdbc6b9f6548f801e7bbdbce798b57fa43d73ddb025b99adba710d55f Stored in directory: /tmp/pip-ephem-wheel-cache-u89w9a9f/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, ptyprocess, parso, nbformat, jupyter-client, testpath, prompt-toolkit, pillow, pickleshare, pexpect, pandocfilters, nbclient, mistune, matplotlib-inline, jupyterlab-pygments, jedi, defusedxml, decorator, bleach, 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/latest Can't uninstall 'pandas'. No files were found to uninstall. Successfully installed attrs-21.4.0 backcall-0.2.0 bleach-4.1.0 debugpy-1.5.1 decorator-5.1.0 defusedxml-0.7.1 entrypoints-0.3 et-xmlfile-1.1.0 importlib-resources-5.4.0 ipykernel-6.6.1 ipython-7.31.0 ipython-genutils-0.2.0 jedi-0.18.1 joblib-1.1.0 jsonschema-4.3.3 jupyter-client-7.1.0 jupyter-core-4.9.1 jupyterlab-pygments-0.1.2 m2r-0.2.1 matplotlib-inline-0.1.3 mistune-0.8.4 nbclient-0.5.9 nbconvert-6.4.0 nbformat-5.1.3 nbsphinx-0.8.8 nest-asyncio-1.5.4 openpyxl-3.0.9 pandas-1.3.5 pandocfilters-1.5.0 parso-0.8.3 pbr-5.8.0 pexpect-4.8.0 pickleshare-0.7.5 pillow-9.0.0 prompt-toolkit-3.0.24 ptyprocess-0.7.0 pyrsistent-0.18.0 pyzmq-22.3.0 scipy-1.7.3 seaborn-0.11.2 sphinxcontrib-apidoc-0.3.0 testpath-0.5.0 tornado-6.1 tqdm-4.62.3 traitlets-5.1.1 wcwidth-0.2.5 webencodings-0.5.1 xlsxwriter-3.0.2 zipp-3.7.0 [rtd-command-info] start-time: 2022-01-05T21:20:53.139519Z, end-time: 2022-01-05T21:20:54.117775Z, duration: 0, 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/latest/lib/python3.8/site-packages (from -r docs/requirements.txt (line 1)) (0.17.1) [rtd-command-info] start-time: 2022-01-05T21:20:55.173100Z, end-time: 2022-01-05T21:20:55.241485Z, 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 = '0.8.1' # -- General configuration --------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', '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': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("feature-v0.8.1", "/en/feature-v0.8.1/"), ], 'downloads': [ ("pdf", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/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': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '881d14d7', } # 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/814858/' 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: 2022-01-05T21:20:55.360138Z, end-time: 2022-01-05T21:21:14.520903Z, duration: 19, 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/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.data_files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.probes.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.reports.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst. [autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.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 [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.assign.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.beta_density_plot.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.beta_mds_plot.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.cli.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.combine_mds.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.drop_nan_probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.exclude_probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.exclude_sex_control_probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.get_sex.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.plot_beta_by_type.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.plot_controls.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.predict.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.qc_signal_intensity.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.read_geo.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.run_pipeline.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.run_qc.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.sample_plot.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.samples.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 11 source files that are out of date updating environment: 37 added, 0 changed, 0 removed reading sources... [ 2%] README reading sources... [ 5%] docs/filtering-probes reading sources... [ 8%] docs/loading-data reading sources... [ 10%] docs/mds-example reading sources... [ 13%] docs/quality-control-example reading sources... [ 16%] docs/release-history reading sources... [ 18%] docs/research_notebooks/postprocessQC_example reading sources... [ 21%] docs/research_notebooks/pval reading sources... [ 24%] docs/research_notebooks/rawQC_example reading sources... [ 27%] docs/source/_autosummary/methylcheck.assign reading sources... [ 29%] docs/source/_autosummary/methylcheck.beta_density_plot reading sources... [ 32%] docs/source/_autosummary/methylcheck.beta_mds_plot reading sources... [ 35%] docs/source/_autosummary/methylcheck.cli reading sources... [ 37%] docs/source/_autosummary/methylcheck.combine_mds reading sources... [ 40%] docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution reading sources... 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/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/latest/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/latest/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)): 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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/methylcheck/probes/filters.py:docstring of methylcheck.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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/latest/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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[rtd-command-info] start-time: 2022-01-05T21:21:14.671132Z, end-time: 2022-01-05T21:21:17.584358Z, duration: 2, exit-code: 0 python -m sphinx -T -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v1.8.6 loading translations [en]... done making output directory... loading pickled environment... done Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.data_files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.probes.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.reports.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst. [autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.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.assign.rst, ..., 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 [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found preparing documents... done assembling single document... docs/loading-data docs/filtering-probes docs/quality-control-example 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 writing... done writing additional files... copying images... 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Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.probes.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.reports.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst. [autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.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.assign.rst, ..., 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/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/latest/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: WARNING: Could not fetch remote image: https://api.codacy.com/project/badge/Grade/aedf5c223e39415180ff35153b2bad89 [404] 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://coveralls.io/repos/github/FoxoTech/methylcheck/badge.svg?t=OVL45Q) README.md:38: 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://img.shields.io/pypi/dm/methylcheck.svg?label=pypi%20downloads&logo=PyPI&logoColor=white: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/latest/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2022-01-05T21:21:29.000465Z, end-time: 2022-01-05T21:21:29.069542Z, 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: 2022-01-05T21:21:29.181673Z, end-time: 2022-01-05T21:21:51.922312Z, duration: 22, 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/filtering-probes::doc' on page 9 undefined on input line 354. LaTeX Warning: Hyper reference `docs/quality-control-example::doc' on page 9 un defined on input line 357. LaTeX Warning: Hyper reference `docs/mds-example::doc' on page 9 undefined on i nput line 360. LaTeX Warning: Hyper reference `docs/quality-control-example:Predicting-Sex' on page 9 undefined on input line 363. [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.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 1/1 [00:00<00:00, 5.92it/s] ! 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See the inputenc package documentation for explanation. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 1/1 [00:00<00:00, 5.92it/s] [10] ! 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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/s] [11] ! 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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 16/16 [00:00<00:00, 1480.91it/s] [12] ! 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.758 ...��███| 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.758 ...��███| 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. 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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.758 ...��███| 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.758 ...��███| 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.758 ...��███| 1/1 [00:00<00:00, 5.41it/s] Overfull \vbox (13.12581pt too high) detected at line 827 [14] ! 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 16/16 [00:00<00:00, 524.09it/s] [15] [16] Underfull \vbox (badness 10000) detected at line 1018 [17 <./docs_loading-data_15_1.png>] [18 <./docs_loading-data_17_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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 1/1 [00:00<00:00, 4.75it/s] [20] Underfull \vbox (badness 10000) detected at line 1285 [21 <./docs_filtering-probes_9_1.png>] [22 <./docs_filtering-probes_11_0.png>] Underfull \vbox (badness 10000) detected at line 1410 [23] Underfull \vbox (badness 10000) detected at line 1429 [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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 1/1 [00:00<00:00, 5.07it/s] [26] Underfull \hbox (badness 10000) in paragraph at lines 1592--1593 []\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 1592--1593 \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 1592--1593 [] [27 <./bead_array_report.png>] Underfull \vbox (badness 10000) detected at line 1630 [28] Underfull \vbox (badness 10000) detected at line 1641 [29 <./docs_quality-control-example_9_0.png>] Underfull \vbox (badness 10000) detected at line 1666 [30 <./docs_quality-control-example_9_1.png>] Underfull \vbox (badness 10000) detected at line 1677 [31 <./docs_quality-control-example_9_3.png>] Underfull \vbox (badness 10000) detected at line 1688 [32 <./docs_quality-control-example_9_4.png>] Underfull \vbox (badness 10000) detected at line 1699 [33 <./docs_quality-control-example_9_5.png>] Underfull \vbox (badness 10000) detected at line 1710 [34 <./docs_quality-control-example_9_6.png>] Underfull \vbox (badness 10000) detected at line 1721 [35 <./docs_quality-control-example_9_7.png>] Underfull \vbox (badness 10000) detected at line 1732 [36 <./docs_quality-control-example_9_8.png>] Underfull \vbox (badness 10000) detected at line 1743 [37 <./docs_quality-control-example_9_9.png>] Underfull \vbox (badness 10000) detected at line 1781 [38 <./docs_quality-control-example_9_10.png>] Underfull \vbox (badness 10000) detected at line 1818 [39 <./docs_quality-control-example_9_13.png>] Underfull \vbox (badness 10000) detected at line 1855 [40 <./docs_quality-control-example_9_16.png>] Underfull \vbox (badness 10000) detected at line 1892 [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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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 1977--1978 []\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 1981--1982 []\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] Underfull \vbox (badness 10000) detected at line 2218 [46] Underfull \vbox (badness 7116) detected at line 2342 [47 <./docs_mds-example_4_1.png>] Underfull \vbox (badness 10000) detected at line 2342 Overfull \vbox (2.68169pt too high) detected at line 2342 [48] [49] [50 <./docs_mds-example_12_1.png>] Underfull \vbox (badness 10000) detected at line 2568 Overfull \vbox (2.68169pt too high) detected at line 2568 [51] Underfull \vbox (badness 10000) detected at line 2607 [52] Underfull \vbox (badness 7116) detected at line 2731 [53 <./docs_mds-example_14_1.png>] Underfull \vbox (badness 10000) detected at line 2731 Overfull \vbox (2.68169pt too high) detected at line 2731 [54] Underfull \vbox (badness 10000) detected at line 2770 [55] Underfull \vbox (badness 7116) detected at line 2894 [56 <./docs_mds-example_16_1.png>] Underfull \vbox (badness 10000) detected at line 2894 Overfull \vbox (2.68169pt too high) detected at line 2894 [57] Underfull \vbox (badness 10000) detected at line 2929 [58] Underfull \vbox (badness 7116) detected at line 3053 [59 <./docs_mds-example_18_1.png>] Underfull \vbox (badness 10000) detected at line 3053 Overfull \vbox (2.68169pt too high) detected at line 3053 [60] Underfull \vbox (badness 10000) detected at line 3090 [61] Underfull \vbox (badness 10000) detected at line 3123 [62 <./docs_mds-example_20_1.png>] LaTeX Warning: Hyper reference `docs/source/_autosummary/methylcheck.cli:module -methylcheck.cli' on page 63 undefined on input line 3148. 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[64] Underfull \hbox (badness 10000) in paragraph at lines 3406--3412 []\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 3417--3422 []\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 3429--3432 []\T1/ptm/m/n/10 [`mean_beta_plot', `beta_density_plot', `cu-mu-la-tive_sum_bet a_distribution', [65] [66] [67] Underfull \hbox (badness 10000) in paragraph at lines 3689--3689 []\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 3689--3689 \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- [68] Underfull \hbox (badness 10000) in paragraph at lines 3742--3742 []\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 3742--3742 \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 3755--3760 []\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 3755--3760 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = [69] Underfull \hbox (badness 10000) in paragraph at lines 3806--3806 []\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 3823--3828 []\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 3823--3828 \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 3881--3883 []\T1/ptm/m/n/10 `non-polymorphic' | [70] Underfull \hbox (badness 10000) in paragraph at lines 3904--3904 []\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 , [71] [72] Underfull \hbox (badness 10000) in paragraph at lines 4102--4103 []\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 4105--4108 []\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 4105--4108 \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 (107 pages, 2222486 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/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.' 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 103 undefined on input line 6659 Reference `docs/source/modules:module-methylcheck.load_processed' on page 103 undefined on input line 6660 Reference `docs/source/modules:module-methylcheck.predict' on page 103 undefined on input line 6661 Reference `docs/source/modules:module-methylcheck.probes' on page 103 undefined on input line 6662 Reference `docs/source/modules:module-methylcheck.qc_plot' on page 103 undefined on input line 6663 Reference `docs/source/modules:module-methylcheck.read_geo_processed' on page 103 undefined on input line 6664 Reference `docs/source/modules:module-methylcheck.reports.qc_report.run_pipeline' on page 103 undefined on input line 6665 Reference `docs/source/modules:module-methylcheck.samples' on page 103 undefined on input line 6666 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 (132 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'... 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.855 ...███| 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.855 ...███| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 16/16 [00:00<00:00, 524.09it/s] [15] [16] Underfull \vbox (badness 10000) detected at line 1018 [17 <./docs_loading-data_15_1.png>] [18 <./docs_loading-data_17_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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 1/1 [00:00<00:00, 4.75it/s] [20] Underfull \vbox (badness 10000) detected at line 1285 [21 <./docs_filtering-probes_9_1.png>] [22 <./docs_filtering-probes_11_0.png>] Underfull \vbox (badness 10000) detected at line 1410 [23] Underfull \vbox (badness 10000) detected at line 1429 [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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 1/1 [00:00<00:00, 5.07it/s] [26] Underfull \hbox (badness 10000) in paragraph at lines 1592--1593 []\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 1592--1593 \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 1592--1593 [] [27 <./bead_array_report.png>] Underfull \vbox (badness 10000) detected at line 1630 [28] Underfull \vbox (badness 10000) detected at line 1641 [29 <./docs_quality-control-example_9_0.png>] Underfull \vbox (badness 10000) detected at line 1666 [30 <./docs_quality-control-example_9_1.png>] Underfull \vbox (badness 10000) detected at line 1677 [31 <./docs_quality-control-example_9_3.png>] Underfull \vbox (badness 10000) detected at line 1688 [32 <./docs_quality-control-example_9_4.png>] Underfull \vbox (badness 10000) detected at line 1699 [33 <./docs_quality-control-example_9_5.png>] Underfull \vbox (badness 10000) detected at line 1710 [34 <./docs_quality-control-example_9_6.png>] Underfull \vbox (badness 10000) detected at line 1721 [35 <./docs_quality-control-example_9_7.png>] Underfull \vbox (badness 10000) detected at line 1732 [36 <./docs_quality-control-example_9_8.png>] Underfull \vbox (badness 10000) detected at line 1743 [37 <./docs_quality-control-example_9_9.png>] Underfull \vbox (badness 10000) detected at line 1781 [38 <./docs_quality-control-example_9_10.png>] Underfull \vbox (badness 10000) detected at line 1818 [39 <./docs_quality-control-example_9_13.png>] Underfull \vbox (badness 10000) detected at line 1855 [40 <./docs_quality-control-example_9_16.png>] Underfull \vbox (badness 10000) detected at line 1892 [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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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 1977--1978 []\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 1981--1982 []\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] Underfull \vbox (badness 10000) detected at line 2218 [46] Underfull \vbox (badness 7116) detected at line 2342 [47 <./docs_mds-example_4_1.png>] Underfull \vbox (badness 10000) detected at line 2342 Overfull \vbox (2.68169pt too high) detected at line 2342 [48] [49] [50 <./docs_mds-example_12_1.png>] Underfull \vbox (badness 10000) detected at line 2568 Overfull \vbox (2.68169pt too high) detected at line 2568 [51] Underfull \vbox (badness 10000) detected at line 2607 [52] Underfull \vbox (badness 7116) detected at line 2731 [53 <./docs_mds-example_14_1.png>] Underfull \vbox (badness 10000) detected at line 2731 Overfull \vbox (2.68169pt too high) detected at line 2731 [54] Underfull \vbox (badness 10000) detected at line 2770 [55] Underfull \vbox (badness 7116) detected at line 2894 [56 <./docs_mds-example_16_1.png>] Underfull \vbox (badness 10000) detected at line 2894 Overfull \vbox (2.68169pt too high) detected at line 2894 [57] Underfull \vbox (badness 10000) detected at line 2929 [58] Underfull \vbox (badness 7116) detected at line 3053 [59 <./docs_mds-example_18_1.png>] Underfull \vbox (badness 10000) detected at line 3053 Overfull \vbox (2.68169pt too high) detected at line 3053 [60] Underfull \vbox (badness 10000) detected at line 3090 [61] Underfull \vbox (badness 10000) detected at line 3123 [62 <./docs_mds-example_20_1.png>] Underfull \hbox (badness 10000) in paragraph at lines 3188--3189 []|[][]\T1/pcr/m/sl/10 methylcheck.plot_controls[][]\T1/ptm/m/n/10 ([path, sub- set, Underfull \hbox (badness 10000) in paragraph at lines 3190--3192 []|\T1/ptm/m/n/10 internal ar-ray QC con-trols (avail-able with the Underfull \hbox (badness 10000) in paragraph at lines 3193--3194 []|[][]\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 3203--3204 []|[][]\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 3213--3214 []|[][]\T1/pcr/m/sl/10 methylcheck.exclude_sex_control_probes[][]\T1/ptm/m/n/10 (df, Underfull \hbox (badness 10000) in paragraph at lines 3218--3219 []|[][]\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 3233--3234 []|[][]\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 3238--3239 []|[][]\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 3243--3244 []|[][]\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 3258--3259 []|[][]\T1/pcr/m/sl/10 methylcheck.cumulative_sum_beta_distribution[][]\T1/ptm/ m/n/10 (df)| [63 <./docs_mds-example_21_0.png>] [64] Underfull \hbox (badness 10000) in paragraph at lines 3406--3412 []\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 3417--3422 []\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 3429--3432 []\T1/ptm/m/n/10 [`mean_beta_plot', `beta_density_plot', `cu-mu-la-tive_sum_bet a_distribution', [65] [66] [67] Underfull \hbox (badness 10000) in paragraph at lines 3689--3689 []\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 3689--3689 \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- [68] Underfull \hbox (badness 10000) in paragraph at lines 3742--3742 []\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 3742--3742 \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 3755--3760 []\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 3755--3760 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = [69] Underfull \hbox (badness 10000) in paragraph at lines 3806--3806 []\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 3823--3828 []\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 3823--3828 \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 3881--3883 []\T1/ptm/m/n/10 `non-polymorphic' | [70] Underfull \hbox (badness 10000) in paragraph at lines 3904--3904 []\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 , [71] [72] Underfull \hbox (badness 10000) in paragraph at lines 4102--4103 []\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 4105--4108 []\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 4105--4108 \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 (110 pages, 2240411 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/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.' 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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Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 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. Type H for immediate help. ... l.434 ...��███| 1/1 [00:00<00:00, 5.92it/s] [10] ! 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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/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.522 ...��███| 1/1 [00:00<00:00, 5.98it/s] [11] ! 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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.590 ...��██| 16/16 [00:00<00:00, 488.67it/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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 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.591 ...�██| 16/16 [00:00<00:00, 1480.91it/s] [12] ! 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.674 ...��██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.675 ...�██| 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.758 ...��███| 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.758 ...��███| 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.758 ...��███| 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.758 ...��███| 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.758 ...��███| 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.758 ...��███| 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.758 ...��███| 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.758 ...��███| 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.758 ...��███| 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.758 ...��███| 1/1 [00:00<00:00, 5.41it/s] Overfull \vbox (13.12581pt too high) detected at line 827 [14] ! 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.855 ...███| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 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.857 ...��██| 16/16 [00:00<00:00, 524.09it/s] [15] [16] Underfull \vbox (badness 10000) detected at line 1018 [17 <./docs_loading-data_15_1.png>] [18 <./docs_loading-data_17_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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 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.1156 ...�███| 1/1 [00:00<00:00, 4.75it/s] [20] Underfull \vbox (badness 10000) detected at line 1285 [21 <./docs_filtering-probes_9_1.png>] [22 <./docs_filtering-probes_11_0.png>] Underfull \vbox (badness 10000) detected at line 1410 [23] Underfull \vbox (badness 10000) detected at line 1429 [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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 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.1478 ...�███| 1/1 [00:00<00:00, 5.07it/s] [26] Underfull \hbox (badness 10000) in paragraph at lines 1592--1593 []\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 1592--1593 \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 1592--1593 [] [27 <./bead_array_report.png>] Underfull \vbox (badness 10000) detected at line 1630 [28] Underfull \vbox (badness 10000) detected at line 1641 [29 <./docs_quality-control-example_9_0.png>] Underfull \vbox (badness 10000) detected at line 1666 [30 <./docs_quality-control-example_9_1.png>] Underfull \vbox (badness 10000) detected at line 1677 [31 <./docs_quality-control-example_9_3.png>] Underfull \vbox (badness 10000) detected at line 1688 [32 <./docs_quality-control-example_9_4.png>] Underfull \vbox (badness 10000) detected at line 1699 [33 <./docs_quality-control-example_9_5.png>] Underfull \vbox (badness 10000) detected at line 1710 [34 <./docs_quality-control-example_9_6.png>] Underfull \vbox (badness 10000) detected at line 1721 [35 <./docs_quality-control-example_9_7.png>] Underfull \vbox (badness 10000) detected at line 1732 [36 <./docs_quality-control-example_9_8.png>] Underfull \vbox (badness 10000) detected at line 1743 [37 <./docs_quality-control-example_9_9.png>] Underfull \vbox (badness 10000) detected at line 1781 [38 <./docs_quality-control-example_9_10.png>] Underfull \vbox (badness 10000) detected at line 1818 [39 <./docs_quality-control-example_9_13.png>] Underfull \vbox (badness 10000) detected at line 1855 [40 <./docs_quality-control-example_9_16.png>] Underfull \vbox (badness 10000) detected at line 1892 [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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1921 ...�██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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.1922 ...██| 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 1977--1978 []\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 1981--1982 []\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] Underfull \vbox (badness 10000) detected at line 2218 [46] Underfull \vbox (badness 7116) detected at line 2342 [47 <./docs_mds-example_4_1.png>] Underfull \vbox (badness 10000) detected at line 2342 Overfull \vbox (2.68169pt too high) detected at line 2342 [48] [49] [50 <./docs_mds-example_12_1.png>] Underfull \vbox (badness 10000) detected at line 2568 Overfull \vbox (2.68169pt too high) detected at line 2568 [51] Underfull \vbox (badness 10000) detected at line 2607 [52] Underfull \vbox (badness 7116) detected at line 2731 [53 <./docs_mds-example_14_1.png>] Underfull \vbox (badness 10000) detected at line 2731 Overfull \vbox (2.68169pt too high) detected at line 2731 [54] Underfull \vbox (badness 10000) detected at line 2770 [55] Underfull \vbox (badness 7116) detected at line 2894 [56 <./docs_mds-example_16_1.png>] Underfull \vbox (badness 10000) detected at line 2894 Overfull \vbox (2.68169pt too high) detected at line 2894 [57] Underfull \vbox (badness 10000) detected at line 2929 [58] Underfull \vbox (badness 7116) detected at line 3053 [59 <./docs_mds-example_18_1.png>] Underfull \vbox (badness 10000) detected at line 3053 Overfull \vbox (2.68169pt too high) detected at line 3053 [60] Underfull \vbox (badness 10000) detected at line 3090 [61] Underfull \vbox (badness 10000) detected at line 3123 [62 <./docs_mds-example_20_1.png>] Underfull \hbox (badness 10000) in paragraph at lines 3188--3189 []|[][]\T1/pcr/m/sl/10 methylcheck.plot_controls[][]\T1/ptm/m/n/10 ([path, sub- set, Underfull \hbox (badness 10000) in paragraph at lines 3190--3192 []|\T1/ptm/m/n/10 internal ar-ray QC con-trols (avail-able with the Underfull \hbox (badness 10000) in paragraph at lines 3193--3194 []|[][]\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 3203--3204 []|[][]\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 3213--3214 []|[][]\T1/pcr/m/sl/10 methylcheck.exclude_sex_control_probes[][]\T1/ptm/m/n/10 (df, Underfull \hbox (badness 10000) in paragraph at lines 3218--3219 []|[][]\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 3233--3234 []|[][]\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 3238--3239 []|[][]\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 3243--3244 []|[][]\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 3258--3259 []|[][]\T1/pcr/m/sl/10 methylcheck.cumulative_sum_beta_distribution[][]\T1/ptm/ m/n/10 (df)| [63 <./docs_mds-example_21_0.png>] [64] Underfull \hbox (badness 10000) in paragraph at lines 3406--3412 []\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 3417--3422 []\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 3429--3432 []\T1/ptm/m/n/10 [`mean_beta_plot', `beta_density_plot', `cu-mu-la-tive_sum_bet a_distribution', [65] [66] [67] Underfull \hbox (badness 10000) in paragraph at lines 3689--3689 []\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 3689--3689 \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- [68] Underfull \hbox (badness 10000) in paragraph at lines 3742--3742 []\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 3742--3742 \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 3755--3760 []\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 3755--3760 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = [69] Underfull \hbox (badness 10000) in paragraph at lines 3806--3806 []\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 3823--3828 []\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 3823--3828 \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 3881--3883 []\T1/ptm/m/n/10 `non-polymorphic' | [70] Underfull \hbox (badness 10000) in paragraph at lines 3904--3904 []\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 , [71] [72] Underfull \hbox (badness 10000) in paragraph at lines 4102--4103 []\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 4105--4108 []\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 4105--4108 \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 4105--4108 \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 4117--4119 []\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 4140--4142 []\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 4140--4142 \T1/ptm/m/n/10 tion27k','IlluminaHumanMethylation450k','IlluminaHumanMethylatio nEPIC', `mouse'} or [73] Underfull \hbox (badness 10000) in paragraph at lines 4199--4199 []\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 4199--4199 \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 4199--4199 \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 , [74] Underfull \hbox (badness 10000) in paragraph at lines 4313--4313 []\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 4313--4313 \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 4313--4313 \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- [75] [76] Underfull \hbox (badness 8132) in paragraph at lines 4531--4531 []\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 4531--4531 \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 , [77] Underfull \hbox (badness 10000) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 This Underfull \hbox (badness 10000) in paragraph at lines 4622--4622 \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 , [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 4746--4746 []\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 4746--4746 \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 4746--4746 \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- [80] Underfull \hbox (badness 7907) in paragraph at lines 4816--4823 []\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 4816--4823 \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 4816--4823 \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. 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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 (110 pages, 2240525 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/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.' 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: 2022-01-05T21:21:52.097100Z, end-time: 2022-01-05T21:21:52.189324Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/latex/life-epigenetics-methylcheck.pdf /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/artifacts/latest/sphinx_pdf/life-epigenetics-methylcheck.pdf [rtd-command-info] start-time: 2022-01-05T21:21:52.307078Z, end-time: 2022-01-05T21:22:04.441814Z, duration: 12, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees -D language=en . _build/epub Running Sphinx v1.8.6 loading translations [en]... done making output directory... loading pickled environment... done Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.data_files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.probes.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.reports.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst. [autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.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.assign.rst, ..., 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 37 source files that are out of date updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found preparing documents... done writing output... 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