Read the Docs build information Build id: 298293 Project: life-epigenetics-methylcheck Version: latest Commit: 34d0bf987d630ac474428e861de7edcf27ba1a5f Date: 2020-03-06T21:12:37.768531Z State: finished Success: True [rtd-command-info] start-time: 2020-03-06T21:12:40.521434Z, end-time: 2020-03-06T21:12:46.785127Z, duration: 6, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/LifeEGX/methylcheck.git . Cloning into '.'... [rtd-command-info] start-time: 2020-03-06T21:12:47.188190Z, end-time: 2020-03-06T21:12:48.545289Z, 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 34d0bf9 Add files via upload [rtd-command-info] start-time: 2020-03-06T21:12:48.699548Z, end-time: 2020-03-06T21:12:48.994395Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-03-06T21:12:50.626097Z, end-time: 2020-03-06T21:12:54.994673Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --no-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.3' 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: 2020-03-06T21:12:55.204419Z, end-time: 2020-03-06T21:12:56.138951Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (20.0.2) [rtd-command-info] start-time: 2020-03-06T21:12:56.735368Z, end-time: 2020-03-06T21:13:07.801308Z, duration: 11, exit-code: 0 python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 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<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 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<1.1 Downloading readthedocs_sphinx_ext-1.0.1-py2.py3-none-any.whl (14 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.1-py2.py3-none-any.whl (126 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting packaging Downloading packaging-20.3-py2.py3-none-any.whl (37 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.0-py2.py3-none-any.whl (39 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting pytz>=2015.7 Downloading pytz-2019.3-py2.py3-none-any.whl (509 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.8-py2.py3-none-any.whl (125 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting certifi>=2017.4.17 Downloading certifi-2019.11.28-py2.py3-none-any.whl (156 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.6-py2.py3-none-any.whl (67 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=23754 sha256=f379c5ce68d2a77892706e77705a767aeb979a2391b9f31c9208046b7b4d414d Stored in directory: /tmp/pip-ephem-wheel-cache-diaqrc79/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b 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=491058 sha256=163d8740830cc8d56a4a684553087409356abadb071ba81c72ca307145132128 Stored in directory: /tmp/pip-ephem-wheel-cache-diaqrc79/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, MarkupSafe, Jinja2, snowballstemmer, pytz, babel, urllib3, idna, certifi, chardet, requests, pyparsing, packaging, sphinxcontrib-websupport, imagesize, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 45.2.0 Uninstalling setuptools-45.2.0: Successfully uninstalled setuptools-45.2.0 Successfully installed Jinja2-2.11.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.3 pillow-5.4.1 pyparsing-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.0 urllib3-1.25.8 [rtd-command-info] start-time: 2020-03-06T21:13:07.967765Z, end-time: 2020-03-06T21:13:39.193922Z, duration: 31, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting numpy Downloading numpy-1.18.1-cp37-cp37m-manylinux1_x86_64.whl (20.1 MB) Collecting pandas Downloading pandas-1.0.1-cp37-cp37m-manylinux1_x86_64.whl (10.1 MB) Collecting scipy Downloading scipy-1.4.1-cp37-cp37m-manylinux1_x86_64.whl (26.1 MB) Collecting matplotlib Downloading matplotlib-3.2.0-cp37-cp37m-manylinux1_x86_64.whl (12.4 MB) Collecting seaborn Downloading seaborn-0.10.0-py3-none-any.whl (215 kB) Collecting pytest Downloading pytest-5.3.5-py3-none-any.whl (235 kB) Collecting coverage Downloading coverage-5.0.3-cp37-cp37m-manylinux1_x86_64.whl (227 kB) Collecting python-coveralls Downloading python_coveralls-2.9.3-py2.py3-none-any.whl (9.9 kB) Requirement already satisfied: sphinx>=1.4 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 10)) (1.8.5) 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 tqdm Downloading tqdm-4.43.0-py2.py3-none-any.whl (59 kB) Collecting ipykernel Downloading ipykernel-5.1.4-py3-none-any.whl (116 kB) Collecting nbsphinx Downloading nbsphinx-0.5.1-py2.py3-none-any.whl (21 kB) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from pandas->-r requirements.txt (line 2)) (2019.3) Collecting python-dateutil>=2.6.1 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.1.0-cp37-cp37m-manylinux1_x86_64.whl (90 kB) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 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)) (2.4.6) Collecting cycler>=0.10 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Collecting py>=1.5.0 Downloading py-1.8.1-py2.py3-none-any.whl (83 kB) Collecting pluggy<1.0,>=0.12 Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from pytest->-r requirements.txt (line 6)) (20.3) Collecting wcwidth Downloading wcwidth-0.1.8-py2.py3-none-any.whl (17 kB) Collecting importlib-metadata>=0.12; python_version < "3.8" Downloading importlib_metadata-1.5.0-py2.py3-none-any.whl (30 kB) Collecting more-itertools>=4.0.0 Downloading more_itertools-8.2.0-py3-none-any.whl (43 kB) Collecting attrs>=17.4.0 Downloading attrs-19.3.0-py2.py3-none-any.whl (39 kB) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from python-coveralls->-r requirements.txt (line 9)) (1.14.0) Collecting PyYAML Downloading PyYAML-5.3.tar.gz (268 kB) Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from python-coveralls->-r requirements.txt (line 9)) (2.23.0) 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>=1.4->-r requirements.txt (line 10)) (1.2.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 10)) (41.0.1) 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>=1.4->-r requirements.txt (line 10)) (2.3.1) 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>=1.4->-r requirements.txt (line 10)) (0.7.12) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 10)) (1.2.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 10)) (2.0.0) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 10)) (2.11.1) 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>=1.4->-r requirements.txt (line 10)) (2.8.0) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 10)) (0.14) Collecting pbr Downloading pbr-5.4.4-py2.py3-none-any.whl (110 kB) Collecting mistune Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Collecting jupyter-client Downloading jupyter_client-6.0.0-py3-none-any.whl (104 kB) Collecting ipython>=5.0.0 Downloading ipython-7.13.0-py3-none-any.whl (780 kB) Collecting traitlets>=4.1.0 Downloading traitlets-4.3.3-py2.py3-none-any.whl (75 kB) Collecting tornado>=4.2 Downloading tornado-6.0.4.tar.gz (496 kB) Collecting nbformat Downloading nbformat-5.0.4-py3-none-any.whl (169 kB) Collecting nbconvert!=5.4 Downloading nbconvert-5.6.1-py2.py3-none-any.whl (455 kB) Collecting zipp>=0.5 Downloading zipp-3.1.0-py3-none-any.whl (4.9 kB) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests->python-coveralls->-r requirements.txt (line 9)) (1.25.8) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests->python-coveralls->-r requirements.txt (line 9)) (2.9) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests->python-coveralls->-r requirements.txt (line 9)) (2019.11.28) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests->python-coveralls->-r requirements.txt (line 9)) (3.0.4) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.4->-r requirements.txt (line 10)) (1.1.1) Collecting pyzmq>=13 Downloading pyzmq-19.0.0-cp37-cp37m-manylinux1_x86_64.whl (1.1 MB) Collecting jupyter-core>=4.6.0 Downloading jupyter_core-4.6.3-py2.py3-none-any.whl (83 kB) Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 Downloading prompt_toolkit-3.0.4-py3-none-any.whl (351 kB) Collecting backcall Downloading backcall-0.1.0.tar.gz (9.7 kB) Collecting decorator Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting pickleshare Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB) Collecting pexpect; sys_platform != "win32" Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB) Collecting jedi>=0.10 Downloading jedi-0.16.0-py2.py3-none-any.whl (1.1 MB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Collecting bleach Downloading bleach-3.1.1-py2.py3-none-any.whl (150 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.4.2.tar.gz (14 kB) Collecting entrypoints>=0.2.2 Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting testpath Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB) Collecting defusedxml Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB) Collecting ptyprocess>=0.5 Downloading ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB) Collecting parso>=0.5.2 Downloading parso-0.6.2-py2.py3-none-any.whl (97 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.15.7.tar.gz (107 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Building wheels for collected packages: m2r, PyYAML, tornado, backcall, pandocfilters, pyrsistent 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=10466 sha256=0d7d37691cddce6432d74d65e93e4a3a5f67613f63196db865abbfad76e41fb0 Stored in directory: /tmp/pip-ephem-wheel-cache-jny69c7a/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f Building wheel for PyYAML (setup.py): started Building wheel for PyYAML (setup.py): finished with status 'done' Created wheel for PyYAML: filename=PyYAML-5.3-cp37-cp37m-linux_x86_64.whl size=44228 sha256=e1d14c00ea018fbdd02245401cffed5aa669a983b8dcb9848bc0edc544e3c822 Stored in directory: /tmp/pip-ephem-wheel-cache-jny69c7a/wheels/8a/55/a4/c0a81d27c33462cfdcb904db018f5550197e88b2b6b85beed2 Building wheel for tornado (setup.py): started Building wheel for tornado (setup.py): finished with status 'done' Created wheel for tornado: filename=tornado-6.0.4-cp37-cp37m-linux_x86_64.whl size=428553 sha256=204048acd59027584e8632264252665729e76b721183007fc57f4e736d9d8561 Stored in directory: /tmp/pip-ephem-wheel-cache-jny69c7a/wheels/7d/14/fa/d88fb5da77d813ea0ffca38a2ab2a052874e9e1142bad0b348 Building wheel for backcall (setup.py): started Building wheel for backcall (setup.py): finished with status 'done' Created wheel for backcall: filename=backcall-0.1.0-py3-none-any.whl size=10413 sha256=ac4d043ccb21aa5b17200df178a8b578134ab343e5c71a450e2bfe4f52f61c99 Stored in directory: /tmp/pip-ephem-wheel-cache-jny69c7a/wheels/9e/56/4f/da13e448a8a5b8671b2954600d5355cf36e557c7aa5020139b Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7856 sha256=0206f4c0d0992c5efe70dd6830695408e5ae9137c4c0140c24c251dd046ed94e Stored in directory: /tmp/pip-ephem-wheel-cache-jny69c7a/wheels/63/99/01/9fe785b86d1e091a6b2a61e06ddb3d8eb1bc9acae5933d4740 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.15.7-cp37-cp37m-linux_x86_64.whl size=115961 sha256=826718d2b4f3cc67a331f97430f3f708ad12181f2ff331e25bc7369e31de6e6b Stored in directory: /tmp/pip-ephem-wheel-cache-jny69c7a/wheels/57/74/e3/61db397ec89f304e49711ec9f68490f15814b80c1c0ee9b8c0 Successfully built m2r PyYAML tornado backcall pandocfilters pyrsistent Installing collected packages: numpy, python-dateutil, pandas, scipy, kiwisolver, cycler, matplotlib, seaborn, py, zipp, importlib-metadata, pluggy, wcwidth, more-itertools, attrs, pytest, coverage, PyYAML, python-coveralls, pbr, sphinxcontrib-apidoc, mistune, m2r, tqdm, tornado, pyzmq, decorator, ipython-genutils, traitlets, jupyter-core, jupyter-client, prompt-toolkit, backcall, pickleshare, ptyprocess, pexpect, parso, jedi, ipython, ipykernel, pyrsistent, jsonschema, nbformat, webencodings, bleach, pandocfilters, entrypoints, testpath, defusedxml, nbconvert, nbsphinx Successfully installed PyYAML-5.3 attrs-19.3.0 backcall-0.1.0 bleach-3.1.1 coverage-5.0.3 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-1.5.0 ipykernel-5.1.4 ipython-7.13.0 ipython-genutils-0.2.0 jedi-0.16.0 jsonschema-3.2.0 jupyter-client-6.0.0 jupyter-core-4.6.3 kiwisolver-1.1.0 m2r-0.2.1 matplotlib-3.2.0 mistune-0.8.4 more-itertools-8.2.0 nbconvert-5.6.1 nbformat-5.0.4 nbsphinx-0.5.1 numpy-1.18.1 pandas-1.0.1 pandocfilters-1.4.2 parso-0.6.2 pbr-5.4.4 pexpect-4.8.0 pickleshare-0.7.5 pluggy-0.13.1 prompt-toolkit-3.0.4 ptyprocess-0.6.0 py-1.8.1 pyrsistent-0.15.7 pytest-5.3.5 python-coveralls-2.9.3 python-dateutil-2.8.1 pyzmq-19.0.0 scipy-1.4.1 seaborn-0.10.0 sphinxcontrib-apidoc-0.3.0 testpath-0.4.4 tornado-6.0.4 tqdm-4.43.0 traitlets-4.3.3 wcwidth-0.1.8 webencodings-0.5.1 zipp-3.1.0 [rtd-command-info] start-time: 2020-03-06T21:13:39.363911Z, end-time: 2020-03-06T21:13:42.667913Z, duration: 3, exit-code: 0 python /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/setup.py install --force running install running bdist_egg running egg_info creating methylcheck.egg-info writing methylcheck.egg-info/PKG-INFO writing dependency_links to methylcheck.egg-info/dependency_links.txt writing entry points to methylcheck.egg-info/entry_points.txt writing requirements to methylcheck.egg-info/requires.txt writing top-level names to methylcheck.egg-info/top_level.txt writing manifest file 'methylcheck.egg-info/SOURCES.txt' reading manifest file 'methylcheck.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'README.rst' writing manifest file 'methylcheck.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/methylcheck copying methylcheck/__init__.py -> build/lib/methylcheck copying methylcheck/postprocessQC.py -> build/lib/methylcheck copying methylcheck/QCreport.py -> build/lib/methylcheck copying methylcheck/cli.py -> build/lib/methylcheck copying methylcheck/filters.py -> build/lib/methylcheck copying methylcheck/__main__.py -> build/lib/methylcheck copying methylcheck/rawQC.py -> build/lib/methylcheck creating build/lib/methylcheck/data_files copying methylcheck/data_files/450k_control.npy -> build/lib/methylcheck/data_files copying methylcheck/data_files/450k_polymorphic_crossRxtve_probes.csv.gz -> build/lib/methylcheck/data_files copying methylcheck/data_files/450k_sex.npy -> build/lib/methylcheck/data_files copying methylcheck/data_files/EPIC+_control.npy -> build/lib/methylcheck/data_files copying methylcheck/data_files/EPIC+_sex.npy -> build/lib/methylcheck/data_files copying methylcheck/data_files/EPIC_control.npy -> build/lib/methylcheck/data_files copying methylcheck/data_files/EPIC_polymorphic_crossRxtve_probes.csv.gz -> build/lib/methylcheck/data_files copying methylcheck/data_files/EPIC_sex.npy -> build/lib/methylcheck/data_files creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/methylcheck creating build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/450k_control.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/EPIC+_sex.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/EPIC_sex.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/EPIC_control.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/450k_sex.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/EPIC+_control.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/EPIC_polymorphic_crossRxtve_probes.csv.gz -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/450k_polymorphic_crossRxtve_probes.csv.gz -> build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/postprocessQC.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/QCreport.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/cli.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/filters.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/__main__.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/rawQC.py -> build/bdist.linux-x86_64/egg/methylcheck byte-compiling build/bdist.linux-x86_64/egg/methylcheck/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/postprocessQC.py to postprocessQC.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/QCreport.py to QCreport.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/cli.py to cli.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/filters.py to filters.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/rawQC.py to rawQC.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying methylcheck.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... creating dist creating 'dist/methylcheck-0.2.5-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing methylcheck-0.2.5-py3.7.egg Copying methylcheck-0.2.5-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Adding methylcheck 0.2.5 to easy-install.pth file Installing methylcheck-cli script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/methylcheck-0.2.5-py3.7.egg Processing dependencies for methylcheck==0.2.5 Searching for scikit-learn Reading https://pypi.org/simple/scikit-learn/ Downloading https://files.pythonhosted.org/packages/41/b6/126263db075fbcc79107749f906ec1c7639f69d2d017807c6574792e517e/scikit_learn-0.22.2.post1-cp37-cp37m-manylinux1_x86_64.whl#sha256=84e759a766c315deb5c85139ff879edbb0aabcddb9358acf499564ed1c21e337 Best match: scikit-learn 0.22.2.post1 Processing scikit_learn-0.22.2.post1-cp37-cp37m-manylinux1_x86_64.whl Installing scikit_learn-0.22.2.post1-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/scikit_learn-0.22.2.post1-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt Adding scikit-learn 0.22.2.post1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/scikit_learn-0.22.2.post1-py3.7-linux-x86_64.egg Searching for joblib>=0.11 Reading https://pypi.org/simple/joblib/ Downloading https://files.pythonhosted.org/packages/28/5c/cf6a2b65a321c4a209efcdf64c2689efae2cb62661f8f6f4bb28547cf1bf/joblib-0.14.1-py2.py3-none-any.whl#sha256=bdb4fd9b72915ffb49fde2229ce482dd7ae79d842ed8c2b4c932441495af1403 Best match: joblib 0.14.1 Processing joblib-0.14.1-py2.py3-none-any.whl Installing joblib-0.14.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Adding joblib 0.14.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/joblib-0.14.1-py3.7.egg Searching for tqdm==4.43.0 Best match: tqdm 4.43.0 Adding tqdm 4.43.0 to easy-install.pth file Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for matplotlib==3.2.0 Best match: matplotlib 3.2.0 Adding matplotlib 3.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for seaborn==0.10.0 Best match: seaborn 0.10.0 Adding seaborn 0.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for pandas==1.0.1 Best match: pandas 1.0.1 Adding pandas 1.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for numpy==1.18.1 Best match: numpy 1.18.1 Adding numpy 1.18.1 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for scipy==1.4.1 Best match: scipy 1.4.1 Adding scipy 1.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for cycler==0.10.0 Best match: cycler 0.10.0 Adding cycler 0.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for python-dateutil==2.8.1 Best match: python-dateutil 2.8.1 Adding python-dateutil 2.8.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for pyparsing==2.4.6 Best match: pyparsing 2.4.6 Adding pyparsing 2.4.6 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for kiwisolver==1.1.0 Best match: kiwisolver 1.1.0 Adding kiwisolver 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for pytz==2019.3 Best match: pytz 2019.3 Adding pytz 2019.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for six==1.14.0 Best match: six 1.14.0 Adding six 1.14.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for setuptools==41.0.1 Best match: setuptools 41.0.1 Adding setuptools 41.0.1 to easy-install.pth file Installing easy_install script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Installing easy_install-3.6 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Finished processing dependencies for methylcheck==0.2.5 [rtd-command-info] start-time: 2020-03-06T21:13:43.969207Z, end-time: 2020-03-06T21:13:44.271101Z, 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 = '2019, Life Epigenetics' author = 'Life Epigenetics' # The short X.Y version version = '0.2' # The full version, including alpha/beta/rc tags release = '0.2' # -- 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' ] # 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 = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_sphinx_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] # source_suffix = '.rst' # The master toctree document. master_doc = 'index' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path . exclude_patterns = ['_sphinx_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' #'alabaster' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_sphinx_static'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # The default sidebars (for documents that don't match any pattern) are # defined by theme itself. Builtin themes are using these templates by # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', # 'searchbox.html']``. # # html_sidebars = {} # -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = 'methylcheckdoc' # -- Options for LaTeX output ------------------------------------------------ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'methylcheck.tex', 'methylcheck Documentation', 'Life Epigenetics', 'manual'), ] # -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'methylcheck', 'methylcheck Documentation', [author], 1) ] # -- Options for Texinfo output ---------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'methylcheck', 'methylcheck Documentation', author, 'methylcheck', 'One line description of project.', 'Miscellaneous'), ] # -- Extension configuration ------------------------------------------------- ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types 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://media.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://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], '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', 'proxied_api_host': '/_', 'github_user': 'LifeEGX', '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, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '34d0bf98', } 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") 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' [rtd-command-info] start-time: 2020-03-06T21:13:44.442694Z, end-time: 2020-03-06T21:13:57.719600Z, duration: 13, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -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.QCreport.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.cli.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.filters.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.postprocessQC.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rawQC.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/modules.rst. building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 10 source files that are out of date updating environment: 10 added, 0 changed, 0 removed reading sources... [ 10%] README reading sources... [ 20%] docs/another-methylcheck-qc-example reading sources... [ 30%] docs/demo-methylprep-to-methylcheck-example reading sources... [ 40%] docs/demo_using_matched_meta_data reading sources... [ 50%] docs/filtering_probes reading sources... [ 60%] docs/methylprep_methylcheck_example reading sources... [ 70%] docs/postprocessQC_example reading sources... [ 80%] docs/rawQC_example reading sources... [ 90%] docs/source/methylcheck reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:98: WARNING: Title level inconsistent: Filter either by the publication source, or by the type of effect (e.g. Polymorphism) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent: (These return a filtered data set) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_probes:11: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:26: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:31: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:34: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:43: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:47: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:57: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:36: WARNING: Unexpected section title. returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:41: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:2: WARNING: Unexpected section title. combine (or segment) datasets how it works ------------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:15: WARNING: Unexpected section title. inputs ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:16: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:18: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:21: WARNING: Unexpected section title. optional keyword arguments -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:32: WARNING: Unexpected section title. analysis parameters ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:34: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Title underline too short. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Unexpected section title. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:39: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. 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/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 10%] README writing output... [ 20%] docs/another-methylcheck-qc-example writing output... [ 30%] docs/demo-methylprep-to-methylcheck-example writing output... [ 40%] docs/demo_using_matched_meta_data writing output... [ 50%] docs/filtering_probes writing output... [ 60%] docs/methylprep_methylcheck_example writing output... [ 70%] docs/postprocessQC_example writing output... [ 80%] docs/rawQC_example writing output... [ 90%] docs/source/methylcheck writing output... [100%] index generating indices... genindex py-modindex copying notebooks ... [ 14%] docs/another-methylcheck-qc-example.ipynb copying notebooks ... [ 28%] docs/demo-methylprep-to-methylcheck-example.ipynb copying notebooks ... [ 42%] docs/demo_using_matched_meta_data.ipynb copying notebooks ... [ 57%] docs/filtering_probes.ipynb copying notebooks ... [ 71%] docs/methylprep_methylcheck_example.ipynb copying notebooks ... [ 85%] docs/postprocessQC_example.ipynb copying notebooks ... [100%] docs/rawQC_example.ipynb writing additional pages... search copying images... [ 4%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_another-methylcheck-qc-example_6_0.png copying images... [ 9%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_another-methylcheck-qc-example_7_0.png copying images... [ 14%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_another-methylcheck-qc-example_8_2.png copying images... [ 19%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_another-methylcheck-qc-example_9_1.png copying images... [ 23%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_demo-methylprep-to-methylcheck-example_7_1.png copying images... [ 28%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_demo-methylprep-to-methylcheck-example_8_0.png copying images... [ 33%] docs/../_build/doctrees-readthedocs/nbsphinx/docs_demo-methylprep-to-methylcheck-example_9_3.png copying images... 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[rtd-command-info] start-time: 2020-03-06T21:13:57.908005Z, end-time: 2020-03-06T21:14:08.059082Z, duration: 10, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia 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.QCreport.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.cli.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.filters.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.postprocessQC.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rawQC.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/modules.rst. building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 24 added, 0 changed, 0 removed reading sources... [ 4%] README reading sources... [ 8%] _build/doctrees-readthedocs/nbsphinx/docs/another-methylcheck-qc-example reading sources... [ 12%] _build/doctrees-readthedocs/nbsphinx/docs/demo-methylprep-to-methylcheck-example reading sources... [ 16%] _build/doctrees-readthedocs/nbsphinx/docs/demo_using_matched_meta_data reading sources... [ 20%] _build/doctrees-readthedocs/nbsphinx/docs/filtering_probes reading sources... [ 25%] _build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example reading sources... [ 29%] _build/doctrees-readthedocs/nbsphinx/docs/postprocessQC_example reading sources... [ 33%] _build/doctrees-readthedocs/nbsphinx/docs/rawQC_example reading sources... [ 37%] _build/html/docs/another-methylcheck-qc-example reading sources... [ 41%] _build/html/docs/demo-methylprep-to-methylcheck-example reading sources... [ 45%] _build/html/docs/demo_using_matched_meta_data reading sources... [ 50%] _build/html/docs/filtering_probes reading sources... [ 54%] _build/html/docs/methylprep_methylcheck_example reading sources... [ 58%] _build/html/docs/postprocessQC_example reading sources... [ 62%] _build/html/docs/rawQC_example reading sources... [ 66%] docs/another-methylcheck-qc-example reading sources... [ 70%] docs/demo-methylprep-to-methylcheck-example reading sources... [ 75%] docs/demo_using_matched_meta_data reading sources... [ 79%] docs/filtering_probes reading sources... [ 83%] docs/methylprep_methylcheck_example reading sources... [ 87%] docs/postprocessQC_example reading sources... [ 91%] docs/rawQC_example reading sources... [ 95%] docs/source/methylcheck reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb:98: WARNING: Title level inconsistent: Filter either by the publication source, or by the type of effect (e.g. Polymorphism) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent: (These return a filtered data set) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/html/docs/filtering_probes.ipynb:98: WARNING: Title level inconsistent: Filter either by the publication source, or by the type of effect (e.g. Polymorphism) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/html/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent: (These return a filtered data set) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:98: WARNING: Title level inconsistent: Filter either by the publication source, or by the type of effect (e.g. Polymorphism) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methylprep_methylcheck_example.ipynb:362: WARNING: Title level inconsistent: (These return a filtered data set) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_probes:11: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:4: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:26: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:31: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:34: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:43: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:47: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:57: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:36: WARNING: Unexpected section title. returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:41: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:2: WARNING: Unexpected section title. combine (or segment) datasets how it works ------------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:15: WARNING: Unexpected section title. inputs ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:16: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:18: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:21: WARNING: Unexpected section title. optional keyword arguments -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:32: WARNING: Unexpected section title. analysis parameters ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:34: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Title underline too short. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Unexpected section title. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:39: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent. 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/_build/doctrees-readthedocs/nbsphinx/docs/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/_build/doctrees-readthedocs/nbsphinx/docs/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/_build/doctrees-readthedocs/nbsphinx/docs/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/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocs/nbsphinx/docs/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees-readthedocs/nbsphinx/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/html/docs/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/_build/html/docs/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/_build/html/docs/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/_build/html/docs/filtering_probes.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/html/docs/methylprep_methylcheck_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/html/docs/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/html/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... docs/demo-methylprep-to-methylcheck-example docs/filtering_probes docs/methylprep_methylcheck_example docs/another-methylcheck-qc-example docs/demo_using_matched_meta_data docs/source/methylcheck writing... done writing additional files... copying images... 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[rtd-command-info] start-time: 2020-03-06T21:14:08.261705Z, end-time: 2020-03-06T21:14:25.489991Z, duration: 17, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex 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.QCreport.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.cli.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.filters.rst. 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Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:26: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:31: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:34: WARNING: Definition list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:43: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:47: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:57: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:36: WARNING: Unexpected section title. returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:41: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:2: WARNING: Unexpected section title. combine (or segment) datasets how it works ------------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:15: WARNING: Unexpected section title. inputs ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:16: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:18: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:21: WARNING: Unexpected section title. optional keyword arguments -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:32: WARNING: Unexpected section title. analysis parameters 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[rtd-command-info] start-time: 2020-03-06T21:14:32.889504Z, end-time: 2020-03-06T21:14:33.190748Z, 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: 2020-03-06T21:14:33.380642Z, end-time: 2020-03-06T21:14:39.528033Z, duration: 6, 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' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylcheck" "methylcheck.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./methylcheck.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[43] [44] LaTeX Warning: Reference `docs/source/methylcheck:module-methylcheck.cli' on pa ge 45 undefined on input line 2404. LaTeX Warning: Reference `docs/source/methylcheck:module-methylcheck.filters' o n page 45 undefined on input line 2405. LaTeX Warning: Reference `docs/source/methylcheck:module-methylcheck.postproces sQC' on page 45 undefined on input line 2406. [45] No file life-epigenetics-methylcheck.ind. (./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 (49 pages, 1022171 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written 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/methylcheck:module-methylcheck.cli' on page 45 undefined on input line 2404 Reference `docs/source/methylcheck:module-methylcheck.filters' on page 45 undefined on input line 2405 Reference `docs/source/methylcheck:module-methylcheck.postprocessQC' on page 45 undefined on input line 2406 Latexmk: Summary of warnings: Latex failed to resolve 3 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 (17 entries accepted, 0 rejected). Sorting entries....done (78 comparisons). Generating output file life-epigenetics-methylcheck.ind....done (46 lines written, 0 warnings). Output written in life-epigenetics-methylcheck.ind. Transcript written in life-epigenetics-methylcheck.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylcheck.aux' 'life-epigenetics-methylcheck.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylcheck" "methylcheck.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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(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 (51 pages, 1028406 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written 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. 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[43] [44] [45] (./life-epigenetics-methylcheck.ind [46] Underfull \hbox (badness 10000) in paragraph at lines 8--10 []\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 10--11 []\T1/pcr/m/n/10 beta_mds_plot() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 15--16 []\T1/pcr/m/n/10 combine_mds() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\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 23--25 []\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 30--32 []\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 35--36 []\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 39--41 []\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 41--42 []\T1/pcr/m/n/10 mean_beta_plot() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule [47]) (./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 (51 pages, 1028590 bytes). Transcript written on life-epigenetics-methylcheck.log. Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written 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: 2020-03-06T21:14:39.701955Z, end-time: 2020-03-06T21:14:40.011020Z, 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: 2020-03-06T21:14:40.240494Z, end-time: 2020-03-06T21:15:19.407291Z, duration: 39, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... 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WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title. Optional Arguments ------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title. 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Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title. Options -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:36: WARNING: Unexpected section title. returns ------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:41: WARNING: Unexpected section title. requires -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:2: WARNING: Unexpected section title. combine (or segment) datasets how it works ------------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:15: WARNING: Unexpected section title. inputs ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:16: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:18: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:21: WARNING: Unexpected section title. optional keyword arguments -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:32: WARNING: Unexpected section title. analysis parameters ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:34: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Title underline too short. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Unexpected section title. returns ------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:39: WARNING: Bullet list ends without a blank line; unexpected unindent. 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for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/rawQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/rawQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/rawQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/html/docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/html/docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/html/docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/html/docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/html/docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/html/docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/_build/html/docs/rawQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees/nbsphinx/docs/rawQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocs/nbsphinx/docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocs/nbsphinx/docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocs/nbsphinx/docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocs/nbsphinx/docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocs/nbsphinx/docs/rawQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/doctrees-readthedocs/nbsphinx/docs/rawQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/_build/html/docs/rawQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/docs/rawQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/html/docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for _build/html/docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for _build/html/docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for _build/html/docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for _build/html/docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for _build/html/docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for _build/html/docs/rawQC_example.ipynb, ignoring WARNING: unknown mimetype for docs/another-methylcheck-qc-example.ipynb, ignoring WARNING: unknown mimetype for docs/demo-methylprep-to-methylcheck-example.ipynb, ignoring WARNING: unknown mimetype for docs/demo_using_matched_meta_data.ipynb, ignoring WARNING: unknown mimetype for docs/filtering_probes.ipynb, ignoring WARNING: unknown mimetype for docs/methylprep_methylcheck_example.ipynb, ignoring WARNING: unknown mimetype for docs/postprocessQC_example.ipynb, ignoring WARNING: unknown mimetype for docs/rawQC_example.ipynb, ignoring writing nav.xhtml file... writing toc.ncx file... writing methylcheck.epub file... build succeeded, 217 warnings. The ePub file is in _build/epub. [rtd-command-info] start-time: 2020-03-06T21:15:19.770227Z, end-time: 2020-03-06T21:15:20.078393Z, 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