Read the Docs build information Build id: 714692 Project: life-epigenetics-methylcheck Version: latest Commit: 2770555ffeb0cf1a633b92ed82c89ae0671d4415 Date: 2021-09-03T20:35:11.102084Z State: finished Success: True [rtd-command-info] start-time: 2021-09-03T20:35:12.629420Z, end-time: 2021-09-03T20:35:46.845072Z, duration: 34, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylcheck.git . Cloning into '.'... Checking out files: 18% (33/174) Checking out files: 19% (34/174) Checking out files: 20% (35/174) Checking out files: 21% (37/174) Checking out files: 22% (39/174) Checking out files: 23% (41/174) Checking out files: 24% (42/174) Checking out files: 25% (44/174) Checking out files: 26% (46/174) Checking out files: 27% (47/174) Checking out files: 28% (49/174) Checking out files: 28% (50/174) Checking out files: 29% (51/174) Checking out files: 30% (53/174) Checking out files: 31% (54/174) Checking out files: 32% (56/174) Checking out files: 33% (58/174) Checking out files: 34% (60/174) Checking out files: 35% (61/174) Checking out files: 36% (63/174) Checking out files: 37% (65/174) Checking out files: 38% (67/174) Checking out files: 39% (68/174) Checking out files: 40% (70/174) Checking out files: 41% (72/174) Checking out files: 42% (74/174) Checking out files: 43% (75/174) Checking out files: 44% (77/174) Checking out files: 45% (79/174) Checking out files: 46% (81/174) Checking out files: 47% (82/174) Checking out files: 48% (84/174) Checking out files: 49% (86/174) Checking out files: 50% (87/174) Checking out files: 51% (89/174) Checking out files: 52% (91/174) Checking out files: 53% (93/174) Checking out files: 54% (94/174) Checking out files: 55% (96/174) Checking out files: 56% (98/174) Checking out files: 57% (100/174) Checking out files: 58% (101/174) Checking out files: 59% (103/174) Checking out files: 60% (105/174) Checking out files: 61% (107/174) Checking out files: 62% (108/174) Checking out files: 63% (110/174) Checking out files: 64% (112/174) Checking out files: 65% (114/174) Checking out files: 66% (115/174) Checking out files: 67% (117/174) Checking out files: 68% (119/174) Checking out files: 69% (121/174) Checking out files: 70% (122/174) Checking out files: 71% (124/174) Checking out files: 72% (126/174) Checking out files: 73% (128/174) Checking out files: 74% (129/174) Checking out files: 75% (131/174) Checking out files: 76% (133/174) Checking out files: 77% (134/174) Checking out files: 78% (136/174) Checking out files: 79% (138/174) Checking out files: 80% (140/174) Checking out files: 81% (141/174) Checking out files: 82% (143/174) Checking out files: 83% (145/174) Checking out files: 84% (147/174) Checking out files: 85% (148/174) Checking out files: 86% (150/174) Checking out files: 87% (152/174) Checking out files: 88% (154/174) Checking out files: 89% (155/174) Checking out files: 90% (157/174) Checking out files: 91% (159/174) Checking out files: 92% (161/174) Checking out files: 93% (162/174) Checking out files: 94% (164/174) Checking out files: 95% (166/174) Checking out files: 96% (168/174) Checking out files: 97% (169/174) Checking out files: 98% (171/174) Checking out files: 99% (173/174) Checking out files: 100% (174/174) Checking out files: 100% (174/174), done. [rtd-command-info] start-time: 2021-09-03T20:35:47.012937Z, end-time: 2021-09-03T20:35:48.248176Z, 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 2770555 Feature/v0.7.5 (#53) [rtd-command-info] start-time: 2021-09-03T20:35:48.352093Z, end-time: 2021-09-03T20:35:48.428812Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-09-03T20:36:07.096650Z, end-time: 2021-09-03T20:36:12.868343Z, duration: 5, 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: 2021-09-03T20:36:12.983138Z, end-time: 2021-09-03T20:36:14.146583Z, 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 (21.2.4) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (57.4.0) [rtd-command-info] start-time: 2021-09-03T20:36:14.284240Z, end-time: 2021-09-03T20:36:23.243857Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.1-py3-none-any.whl (133 kB) Collecting Pygments>=2.0 Downloading Pygments-2.10.0-py3-none-any.whl (1.0 MB) Collecting packaging Downloading packaging-21.0-py3-none-any.whl (40 kB) Collecting setuptools Downloading setuptools-57.4.0-py3-none-any.whl (819 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-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 requests>=2.0.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (31 kB) Collecting idna<4,>=2.5 Downloading idna-3.2-py3-none-any.whl (59 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.5.30-py2.py3-none-any.whl (145 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.4-py3-none-any.whl (36 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.6-py2.py3-none-any.whl (138 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=2167b4534e99ec209677e75a023d589a56880d199f8d556df8fdfd786c9c777b Stored in directory: /tmp/pip-ephem-wheel-cache-4025qn8e/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=22f57e9fca3902bf8fa8fb36f761c4a982cde739fe03f8aabb82c0638413ef42 Stored in directory: /tmp/pip-ephem-wheel-cache-4025qn8e/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-3.0.1 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.5.30 charset-normalizer-2.0.4 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.2 imagesize-1.2.0 mock-1.0.1 packaging-21.0 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 setuptools-57.4.0 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.6 [rtd-command-info] start-time: 2021-09-03T20:36:23.389114Z, end-time: 2021-09-03T20:36:39.357936Z, duration: 15, 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) Collecting pandas<1.3.0,>=1.2 Downloading pandas-1.2.5-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (9.9 MB) 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-0.11.2-py3-none-any.whl (292 kB) Collecting tqdm Downloading tqdm-4.62.2-py2.py3-none-any.whl (76 kB) Collecting sphinxcontrib-apidoc Downloading sphinxcontrib_apidoc-0.3.0-py2.py3-none-any.whl (8.5 kB) Collecting m2r Downloading m2r-0.2.1.tar.gz (16 kB) Collecting nbsphinx Downloading nbsphinx-0.8.7-py3-none-any.whl (25 kB) Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 11)) (1.8.5) Collecting ipykernel Downloading ipykernel-6.3.1-py3-none-any.whl (123 kB) Collecting joblib Downloading joblib-1.0.1-py3-none-any.whl (303 kB) Collecting xlsxwriter Downloading XlsxWriter-3.0.1-py3-none-any.whl (148 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<1.3.0,>=1.2->-r requirements.txt (line 2)) (2.8.1) Requirement already satisfied: pytz>=2017.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from pandas<1.3.0,>=1.2->-r requirements.txt (line 2)) (2021.1) 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 pillow>=6.2.0 Downloading Pillow-8.3.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.0 MB) 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)) (2021.5.30) 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: 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 pbr Downloading pbr-5.6.0-py2.py3-none-any.whl (111 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)) (0.17.1) Collecting nbformat Downloading nbformat-5.1.3-py3-none-any.whl (178 kB) Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from nbsphinx->-r requirements.txt (line 10)) (3.0.1) Collecting nbconvert!=5.4 Downloading nbconvert-6.1.0-py3-none-any.whl (551 kB) Collecting traitlets Downloading traitlets-5.1.0-py3-none-any.whl (101 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)) (2.9.1) 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: 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: Pygments>=2.0 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)) (2.10.0) Requirement already satisfied: setuptools 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)) (57.4.0) 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: 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)) (2.26.0) 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 sphinx->-r requirements.txt (line 11)) (1.16.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (21.0) 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) Collecting argcomplete>=1.12.3 Downloading argcomplete-1.12.3-py2.py3-none-any.whl (38 kB) Collecting ipython<8.0,>=7.23.1 Downloading ipython-7.27.0-py3-none-any.whl (787 kB) Collecting tornado<7.0,>=4.2 Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB) Collecting jupyter-client<8.0 Downloading jupyter_client-7.0.2-py3-none-any.whl (122 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting matplotlib-inline<0.2.0,>=0.1.0 Downloading matplotlib_inline-0.1.2-py3-none-any.whl (8.2 kB) Collecting importlib-metadata<5 Downloading importlib_metadata-4.8.1-py3-none-any.whl (17 kB) Collecting debugpy<2.0,>=1.0.0 Downloading debugpy-1.4.1-cp37-cp37m-manylinux2014_x86_64.whl (4.6 MB) Collecting et-xmlfile Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB) Collecting zipp>=0.5 Downloading zipp-3.5.0-py3-none-any.whl (5.7 kB) Collecting typing-extensions>=3.6.4 Downloading typing_extensions-3.10.0.2-py3-none-any.whl (26 kB) Collecting pickleshare Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB) Collecting pexpect>4.3 Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB) Collecting jedi>=0.16 Downloading jedi-0.18.0-py2.py3-none-any.whl (1.4 MB) Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 Downloading prompt_toolkit-3.0.20-py3-none-any.whl (370 kB) Collecting backcall Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB) Collecting decorator Downloading decorator-5.0.9-py3-none-any.whl (8.9 kB) Collecting parso<0.9.0,>=0.8.0 Downloading parso-0.8.2-py2.py3-none-any.whl (94 kB) Requirement already satisfied: MarkupSafe>=2.0 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)) (2.0.1) Collecting jupyter-core>=4.6.0 Downloading jupyter_core-4.7.1-py3-none-any.whl (82 kB) Collecting entrypoints Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting nest-asyncio>=1.5 Downloading nest_asyncio-1.5.1-py3-none-any.whl (5.0 kB) Collecting pyzmq>=13 Downloading pyzmq-22.2.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB) Collecting nbclient<0.6.0,>=0.5.0 Downloading nbclient-0.5.4-py3-none-any.whl (66 kB) Collecting defusedxml Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Collecting jupyterlab-pygments Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.4.3.tar.gz (16 kB) Collecting bleach Downloading bleach-4.1.0-py2.py3-none-any.whl (157 kB) Collecting testpath Downloading testpath-0.5.0-py3-none-any.whl (84 kB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Collecting attrs>=17.4.0 Downloading attrs-21.2.0-py2.py3-none-any.whl (53 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.18.0-cp37-cp37m-manylinux1_x86_64.whl (119 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) Requirement already satisfied: charset-normalizer~=2.0.0 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)) (2.0.4) 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)) (1.26.6) Requirement already satisfied: idna<4,>=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)) (3.2) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->sphinx->-r requirements.txt (line 11)) (1.1.5) Building wheels for collected packages: m2r, pandocfilters Building wheel for m2r (setup.py): started Building wheel for m2r (setup.py): finished with status 'done' Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10475 sha256=c68afe41bdfd765d7e6b0d998004718a86c84e84bf9cd459cccfde73c1d86e2b Stored in directory: /tmp/pip-ephem-wheel-cache-ei81lgo_/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=8006 sha256=483b7470c00ceb0ac3093a17c43dd16fe9c0a643dd35e0cc331113c08385c102 Stored in directory: /tmp/pip-ephem-wheel-cache-ei81lgo_/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000 Successfully built m2r pandocfilters Installing collected packages: zipp, typing-extensions, traitlets, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, nest-asyncio, jupyter-core, jsonschema, ipython-genutils, entrypoints, webencodings, wcwidth, ptyprocess, parso, nbformat, jupyter-client, testpath, prompt-toolkit, pillow, pickleshare, pexpect, pandocfilters, nbclient, mistune, matplotlib-inline, jupyterlab-pygments, jedi, defusedxml, decorator, bleach, backcall, pbr, pandas, nbconvert, ipython, et-xmlfile, debugpy, argcomplete, xlsxwriter, tqdm, sphinxcontrib-apidoc, seaborn, openpyxl, nbsphinx, m2r, joblib, ipykernel Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Attempting uninstall: pandas Found existing installation: pandas 1.1.3 Not uninstalling pandas at /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest Can't uninstall 'pandas'. No files were found to uninstall. Successfully installed argcomplete-1.12.3 attrs-21.2.0 backcall-0.2.0 bleach-4.1.0 debugpy-1.4.1 decorator-5.0.9 defusedxml-0.7.1 entrypoints-0.3 et-xmlfile-1.1.0 importlib-metadata-4.8.1 ipykernel-6.3.1 ipython-7.27.0 ipython-genutils-0.2.0 jedi-0.18.0 joblib-1.0.1 jsonschema-3.2.0 jupyter-client-7.0.2 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 m2r-0.2.1 matplotlib-inline-0.1.2 mistune-0.8.4 nbclient-0.5.4 nbconvert-6.1.0 nbformat-5.1.3 nbsphinx-0.8.7 nest-asyncio-1.5.1 openpyxl-3.0.7 pandas-1.2.5 pandocfilters-1.4.3 parso-0.8.2 pbr-5.6.0 pexpect-4.8.0 pickleshare-0.7.5 pillow-8.3.2 prompt-toolkit-3.0.20 ptyprocess-0.7.0 pyrsistent-0.18.0 pyzmq-22.2.1 seaborn-0.11.2 sphinxcontrib-apidoc-0.3.0 testpath-0.5.0 tornado-6.1 tqdm-4.62.2 traitlets-5.1.0 typing-extensions-3.10.0.2 wcwidth-0.2.5 webencodings-0.5.1 xlsxwriter-3.0.1 zipp-3.5.0 [rtd-command-info] start-time: 2021-09-03T20:36:40.368337Z, end-time: 2021-09-03T20:36:40.439843Z, 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 = '2021, FOXO Technologies, inc.' author = 'FOXO Technologies, inc.' # The short X.Y version version = '0.7' # The full version, including alpha/beta/rc tags release = '0.7.4' # -- General configuration --------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', 'sphinxcontrib.apidoc', 'm2r', 'nbsphinx', 'sphinx.ext.autosummary' ] # instead of CLI "sphinx-autodoc . _build/html" you write this apidoc_module_dir = '.' apidoc_output_dir = '_sphinx_build' apidoc_excluded_paths = ['tests'] apidoc_separate_modules = False # Add any paths that contain templates here, relative to this directory. templates_path = ['_sphinx_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] # source_suffix = '.rst' # The master toctree document. master_doc = 'index' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path . exclude_patterns = ['_sphinx_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' #'alabaster' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_sphinx_static'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # The default sidebars (for documents that don't match any pattern) are # defined by theme itself. Builtin themes are using these templates by # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', # 'searchbox.html']``. # # html_sidebars = {} # -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = 'methylcheckdoc' # -- Options for LaTeX output ------------------------------------------------ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'methylcheck.tex', 'methylcheck Documentation', 'FOXO Technologies, inc', 'manual'), ] # -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'methylcheck', 'methylcheck Documentation', [author], 1) ] # -- Options for Texinfo output ---------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'methylcheck', 'methylcheck Documentation', author, 'methylcheck', '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 shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("feature-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': '2770555f', } # 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/714692/' 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: 2021-09-03T20:36:40.548840Z, end-time: 2021-09-03T20:37:57.859985Z, duration: 77, 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. 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 [html]: targets for 25 source files that are out of date updating environment: 25 added, 0 changed, 0 removed reading sources... [ 4%] README reading sources... [ 8%] docs/bead-array reading sources... [ 12%] docs/example_notebooks/another-methylcheck-qc-example reading sources... [ 16%] docs/example_notebooks/demo-methylprep-to-methylcheck-example reading sources... [ 20%] docs/example_notebooks/demo_read_geo_processed reading sources... [ 24%] docs/example_notebooks/demo_using_matched_meta_data reading sources... [ 28%] docs/example_notebooks/examples reading sources... [ 32%] docs/example_notebooks/interactive-mds-filtering reading sources... [ 36%] docs/example_notebooks/methylcheck-cli reading sources... [ 40%] docs/example_notebooks/methylprep-methylcheck-qc-example reading sources... [ 44%] docs/example_notebooks/outdated-methylprep-methylcheck-example reading sources... [ 48%] docs/example_notebooks/postprocessQC_example reading sources... [ 52%] docs/example_notebooks/pval reading sources... [ 56%] docs/example_notebooks/qc-sex-check reading sources... [ 60%] docs/example_notebooks/rawQC_example reading sources... [ 64%] docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2 reading sources... [ 68%] docs/filtering-probes reading sources... [ 72%] docs/loading-data reading sources... [ 76%] docs/quality-control-example reading sources... [ 80%] docs/release-history reading sources... [ 84%] docs/research_notebooks/postprocessQC_example reading sources... [ 88%] docs/research_notebooks/pval reading sources... [ 92%] docs/research_notebooks/rawQC_example reading sources... [ 96%] 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)): Matplotlib is building the font cache; this may take a moment. reading sources... [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/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: docs/example_notebooks/tutorial_figs/fig3.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/fig4.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/fig5.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/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. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:912: WARNING: Title level inconsistent: Loading CSVs using Pandas ~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:1211: WARNING: Title level inconsistent: 'm\_value' ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb:1: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb:1: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_qc' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.read_geo' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load_both' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_controls' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.list_problem_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.drop_nan_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.sample_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_density_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_compare' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_mds_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.combine_mds' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.predict' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:87: WARNING: Unknown directive type "todo". .. todo:: - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs - DONE: meth_df deal with batches of files /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title. example: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation. 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:11: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot: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:36: 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: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.beta_mds_plot:52: 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:57: 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:61: WARNING: Unknown directive type "todo". .. todo:: - Reads the manifest file for the array, or at least a list of probe names to exclude/include. - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']] - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values df_no_sex_probes = df[probe_names_no_sex_probes] df_no_sex_probes.head() /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition. -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title. how it works: -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition. ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title. inputs: ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title. optional keyword arguments: --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title. analysis parameters: -------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title. returns: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo". .. todo:: - TODO: one dataframe of the retained samples, cutoff box is avg of datasets - TODO: each dataset's results as a transformed file - default: list of samples retained or excluded - option: a list of pyplot subplot objects /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title. input (one of these): ===================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title. optional params: ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title. returns: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title. input (choose one of these): ============================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent. /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'; 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 'methylcheck.qc_report' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/another-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo-methylprep-to-methylcheck-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_read_geo_processed.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_using_matched_meta_data.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/interactive-mds-filtering.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/pval.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/qc-sex-check.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 4%] README writing output... [ 8%] docs/bead-array writing output... [ 12%] docs/example_notebooks/another-methylcheck-qc-example writing output... [ 16%] docs/example_notebooks/demo-methylprep-to-methylcheck-example writing output... [ 20%] docs/example_notebooks/demo_read_geo_processed writing output... [ 24%] docs/example_notebooks/demo_using_matched_meta_data writing output... [ 28%] docs/example_notebooks/examples writing output... [ 32%] docs/example_notebooks/interactive-mds-filtering writing output... [ 36%] docs/example_notebooks/methylcheck-cli writing output... [ 40%] docs/example_notebooks/methylprep-methylcheck-qc-example writing output... [ 44%] docs/example_notebooks/outdated-methylprep-methylcheck-example writing output... [ 48%] docs/example_notebooks/postprocessQC_example writing output... [ 52%] docs/example_notebooks/pval writing output... [ 56%] docs/example_notebooks/qc-sex-check writing output... [ 60%] docs/example_notebooks/rawQC_example writing output... [ 64%] docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2 writing output... [ 68%] docs/filtering-probes writing output... [ 72%] docs/loading-data writing output... [ 76%] docs/quality-control-example writing output... [ 80%] docs/release-history writing output... [ 84%] docs/research_notebooks/postprocessQC_example writing output... [ 88%] docs/research_notebooks/pval writing output... [ 92%] docs/research_notebooks/rawQC_example writing output... [ 96%] docs/source/modules writing output... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:91: WARNING: Could not lex literal_block as "bash". Highlighting skipped. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.combine_mds' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.predict' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.get_sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.assign' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.combine_mds' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.predict' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.get_sex' b'':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.assign' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.combine_mds' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.predict' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.get_sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.assign' generating indices... genindex py-modindex copying notebooks ... [ 5%] docs/example_notebooks/another-methylcheck-qc-example.ipynb copying notebooks ... [ 11%] docs/example_notebooks/demo-methylprep-to-methylcheck-example.ipynb copying notebooks ... [ 16%] docs/example_notebooks/demo_read_geo_processed.ipynb copying notebooks ... [ 22%] docs/example_notebooks/demo_using_matched_meta_data.ipynb copying notebooks ... [ 27%] docs/example_notebooks/interactive-mds-filtering.ipynb copying notebooks ... [ 33%] docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb copying notebooks ... [ 38%] docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb copying notebooks ... [ 44%] docs/example_notebooks/postprocessQC_example.ipynb copying notebooks ... [ 50%] docs/example_notebooks/pval.ipynb copying notebooks ... [ 55%] docs/example_notebooks/qc-sex-check.ipynb copying notebooks ... [ 61%] docs/example_notebooks/rawQC_example.ipynb copying notebooks ... [ 66%] docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb copying notebooks ... [ 72%] docs/filtering-probes.ipynb copying notebooks ... [ 77%] docs/loading-data.ipynb copying notebooks ... [ 83%] docs/quality-control-example.ipynb copying notebooks ... [ 88%] docs/research_notebooks/postprocessQC_example.ipynb copying notebooks ... [ 94%] docs/research_notebooks/pval.ipynb copying notebooks ... [100%] docs/research_notebooks/rawQC_example.ipynb writing additional pages... search copying images... [ 0%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_another-methylcheck-qc-example_6_0.png copying images... [ 1%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_another-methylcheck-qc-example_7_0.png copying images... [ 2%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_another-methylcheck-qc-example_8_2.png copying images... [ 3%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_another-methylcheck-qc-example_9_1.png copying images... [ 4%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo-methylprep-to-methylcheck-example_7_1.png copying images... [ 4%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo-methylprep-to-methylcheck-example_8_0.png copying images... [ 5%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo-methylprep-to-methylcheck-example_9_3.png copying images... [ 6%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_1.png copying images... [ 7%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_3.png copying images... [ 8%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_5.png copying images... [ 9%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_7.png copying images... [ 9%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_11.png copying images... [ 10%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_13.png copying images... [ 11%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_15.png copying images... [ 12%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_interactive-mds-filtering_3_1.png copying images... [ 13%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_interactive-mds-filtering_3_3.png copying images... [ 13%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_interactive-mds-filtering_3_6.png copying images... [ 14%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_interactive-mds-filtering_3_8.png copying images... [ 15%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_13_0.png copying images... [ 16%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_15_0.png copying images... [ 17%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_17_0.png copying images... [ 18%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_18_3.png copying images... [ 18%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_19_0.png copying images... [ 19%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_20_2.png copying images... [ 20%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_0.png copying images... [ 21%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_1.png copying images... [ 22%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_2.png copying images... [ 22%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_3.png copying images... [ 23%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_4.png copying images... [ 24%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_5.png copying images... [ 25%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_6.png copying images... [ 26%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_7.png copying images... [ 27%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_8.png copying images... [ 27%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_9.png copying images... [ 28%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_12.png copying images... [ 29%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_14.png copying images... [ 30%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_16.png copying images... [ 31%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_18.png copying images... [ 31%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_13_0.png copying images... [ 32%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_15_0.png copying images... [ 33%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_17_0.png copying images... [ 34%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_18_3.png copying images... [ 35%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_19_0.png copying images... [ 36%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_20_2.png copying images... [ 36%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_0.png copying images... [ 37%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_1.png copying images... [ 38%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_2.png copying images... [ 39%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_3.png copying images... [ 40%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_4.png copying images... [ 40%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_5.png copying images... [ 41%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_6.png copying images... [ 42%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_7.png copying images... [ 43%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_8.png copying images... [ 44%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_9.png copying images... [ 45%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_12.png copying images... [ 45%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_14.png copying images... [ 46%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_16.png copying images... [ 47%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_18.png copying images... [ 48%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_postprocessQC_example_7_0.png copying images... [ 49%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_postprocessQC_example_8_0.png copying images... [ 50%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_postprocessQC_example_13_0.png copying images... [ 50%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_postprocessQC_example_15_0.png copying images... [ 51%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_12_0.png copying images... [ 52%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_14_0.png copying images... [ 53%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_14_1.png copying images... [ 54%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_15_1.png copying images... [ 54%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_16_2.png copying images... [ 55%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_16_4.png copying images... [ 56%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_16_6.png copying images... [ 57%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_16_8.png copying images... [ 58%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_0.png copying images... [ 59%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_1.png copying images... [ 59%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_3.png copying images... [ 60%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_4.png copying images... [ 61%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_5.png copying images... [ 62%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_6.png copying images... [ 63%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_7.png copying images... [ 63%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_8.png copying images... [ 64%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_18_1.png copying images... [ 65%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_3_1.png copying images... [ 66%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_4_1.png copying images... [ 67%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_5_2.png copying images... [ 68%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_6_1.png copying images... [ 68%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_6_2.png copying images... [ 69%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_6_3.png copying images... [ 70%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_7_1.png copying images... [ 71%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_8_1.png copying images... [ 72%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_11_1.png copying images... [ 72%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_13_1.png copying images... [ 73%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_14_0.png copying images... [ 74%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_0.png copying images... [ 75%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_1.png copying images... [ 76%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_2.png copying images... [ 77%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_3.png copying images... [ 77%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_4.png copying images... [ 78%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_5.png copying images... [ 79%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_6.png copying images... [ 80%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_7.png copying images... [ 81%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_8.png copying images... [ 81%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_9.png copying images... [ 82%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_12.png copying images... [ 83%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_15.png copying images... [ 84%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_18.png copying images... [ 85%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_21.png copying images... [ 86%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_0.png copying images... [ 86%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_1.png copying images... [ 87%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_2.png copying images... [ 88%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_3.png copying images... [ 89%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_4.png copying images... [ 90%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_5.png copying images... [ 90%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_6.png copying images... [ 91%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_7.png copying images... [ 92%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_8.png copying images... [ 93%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_9.png copying images... [ 94%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_12.png copying images... [ 95%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_14.png copying images... [ 95%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_16.png copying images... [ 96%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_18.png copying images... [ 97%] docs/research_notebooks/../../_build/doctrees/nbsphinx/docs_research_notebooks_postprocessQC_example_7_0.png copying images... [ 98%] docs/research_notebooks/../../_build/doctrees/nbsphinx/docs_research_notebooks_postprocessQC_example_8_0.png copying images... [ 99%] docs/research_notebooks/../../_build/doctrees/nbsphinx/docs_research_notebooks_postprocessQC_example_13_0.png copying images... [100%] docs/research_notebooks/../../_build/doctrees/nbsphinx/docs_research_notebooks_postprocessQC_example_15_0.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 204 warnings. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-09-03T20:37:58.070782Z, end-time: 2021-09-03T20:38:01.960226Z, 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. 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 [readthedocssinglehtmllocalmedia]: all documents 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: docs/example_notebooks/tutorial_figs/fig3.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/fig4.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/fig5.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/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/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_qc' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.read_geo' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load_both' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_controls' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.list_problem_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.drop_nan_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.sample_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_density_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_compare' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_mds_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.combine_mds' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.predict' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:87: WARNING: Unknown directive type "todo". .. todo:: - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs - DONE: meth_df deal with batches of files /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title. example: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation. 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:11: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot: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:36: 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: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.beta_mds_plot:52: 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:57: 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:61: WARNING: Unknown directive type "todo". .. todo:: - Reads the manifest file for the array, or at least a list of probe names to exclude/include. - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']] - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values df_no_sex_probes = df[probe_names_no_sex_probes] df_no_sex_probes.head() /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition. -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title. how it works: -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition. ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title. inputs: ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title. optional keyword arguments: --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title. analysis parameters: -------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title. returns: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo". .. todo:: - TODO: one dataframe of the retained samples, cutoff box is avg of datasets - TODO: each dataset's results as a transformed file - default: list of samples retained or excluded - option: a list of pyplot subplot objects /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title. input (one of these): ===================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title. optional params: ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title. returns: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title. input (choose one of these): ============================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent. /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'; 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 'methylcheck.qc_report' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/another-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo-methylprep-to-methylcheck-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_read_geo_processed.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_using_matched_meta_data.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/interactive-mds-filtering.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/pval.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/qc-sex-check.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... docs/loading-data docs/quality-control-example docs/bead-array docs/filtering-probes docs/example_notebooks/examples docs/source/modules docs/source/_autosummary/methylcheck.cli /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.cli' docs/source/_autosummary/methylcheck.run_pipeline /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_pipeline' docs/source/_autosummary/methylcheck.run_qc /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_qc' docs/source/_autosummary/methylcheck.read_geo /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.read_geo' docs/source/_autosummary/methylcheck.load /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.load' docs/source/_autosummary/methylcheck.load_both /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.load_both' docs/source/_autosummary/methylcheck.qc_signal_intensity /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.qc_signal_intensity' docs/source/_autosummary/methylcheck.plot_M_vs_U /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.plot_M_vs_U' docs/source/_autosummary/methylcheck.plot_controls /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.plot_controls' docs/source/_autosummary/methylcheck.plot_beta_by_type /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.plot_beta_by_type' docs/source/_autosummary/methylcheck.probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.probes' docs/source/_autosummary/methylcheck.list_problem_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.list_problem_probes' docs/source/_autosummary/methylcheck.exclude_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.exclude_probes' docs/source/_autosummary/methylcheck.exclude_sex_control_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' docs/source/_autosummary/methylcheck.drop_nan_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.drop_nan_probes' docs/source/_autosummary/methylcheck.samples /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.samples' docs/source/_autosummary/methylcheck.sample_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.sample_plot' docs/source/_autosummary/methylcheck.beta_density_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.beta_density_plot' docs/source/_autosummary/methylcheck.mean_beta_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.mean_beta_plot' docs/source/_autosummary/methylcheck.mean_beta_compare /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.mean_beta_compare' docs/source/_autosummary/methylcheck.beta_mds_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.beta_mds_plot' docs/source/_autosummary/methylcheck.combine_mds /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.combine_mds' docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' docs/source/_autosummary/methylcheck.predict /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.predict' docs/source/_autosummary/methylcheck.get_sex /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.get_sex' docs/source/_autosummary/methylcheck.assign /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.assign' docs/release-history writing... WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.combine_mds' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.predict' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.get_sex' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.assign' done writing additional files... copying images... [ 3%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_0.png copying images... [ 6%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_1.png copying images... [ 9%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_2.png copying images... [ 12%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_3.png copying images... [ 15%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_4.png copying images... [ 18%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_5.png copying images... [ 21%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_6.png copying images... [ 25%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_7.png copying images... [ 28%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_8.png copying images... [ 31%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_9.png copying images... [ 34%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_12.png copying images... [ 37%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_15.png copying images... [ 40%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_18.png copying images... [ 43%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_21.png copying images... [ 46%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_0.png copying images... [ 50%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_1.png copying images... [ 53%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_2.png copying images... [ 56%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_3.png copying images... [ 59%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_4.png copying images... [ 62%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_5.png copying images... [ 65%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_6.png copying images... [ 68%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_7.png copying images... [ 71%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_8.png copying images... [ 75%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_9.png copying images... [ 78%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_12.png copying images... [ 81%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_14.png copying images... [ 84%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_16.png copying images... [ 87%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_18.png copying images... [ 90%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_8_1.png copying images... [ 93%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_11_1.png copying images... [ 96%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_13_1.png copying images... [100%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_14_0.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_static' does not exist done copying extra files... done dumping object inventory... done build succeeded, 160 warnings. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-09-03T20:38:02.107997Z, end-time: 2021-09-03T20:38:09.733123Z, duration: 7, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex 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 [latex]: all documents 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: docs/example_notebooks/tutorial_figs/fig3.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/fig4.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/fig5.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/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/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_qc' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.read_geo' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load_both' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_controls' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.list_problem_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.drop_nan_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.sample_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_density_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_compare' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_mds_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.combine_mds' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.predict' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:87: WARNING: Unknown directive type "todo". .. todo:: - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs - DONE: meth_df deal with batches of files /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title. example: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation. 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:11: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot: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:36: 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: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.beta_mds_plot:52: 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:57: 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:61: WARNING: Unknown directive type "todo". .. todo:: - Reads the manifest file for the array, or at least a list of probe names to exclude/include. - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']] - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values df_no_sex_probes = df[probe_names_no_sex_probes] df_no_sex_probes.head() /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition. -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title. how it works: -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition. ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title. inputs: ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title. optional keyword arguments: --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title. analysis parameters: -------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title. returns: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo". .. todo:: - TODO: one dataframe of the retained samples, cutoff box is avg of datasets - TODO: each dataset's results as a transformed file - default: list of samples retained or excluded - option: a list of pyplot subplot objects /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title. input (one of these): ===================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title. optional params: ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title. returns: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title. input (choose one of these): ============================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent. /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'; 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 'methylcheck.qc_report' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/another-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo-methylprep-to-methylcheck-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_read_geo_processed.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_using_matched_meta_data.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/interactive-mds-filtering.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/pval.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/qc-sex-check.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree done processing methylcheck.tex...index docs/loading-data docs/quality-control-example docs/bead-array docs/filtering-probes docs/example_notebooks/examples docs/source/modules docs/source/_autosummary/methylcheck.cli /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/builders/latex/__init__.py:201: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. if toctrees[0].get('maxdepth') > 0: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.cli' docs/source/_autosummary/methylcheck.run_pipeline /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_pipeline' docs/source/_autosummary/methylcheck.run_qc /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_qc' docs/source/_autosummary/methylcheck.read_geo /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.read_geo' docs/source/_autosummary/methylcheck.load /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.load' docs/source/_autosummary/methylcheck.load_both /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.load_both' docs/source/_autosummary/methylcheck.qc_signal_intensity /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.qc_signal_intensity' docs/source/_autosummary/methylcheck.plot_M_vs_U /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.plot_M_vs_U' docs/source/_autosummary/methylcheck.plot_controls /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.plot_controls' docs/source/_autosummary/methylcheck.plot_beta_by_type /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.plot_beta_by_type' docs/source/_autosummary/methylcheck.probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.probes' docs/source/_autosummary/methylcheck.list_problem_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.list_problem_probes' docs/source/_autosummary/methylcheck.exclude_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.exclude_probes' docs/source/_autosummary/methylcheck.exclude_sex_control_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' docs/source/_autosummary/methylcheck.drop_nan_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.drop_nan_probes' docs/source/_autosummary/methylcheck.samples /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.samples' docs/source/_autosummary/methylcheck.sample_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.sample_plot' docs/source/_autosummary/methylcheck.beta_density_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.beta_density_plot' docs/source/_autosummary/methylcheck.mean_beta_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.mean_beta_plot' docs/source/_autosummary/methylcheck.mean_beta_compare /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.mean_beta_compare' docs/source/_autosummary/methylcheck.beta_mds_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.beta_mds_plot' docs/source/_autosummary/methylcheck.combine_mds /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.combine_mds' docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' docs/source/_autosummary/methylcheck.predict /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.predict' docs/source/_autosummary/methylcheck.get_sex /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.get_sex' docs/source/_autosummary/methylcheck.assign /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.assign' docs/release-history resolving references... README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://readthedocs.com/projects/life-epigenetics-methylcheck/badge/?version=latest) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/badge/License-MIT-yellow.svg) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://circleci.com/gh/FoxoTech/methylcheck.svg?style=shield) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://api.codacy.com/project/badge/Grade/aedf5c223e39415180ff35153b2bad89) README.md:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://coveralls.io/repos/github/FoxoTech/methylcheck/badge.svg?t=OVL45Q) README.md:38: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/dm/methylcheck.svg?label=pypi%20downloads&logo=PyPI&logoColor=white:target:https://img.shields.io/pypi/dm/methylcheck.svg?label=pypi%20downloads&logo=PyPI&logoColor=white:alt:PyPI-Downloads:raw-html-m2r:``) writing... done copying images... [ 2%] https://raw.githubusercontent.com/FoxoTech/methylcheck/master/docs/methylcheck_overview.png copying images... [ 5%] https://raw.githubusercontent.com/FoxoTech/methylcheck/master/docs/methylcheck_functions.png copying images... [ 8%] https://raw.githubusercontent.com/FoxoTech/methylcheck/master/docs/example_controls_report.png copying images... [ 10%] https://raw.githubusercontent.com/FoxoTech/methylcheck/master/docs/example_ReportPDF.png copying images... [ 13%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_0.png copying images... [ 16%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_1.png copying images... [ 18%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_2.png copying images... [ 21%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_3.png copying images... [ 24%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_4.png copying images... [ 27%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_5.png copying images... [ 29%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_6.png copying images... [ 32%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_7.png copying images... [ 35%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_8.png copying images... [ 37%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_9.png copying images... [ 40%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_12.png copying images... [ 43%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_15.png copying images... [ 45%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_18.png copying images... [ 48%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_21.png copying images... [ 51%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_0.png copying images... [ 54%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_1.png copying images... [ 56%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_2.png copying images... [ 59%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_3.png copying images... [ 62%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_4.png copying images... [ 64%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_5.png copying images... [ 67%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_6.png copying images... [ 70%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_7.png copying images... [ 72%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_8.png copying images... [ 75%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_9.png copying images... [ 78%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_12.png copying images... [ 81%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_14.png copying images... [ 83%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_16.png copying images... [ 86%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_18.png copying images... [ 89%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_8_1.png copying images... [ 91%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_11_1.png copying images... [ 94%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_13_1.png copying images... [ 97%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_14_0.png copying images... [100%] https://raw.githubusercontent.com/FoxoTech/methylcheck/master/docs/plot_M_vs_U_compare_dye_noob_to_raw.png copying TeX support files... done build succeeded, 139 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2021-09-03T20:38:15.937356Z, end-time: 2021-09-03T20:38:16.018540Z, 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: 2021-09-03T20:38:16.124726Z, end-time: 2021-09-03T20:38:45.359967Z, duration: 29, 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. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylcheck" "methylcheck.tex"' ------------ This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./methylcheck.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file life-epigenetics-methylcheck.idx (./life-epigenetics-methylcheck.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.228 ...3083485633693ce12e4792f1127c13dbb3}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.228 ...3083485633693ce12e4792f1127c13dbb3}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.230 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.230 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.232 ...f26a5b78d7ab1b7a7e141a/methylcheck}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.232 ...f26a5b78d7ab1b7a7e141a/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 ...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.234 ...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 ...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.236 ...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 23 8. ! LaTeX Error: Unknown graphics extension: .png"height="50">`. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.238 ...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 23 8. ! LaTeX Error: Unknown graphics extension: .png"height="50">`. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.238 ...dd9574bfece/python3.6}.png"height="50">`} Overfull \hbox (975.67087pt too wide) in paragraph at lines 2--241 [][][][][][] [1] [2 <./methylcheck_overview.png>] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (298.86465pt too wide) in paragraph at lines 2--248 [][][][][][] [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--371 [][][][][][] [11] [12 <./example_controls_report.png>] Overfull \hbox (204.79077pt too wide) in paragraph at lines 2--401 [][][][][][] [13] Overfull \vbox (162.62206pt too high) has occurred while \output is active [14 <./example_ReportPDF.png>] 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 6/6 [00:00<00:00, 2400.86it/s] Overfull \vbox (1.63934pt too high) detected at line 668 [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.699 ...███| 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, 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, 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, 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, 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, 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, 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, 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, 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, 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.741 ...███| 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, 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, 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, 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, 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, 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, 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, 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, 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, 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 6/6 [00:01<00:00, 3.68it/s] Overfull \vbox (1.32576pt too high) detected at line 890 [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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 1/1 [00:00<00:00, 6.61it/s] Underfull \vbox (badness 3492) detected at line 1153 [24] Underfull \vbox (badness 10000) detected at line 1164 [25 <./docs_quality-control-example_5_0.png>] Underfull \vbox (badness 10000) detected at line 1175 [26 <./docs_quality-control-example_5_1.png>] Underfull \vbox (badness 10000) detected at line 1186 [27 <./docs_quality-control-example_5_2.png>] Underfull \vbox (badness 10000) detected at line 1197 [28 <./docs_quality-control-example_5_3.png>] Underfull \vbox (badness 10000) detected at line 1208 [29 <./docs_quality-control-example_5_4.png>] Underfull \vbox (badness 10000) detected at line 1219 [30 <./docs_quality-control-example_5_5.png>] Underfull \vbox (badness 10000) detected at line 1230 [31 <./docs_quality-control-example_5_6.png>] Underfull \vbox (badness 10000) detected at line 1241 [32 <./docs_quality-control-example_5_7.png>] Underfull \vbox (badness 10000) detected at line 1252 [33 <./docs_quality-control-example_5_8.png>] Underfull \vbox (badness 10000) detected at line 1290 [34 <./docs_quality-control-example_5_9.png>] Underfull \vbox (badness 10000) detected at line 1327 [35 <./docs_quality-control-example_5_12.png>] Underfull \vbox (badness 10000) detected at line 1364 [36 <./docs_quality-control-example_5_15.png>] Underfull \vbox (badness 10000) detected at line 1401 [37 <./docs_quality-control-example_5_18.png>] Underfull \vbox (badness 10000) detected at line 1422 [38 <./docs_quality-control-example_5_21.png>] Underfull \vbox (badness 10000) detected at line 1433 [39 <./docs_quality-control-example_6_0.png>] Underfull \vbox (badness 10000) detected at line 1444 [40 <./docs_quality-control-example_6_1.png>] Underfull \vbox (badness 10000) detected at line 1455 [41 <./docs_quality-control-example_6_2.png>] Underfull \vbox (badness 10000) detected at line 1466 [42 <./docs_quality-control-example_6_3.png>] Underfull \vbox (badness 10000) detected at line 1477 [43 <./docs_quality-control-example_6_4.png>] Underfull \vbox (badness 10000) detected at line 1488 [44 <./docs_quality-control-example_6_5.png>] Underfull \vbox (badness 10000) detected at line 1499 [45 <./docs_quality-control-example_6_6.png>] Underfull \vbox (badness 10000) detected at line 1510 [46 <./docs_quality-control-example_6_7.png>] Underfull \vbox (badness 10000) detected at line 1521 [47 <./docs_quality-control-example_6_8.png>] Underfull \vbox (badness 10000) detected at line 1558 [48 <./docs_quality-control-example_6_9.png>] Underfull \vbox (badness 10000) detected at line 1582 [49 <./docs_quality-control-example_6_12.png>] Underfull \vbox (badness 10000) detected at line 1606 [50 <./docs_quality-control-example_6_14.png>] Underfull \vbox (badness 10000) detected at line 1630 [51 <./docs_quality-control-example_6_16.png>] [52 <./docs_quality-control-exam ple_6_18.png>] [53] Overfull \hbox (2028.37567pt too wide) in paragraph at lines 2--1764 [][][][][][] [54] Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 []\T1/phv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 \T1/phv/m/n/10 gu- Overfull \hbox (7.23338pt too wide) in paragraph at lines 1865--1865 \T1/phv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 []\T1/phv/m/n/10 De- Overfull \hbox (1.02771pt too wide) in paragraph at lines 1865--1865 \T1/phv/m/n/10 fault| Overfull \hbox (17.77328pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 data_dir| Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 path Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 \T1/ptm/b/n/10 RE- Overfull \hbox (22.32765pt too wide) in paragraph at lines 1865--1865 \T1/ptm/b/n/10 QUIRED| Overfull \hbox (1.11351pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 out- Overfull \hbox (15.00327pt too wide) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 filepath| Overfull \hbox (6.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 None| Overfull \hbox (0.55345pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 col- Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 or- Overfull \hbox (5.56345pt too wide) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 blind| Overfull \hbox (12.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 False| Overfull \hbox (22.5233pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 bg_offset| Overfull \hbox (2.42802pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 3000| Overfull \hbox (0.55345pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 cut- Overfull \hbox (25.30319pt too wide) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 off_adjust| Overfull \hbox (10.75363pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 legacy| Overfull \hbox (12.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 False| Overfull \hbox (11.66357pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 round- Overfull \hbox (1.9735pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 pval| Overfull \hbox (6.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 True| Overfull \hbox (18.64328pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 pval_sig| Overfull \hbox (5.55334pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 pass- [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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 6/6 [00:49<00:00, 8.26s/it] Underfull \vbox (badness 10000) detected at line 2067 [57] Underfull \vbox (badness 10000) detected at line 2103 [58 <./docs_filtering-probes_8_1.png>] Underfull \vbox (badness 10000) detected at line 2139 [59 <./docs_filtering-probes_11_1.png>] Underfull \vbox (badness 10000) detected at line 2159 [60 <./docs_filtering-probes_13_1.png>] [61 <./docs_filtering-probes_14_0.png>] Overfull \hbox (909.45023pt too wide) in paragraph at lines 2--2215 [][][][][][] [62] Overfull \vbox (686.56174pt too high) has occurred while \output is active [63 <./5146fdf952a8919a55a6efc634c173948bb008a6.png>] Underfull \hbox (badness 10000) in paragraph at lines 2277--2278 []|\T1/pcr/m/n/10 methylcheck.plot_controls\T1/ptm/m/n/10 ([path, sub-set, Underfull \hbox (badness 10000) in paragraph at lines 2279--2281 []|\T1/ptm/m/n/10 internal ar-ray QC con-trols (avail-able with the Underfull \hbox (badness 10000) in paragraph at lines 2282--2283 []|\T1/pcr/m/n/10 methylcheck.plot_beta_by_type\T1/ptm/m/n/10 (beta_df[, LaTeX Warning: Hyper reference `docs/source/modules:module-methylcheck.probes' on page 64 undefined on input line 2287. Underfull \hbox (badness 10000) in paragraph at lines 2292--2293 []|\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 2302--2303 []|\T1/pcr/m/n/10 methylcheck.exclude_sex_control_probes\T1/ptm/m/n/10 (df, Underfull \hbox (badness 10000) in paragraph at lines 2307--2308 []|\T1/pcr/m/n/10 methylcheck.drop_nan_probes\T1/ptm/m/n/10 (df[, silent, LaTeX Warning: Hyper reference `docs/source/modules:module-methylcheck.samples' on page 64 undefined on input line 2312. Underfull \hbox (badness 10000) in paragraph at lines 2322--2323 []|\T1/pcr/m/n/10 methylcheck.beta_density_plot\T1/ptm/m/n/10 (df[, ver- Underfull \hbox (badness 10000) in paragraph at lines 2327--2328 []|\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 2332--2333 []|\T1/pcr/m/n/10 methylcheck.mean_beta_compare\T1/ptm/m/n/10 (df1, df2[, Overfull \hbox (56.71234pt too wide) in paragraph at lines 2347--2348 []|\T1/pcr/m/n/10 methylcheck.cumulative_sum_beta_distribution\T1/ptm/m/n/10 (d f)| LaTeX Warning: Hyper reference `docs/source/modules:module-methylcheck.predict' on page 64 undefined on input line 2352. Package longtable Warning: Column widths have changed (longtable) in table 1 on input line 2367. Underfull \hbox (badness 10000) in paragraph at lines 2374--2374 \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 , [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 2491--2491 []\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 2491--2491 \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 2491--2491 \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- [66] Underfull \hbox (badness 7907) in paragraph at lines 2561--2568 []\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 2561--2568 \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 2561--2568 \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 2575--2575 []\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 2575--2575 \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 2575--2575 \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 , [67] Underfull \hbox (badness 10000) in paragraph at lines 2643--2643 []\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 2643--2643 \T1/ptm/m/it/10 turn_sample_column_names=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2647--2654 []\T1/ptm/m/n/10 betas non-normalized ma-trix_processed ma-trix_signal se-ries_ matrix ^^U read_series_matrix(file, de- Underfull \hbox (badness 10000) in paragraph at lines 2684--2686 []\T1/ptm/m/n/10 {`27k', `450k', `EPIC', `EPIC-PLUS', `MOUSE'} or {`Il-lu-mi-na Hu-man-Methy-la- Underfull \hbox (badness 10000) in paragraph at lines 2684--2686 \T1/ptm/m/n/10 tion27k','IlluminaHumanMethylation450k','IlluminaHumanMethylatio nEPIC', `mouse'} or [68] Underfull \hbox (badness 10000) in paragraph at lines 2723--2724 []\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 2726--2729 []\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 2726--2729 \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 2726--2729 \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 2738--2740 []\T1/ptm/m/n/10 ref: [][]$https : / / bioconductor . org / packages / devel / bioc / vignettes / sesame / inst / doc / sesame . html # [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 2980--2982 []\T1/ptm/m/n/10 This [71] Underfull \hbox (badness 10000) in paragraph at lines 3029--3029 []\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 3029--3029 \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 3029--3029 \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 3029--3029 \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 , [72] Underfull \hbox (badness 10000) in paragraph at lines 3123--3123 []\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 3123--3123 \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 , Underfull \hbox (badness 10000) in paragraph at lines 3123--3123 \T1/ptm/m/it/10 plot_removed=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nafill='quic k'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=None\T1/ptm/m/n/10 , Overfull \hbox (57.53044pt too wide) in paragraph at lines 3155--3157 [] Overfull \hbox (205.40927pt too wide) in paragraph at lines 3158--3161 [] [73] Underfull \hbox (badness 10000) in paragraph at lines 3332--3332 []\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 , [74] Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 []\T1/ptm/m/it/10 data_containers=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path=Non e\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 un-meth=None\T1/ptm/m /n/10 , \T1/ptm/m/it/10 poobah=None\T1/ptm/m/n/10 , Underfull \hbox (badness 7558) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 palette=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- Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot=True\T1/ptm/m/n /10 , \T1/ptm/m/it/10 cut-off_line=True\T1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 3365--3370 []\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 3365--3370 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = Underfull \hbox (badness 6910) in paragraph at lines 3413--3413 \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 , [75] Underfull \hbox (badness 6944) in paragraph at lines 3430--3435 []\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 3430--3435 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = Underfull \hbox (badness 10000) in paragraph at lines 3485--3487 []\T1/ptm/m/n/10 `non-polymorphic' | Underfull \hbox (badness 10000) in paragraph at lines 3505--3505 []\T1/ptm/m/it/10 path_or_df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 use_median=False\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3517--3517 []\T1/ptm/m/it/10 data_source\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3517--3517 \T1/ptm/m/it/10 save=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 - Underfull \hbox (badness 10000) in paragraph at lines 3517--3517 \T1/ptm/m/it/10 clude_probe_failure_percent=True\T1/ptm/m/n/10 , \T1/ptm/m/it/1 0 poobah_cutoff=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cus- [76] [77] [78] Overfull \hbox (33.52034pt too wide) in paragraph at lines 3737--3739 [] [79] [80] [81] [82] Chapter 7. [83] [84] LaTeX Warning: Reference `docs/source/modules:module-methylcheck.load_processed ' on page 85 undefined on input line 3950. LaTeX Warning: Reference `docs/source/modules:module-methylcheck.predict' on pa ge 85 undefined on input line 3951. LaTeX Warning: Reference `docs/source/modules:module-methylcheck.probes' on pag e 85 undefined on input line 3952. LaTeX Warning: Reference `docs/source/modules:module-methylcheck.qc_plot' on pa ge 85 undefined on input line 3953. LaTeX Warning: Reference `docs/source/modules:module-methylcheck.read_geo_proce ssed' on page 85 undefined on input line 3954. LaTeX Warning: Reference `docs/source/modules:module-methylcheck.samples' on pa ge 85 undefined on input line 3955. [85] 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 (89 pages, 2996182 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.' Latexmk: Missing input file: 'life-epigenetics-methylcheck.ind' from line 'No file life-epigenetics-methylcheck.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Latexmk: List of undefined refs and citations: Reference `docs/source/modules:module-methylcheck.load_processed' on page 85 undefined on input line 3950 Reference `docs/source/modules:module-methylcheck.predict' on page 85 undefined on input line 3951 Reference `docs/source/modules:module-methylcheck.probes' on page 85 undefined on input line 3952 Reference `docs/source/modules:module-methylcheck.qc_plot' on page 85 undefined on input line 3953 Reference `docs/source/modules:module-methylcheck.read_geo_processed' on page 85 undefined on input line 3954 Reference `docs/source/modules:module-methylcheck.samples' on page 85 undefined on input line 3955 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 (32 entries accepted, 0 rejected). Sorting entries....done (154 comparisons). Generating output file life-epigenetics-methylcheck.ind....done (79 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. (./sphinxmanual.cls Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file life-epigenetics-methylcheck.idx (./life-epigenetics-methylcheck.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./life-epigenetics-methylcheck.out) (./life-epigenetics-methylcheck.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./life-epigenetics-methylcheck.toc (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1]) [2] ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.228 ...3083485633693ce12e4792f1127c13dbb3}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.228 ...3083485633693ce12e4792f1127c13dbb3}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.230 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.230 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.232 ...f26a5b78d7ab1b7a7e141a/methylcheck}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.232 ...f26a5b78d7ab1b7a7e141a/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 ...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.234 ...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 ...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.236 ...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 23 8. ! LaTeX Error: Unknown graphics extension: .png"height="50">`. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.238 ...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 23 8. ! LaTeX Error: Unknown graphics extension: .png"height="50">`. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.238 ...dd9574bfece/python3.6}.png"height="50">`} Overfull \hbox (975.67087pt too wide) in paragraph at lines 2--241 [][][][][][] [1] [2 <./methylcheck_overview.png>] Chapter 1. Overfull \hbox (298.86465pt too wide) in paragraph at lines 2--248 [][][][][][] [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--371 [][][][][][] [11] [12 <./example_controls_report.png>] Overfull \hbox (204.79077pt too wide) in paragraph at lines 2--401 [][][][][][] [13] Overfull \vbox (162.62206pt too high) has occurred while \output is active [14 <./example_ReportPDF.png>] 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 6/6 [00:00<00:00, 2400.86it/s] Overfull \vbox (1.63934pt too high) detected at line 668 [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.699 ...███| 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, 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, 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, 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, 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, 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, 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, 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, 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, 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.741 ...███| 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, 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, 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, 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, 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, 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, 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, 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, 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, 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 6/6 [00:01<00:00, 3.68it/s] Overfull \vbox (1.32576pt too high) detected at line 890 [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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 1/1 [00:00<00:00, 6.61it/s] Underfull \vbox (badness 3492) detected at line 1153 [24] Underfull \vbox (badness 10000) detected at line 1164 [25 <./docs_quality-control-example_5_0.png>] Underfull \vbox (badness 10000) detected at line 1175 [26 <./docs_quality-control-example_5_1.png>] Underfull \vbox (badness 10000) detected at line 1186 [27 <./docs_quality-control-example_5_2.png>] Underfull \vbox (badness 10000) detected at line 1197 [28 <./docs_quality-control-example_5_3.png>] Underfull \vbox (badness 10000) detected at line 1208 [29 <./docs_quality-control-example_5_4.png>] Underfull \vbox (badness 10000) detected at line 1219 [30 <./docs_quality-control-example_5_5.png>] Underfull \vbox (badness 10000) detected at line 1230 [31 <./docs_quality-control-example_5_6.png>] Underfull \vbox (badness 10000) detected at line 1241 [32 <./docs_quality-control-example_5_7.png>] Underfull \vbox (badness 10000) detected at line 1252 [33 <./docs_quality-control-example_5_8.png>] Underfull \vbox (badness 10000) detected at line 1290 [34 <./docs_quality-control-example_5_9.png>] Underfull \vbox (badness 10000) detected at line 1327 [35 <./docs_quality-control-example_5_12.png>] Underfull \vbox (badness 10000) detected at line 1364 [36 <./docs_quality-control-example_5_15.png>] Underfull \vbox (badness 10000) detected at line 1401 [37 <./docs_quality-control-example_5_18.png>] Underfull \vbox (badness 10000) detected at line 1422 [38 <./docs_quality-control-example_5_21.png>] Underfull \vbox (badness 10000) detected at line 1433 [39 <./docs_quality-control-example_6_0.png>] Underfull \vbox (badness 10000) detected at line 1444 [40 <./docs_quality-control-example_6_1.png>] Underfull \vbox (badness 10000) detected at line 1455 [41 <./docs_quality-control-example_6_2.png>] Underfull \vbox (badness 10000) detected at line 1466 [42 <./docs_quality-control-example_6_3.png>] Underfull \vbox (badness 10000) detected at line 1477 [43 <./docs_quality-control-example_6_4.png>] Underfull \vbox (badness 10000) detected at line 1488 [44 <./docs_quality-control-example_6_5.png>] Underfull \vbox (badness 10000) detected at line 1499 [45 <./docs_quality-control-example_6_6.png>] Underfull \vbox (badness 10000) detected at line 1510 [46 <./docs_quality-control-example_6_7.png>] Underfull \vbox (badness 10000) detected at line 1521 [47 <./docs_quality-control-example_6_8.png>] Underfull \vbox (badness 10000) detected at line 1558 [48 <./docs_quality-control-example_6_9.png>] Underfull \vbox (badness 10000) detected at line 1582 [49 <./docs_quality-control-example_6_12.png>] Underfull \vbox (badness 10000) detected at line 1606 [50 <./docs_quality-control-example_6_14.png>] Underfull \vbox (badness 10000) detected at line 1630 [51 <./docs_quality-control-example_6_16.png>] [52 <./docs_quality-control-exam ple_6_18.png>] [53] Overfull \hbox (2028.37567pt too wide) in paragraph at lines 2--1764 [][][][][][] [54] Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 []\T1/phv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 \T1/phv/m/n/10 gu- Overfull \hbox (7.23338pt too wide) in paragraph at lines 1865--1865 \T1/phv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 []\T1/phv/m/n/10 De- Overfull \hbox (1.02771pt too wide) in paragraph at lines 1865--1865 \T1/phv/m/n/10 fault| Overfull \hbox (17.77328pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 data_dir| Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 path Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 \T1/ptm/b/n/10 RE- Overfull \hbox (22.32765pt too wide) in paragraph at lines 1865--1865 \T1/ptm/b/n/10 QUIRED| Overfull \hbox (1.11351pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 out- Overfull \hbox (15.00327pt too wide) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 filepath| Overfull \hbox (6.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 None| Overfull \hbox (0.55345pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 col- Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 or- Overfull \hbox (5.56345pt too wide) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 blind| Overfull \hbox (12.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 False| Overfull \hbox (22.5233pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 bg_offset| Overfull \hbox (2.42802pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 3000| Overfull \hbox (0.55345pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 cut- Overfull \hbox (25.30319pt too wide) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 off_adjust| Overfull \hbox (10.75363pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 legacy| Overfull \hbox (12.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 False| Overfull \hbox (11.66357pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 round- Overfull \hbox (1.9735pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 pval| Overfull \hbox (6.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 True| Overfull \hbox (18.64328pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 pval_sig| Overfull \hbox (5.55334pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 pass- [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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 6/6 [00:49<00:00, 8.26s/it] Underfull \vbox (badness 10000) detected at line 2067 [57] Underfull \vbox (badness 10000) detected at line 2103 [58 <./docs_filtering-probes_8_1.png>] Underfull \vbox (badness 10000) detected at line 2139 [59 <./docs_filtering-probes_11_1.png>] Underfull \vbox (badness 10000) detected at line 2159 [60 <./docs_filtering-probes_13_1.png>] [61 <./docs_filtering-probes_14_0.png>] Overfull \hbox (909.45023pt too wide) in paragraph at lines 2--2215 [][][][][][] [62] Overfull \vbox (686.56174pt too high) has occurred while \output is active [63 <./5146fdf952a8919a55a6efc634c173948bb008a6.png>] Underfull \hbox (badness 10000) in paragraph at lines 2277--2278 []|\T1/pcr/m/n/10 methylcheck.plot_controls\T1/ptm/m/n/10 ([path, sub-set, Underfull \hbox (badness 10000) in paragraph at lines 2279--2281 []|\T1/ptm/m/n/10 internal ar-ray QC con-trols (avail-able with the Underfull \hbox (badness 10000) in paragraph at lines 2282--2283 []|\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 2292--2293 []|\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 2302--2303 []|\T1/pcr/m/n/10 methylcheck.exclude_sex_control_probes\T1/ptm/m/n/10 (df, Underfull \hbox (badness 10000) in paragraph at lines 2307--2308 []|\T1/pcr/m/n/10 methylcheck.drop_nan_probes\T1/ptm/m/n/10 (df[, silent, Underfull \hbox (badness 10000) in paragraph at lines 2322--2323 []|\T1/pcr/m/n/10 methylcheck.beta_density_plot\T1/ptm/m/n/10 (df[, ver- Underfull \hbox (badness 10000) in paragraph at lines 2327--2328 []|\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 2332--2333 []|\T1/pcr/m/n/10 methylcheck.mean_beta_compare\T1/ptm/m/n/10 (df1, df2[, Overfull \hbox (56.71234pt too wide) in paragraph at lines 2347--2348 []|\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 2374--2374 \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 , [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 2491--2491 []\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 2491--2491 \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 2491--2491 \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- [66] Underfull \hbox (badness 7907) in paragraph at lines 2561--2568 []\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 2561--2568 \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 2561--2568 \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 2575--2575 []\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 2575--2575 \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 2575--2575 \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 , [67] Underfull \hbox (badness 10000) in paragraph at lines 2643--2643 []\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 2643--2643 \T1/ptm/m/it/10 turn_sample_column_names=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2647--2654 []\T1/ptm/m/n/10 betas non-normalized ma-trix_processed ma-trix_signal se-ries_ matrix ^^U read_series_matrix(file, de- Underfull \hbox (badness 10000) in paragraph at lines 2684--2686 []\T1/ptm/m/n/10 {`27k', `450k', `EPIC', `EPIC-PLUS', `MOUSE'} or {`Il-lu-mi-na Hu-man-Methy-la- Underfull \hbox (badness 10000) in paragraph at lines 2684--2686 \T1/ptm/m/n/10 tion27k','IlluminaHumanMethylation450k','IlluminaHumanMethylatio nEPIC', `mouse'} or [68] Underfull \hbox (badness 10000) in paragraph at lines 2723--2724 []\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 2726--2729 []\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 2726--2729 \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 2726--2729 \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 2738--2740 []\T1/ptm/m/n/10 ref: [][]$https : / / bioconductor . org / packages / devel / bioc / vignettes / sesame / inst / doc / sesame . html # [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 2980--2982 []\T1/ptm/m/n/10 This [71] Underfull \hbox (badness 10000) in paragraph at lines 3029--3029 []\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 3029--3029 \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 3029--3029 \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 3029--3029 \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 , [72] Underfull \hbox (badness 10000) in paragraph at lines 3123--3123 []\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 3123--3123 \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 , Underfull \hbox (badness 10000) in paragraph at lines 3123--3123 \T1/ptm/m/it/10 plot_removed=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nafill='quic k'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=None\T1/ptm/m/n/10 , Overfull \hbox (57.53044pt too wide) in paragraph at lines 3155--3157 [] Overfull \hbox (205.40927pt too wide) in paragraph at lines 3158--3161 [] [73] Underfull \hbox (badness 10000) in paragraph at lines 3332--3332 []\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 , [74] Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 []\T1/ptm/m/it/10 data_containers=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path=Non e\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 un-meth=None\T1/ptm/m /n/10 , \T1/ptm/m/it/10 poobah=None\T1/ptm/m/n/10 , Underfull \hbox (badness 7558) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 palette=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- Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot=True\T1/ptm/m/n /10 , \T1/ptm/m/it/10 cut-off_line=True\T1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 3365--3370 []\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 3365--3370 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = Underfull \hbox (badness 6910) in paragraph at lines 3413--3413 \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 , [75] Underfull \hbox (badness 6944) in paragraph at lines 3430--3435 []\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 3430--3435 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = Underfull \hbox (badness 10000) in paragraph at lines 3485--3487 []\T1/ptm/m/n/10 `non-polymorphic' | Underfull \hbox (badness 10000) in paragraph at lines 3505--3505 []\T1/ptm/m/it/10 path_or_df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 use_median=False\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3517--3517 []\T1/ptm/m/it/10 data_source\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3517--3517 \T1/ptm/m/it/10 save=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 - Underfull \hbox (badness 10000) in paragraph at lines 3517--3517 \T1/ptm/m/it/10 clude_probe_failure_percent=True\T1/ptm/m/n/10 , \T1/ptm/m/it/1 0 poobah_cutoff=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cus- [76] [77] [78] Overfull \hbox (33.52034pt too wide) in paragraph at lines 3737--3739 [] [79] [80] [81] [82] Chapter 7. [83] [84] [85] (./life-epigenetics-methylcheck.ind [86] 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 14--16 []\T1/pcr/m/n/10 bis_conversion_control() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\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 22--24 []\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 27--29 []\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 29--30 []\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 34--36 []\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 43--44 []\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 45--46 []\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 49--50 []\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 50--51 []\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 55--56 []\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 60--61 []\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 61--62 []\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 64--65 []\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 68--69 []\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 72--73 []\T1/pcr/m/n/10 read_geo() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule [87]) (./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'. ) (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 (91 pages, 3009009 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.' Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylcheck.aux' 'life-epigenetics-methylcheck.out' 'life-epigenetics-methylcheck.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ 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. (./sphinxmanual.cls Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file life-epigenetics-methylcheck.idx (./life-epigenetics-methylcheck.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./life-epigenetics-methylcheck.out) (./life-epigenetics-methylcheck.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./life-epigenetics-methylcheck.toc (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1]) [2] ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.228 ...3083485633693ce12e4792f1127c13dbb3}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.228 ...3083485633693ce12e4792f1127c13dbb3}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.230 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.230 ...c38de6bb2bf7b78/License-MIT-yellow}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.232 ...f26a5b78d7ab1b7a7e141a/methylcheck}.svg}} ^^M ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.232 ...f26a5b78d7ab1b7a7e141a/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 ...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.234 ...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 ...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.236 ...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 23 8. ! LaTeX Error: Unknown graphics extension: .png"height="50">`. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.238 ...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 23 8. ! LaTeX Error: Unknown graphics extension: .png"height="50">`. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.238 ...dd9574bfece/python3.6}.png"height="50">`} Overfull \hbox (975.67087pt too wide) in paragraph at lines 2--241 [][][][][][] [1] [2 <./methylcheck_overview.png>] Chapter 1. Overfull \hbox (298.86465pt too wide) in paragraph at lines 2--248 [][][][][][] [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--371 [][][][][][] [11] [12 <./example_controls_report.png>] Overfull \hbox (204.79077pt too wide) in paragraph at lines 2--401 [][][][][][] [13] Overfull \vbox (162.62206pt too high) has occurred while \output is active [14 <./example_ReportPDF.png>] 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.493 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.497 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.608 ...��███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 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.612 ...███| 6/6 [00:00<00:00, 2400.86it/s] Overfull \vbox (1.63934pt too high) detected at line 668 [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.699 ...███| 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, 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, 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, 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, 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, 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, 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, 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, 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, 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.700 ...███| 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.741 ...███| 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, 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, 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, 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, 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, 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, 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, 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, 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, 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.742 ...███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 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.781 ...��███| 6/6 [00:01<00:00, 3.68it/s] Overfull \vbox (1.32576pt too high) detected at line 890 [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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.902 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.987 ...��███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1101 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 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.1105 ...�███| 1/1 [00:00<00:00, 6.61it/s] Underfull \vbox (badness 3492) detected at line 1153 [24] Underfull \vbox (badness 10000) detected at line 1164 [25 <./docs_quality-control-example_5_0.png>] Underfull \vbox (badness 10000) detected at line 1175 [26 <./docs_quality-control-example_5_1.png>] Underfull \vbox (badness 10000) detected at line 1186 [27 <./docs_quality-control-example_5_2.png>] Underfull \vbox (badness 10000) detected at line 1197 [28 <./docs_quality-control-example_5_3.png>] Underfull \vbox (badness 10000) detected at line 1208 [29 <./docs_quality-control-example_5_4.png>] Underfull \vbox (badness 10000) detected at line 1219 [30 <./docs_quality-control-example_5_5.png>] Underfull \vbox (badness 10000) detected at line 1230 [31 <./docs_quality-control-example_5_6.png>] Underfull \vbox (badness 10000) detected at line 1241 [32 <./docs_quality-control-example_5_7.png>] Underfull \vbox (badness 10000) detected at line 1252 [33 <./docs_quality-control-example_5_8.png>] Underfull \vbox (badness 10000) detected at line 1290 [34 <./docs_quality-control-example_5_9.png>] Underfull \vbox (badness 10000) detected at line 1327 [35 <./docs_quality-control-example_5_12.png>] Underfull \vbox (badness 10000) detected at line 1364 [36 <./docs_quality-control-example_5_15.png>] Underfull \vbox (badness 10000) detected at line 1401 [37 <./docs_quality-control-example_5_18.png>] Underfull \vbox (badness 10000) detected at line 1422 [38 <./docs_quality-control-example_5_21.png>] Underfull \vbox (badness 10000) detected at line 1433 [39 <./docs_quality-control-example_6_0.png>] Underfull \vbox (badness 10000) detected at line 1444 [40 <./docs_quality-control-example_6_1.png>] Underfull \vbox (badness 10000) detected at line 1455 [41 <./docs_quality-control-example_6_2.png>] Underfull \vbox (badness 10000) detected at line 1466 [42 <./docs_quality-control-example_6_3.png>] Underfull \vbox (badness 10000) detected at line 1477 [43 <./docs_quality-control-example_6_4.png>] Underfull \vbox (badness 10000) detected at line 1488 [44 <./docs_quality-control-example_6_5.png>] Underfull \vbox (badness 10000) detected at line 1499 [45 <./docs_quality-control-example_6_6.png>] Underfull \vbox (badness 10000) detected at line 1510 [46 <./docs_quality-control-example_6_7.png>] Underfull \vbox (badness 10000) detected at line 1521 [47 <./docs_quality-control-example_6_8.png>] Underfull \vbox (badness 10000) detected at line 1558 [48 <./docs_quality-control-example_6_9.png>] Underfull \vbox (badness 10000) detected at line 1582 [49 <./docs_quality-control-example_6_12.png>] Underfull \vbox (badness 10000) detected at line 1606 [50 <./docs_quality-control-example_6_14.png>] Underfull \vbox (badness 10000) detected at line 1630 [51 <./docs_quality-control-example_6_16.png>] [52 <./docs_quality-control-exam ple_6_18.png>] [53] Overfull \hbox (2028.37567pt too wide) in paragraph at lines 2--1764 [][][][][][] [54] Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 []\T1/phv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 \T1/phv/m/n/10 gu- Overfull \hbox (7.23338pt too wide) in paragraph at lines 1865--1865 \T1/phv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 []\T1/phv/m/n/10 De- Overfull \hbox (1.02771pt too wide) in paragraph at lines 1865--1865 \T1/phv/m/n/10 fault| Overfull \hbox (17.77328pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 data_dir| Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 path Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 \T1/ptm/b/n/10 RE- Overfull \hbox (22.32765pt too wide) in paragraph at lines 1865--1865 \T1/ptm/b/n/10 QUIRED| Overfull \hbox (1.11351pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 out- Overfull \hbox (15.00327pt too wide) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 filepath| Overfull \hbox (6.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 None| Overfull \hbox (0.55345pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 col- Underfull \hbox (badness 10000) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 or- Overfull \hbox (5.56345pt too wide) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 blind| Overfull \hbox (12.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 False| Overfull \hbox (22.5233pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 bg_offset| Overfull \hbox (2.42802pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 3000| Overfull \hbox (0.55345pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 cut- Overfull \hbox (25.30319pt too wide) in paragraph at lines 1865--1865 \T1/ptm/m/n/10 off_adjust| Overfull \hbox (10.75363pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 legacy| Overfull \hbox (12.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 False| Overfull \hbox (11.66357pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 round- Overfull \hbox (1.9735pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 pval| Overfull \hbox (6.42802pt too wide) in paragraph at lines 1865--1865 []\T1/pcr/m/n/10 True| Overfull \hbox (18.64328pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 pval_sig| Overfull \hbox (5.55334pt too wide) in paragraph at lines 1865--1865 []\T1/ptm/m/n/10 pass- [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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1983 ...�██| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 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.1985 ...�███| 6/6 [00:49<00:00, 8.26s/it] Underfull \vbox (badness 10000) detected at line 2067 [57] Underfull \vbox (badness 10000) detected at line 2103 [58 <./docs_filtering-probes_8_1.png>] Underfull \vbox (badness 10000) detected at line 2139 [59 <./docs_filtering-probes_11_1.png>] Underfull \vbox (badness 10000) detected at line 2159 [60 <./docs_filtering-probes_13_1.png>] [61 <./docs_filtering-probes_14_0.png>] Overfull \hbox (909.45023pt too wide) in paragraph at lines 2--2215 [][][][][][] [62] Overfull \vbox (686.56174pt too high) has occurred while \output is active [63 <./5146fdf952a8919a55a6efc634c173948bb008a6.png>] Underfull \hbox (badness 10000) in paragraph at lines 2277--2278 []|\T1/pcr/m/n/10 methylcheck.plot_controls\T1/ptm/m/n/10 ([path, sub-set, Underfull \hbox (badness 10000) in paragraph at lines 2279--2281 []|\T1/ptm/m/n/10 internal ar-ray QC con-trols (avail-able with the Underfull \hbox (badness 10000) in paragraph at lines 2282--2283 []|\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 2292--2293 []|\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 2302--2303 []|\T1/pcr/m/n/10 methylcheck.exclude_sex_control_probes\T1/ptm/m/n/10 (df, Underfull \hbox (badness 10000) in paragraph at lines 2307--2308 []|\T1/pcr/m/n/10 methylcheck.drop_nan_probes\T1/ptm/m/n/10 (df[, silent, Underfull \hbox (badness 10000) in paragraph at lines 2322--2323 []|\T1/pcr/m/n/10 methylcheck.beta_density_plot\T1/ptm/m/n/10 (df[, ver- Underfull \hbox (badness 10000) in paragraph at lines 2327--2328 []|\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 2332--2333 []|\T1/pcr/m/n/10 methylcheck.mean_beta_compare\T1/ptm/m/n/10 (df1, df2[, Overfull \hbox (56.71234pt too wide) in paragraph at lines 2347--2348 []|\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 2374--2374 \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 , [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 2491--2491 []\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 2491--2491 \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 2491--2491 \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- [66] Underfull \hbox (badness 7907) in paragraph at lines 2561--2568 []\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 2561--2568 \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 2561--2568 \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 2575--2575 []\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 2575--2575 \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 2575--2575 \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 , [67] Underfull \hbox (badness 10000) in paragraph at lines 2643--2643 []\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 2643--2643 \T1/ptm/m/it/10 turn_sample_column_names=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2647--2654 []\T1/ptm/m/n/10 betas non-normalized ma-trix_processed ma-trix_signal se-ries_ matrix ^^U read_series_matrix(file, de- Underfull \hbox (badness 10000) in paragraph at lines 2684--2686 []\T1/ptm/m/n/10 {`27k', `450k', `EPIC', `EPIC-PLUS', `MOUSE'} or {`Il-lu-mi-na Hu-man-Methy-la- Underfull \hbox (badness 10000) in paragraph at lines 2684--2686 \T1/ptm/m/n/10 tion27k','IlluminaHumanMethylation450k','IlluminaHumanMethylatio nEPIC', `mouse'} or [68] Underfull \hbox (badness 10000) in paragraph at lines 2723--2724 []\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 2726--2729 []\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 2726--2729 \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 2726--2729 \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 2738--2740 []\T1/ptm/m/n/10 ref: [][]$https : / / bioconductor . org / packages / devel / bioc / vignettes / sesame / inst / doc / sesame . html # [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 2980--2982 []\T1/ptm/m/n/10 This [71] Underfull \hbox (badness 10000) in paragraph at lines 3029--3029 []\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 3029--3029 \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 3029--3029 \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 3029--3029 \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 , [72] Underfull \hbox (badness 10000) in paragraph at lines 3123--3123 []\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 3123--3123 \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 , Underfull \hbox (badness 10000) in paragraph at lines 3123--3123 \T1/ptm/m/it/10 plot_removed=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nafill='quic k'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=None\T1/ptm/m/n/10 , Overfull \hbox (57.53044pt too wide) in paragraph at lines 3155--3157 [] Overfull \hbox (205.40927pt too wide) in paragraph at lines 3158--3161 [] [73] Underfull \hbox (badness 10000) in paragraph at lines 3332--3332 []\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 , [74] Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 []\T1/ptm/m/it/10 data_containers=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path=Non e\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 meth=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 un-meth=None\T1/ptm/m /n/10 , \T1/ptm/m/it/10 poobah=None\T1/ptm/m/n/10 , Underfull \hbox (badness 7558) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 palette=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- Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot=True\T1/ptm/m/n /10 , \T1/ptm/m/it/10 cut-off_line=True\T1/ptm/m/n/10 , Underfull \hbox (badness 6944) in paragraph at lines 3365--3370 []\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 3365--3370 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = Underfull \hbox (badness 6910) in paragraph at lines 3413--3413 \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 , [75] Underfull \hbox (badness 6944) in paragraph at lines 3430--3435 []\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 3430--3435 \T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl') un-meth = Underfull \hbox (badness 10000) in paragraph at lines 3485--3487 []\T1/ptm/m/n/10 `non-polymorphic' | Underfull \hbox (badness 10000) in paragraph at lines 3505--3505 []\T1/ptm/m/it/10 path_or_df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 use_median=False\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3517--3517 []\T1/ptm/m/it/10 data_source\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3517--3517 \T1/ptm/m/it/10 save=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 - Underfull \hbox (badness 10000) in paragraph at lines 3517--3517 \T1/ptm/m/it/10 clude_probe_failure_percent=True\T1/ptm/m/n/10 , \T1/ptm/m/it/1 0 poobah_cutoff=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cus- [76] [77] [78] Overfull \hbox (33.52034pt too wide) in paragraph at lines 3737--3739 [] [79] [80] [81] [82] Chapter 7. [83] [84] [85] (./life-epigenetics-methylcheck.ind [86] 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 14--16 []\T1/pcr/m/n/10 bis_conversion_control() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\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 22--24 []\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 27--29 []\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 29--30 []\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 34--36 []\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 43--44 []\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 45--46 []\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 49--50 []\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 50--51 []\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 55--56 []\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 60--61 []\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 61--62 []\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 64--65 []\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 68--69 []\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 72--73 []\T1/pcr/m/n/10 read_geo() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule [87]) (./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 (91 pages, 3009012 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23' Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line 'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.' Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2021-09-03T20:38:45.582717Z, end-time: 2021-09-03T20:38:45.668822Z, 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: 2021-09-03T20:38:45.797470Z, end-time: 2021-09-03T20:39:01.711399Z, duration: 15, 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: docs/example_notebooks/tutorial_figs/fig3.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/fig4.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/fig5.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/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/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_qc' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.read_geo' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load_both' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_controls' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.list_problem_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.drop_nan_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.sample_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_density_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_compare' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_mds_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.combine_mds' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.predict' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:87: WARNING: Unknown directive type "todo". .. todo:: - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs - DONE: meth_df deal with batches of files /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title. options: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title. example: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation. 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:11: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot: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:36: 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: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.beta_mds_plot:52: 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:57: 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:61: WARNING: Unknown directive type "todo". .. todo:: - Reads the manifest file for the array, or at least a list of probe names to exclude/include. - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']] - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values df_no_sex_probes = df[probe_names_no_sex_probes] df_no_sex_probes.head() /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition. -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title. how it works: -------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition. ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title. inputs: ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title. optional keyword arguments: --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title. analysis parameters: -------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title. returns: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo". .. todo:: - TODO: one dataframe of the retained samples, cutoff box is avg of datasets - TODO: each dataset's results as a transformed file - default: list of samples retained or excluded - option: a list of pyplot subplot objects /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title. input (one of these): ===================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title. optional params: ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title. returns: ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title. input (choose one of these): ============================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent. /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'; 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 'methylcheck.qc_report' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/another-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo-methylprep-to-methylcheck-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_read_geo_processed.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_using_matched_meta_data.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/interactive-mds-filtering.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/pval.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/qc-sex-check.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 4%] README writing output... [ 8%] docs/bead-array writing output... [ 12%] docs/example_notebooks/another-methylcheck-qc-example writing output... [ 16%] docs/example_notebooks/demo-methylprep-to-methylcheck-example writing output... [ 20%] docs/example_notebooks/demo_read_geo_processed writing output... [ 24%] docs/example_notebooks/demo_using_matched_meta_data writing output... [ 28%] docs/example_notebooks/examples writing output... [ 32%] docs/example_notebooks/interactive-mds-filtering writing output... [ 36%] docs/example_notebooks/methylcheck-cli writing output... [ 40%] docs/example_notebooks/methylprep-methylcheck-qc-example writing output... [ 44%] docs/example_notebooks/outdated-methylprep-methylcheck-example writing output... [ 48%] docs/example_notebooks/postprocessQC_example writing output... [ 52%] docs/example_notebooks/pval writing output... [ 56%] docs/example_notebooks/qc-sex-check writing output... [ 60%] docs/example_notebooks/rawQC_example writing output... [ 64%] docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2 writing output... [ 68%] docs/filtering-probes writing output... [ 72%] docs/loading-data writing output... [ 76%] docs/quality-control-example writing output... [ 80%] docs/release-history writing output... [ 84%] docs/research_notebooks/postprocessQC_example writing output... [ 88%] docs/research_notebooks/pval writing output... [ 92%] docs/research_notebooks/rawQC_example writing output... [ 96%] docs/source/modules writing output... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:91: WARNING: Could not lex literal_block as "bash". Highlighting skipped. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.combine_mds' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.predict' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.get_sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41::: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.assign' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.combine_mds' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.predict' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.get_sex' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/index.rst:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.assign' generating indices... genindex py-modindex writing additional pages... copying images... [ 0%] https://readthedocs.com/projects/life-epigenetics-methylcheck/badge/?version=latest copying images... [ 1%] https://img.shields.io/badge/License-MIT-yellow.svg copying images... [ 2%] https://circleci.com/gh/FoxoTech/methylcheck.svg?style=shield copying images... [ 3%] https://api.codacy.com/project/badge/Grade/aedf5c223e39415180ff35153b2bad89 copying images... [ 3%] https://coveralls.io/repos/github/FoxoTech/methylcheck/badge.svg?t=OVL45Q copying images... [ 4%] https://img.shields.io/pypi/dm/methylcheck.svg?label=pypi%20downloads&logo=PyPI&logoColor=white:target:https://img.shields.io/pypi/dm/methylcheck.svg?label=pypi%20downloads&logo=PyPI&logoColor=white:alt:PyPI-Downloads:raw-html-m2r:`` copying images... [ 5%] https://raw.githubusercontent.com/FoxoTech/methylcheck/master/docs/methylcheck_overview.png copying images... [ 6%] https://raw.githubusercontent.com/FoxoTech/methylcheck/master/docs/methylcheck_functions.png copying images... [ 6%] https://raw.githubusercontent.com/FoxoTech/methylcheck/master/docs/example_controls_report.png copying images... [ 7%] https://raw.githubusercontent.com/FoxoTech/methylcheck/master/docs/example_ReportPDF.png copying images... [ 8%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_another-methylcheck-qc-example_6_0.png copying images... [ 9%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_another-methylcheck-qc-example_7_0.png copying images... [ 9%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_another-methylcheck-qc-example_8_2.png copying images... [ 10%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_another-methylcheck-qc-example_9_1.png copying images... [ 11%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo-methylprep-to-methylcheck-example_7_1.png copying images... [ 12%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo-methylprep-to-methylcheck-example_8_0.png copying images... [ 12%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo-methylprep-to-methylcheck-example_9_3.png copying images... [ 13%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_1.png copying images... [ 14%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_3.png copying images... [ 15%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_5.png copying images... [ 15%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_7.png copying images... [ 16%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_11.png copying images... [ 17%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_13.png copying images... [ 18%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_demo_read_geo_processed_1_15.png copying images... [ 18%] https://raw.githubusercontent.com/FoxoTech/methylcheck/master/docs/plot_M_vs_U_compare_dye_noob_to_raw.png copying images... [ 19%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_interactive-mds-filtering_3_1.png copying images... [ 20%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_interactive-mds-filtering_3_3.png copying images... [ 21%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_interactive-mds-filtering_3_6.png copying images... [ 21%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_interactive-mds-filtering_3_8.png copying images... [ 22%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_13_0.png copying images... [ 23%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_15_0.png copying images... [ 24%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_17_0.png copying images... [ 24%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_18_3.png copying images... [ 25%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_19_0.png copying images... [ 26%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_20_2.png copying images... [ 27%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_0.png copying images... [ 27%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_1.png copying images... [ 28%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_2.png copying images... [ 29%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_3.png copying images... [ 30%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_4.png copying images... [ 30%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_5.png copying images... [ 31%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_6.png copying images... [ 32%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_7.png copying images... [ 33%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_8.png copying images... [ 33%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_9.png copying images... [ 34%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_12.png copying images... [ 35%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_14.png copying images... [ 36%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_16.png copying images... [ 36%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_methylprep-methylcheck-qc-example_22_18.png copying images... [ 37%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_13_0.png copying images... [ 38%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_15_0.png copying images... [ 39%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_17_0.png copying images... [ 39%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_18_3.png copying images... [ 40%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_19_0.png copying images... [ 41%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_20_2.png copying images... [ 42%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_0.png copying images... [ 42%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_1.png copying images... [ 43%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_2.png copying images... [ 44%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_3.png copying images... [ 45%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_4.png copying images... [ 45%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_5.png copying images... [ 46%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_6.png copying images... [ 47%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_7.png copying images... [ 48%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_8.png copying images... [ 48%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_9.png copying images... [ 49%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_12.png copying images... [ 50%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_14.png copying images... [ 51%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_16.png copying images... [ 51%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_outdated-methylprep-methylcheck-example_22_18.png copying images... [ 52%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_postprocessQC_example_7_0.png copying images... [ 53%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_postprocessQC_example_8_0.png copying images... [ 54%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_postprocessQC_example_13_0.png copying images... [ 54%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_postprocessQC_example_15_0.png copying images... [ 55%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_12_0.png copying images... [ 56%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_14_0.png copying images... [ 57%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_14_1.png copying images... [ 57%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_15_1.png copying images... [ 58%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_16_2.png copying images... [ 59%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_16_4.png copying images... [ 60%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_16_6.png copying images... [ 60%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_16_8.png copying images... [ 61%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_0.png copying images... [ 62%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_1.png copying images... [ 63%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_3.png copying images... [ 63%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_4.png copying images... [ 64%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_5.png copying images... [ 65%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_6.png copying images... [ 66%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_7.png copying images... [ 66%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_17_8.png copying images... [ 67%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_qc-sex-check_18_1.png copying images... [ 68%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_3_1.png copying images... [ 69%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_4_1.png copying images... [ 69%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_5_2.png copying images... [ 70%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_6_1.png copying images... [ 71%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_6_2.png copying images... [ 72%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_6_3.png copying images... [ 72%] docs/example_notebooks/../../_build/doctrees/nbsphinx/docs_example_notebooks_testing_sns_upgrade_methylcheck_v0.6.2_7_1.png copying images... [ 73%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_8_1.png copying images... [ 74%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_11_1.png copying images... [ 75%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_13_1.png copying images... [ 75%] docs/../_build/doctrees/nbsphinx/docs_filtering-probes_14_0.png copying images... [ 76%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_0.png copying images... [ 77%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_1.png copying images... [ 78%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_2.png copying images... [ 78%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_3.png copying images... [ 79%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_4.png copying images... [ 80%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_5.png copying images... [ 81%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_6.png copying images... [ 81%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_7.png copying images... [ 82%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_8.png copying images... [ 83%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_9.png copying images... [ 84%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_12.png copying images... [ 84%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_15.png copying images... [ 85%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_18.png copying images... [ 86%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_5_21.png copying images... [ 87%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_0.png copying images... [ 87%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_1.png copying images... [ 88%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_2.png copying images... [ 89%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_3.png copying images... [ 90%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_4.png copying images... [ 90%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_5.png copying images... [ 91%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_6.png copying images... [ 92%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_7.png copying images... [ 93%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_8.png copying images... [ 93%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_9.png copying images... [ 94%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_12.png copying images... [ 95%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_14.png copying images... [ 96%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_16.png copying images... [ 96%] docs/../_build/doctrees/nbsphinx/docs_quality-control-example_6_18.png copying images... [ 97%] docs/research_notebooks/../../_build/doctrees/nbsphinx/docs_research_notebooks_postprocessQC_example_7_0.png copying images... [ 98%] docs/research_notebooks/../../_build/doctrees/nbsphinx/docs_research_notebooks_postprocessQC_example_8_0.png copying images... [ 99%] docs/research_notebooks/../../_build/doctrees/nbsphinx/docs_research_notebooks_postprocessQC_example_13_0.png copying images... [100%] docs/research_notebooks/../../_build/doctrees/nbsphinx/docs_research_notebooks_postprocessQC_example_15_0.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_static' does not exist done copying extra files... done WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.combine_mds' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.predict' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.get_sex' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.assign' writing mimetype file... writing META-INF/container.xml file... writing content.opf file... WARNING: unknown mimetype for _images/python3.6.png"height="50">`, ignoring writing nav.xhtml file... WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.combine_mds' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.predict' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.get_sex' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.assign' writing toc.ncx file... WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.combine_mds' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.predict' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.get_sex' WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.assign' writing methylcheck.epub file... build succeeded, 240 warnings. The ePub file is in _build/epub. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-09-03T20:39:01.831485Z, end-time: 2021-09-03T20:39:01.903398Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/epub/methylcheck.epub /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/artifacts/latest/sphinx_epub/life-epigenetics-methylcheck.epub