Read the Docs build information Build id: 508305 Project: life-epigenetics-methylcheck Version: latest Commit: 2ae6ad66390dcaeda3aaecdd02df906a2a5add29 Date: 2020-12-15T16:18:59.562257Z State: finished Success: True [rtd-command-info] start-time: 2020-12-15T16:19:01.137664Z, end-time: 2020-12-15T16:19:13.880311Z, duration: 12, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylcheck.git . Cloning into '.'... 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[rtd-command-info] start-time: 2020-12-15T16:19:14.342911Z, end-time: 2020-12-15T16:19:15.806790Z, 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 2ae6ad6 mouse array support and unit testing [rtd-command-info] start-time: 2020-12-15T16:19:15.988335Z, end-time: 2020-12-15T16:19:16.045041Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-12-15T16:19:19.884917Z, end-time: 2020-12-15T16:19:25.026135Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-12-15T16:19:25.199703Z, end-time: 2020-12-15T16:19:26.948337Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (20.3.3) [rtd-command-info] start-time: 2020-12-15T16:19:27.077097Z, end-time: 2020-12-15T16:19:36.338871Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 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.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.1-py2.py3-none-any.whl (13 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting six Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting Jinja2>=2.9 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting Pygments>=2.0 Downloading Pygments-2.7.3-py3-none-any.whl (950 kB) Collecting pytz>=2015.7 Downloading pytz-2020.4-py2.py3-none-any.whl (509 kB) Collecting requests Downloading requests-2.25.0-py2.py3-none-any.whl (61 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.2-py2.py3-none-any.whl (136 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting packaging Downloading packaging-20.8-py2.py3-none-any.whl (39 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=f433a272a4bb41135df35ef7b4c44ca414580f831a13595614fdf9450e96a270 Stored in directory: /tmp/pip-ephem-wheel-cache-452zllbb/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=32638a1beb195682f278afccb3ac60fd4d9e1deff3f13d5563cf80be738ac495 Stored in directory: /tmp/pip-ephem-wheel-cache-452zllbb/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.3 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.8 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.25.0 setuptools-51.0.0 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2 [rtd-command-info] start-time: 2020-12-15T16:19:36.510669Z, end-time: 2020-12-15T16:19:48.662087Z, duration: 12, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: numpy in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (1.19.2) Requirement already satisfied: pandas in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 2)) (1.1.3) Requirement already satisfied: scipy in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 3)) (1.5.3) Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 11)) (1.8.5) Collecting matplotlib<3.1.3 Downloading matplotlib-3.1.2-cp37-cp37m-manylinux1_x86_64.whl (13.1 MB) 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<3.1.3->-r requirements.txt (line 4)) (2.4.7) Requirement already satisfied: python-dateutil>=2.1 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib<3.1.3->-r requirements.txt (line 4)) (2.8.1) Requirement already satisfied: cycler>=0.10 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib<3.1.3->-r requirements.txt (line 4)) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib<3.1.3->-r requirements.txt (line 4)) (1.2.0) Collecting xlrd>=1.0.0 Downloading xlrd-2.0.1-py2.py3-none-any.whl (96 kB) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from cycler>=0.10->matplotlib<3.1.3->-r requirements.txt (line 4)) (1.15.0) Collecting ipykernel Downloading ipykernel-5.4.2-py3-none-any.whl (119 kB) Collecting ipython>=5.0.0 Downloading ipython-7.19.0-py3-none-any.whl (784 kB) Requirement already satisfied: pygments in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 12)) (2.7.3) Requirement already satisfied: setuptools>=18.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 12)) (51.0.0) Collecting jedi>=0.10 Downloading jedi-0.17.2-py2.py3-none-any.whl (1.4 MB) Collecting parso<0.8.0,>=0.7.0 Downloading parso-0.7.1-py2.py3-none-any.whl (109 kB) Collecting pexpect>4.3 Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB) Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 Downloading prompt_toolkit-3.0.8-py3-none-any.whl (355 kB) Collecting ptyprocess>=0.5 Downloading ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB) Collecting tornado>=4.2 Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB) Collecting traitlets>=4.1.0 Downloading traitlets-5.0.5-py3-none-any.whl (100 kB) Collecting m2r Downloading m2r-0.2.1.tar.gz (16 kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from m2r->-r requirements.txt (line 9)) (0.14) Collecting nbsphinx Downloading nbsphinx-0.8.0-py3-none-any.whl (24 kB) Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from nbsphinx->-r requirements.txt (line 10)) (2.11.2) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (2.9.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (0.7.12) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.2.4) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.2.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (2.0.0) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (2.25.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (20.8) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx->-r requirements.txt (line 11)) (2020.4) 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->nbsphinx->-r requirements.txt (line 10)) (1.1.1) Collecting nbconvert!=5.4 Downloading nbconvert-6.0.7-py3-none-any.whl (552 kB) Collecting entrypoints>=0.2.2 Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting mistune Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Collecting nbclient<0.6.0,>=0.5.0 Downloading nbclient-0.5.1-py3-none-any.whl (65 kB) Collecting jupyter-client Downloading jupyter_client-6.1.7-py3-none-any.whl (108 kB) Collecting jupyter-core Downloading jupyter_core-4.7.0-py3-none-any.whl (82 kB) Collecting nbformat Downloading nbformat-5.0.8-py3-none-any.whl (172 kB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Collecting attrs>=17.4.0 Downloading attrs-20.3.0-py2.py3-none-any.whl (49 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.4.3.tar.gz (16 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.17.3.tar.gz (106 kB) Collecting pyzmq>=13 Downloading pyzmq-20.0.0-cp37-cp37m-manylinux1_x86_64.whl (1.1 MB) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (2.10) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (3.0.4) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (1.26.2) 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>=2.0.0->sphinx->-r requirements.txt (line 11)) (2020.12.5) Collecting seaborn Downloading seaborn-0.11.0-py3-none-any.whl (283 kB) Collecting sphinxcontrib-apidoc Downloading sphinxcontrib_apidoc-0.3.0-py2.py3-none-any.whl (8.5 kB) Collecting tqdm Downloading tqdm-4.54.1-py2.py3-none-any.whl (69 kB) Collecting async-generator Downloading async_generator-1.10-py3-none-any.whl (18 kB) Collecting backcall Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB) Collecting bleach Downloading bleach-3.2.1-py2.py3-none-any.whl (145 kB) Collecting decorator Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting defusedxml Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB) Collecting importlib-metadata Downloading importlib_metadata-3.3.0-py3-none-any.whl (10 kB) Collecting typing-extensions>=3.6.4 Downloading typing_extensions-3.7.4.3-py3-none-any.whl (22 kB) Collecting zipp>=0.5 Downloading zipp-3.4.0-py3-none-any.whl (5.2 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting jupyterlab-pygments Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB) Collecting nest-asyncio Downloading nest_asyncio-1.4.3-py3-none-any.whl (5.3 kB) Collecting pbr Downloading pbr-5.5.1-py2.py3-none-any.whl (106 kB) Collecting pickleshare Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->sphinx->-r requirements.txt (line 11)) (1.1.4) Collecting testpath Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB) Collecting wcwidth Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Building wheels for collected packages: m2r, 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=10465 sha256=13f37e703ffbbe8952a7c0f16c3f8cfb91cf462ff79e837c9cb29f3799f42101 Stored in directory: /tmp/pip-ephem-wheel-cache-cdmgk5ns/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=7992 sha256=43e94a61f373868805d27fcf55fd81ccab1ed65cd3267e331e5e028c8c10d459 Stored in directory: /tmp/pip-ephem-wheel-cache-cdmgk5ns/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp37-cp37m-linux_x86_64.whl size=115337 sha256=75ed2652ad39094f27d98977c35101ef01a12c11ddacb21e1530443648882493 Stored in directory: /tmp/pip-ephem-wheel-cache-cdmgk5ns/wheels/a5/52/bf/71258a1d7b3c8cbe1ee53f9314c6f65f20385481eaee573cc5 Successfully built m2r pandocfilters pyrsistent Installing collected packages: zipp, typing-extensions, ipython-genutils, traitlets, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, jupyter-core, jsonschema, webencodings, wcwidth, ptyprocess, parso, nest-asyncio, nbformat, jupyter-client, async-generator, testpath, prompt-toolkit, pickleshare, pexpect, pandocfilters, nbclient, mistune, jupyterlab-pygments, jedi, entrypoints, defusedxml, decorator, bleach, backcall, pbr, nbconvert, matplotlib, ipython, xlrd, tqdm, sphinxcontrib-apidoc, seaborn, nbsphinx, m2r, ipykernel Attempting uninstall: matplotlib Found existing installation: matplotlib 3.3.2 Not uninstalling matplotlib at /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest Can't uninstall 'matplotlib'. No files were found to uninstall. Successfully installed async-generator-1.10 attrs-20.3.0 backcall-0.2.0 bleach-3.2.1 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-3.3.0 ipykernel-5.4.2 ipython-7.19.0 ipython-genutils-0.2.0 jedi-0.17.2 jsonschema-3.2.0 jupyter-client-6.1.7 jupyter-core-4.7.0 jupyterlab-pygments-0.1.2 m2r-0.2.1 matplotlib-3.1.2 mistune-0.8.4 nbclient-0.5.1 nbconvert-6.0.7 nbformat-5.0.8 nbsphinx-0.8.0 nest-asyncio-1.4.3 pandocfilters-1.4.3 parso-0.7.1 pbr-5.5.1 pexpect-4.8.0 pickleshare-0.7.5 prompt-toolkit-3.0.8 ptyprocess-0.6.0 pyrsistent-0.17.3 pyzmq-20.0.0 seaborn-0.11.0 sphinxcontrib-apidoc-0.3.0 testpath-0.4.4 tornado-6.1 tqdm-4.54.1 traitlets-5.0.5 typing-extensions-3.7.4.3 wcwidth-0.2.5 webencodings-0.5.1 xlrd-2.0.1 zipp-3.4.0 [rtd-command-info] start-time: 2020-12-15T16:19:48.790466Z, end-time: 2020-12-15T16:19:51.254004Z, duration: 2, 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/qc_report.py -> build/lib/methylcheck copying methylcheck/progress_bar.py -> build/lib/methylcheck copying methylcheck/__init__.py -> build/lib/methylcheck copying methylcheck/read_geo_processed.py -> build/lib/methylcheck copying methylcheck/version.py -> build/lib/methylcheck copying methylcheck/qc_plot.py -> build/lib/methylcheck copying methylcheck/cli.py -> build/lib/methylcheck copying methylcheck/__main__.py -> build/lib/methylcheck copying methylcheck/p_value_probe_detection.py -> build/lib/methylcheck copying methylcheck/load_processed.py -> build/lib/methylcheck creating build/lib/methylcheck/data_files copying methylcheck/data_files/__init__.py -> build/lib/methylcheck/data_files creating build/lib/methylcheck/samples copying methylcheck/samples/sklearn_mds.py -> build/lib/methylcheck/samples copying methylcheck/samples/assign_groups.py -> build/lib/methylcheck/samples copying methylcheck/samples/__init__.py -> build/lib/methylcheck/samples copying methylcheck/samples/postprocessQC.py -> build/lib/methylcheck/samples creating build/lib/methylcheck/predict copying methylcheck/predict/__init__.py -> build/lib/methylcheck/predict copying methylcheck/predict/sex.py -> build/lib/methylcheck/predict creating build/lib/methylcheck/probes copying methylcheck/probes/__init__.py -> build/lib/methylcheck/probes copying methylcheck/probes/filters.py -> build/lib/methylcheck/probes 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 copying methylcheck/data_files/illumina_sketchy_probes_996.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 copying build/lib/methylcheck/qc_report.py -> build/bdist.linux-x86_64/egg/methylcheck creating build/bdist.linux-x86_64/egg/methylcheck/data_files copying build/lib/methylcheck/data_files/illumina_sketchy_probes_996.npy -> 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/__init__.py -> 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/progress_bar.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck creating build/bdist.linux-x86_64/egg/methylcheck/samples copying build/lib/methylcheck/samples/sklearn_mds.py -> build/bdist.linux-x86_64/egg/methylcheck/samples copying build/lib/methylcheck/samples/assign_groups.py -> build/bdist.linux-x86_64/egg/methylcheck/samples copying build/lib/methylcheck/samples/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck/samples copying build/lib/methylcheck/samples/postprocessQC.py -> build/bdist.linux-x86_64/egg/methylcheck/samples copying build/lib/methylcheck/read_geo_processed.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/version.py -> build/bdist.linux-x86_64/egg/methylcheck creating build/bdist.linux-x86_64/egg/methylcheck/predict copying build/lib/methylcheck/predict/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck/predict copying build/lib/methylcheck/predict/sex.py -> build/bdist.linux-x86_64/egg/methylcheck/predict copying build/lib/methylcheck/qc_plot.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/cli.py -> build/bdist.linux-x86_64/egg/methylcheck creating build/bdist.linux-x86_64/egg/methylcheck/probes copying build/lib/methylcheck/probes/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck/probes copying build/lib/methylcheck/probes/filters.py -> build/bdist.linux-x86_64/egg/methylcheck/probes copying build/lib/methylcheck/__main__.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/p_value_probe_detection.py -> build/bdist.linux-x86_64/egg/methylcheck copying build/lib/methylcheck/load_processed.py -> build/bdist.linux-x86_64/egg/methylcheck byte-compiling build/bdist.linux-x86_64/egg/methylcheck/qc_report.py to qc_report.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/data_files/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/progress_bar.py to progress_bar.cpython-37.pyc 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/samples/sklearn_mds.py to sklearn_mds.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/samples/assign_groups.py to assign_groups.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/samples/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/samples/postprocessQC.py to postprocessQC.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/read_geo_processed.py to read_geo_processed.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/version.py to version.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/predict/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/predict/sex.py to sex.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/qc_plot.py to qc_plot.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/probes/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/probes/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/p_value_probe_detection.py to p_value_probe_detection.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/methylcheck/load_processed.py to load_processed.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-0.6.5-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-0.6.5-py3.7.egg Copying methylcheck-0.6.5-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Adding methylcheck 0.6.5 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-0.6.5-py3.7.egg Processing dependencies for methylcheck==0.6.5 Searching for statsmodels Reading https://pypi.org/simple/statsmodels/ Downloading https://files.pythonhosted.org/packages/93/97/67bf20df36a88ce8dd84828f83453b91177e1ff0abd8c92f2e0a47782689/statsmodels-0.12.1-cp37-cp37m-manylinux1_x86_64.whl#sha256=588c0f7e29403161ca952dcdad3d67970583742e9f11f66c7c5b08ac97a0408c Best match: statsmodels 0.12.1 Processing statsmodels-0.12.1-cp37-cp37m-manylinux1_x86_64.whl Installing statsmodels-0.12.1-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/statsmodels-0.12.1-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt Adding statsmodels 0.12.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/statsmodels-0.12.1-py3.7-linux-x86_64.egg Searching for patsy>=0.5 Reading https://pypi.org/simple/patsy/ Downloading https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl#sha256=5465be1c0e670c3a965355ec09e9a502bf2c4cbe4875e8528b0221190a8a5d40 Best match: patsy 0.5.1 Processing patsy-0.5.1-py2.py3-none-any.whl Installing patsy-0.5.1-py2.py3-none-any.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/patsy-0.5.1-py3.7.egg/EGG-INFO/requires.txt Adding patsy 0.5.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/patsy-0.5.1-py3.7.egg Searching for tqdm==4.54.1 Best match: tqdm 4.54.1 Adding tqdm 4.54.1 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 seaborn==0.11.0 Best match: seaborn 0.11.0 Adding seaborn 0.11.0 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 matplotlib==3.1.2 Best match: matplotlib 3.1.2 Adding matplotlib 3.1.2 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==1.1.3 Best match: pandas 1.1.3 Adding pandas 1.1.3 to easy-install.pth file Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for numpy==1.19.2 Best match: numpy 1.19.2 numpy 1.19.2 is already the active version in easy-install.pth 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/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for scipy==1.5.3 Best match: scipy 1.5.3 scipy 1.5.3 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for cycler==0.10.0 Best match: cycler 0.10.0 cycler 0.10.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for kiwisolver==1.2.0 Best match: kiwisolver 1.2.0 kiwisolver 1.2.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for pyparsing==2.4.7 Best match: pyparsing 2.4.7 Adding pyparsing 2.4.7 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 python-dateutil 2.8.1 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for pytz==2020.4 Best match: pytz 2020.4 Adding pytz 2020.4 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==1.15.0 Best match: six 1.15.0 Adding six 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Finished processing dependencies for methylcheck==0.6.5 [rtd-command-info] start-time: 2020-12-15T16:19:52.608149Z, end-time: 2020-12-15T16:19:52.688509Z, 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', 'sphinx.ext.autosummary' ] # instead of CLI "sphinx-autodoc . _build/html" you write this apidoc_module_dir = '.' apidoc_output_dir = '_sphinx_build' apidoc_excluded_paths = ['tests'] apidoc_separate_modules = 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://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("feature-mouse", "/en/feature-mouse/"), ], 'downloads': [ ("html", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylcheck', 'name': u'methylcheck', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://life-epigenetics-methylcheck.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'FOXOBioScience', 'proxied_api_host': '/_', 'github_repo': 'methylcheck', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '2ae6ad66', } 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' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2020-12-15T16:19:52.884728Z, end-time: 2020-12-15T16:20:14.860287Z, duration: 21, exit-code: 0 python sphinx-build -T -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.cli.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.load_processed.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.p_value_probe_detection.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.progress_bar.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.qc_plot.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.qc_report.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.read_geo_processed.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.version.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.data_files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.sex.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.probes.filters.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.probes.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.assign_groups.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.postprocessQC.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.sklearn_mds.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst. building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 15 source files that are out of date updating environment: 15 added, 0 changed, 0 removed reading sources... [ 6%] README reading sources... [ 13%] docs/another-methylcheck-qc-example reading sources... [ 20%] docs/demo-methylprep-to-methylcheck-example reading sources... [ 26%] docs/demo_qc_functions reading sources... [ 33%] docs/demo_read_geo_processed reading sources... [ 40%] docs/demo_using_matched_meta_data reading sources... [ 46%] docs/filtering_probes reading sources... [ 53%] docs/methylprep_methylcheck_example reading sources... [ 60%] docs/postprocessQC_example reading sources... [ 66%] docs/pval reading sources... [ 73%] docs/rawQC_example reading sources... [ 80%] docs/release-history reading sources... [ 86%] docs/source/methylcheck reading sources... [ 93%] docs/testing_sns_upgrade_methylcheck_v0.6.2 reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:106: 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:404: WARNING: Title level inconsistent: (These return a filtered data set) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb:6: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb:6: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.cli /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.run_pipeline /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.run_qc /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.read_geo /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.load /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.load_both /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.qc_signal_intensity /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_M_vs_U /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_controls /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_beta_by_type /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.list_problem_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.exclude_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.exclude_sex_control_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.drop_nan_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.samples /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.sample_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.beta_density_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.mean_beta_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.mean_beta_compare /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.beta_mds_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.combine_mds /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.cumulative_sum_beta_distribution /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.predict /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.get_sex /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.assign WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised: No module named 'joblib' WARNING: autodoc: failed to import module 'probes' from module 'methylcheck'; the following exception was raised: No module named 'joblib' WARNING: autodoc: failed to import module 'samples' from module 'methylcheck'; the following exception was raised: No module named 'joblib' WARNING: autodoc: failed to import module 'predict' from module 'methylcheck'; the following exception was raised: No module named 'joblib' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/testing_sns_upgrade_methylcheck_v0.6.2.ipynb:6: WARNING: Each notebook should have at least one section title 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/pval.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 /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2020-12-15T16:20:15.252406Z, end-time: 2020-12-15T16:20:21.771548Z, duration: 6, 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.cli.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.load_processed.rst. 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:106: 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:404: WARNING: Title level inconsistent: (These return a filtered data set) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/postprocessQC_example.ipynb:6: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb:6: WARNING: Each notebook should have at least one section title /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.cli /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.run_pipeline /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.run_qc /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.read_geo /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.load /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.load_both /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.qc_signal_intensity /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_M_vs_U /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_controls /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.plot_beta_by_type /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.list_problem_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.exclude_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.exclude_sex_control_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.drop_nan_probes /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.samples /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.sample_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.beta_density_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.mean_beta_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.mean_beta_compare /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.beta_mds_plot /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.combine_mds /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.cumulative_sum_beta_distribution /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.predict /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.get_sex /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/methylcheck.rst:4: WARNING: failed to import methylcheck.assign WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised: No module named 'joblib' WARNING: autodoc: failed to import module 'probes' from module 'methylcheck'; the following exception was raised: No module named 'joblib' WARNING: autodoc: failed to import module 'samples' from module 'methylcheck'; the following exception was raised: No module named 'joblib' WARNING: autodoc: failed to import module 'predict' from module 'methylcheck'; the following exception was raised: No module named 'joblib' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/testing_sns_upgrade_methylcheck_v0.6.2.ipynb:6: WARNING: Each notebook should have at least one section title 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 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