Read the Docs build information Build id: 609322 Project: life-epigenetics-methylcheck Version: latest Commit: be5dfa52903d3577c500ce03cef852ea15b32c1a Date: 2021-04-08T20:44:37.693466Z State: finished Success: True [rtd-command-info] start-time: 2021-04-08T20:44:39.173612Z, end-time: 2021-04-08T20:44:51.908350Z, duration: 12, 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: 2021-04-08T20:44:52.065046Z, end-time: 2021-04-08T20:44:53.604603Z, 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 be5dfa5 Feature/v0.7.1 (#44) [rtd-command-info] start-time: 2021-04-08T20:44:53.756559Z, end-time: 2021-04-08T20:44:53.821527Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-04-08T20:44:57.741228Z, end-time: 2021-04-08T20:45:02.668111Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python3.7 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: 2021-04-08T20:45:02.806121Z, end-time: 2021-04-08T20:45:04.450805Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (21.0.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (54.2.0) [rtd-command-info] start-time: 2021-04-08T20:45:04.588009Z, end-time: 2021-04-08T20:45:14.606703Z, duration: 10, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17-py2.py3-none-any.whl (575 kB) Collecting Jinja2>=2.9 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) Collecting requests Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting Pygments>=2.0 Downloading Pygments-2.8.1-py3-none-any.whl (983 kB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting setuptools Downloading setuptools-54.2.0-py3-none-any.whl (785 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux2010_x86_64.whl (33 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.4-py2.py3-none-any.whl (153 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=2922bfa574868a39bc7e99405a2870edcd86f233d5bb0316f7aa6963c8c66631 Stored in directory: /tmp/pip-ephem-wheel-cache-0_8tmh58/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=36d8ddd62a6624c97ff20e1dcd4a2f2f15b9082fa948fa61cc6dc7f1109987fb Stored in directory: /tmp/pip-ephem-wheel-cache-0_8tmh58/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.8.1 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.17 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 setuptools-54.2.0 six-1.15.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.4 [rtd-command-info] start-time: 2021-04-08T20:45:14.729645Z, end-time: 2021-04-08T20:45:27.482503Z, duration: 12, 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/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (1.19.2) Requirement already satisfied: pandas>=1.0 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 2)) (1.1.3) Requirement already satisfied: scipy in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 3)) (1.5.3) Requirement already satisfied: matplotlib in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 4)) (3.3.2) Collecting seaborn Downloading seaborn-0.11.1-py3-none-any.whl (285 kB) Collecting tqdm Downloading tqdm-4.60.0-py2.py3-none-any.whl (75 kB) Collecting sphinxcontrib-apidoc Downloading sphinxcontrib_apidoc-0.3.0-py2.py3-none-any.whl (8.5 kB) Collecting m2r Downloading m2r-0.2.1.tar.gz (16 kB) Collecting nbsphinx Downloading nbsphinx-0.8.2-py3-none-any.whl (24 kB) Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 11)) (1.8.5) Collecting ipykernel Downloading ipykernel-5.5.3-py3-none-any.whl (120 kB) Collecting joblib Downloading joblib-1.0.1-py3-none-any.whl (303 kB) Collecting xlsxwriter Downloading XlsxWriter-1.3.8-py2.py3-none-any.whl (145 kB) Collecting openpyxl Downloading openpyxl-3.0.7-py2.py3-none-any.whl (243 kB) Requirement already satisfied: python-dateutil>=2.7.3 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from pandas>=1.0->-r requirements.txt (line 2)) (2.8.1) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from pandas>=1.0->-r requirements.txt (line 2)) (2021.1) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from python-dateutil>=2.7.3->pandas>=1.0->-r requirements.txt (line 2)) (1.15.0) Collecting ipython>=5.0.0 Downloading ipython-7.22.0-py3-none-any.whl (785 kB) Collecting jupyter-client Downloading jupyter_client-6.1.12-py3-none-any.whl (112 kB) Collecting traitlets>=4.1.0 Downloading traitlets-5.0.5-py3-none-any.whl (100 kB) Collecting tornado>=4.2 Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB) Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 Downloading prompt_toolkit-3.0.18-py3-none-any.whl (367 kB) Collecting backcall Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB) Collecting pexpect>4.3 Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB) Requirement already satisfied: setuptools>=18.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 12)) (54.2.0) Requirement already satisfied: pygments in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 12)) (2.8.1) Collecting jedi>=0.16 Downloading jedi-0.18.0-py2.py3-none-any.whl (1.4 MB) Collecting pickleshare Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB) Collecting decorator Downloading decorator-5.0.6-py3-none-any.whl (8.8 kB) Collecting parso<0.9.0,>=0.8.0 Downloading parso-0.8.2-py2.py3-none-any.whl (94 kB) Collecting ptyprocess>=0.5 Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB) Collecting wcwidth Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting mistune Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from m2r->-r requirements.txt (line 9)) (0.17) 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/python3.7/site-packages (from matplotlib->-r requirements.txt (line 4)) (2.4.7) Collecting pillow>=6.2.0 Downloading Pillow-8.2.0-cp37-cp37m-manylinux1_x86_64.whl (3.0 MB) Requirement already satisfied: cycler>=0.10 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 4)) (0.10.0) Requirement already satisfied: certifi>=2020.06.20 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 4)) (2020.12.5) Requirement already satisfied: kiwisolver>=1.0.1 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 4)) (1.2.0) Collecting nbconvert!=5.4 Downloading nbconvert-6.0.7-py3-none-any.whl (552 kB) Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from nbsphinx->-r requirements.txt (line 10)) (2.11.3) Collecting nbformat Downloading nbformat-5.1.3-py3-none-any.whl (178 kB) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (2.9.0) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.2.4) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (2.25.1) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.2.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (2.1.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (0.7.12) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (20.9) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from jinja2->nbsphinx->-r requirements.txt (line 10)) (1.1.1) Collecting bleach Downloading bleach-3.3.0-py2.py3-none-any.whl (283 kB) Collecting jupyter-core Downloading jupyter_core-4.7.1-py3-none-any.whl (82 kB) Collecting jupyterlab-pygments Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB) Collecting entrypoints>=0.2.2 Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.4.3.tar.gz (16 kB) Collecting defusedxml Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Collecting nbclient<0.6.0,>=0.5.0 Downloading nbclient-0.5.3-py3-none-any.whl (82 kB) Collecting testpath Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB) Collecting async-generator Downloading async_generator-1.10-py3-none-any.whl (18 kB) Collecting nest-asyncio Downloading nest_asyncio-1.5.1-py3-none-any.whl (5.0 kB) Collecting pyzmq>=13 Downloading pyzmq-22.0.3-cp37-cp37m-manylinux1_x86_64.whl (1.1 MB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Collecting importlib-metadata Downloading importlib_metadata-3.10.0-py3-none-any.whl (14 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.17.3.tar.gz (106 kB) Collecting attrs>=17.4.0 Downloading attrs-20.3.0-py2.py3-none-any.whl (49 kB) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (1.26.4) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (2.10) Requirement already satisfied: chardet<5,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (4.0.0) Collecting et-xmlfile Downloading et_xmlfile-1.0.1.tar.gz (8.4 kB) Collecting pbr Downloading pbr-5.5.1-py2.py3-none-any.whl (106 kB) Collecting webencodings 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sha256=488e3277ce07419ee67a086ad25fc544464862319da26b5f02f643a673307844 Stored in directory: /tmp/pip-ephem-wheel-cache-gk9n1r_m/wheels/e2/bd/55/048b4fd505716c4c298f42ee02dffd9496bb6d212b266c7f31 Successfully built m2r pandocfilters pyrsistent et-xmlfile Installing collected packages: zipp, typing-extensions, ipython-genutils, traitlets, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, jupyter-core, jsonschema, webencodings, wcwidth, ptyprocess, parso, nest-asyncio, nbformat, jupyter-client, async-generator, testpath, prompt-toolkit, pillow, pickleshare, pexpect, pandocfilters, nbclient, mistune, jupyterlab-pygments, jedi, entrypoints, defusedxml, decorator, bleach, backcall, pbr, nbconvert, ipython, et-xmlfile, 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 Successfully installed async-generator-1.10 attrs-20.3.0 backcall-0.2.0 bleach-3.3.0 decorator-5.0.6 defusedxml-0.7.1 entrypoints-0.3 et-xmlfile-1.0.1 importlib-metadata-3.10.0 ipykernel-5.5.3 ipython-7.22.0 ipython-genutils-0.2.0 jedi-0.18.0 joblib-1.0.1 jsonschema-3.2.0 jupyter-client-6.1.12 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 m2r-0.2.1 mistune-0.8.4 nbclient-0.5.3 nbconvert-6.0.7 nbformat-5.1.3 nbsphinx-0.8.2 nest-asyncio-1.5.1 openpyxl-3.0.7 pandocfilters-1.4.3 parso-0.8.2 pbr-5.5.1 pexpect-4.8.0 pickleshare-0.7.5 pillow-8.2.0 prompt-toolkit-3.0.18 ptyprocess-0.7.0 pyrsistent-0.17.3 pyzmq-22.0.3 seaborn-0.11.1 sphinxcontrib-apidoc-0.3.0 testpath-0.4.4 tornado-6.1 tqdm-4.60.0 traitlets-5.0.5 typing-extensions-3.7.4.3 wcwidth-0.2.5 webencodings-0.5.1 xlsxwriter-1.3.8 zipp-3.4.1 [rtd-command-info] start-time: 2021-04-08T20:45:28.551119Z, end-time: 2021-04-08T20:45:28.638500Z, 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 = '2020, FOXO Bioscience' author = 'FOXO Bioscience' # The short X.Y version version = '0.7' # The full version, including alpha/beta/rc tags release = '0.7' # -- 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' ] # 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', 'Life Epigenetics', 'manual'), ] # -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, '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', 'One line description of project.', 'Miscellaneous'), ] # -- Extension configuration ------------------------------------------------- ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file should't rely on extra depencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("feature-mouse", "/en/feature-mouse/"), ], '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': 'be5dfa52', } # 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/609322/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-04-08T20:45:28.752749Z, end-time: 2021-04-08T20:45:59.320619Z, duration: 30, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-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. 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md:170: WARNING: Title level inconsistent: run_qc() ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not 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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig6.png /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig7.png /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb:295: WARNING: Title level inconsistent: next, remove all probes that researchers have deemed inreliable ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb:404: WARNING: Title level inconsistent: MDS filtering ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb:295: WARNING: Title level inconsistent: next, remove all probes that researchers have deemed inreliable ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb:404: WARNING: Title level inconsistent: MDS filtering ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_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/example_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/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.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/filtering-probes.ipynb:399: WARNING: Title level inconsistent: Be careful -- you can apply the a probe list for EPIC to a 450k dataset, and it will work, but won't be good filtering. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering-probes.ipynb:451: WARNING: Title level inconsistent: Maximum filtering happens by default. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering-probes.ipynb:524: WARNING: Title level inconsistent: Take a look at other quality control methods, such as MDS and cumulative\_sum found in other example notebooks. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:683: WARNING: Title level inconsistent: 'meth\_df' format ~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:758: WARNING: Title level inconsistent: 'noob\_df' format ~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:833: WARNING: Title level inconsistent: 'meth' format will return a list of Python SampleDataContainer objects. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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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. WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised: No module named 'methylcheck.qc_report' /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:10: 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:25: 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:4: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:31: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:42: 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.beta_mds_plot:47: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title. notes ----- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:56: 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:26: 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.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_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.qc_plot.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.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title. inputs: ======= WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; 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[rtd-command-info] start-time: 2021-04-08T20:45:59.500889Z, end-time: 2021-04-08T20:46:03.129569Z, duration: 3, exit-code: 0 python -m sphinx -T -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading pickled environment... done Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-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. 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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. WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised: No module named 'methylcheck.qc_report' /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:10: 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:25: WARNING: Unexpected section title. 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Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:31: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:42: 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.beta_mds_plot:47: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title. notes ----- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:56: 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:26: WARNING: Unexpected section title. optional params: ================ 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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title. inputs: ======= WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; the following exception was raised: No module named 'statsmodels' WARNING: autodoc: failed to import module 'qc_report.ReportPDF' from module 'methylcheck'; the following exception was raised: No module named 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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:25: WARNING: Unexpected section title. 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Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:31: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:42: 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.beta_mds_plot:47: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title. notes ----- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:56: 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:26: WARNING: Unexpected section title. optional params: ================ 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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title. inputs: ======= WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; the following exception was raised: No module named 'statsmodels' WARNING: autodoc: failed to import module 'qc_report.ReportPDF' from module 'methylcheck'; the following exception was raised: No module named 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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: 2021-04-08T20:46:18.035440Z, end-time: 2021-04-08T20:46:18.114695Z, 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: 2021-04-08T20:46:18.240173Z, end-time: 2021-04-08T20:46:30.774860Z, duration: 12, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=life-epigenetics-methylcheck -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. 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Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/s] [18] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] Overfull \vbox (1.63934pt too high) detected at line 667 [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.698 ...███| 6/6 [00:00<00:00, 2850.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.698 ...███| 6/6 [00:00<00:00, 2850.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.698 ...███| 6/6 [00:00<00:00, 2850.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.698 ...███| 6/6 [00:00<00:00, 2850.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.698 ...███| 6/6 [00:00<00:00, 2850.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.698 ...███| 6/6 [00:00<00:00, 2850.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.698 ...███| 6/6 [00:00<00:00, 2850.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.698 ...███| 6/6 [00:00<00:00, 2850.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.698 ...███| 6/6 [00:00<00:00, 2850.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.698 ...███| 6/6 [00:00<00:00, 2850.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] [20] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] Overfull \vbox (1.32576pt too high) detected at line 889 [21] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] [22] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] [23] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/it] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. 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Underfull \hbox (badness 10000) in paragraph at lines 2367--2367 \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 , [62] [63] Underfull \hbox (badness 10000) in paragraph at lines 2481--2481 []\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 2481--2481 \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 2481--2481 \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- [64] Underfull \hbox (badness 7907) in paragraph at lines 2551--2558 []\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 2551--2558 \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 2551--2558 \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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Underfull \hbox (badness 10000) in paragraph at lines 2714--2717 \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 2726--2728 []\T1/ptm/m/n/10 ref: [][]$https : / / bioconductor . org / packages / devel / bioc / vignettes / sesame / inst / doc / sesame . html # [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 3016--3016 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 3016--3016 \T1/ptm/m/it/10 re-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 , Underfull \hbox (badness 10000) in paragraph at lines 3016--3016 \T1/ptm/m/it/10 re-turn_fig=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 full_range=Fa lse\T1/ptm/m/n/10 , \T1/ptm/m/it/10 high- Underfull \hbox (badness 10000) in paragraph at lines 3016--3016 \T1/ptm/m/it/10 light_samples=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 , [69] Underfull \hbox (badness 10000) in paragraph at lines 3109--3109 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 3109--3109 \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 multi_params={'dra w_box': True}\T1/ptm/m/n/10 , [70] [71] Underfull \hbox (badness 10000) in paragraph at lines 3311--3311 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 3331--3331 \T1/ptm/m/it/10 un-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 , Underfull \hbox (badness 10000) in paragraph at lines 3331--3331 \T1/ptm/m/it/10 noob=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 silent=False\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 3331--3331 \T1/ptm/m/it/10 plot=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bad_sample_cutoff=10. 5\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 6944) in paragraph at lines 3344--3349 []\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 3344--3349 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = [72] Underfull \hbox (badness 6910) in paragraph at lines 3385--3385 \T1/ptm/m/it/10 poobah=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 noob=True\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=Fa lse\T1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 3402--3407 []\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 3402--3407 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = [73] Underfull \hbox (badness 10000) in paragraph at lines 3455--3457 []\T1/ptm/m/n/10 `non-polymorphic' | Underfull \hbox (badness 10000) in paragraph at lines 3478--3478 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 3478--3478 \T1/ptm/m/it/10 plot=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 on_lambda=False\T1/p tm/m/n/10 , \T1/ptm/m/it/10 median_cutoff=-2\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in - Overfull \hbox (33.52034pt too wide) in paragraph at lines 3526--3528 [] [74] [75] [76] [77] [78] Chapter 7. [79] [80] LaTeX Warning: Reference `docs/source/modules:module-methylcheck.load_processed ' on page 81 undefined on input line 3739. LaTeX Warning: Reference `docs/source/modules:module-methylcheck.predict' on pa ge 81 undefined on input line 3740. LaTeX Warning: Reference `docs/source/modules:module-methylcheck.probes' on pag e 81 undefined on input line 3741. LaTeX Warning: Reference `docs/source/modules:module-methylcheck.qc_plot' on pa ge 81 undefined on input line 3742. LaTeX Warning: Reference `docs/source/modules:module-methylcheck.read_geo_proce ssed' on page 81 undefined on input line 3743. LaTeX Warning: Reference `docs/source/modules:module-methylcheck.samples' on pa ge 81 undefined on input line 3744. [81] No file life-epigenetics-methylcheck.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. (./life-epigenetics-methylcheck.aux) Package rerunfilecheck Warning: File `life-epigenetics-methylcheck.out' has cha nged. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on life-epigenetics-methylcheck.pdf (85 pages, 2595825 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 24' 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 240.' 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 24' 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 240.' Latexmk: Missing input file: 'life-epigenetics-methylcheck.ind' from line 'No file life-epigenetics-methylcheck.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Latexmk: List of undefined refs and citations: Reference `docs/source/modules:module-methylcheck.load_processed' on page 81 undefined on input line 3739 Reference `docs/source/modules:module-methylcheck.predict' on page 81 undefined on input line 3740 Reference `docs/source/modules:module-methylcheck.probes' on page 81 undefined on input line 3741 Reference `docs/source/modules:module-methylcheck.qc_plot' on page 81 undefined on input line 3742 Reference `docs/source/modules:module-methylcheck.read_geo_processed' on page 81 undefined on input line 3743 Reference `docs/source/modules:module-methylcheck.samples' on page 81 undefined on input line 3744 Latexmk: Summary of warnings: Latex failed to resolve 6 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' ------------ ------------ Running 'makeindex -s python.ist -o "life-epigenetics-methylcheck.ind" "life-epigenetics-methylcheck.idx"' ------------ Latexmk: applying rule 'makeindex 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 (31 entries accepted, 0 rejected). Sorting entries....done (155 comparisons). Generating output file life-epigenetics-methylcheck.ind....done (77 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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LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.232 ...be9e8894ddc966dbda9dbb/methylcheck}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.234 ...1e8a2a85a8e7b521b468/circleci-docs}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.234 ...1e8a2a85a8e7b521b468/circleci-docs}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.236 ...3/aedf5c223e39415180ff35153b2bad89}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.236 ...3/aedf5c223e39415180ff35153b2bad89}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.238 ...b0ce2b045ce852c84a26def8403e/badge}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.238 ...b0ce2b045ce852c84a26def8403e/badge}.svg}} ^^M LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epi genetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607 c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 24 0. ! LaTeX Error: Unknown graphics extension: .png"height="50">`. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.240 ...dd9574bfece/python3.6}.png"height="50">`} LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epi genetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607 c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 24 0. ! LaTeX Error: Unknown graphics extension: .png"height="50">`. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.240 ...dd9574bfece/python3.6}.png"height="50">`} Overfull \hbox (975.67087pt too wide) in paragraph at lines 2--243 [][][][][][] [1] [2 <./methylcheck_overview.png>] Chapter 1. Overfull \hbox (298.86465pt too wide) in paragraph at lines 2--250 [][][][][][] [3] [4 <./methylcheck_functions.png>] Chapter 2. [5] [6] Chapter 3. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [8] [9] [10] Chapter 4. Overfull \hbox (2028.37567pt too wide) in paragraph at lines 2--388 [][][][][][] [11] Overfull \hbox (204.79077pt too wide) in paragraph at lines 2--400 [][][][][][] [12 <./example_controls_report.png>] Overfull \vbox (162.62206pt too high) has occurred while \output is active [13 <./example_ReportPDF.png>] [14] Chapter 5. [15] [16] Chapter 6. [17] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.492 ...��███| 1/1 [00:00<00:00, 50.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.492 ...��███| 1/1 [00:00<00:00, 50.68it/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.492 ...��███| 1/1 [00:00<00:00, 50.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.492 ...��███| 1/1 [00:00<00:00, 50.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.492 ...��███| 1/1 [00:00<00:00, 50.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.496 ...��███| 1/1 [00:00<00:00, 9.42it/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.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.607 ...��███| 6/6 [00:00<00:00, 8.74it/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.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.611 ...███| 6/6 [00:00<00:00, 2400.86it/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.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.699 ...███| 6/6 [00:00<00:00, 2738.39it/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.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/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.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] [20] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] Overfull \vbox (1.32576pt too high) detected at line 889 [21] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] [22] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] [23] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] Underfull \vbox (badness 3492) detected at line 1152 [24] Underfull \vbox (badness 10000) detected at line 1163 [25 <./docs_quality-control-example_5_0.png>] Underfull \vbox (badness 10000) detected at line 1174 [26 <./docs_quality-control-example_5_1.png>] Underfull \vbox (badness 10000) detected at line 1185 [27 <./docs_quality-control-example_5_2.png>] Underfull \vbox (badness 10000) detected at line 1196 [28 <./docs_quality-control-example_5_3.png>] Underfull \vbox (badness 10000) detected at line 1207 [29 <./docs_quality-control-example_5_4.png>] Underfull \vbox (badness 10000) detected at line 1218 [30 <./docs_quality-control-example_5_5.png>] Underfull \vbox (badness 10000) detected at line 1229 [31 <./docs_quality-control-example_5_6.png>] Underfull \vbox (badness 10000) detected at line 1240 [32 <./docs_quality-control-example_5_7.png>] Underfull \vbox (badness 10000) detected at line 1251 [33 <./docs_quality-control-example_5_8.png>] Underfull \vbox (badness 10000) detected at line 1289 [34 <./docs_quality-control-example_5_9.png>] Underfull \vbox (badness 10000) detected at line 1326 [35 <./docs_quality-control-example_5_12.png>] Underfull \vbox (badness 10000) detected at line 1363 [36 <./docs_quality-control-example_5_15.png>] Underfull \vbox (badness 10000) detected at line 1400 [37 <./docs_quality-control-example_5_18.png>] Underfull \vbox (badness 10000) detected at line 1421 [38 <./docs_quality-control-example_5_21.png>] Underfull \vbox (badness 10000) detected at line 1432 [39 <./docs_quality-control-example_6_0.png>] Underfull \vbox (badness 10000) detected at line 1443 [40 <./docs_quality-control-example_6_1.png>] Underfull \vbox (badness 10000) detected at line 1454 [41 <./docs_quality-control-example_6_2.png>] Underfull \vbox (badness 10000) detected at line 1465 [42 <./docs_quality-control-example_6_3.png>] Underfull \vbox (badness 10000) detected at line 1476 [43 <./docs_quality-control-example_6_4.png>] Underfull \vbox (badness 10000) detected at line 1487 [44 <./docs_quality-control-example_6_5.png>] Underfull \vbox (badness 10000) detected at line 1498 [45 <./docs_quality-control-example_6_6.png>] Underfull \vbox (badness 10000) detected at line 1509 [46 <./docs_quality-control-example_6_7.png>] Underfull \vbox (badness 10000) detected at line 1520 [47 <./docs_quality-control-example_6_8.png>] Underfull \vbox (badness 10000) detected at line 1557 [48 <./docs_quality-control-example_6_9.png>] Underfull \vbox (badness 10000) detected at line 1581 [49 <./docs_quality-control-example_6_12.png>] Underfull \vbox (badness 10000) detected at line 1605 [50 <./docs_quality-control-example_6_14.png>] Underfull \vbox (badness 10000) detected at line 1629 [51 <./docs_quality-control-example_6_16.png>] [52 <./docs_quality-control-exam ple_6_18.png>] [53] Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 []\T1/phv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 \T1/phv/m/n/10 gu- Overfull \hbox (7.23338pt too wide) in paragraph at lines 1870--1870 \T1/phv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 []\T1/phv/m/n/10 De- Overfull \hbox (1.02771pt too wide) in paragraph at lines 1870--1870 \T1/phv/m/n/10 fault| Overfull \hbox (17.77328pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 data_dir| Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 path Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 \T1/ptm/b/n/10 RE- Overfull \hbox (22.32765pt too wide) in paragraph at lines 1870--1870 \T1/ptm/b/n/10 QUIRED| Overfull \hbox (1.11351pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 out- Overfull \hbox (15.00327pt too wide) in paragraph at lines 1870--1870 \T1/ptm/m/n/10 filepath| Overfull \hbox (6.42802pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/10 None| Overfull \hbox (0.55345pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 col- Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 \T1/ptm/m/n/10 or- Overfull \hbox (5.56345pt too wide) in paragraph at lines 1870--1870 \T1/ptm/m/n/10 blind| Overfull \hbox (12.42802pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/10 False| Overfull \hbox (22.5233pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 bg_offset| Overfull \hbox (2.42802pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 3000| Overfull \hbox (0.55345pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 cut- Overfull \hbox (25.30319pt too wide) in paragraph at lines 1870--1870 \T1/ptm/m/n/10 off_adjust| Overfull \hbox (10.75363pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 legacy| Overfull \hbox (12.42802pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/10 False| Overfull \hbox (11.66357pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 round- Overfull \hbox (1.9735pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 pval| Overfull \hbox (6.42802pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/10 True| Overfull \hbox (18.64328pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 pval_sig| Overfull \hbox (5.55334pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 pass- [54] [55] [56] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/it] Underfull \vbox (badness 10000) detected at line 2072 [57] Underfull \vbox (badness 10000) detected at line 2108 [58 <./docs_filtering-probes_8_1.png>] Underfull \vbox (badness 10000) detected at line 2144 [59 <./docs_filtering-probes_11_1.png>] Underfull \vbox (badness 10000) detected at line 2164 [60 <./docs_filtering-probes_13_1.png>] Underfull \hbox (badness 10000) in paragraph at lines 2270--2271 []|\T1/pcr/m/n/10 methylcheck.plot_controls\T1/ptm/m/n/10 ([path, sub-set, Underfull \hbox (badness 10000) in paragraph at lines 2272--2274 []|\T1/ptm/m/n/10 internal ar-ray QC con-trols (avail-able with the Underfull \hbox (badness 10000) in paragraph at lines 2275--2276 []|\T1/pcr/m/n/10 methylcheck.plot_beta_by_type\T1/ptm/m/n/10 (beta_df[, Underfull \hbox (badness 10000) in paragraph at lines 2285--2286 []|\T1/pcr/m/n/10 methylcheck.list_problem_probes\T1/ptm/m/n/10 (array[, Overfull \hbox (19.88239pt too wide) in paragraph at lines 2295--2296 []|\T1/pcr/m/n/10 methylcheck.exclude_sex_control_probes\T1/ptm/m/n/10 (df, Underfull \hbox (badness 10000) in paragraph at lines 2300--2301 []|\T1/pcr/m/n/10 methylcheck.drop_nan_probes\T1/ptm/m/n/10 (df[, silent, Underfull \hbox (badness 10000) in paragraph at lines 2315--2316 []|\T1/pcr/m/n/10 methylcheck.beta_density_plot\T1/ptm/m/n/10 (df[, ver- Underfull \hbox (badness 10000) in paragraph at lines 2320--2321 []|\T1/pcr/m/n/10 methylcheck.mean_beta_plot\T1/ptm/m/n/10 (df[, ver-bose, Underfull \hbox (badness 6284) in paragraph at lines 2325--2326 []|\T1/pcr/m/n/10 methylcheck.mean_beta_compare\T1/ptm/m/n/10 (df1, df2[, [61 <./docs_filtering-probes_14_0.png>] Overfull \hbox (56.71234pt too wide) in paragraph at lines 2340--2341 []|\T1/pcr/m/n/10 methylcheck.cumulative_sum_beta_distribution\T1/ptm/m/n/10 (d f)| Underfull \hbox (badness 10000) in paragraph at lines 2367--2367 \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 , [62] [63] Underfull \hbox (badness 10000) in paragraph at lines 2481--2481 []\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 2481--2481 \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 2481--2481 \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- [64] Underfull \hbox (badness 7907) in paragraph at lines 2551--2558 []\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 2551--2558 \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 2551--2558 \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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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on life-epigenetics-methylcheck.pdf (87 pages, 2608426 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 24' 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 240.' 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 24' 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 240.' Latexmk: References changed. 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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.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.740 ...███| 6/6 [00:00<00:00, 1549.62it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.741 ...███| 6/6 [00:00<00:00, 2265.76it/s] [20] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.780 ...��███| 6/6 [00:01<00:00, 3.68it/s] Overfull \vbox (1.32576pt too high) detected at line 889 [21] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.901 ...��███| 1/1 [00:00<00:00, 50.02it/s] [22] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.986 ...��███| 1/1 [00:00<00:00, 8.26it/s] [23] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1100 ...�███| 1/1 [00:00<00:00, 35.83it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1104 ...�███| 1/1 [00:00<00:00, 6.61it/s] Underfull \vbox (badness 3492) detected at line 1152 [24] Underfull \vbox (badness 10000) detected at line 1163 [25 <./docs_quality-control-example_5_0.png>] Underfull \vbox (badness 10000) detected at line 1174 [26 <./docs_quality-control-example_5_1.png>] Underfull \vbox (badness 10000) detected at line 1185 [27 <./docs_quality-control-example_5_2.png>] Underfull \vbox (badness 10000) detected at line 1196 [28 <./docs_quality-control-example_5_3.png>] Underfull \vbox (badness 10000) detected at line 1207 [29 <./docs_quality-control-example_5_4.png>] Underfull \vbox (badness 10000) detected at line 1218 [30 <./docs_quality-control-example_5_5.png>] Underfull \vbox (badness 10000) detected at line 1229 [31 <./docs_quality-control-example_5_6.png>] Underfull \vbox (badness 10000) detected at line 1240 [32 <./docs_quality-control-example_5_7.png>] Underfull \vbox (badness 10000) detected at line 1251 [33 <./docs_quality-control-example_5_8.png>] Underfull \vbox (badness 10000) detected at line 1289 [34 <./docs_quality-control-example_5_9.png>] Underfull \vbox (badness 10000) detected at line 1326 [35 <./docs_quality-control-example_5_12.png>] Underfull \vbox (badness 10000) detected at line 1363 [36 <./docs_quality-control-example_5_15.png>] Underfull \vbox (badness 10000) detected at line 1400 [37 <./docs_quality-control-example_5_18.png>] Underfull \vbox (badness 10000) detected at line 1421 [38 <./docs_quality-control-example_5_21.png>] Underfull \vbox (badness 10000) detected at line 1432 [39 <./docs_quality-control-example_6_0.png>] Underfull \vbox (badness 10000) detected at line 1443 [40 <./docs_quality-control-example_6_1.png>] Underfull \vbox (badness 10000) detected at line 1454 [41 <./docs_quality-control-example_6_2.png>] Underfull \vbox (badness 10000) detected at line 1465 [42 <./docs_quality-control-example_6_3.png>] Underfull \vbox (badness 10000) detected at line 1476 [43 <./docs_quality-control-example_6_4.png>] Underfull \vbox (badness 10000) detected at line 1487 [44 <./docs_quality-control-example_6_5.png>] Underfull \vbox (badness 10000) detected at line 1498 [45 <./docs_quality-control-example_6_6.png>] Underfull \vbox (badness 10000) detected at line 1509 [46 <./docs_quality-control-example_6_7.png>] Underfull \vbox (badness 10000) detected at line 1520 [47 <./docs_quality-control-example_6_8.png>] Underfull \vbox (badness 10000) detected at line 1557 [48 <./docs_quality-control-example_6_9.png>] Underfull \vbox (badness 10000) detected at line 1581 [49 <./docs_quality-control-example_6_12.png>] Underfull \vbox (badness 10000) detected at line 1605 [50 <./docs_quality-control-example_6_14.png>] Underfull \vbox (badness 10000) detected at line 1629 [51 <./docs_quality-control-example_6_16.png>] [52 <./docs_quality-control-exam ple_6_18.png>] [53] Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 []\T1/phv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 \T1/phv/m/n/10 gu- Overfull \hbox (7.23338pt too wide) in paragraph at lines 1870--1870 \T1/phv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 []\T1/phv/m/n/10 De- Overfull \hbox (1.02771pt too wide) in paragraph at lines 1870--1870 \T1/phv/m/n/10 fault| Overfull \hbox (17.77328pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 data_dir| Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 path Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 \T1/ptm/b/n/10 RE- Overfull \hbox (22.32765pt too wide) in paragraph at lines 1870--1870 \T1/ptm/b/n/10 QUIRED| Overfull \hbox (1.11351pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 out- Overfull \hbox (15.00327pt too wide) in paragraph at lines 1870--1870 \T1/ptm/m/n/10 filepath| Overfull \hbox (6.42802pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/10 None| Overfull \hbox (0.55345pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 col- Underfull \hbox (badness 10000) in paragraph at lines 1870--1870 \T1/ptm/m/n/10 or- Overfull \hbox (5.56345pt too wide) in paragraph at lines 1870--1870 \T1/ptm/m/n/10 blind| Overfull \hbox (12.42802pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/10 False| Overfull \hbox (22.5233pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 bg_offset| Overfull \hbox (2.42802pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 3000| Overfull \hbox (0.55345pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 cut- Overfull \hbox (25.30319pt too wide) in paragraph at lines 1870--1870 \T1/ptm/m/n/10 off_adjust| Overfull \hbox (10.75363pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 legacy| Overfull \hbox (12.42802pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/10 False| Overfull \hbox (11.66357pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 round- Overfull \hbox (1.9735pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 pval| Overfull \hbox (6.42802pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/10 True| Overfull \hbox (18.64328pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 pval_sig| Overfull \hbox (5.55334pt too wide) in paragraph at lines 1870--1870 []\T1/ptm/m/n/10 pass- [54] [55] [56] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1988 ...�██| 6/6 [00:00<00:00, 16215.09it/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/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.1990 ...�███| 6/6 [00:49<00:00, 8.26s/it] Underfull \vbox (badness 10000) detected at line 2072 [57] Underfull \vbox (badness 10000) detected at line 2108 [58 <./docs_filtering-probes_8_1.png>] Underfull \vbox (badness 10000) detected at line 2144 [59 <./docs_filtering-probes_11_1.png>] Underfull \vbox (badness 10000) detected at line 2164 [60 <./docs_filtering-probes_13_1.png>] Underfull \hbox (badness 10000) in paragraph at lines 2270--2271 []|\T1/pcr/m/n/10 methylcheck.plot_controls\T1/ptm/m/n/10 ([path, sub-set, Underfull \hbox (badness 10000) in paragraph at lines 2272--2274 []|\T1/ptm/m/n/10 internal ar-ray QC con-trols (avail-able with the Underfull \hbox (badness 10000) in paragraph at lines 2275--2276 []|\T1/pcr/m/n/10 methylcheck.plot_beta_by_type\T1/ptm/m/n/10 (beta_df[, Underfull \hbox (badness 10000) in paragraph at lines 2285--2286 []|\T1/pcr/m/n/10 methylcheck.list_problem_probes\T1/ptm/m/n/10 (array[, Overfull \hbox (19.88239pt too wide) in paragraph at lines 2295--2296 []|\T1/pcr/m/n/10 methylcheck.exclude_sex_control_probes\T1/ptm/m/n/10 (df, Underfull \hbox (badness 10000) in paragraph at lines 2300--2301 []|\T1/pcr/m/n/10 methylcheck.drop_nan_probes\T1/ptm/m/n/10 (df[, silent, Underfull \hbox (badness 10000) in paragraph at lines 2315--2316 []|\T1/pcr/m/n/10 methylcheck.beta_density_plot\T1/ptm/m/n/10 (df[, ver- Underfull \hbox (badness 10000) in paragraph at lines 2320--2321 []|\T1/pcr/m/n/10 methylcheck.mean_beta_plot\T1/ptm/m/n/10 (df[, ver-bose, Underfull \hbox (badness 6284) in paragraph at lines 2325--2326 []|\T1/pcr/m/n/10 methylcheck.mean_beta_compare\T1/ptm/m/n/10 (df1, df2[, [61 <./docs_filtering-probes_14_0.png>] Overfull \hbox (56.71234pt too wide) in paragraph at lines 2340--2341 []|\T1/pcr/m/n/10 methylcheck.cumulative_sum_beta_distribution\T1/ptm/m/n/10 (d f)| Underfull \hbox (badness 10000) in paragraph at lines 2367--2367 \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 , [62] [63] Underfull \hbox (badness 10000) in paragraph at lines 2481--2481 []\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 2481--2481 \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 2481--2481 \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- [64] Underfull \hbox (badness 7907) in paragraph at lines 2551--2558 []\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 2551--2558 \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 2551--2558 \T1/pcr/m/n/10 containers = m.load(files, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 meth\ TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ) df = m.load_processed. Underfull \hbox (badness 10000) in paragraph at lines 2565--2565 []\T1/ptm/m/it/10 filepath\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/pt m/m/n/10 , \T1/ptm/m/it/10 de-bug=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2565--2565 \T1/ptm/m/it/10 as_beta=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 col-umn_pattern=No ne\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2565--2565 \T1/ptm/m/it/10 test_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-name_probe_c olumn=True\T1/ptm/m/n/10 , [65] Underfull \hbox (badness 10000) in paragraph at lines 2632--2632 []\T1/ptm/m/it/10 test\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Overfull \hbox (22.45381pt too wide) in paragraph at lines 2632--2632 \T1/ptm/m/it/10 turn_sample_column_names=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2673--2674 []\T1/ptm/m/n/10 {`27k', `450k', `EPIC', `MOUSE'} or {`Il-lu-mi-naHu-man-Methy- la- [66] Underfull \hbox (badness 10000) in paragraph at lines 2711--2712 []\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 2714--2717 []\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 2714--2717 \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 2714--2717 \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 2726--2728 []\T1/ptm/m/n/10 ref: [][]$https : / / bioconductor . org / packages / devel / bioc / vignettes / sesame / inst / doc / sesame . html # [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 3016--3016 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 3016--3016 \T1/ptm/m/it/10 re-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 , Underfull \hbox (badness 10000) in paragraph at lines 3016--3016 \T1/ptm/m/it/10 re-turn_fig=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 full_range=Fa lse\T1/ptm/m/n/10 , \T1/ptm/m/it/10 high- Underfull \hbox (badness 10000) in paragraph at lines 3016--3016 \T1/ptm/m/it/10 light_samples=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 , [69] Underfull \hbox (badness 10000) in paragraph at lines 3109--3109 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 3109--3109 \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 multi_params={'dra w_box': True}\T1/ptm/m/n/10 , [70] [71] Underfull \hbox (badness 10000) in paragraph at lines 3311--3311 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 3331--3331 \T1/ptm/m/it/10 un-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 , Underfull \hbox (badness 10000) in paragraph at lines 3331--3331 \T1/ptm/m/it/10 noob=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 silent=False\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 3331--3331 \T1/ptm/m/it/10 plot=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bad_sample_cutoff=10. 5\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 6944) in paragraph at lines 3344--3349 []\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 3344--3349 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = [72] Underfull \hbox (badness 6910) in paragraph at lines 3385--3385 \T1/ptm/m/it/10 poobah=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 noob=True\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 silent=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=Fa lse\T1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 3402--3407 []\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 3402--3407 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = [73] Underfull \hbox (badness 10000) in paragraph at lines 3455--3457 []\T1/ptm/m/n/10 `non-polymorphic' | Underfull \hbox (badness 10000) in paragraph at lines 3478--3478 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 3478--3478 \T1/ptm/m/it/10 plot=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 on_lambda=False\T1/p tm/m/n/10 , \T1/ptm/m/it/10 median_cutoff=-2\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in - Overfull \hbox (33.52034pt too wide) in paragraph at lines 3526--3528 [] [74] [75] [76] [77] [78] Chapter 7. [79] [80] [81] (./life-epigenetics-methylcheck.ind [82] Underfull \hbox (badness 10000) in paragraph at lines 12--13 []\T1/pcr/m/n/10 beta_density_plot() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 18--20 []\T1/pcr/m/n/10 container_to_pkl() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/pcr/m/n/10 cumulative_sum_beta_distribution() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/pcr/m/n/10 detect_header_pattern() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 27--28 []\T1/pcr/m/n/10 drop_nan_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 32--34 []\T1/pcr/m/n/10 exclude_sex_control_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 41--42 []\T1/pcr/m/n/10 list_problem_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 43--44 []\T1/pcr/m/n/10 load_both() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 47--48 []\T1/pcr/m/n/10 mean_beta_compare() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 48--49 []\T1/pcr/m/n/10 mean_beta_plot() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 53--54 []\T1/pcr/m/n/10 methylcheck.read_geo_processed \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mod-ule\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 58--59 []\T1/pcr/m/n/10 plot_assigned_groups() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 59--60 []\T1/pcr/m/n/10 plot_beta_by_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 62--63 []\T1/pcr/m/n/10 problem_probe_reasons() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 66--67 []\T1/pcr/m/n/10 qc_signal_intensity() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 70--71 []\T1/pcr/m/n/10 read_geo() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule [83]) (./life-epigenetics-methylcheck.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on life-epigenetics-methylcheck.pdf (87 pages, 2608198 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 24' 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 240.' 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 24' 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 240.' Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2021-04-08T20:46:30.973299Z, end-time: 2021-04-08T20:46:31.052310Z, 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: 2021-04-08T20:46:31.162062Z, end-time: 2021-04-08T20:46:48.601552Z, duration: 17, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading pickled environment... done Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-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. building [mo]: targets for 0 po files that are out of date building [epub]: targets for 25 source files that are out of date updating environment: [] 0 added, 2 changed, 0 removed reading sources... [ 50%] docs/example_notebooks/methylcheck-cli reading sources... [100%] docs/source/modules /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig1.png /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig2.png /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: 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WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised: No module named 'methylcheck.qc_report' /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:10: 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:25: WARNING: Unexpected section title. 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Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:31: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:42: 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.beta_mds_plot:47: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title. notes ----- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:56: 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; 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