Read the Docs build information Build id: 445659 Project: life-epigenetics-methylcheck Version: latest Commit: c1856ac8e437146807c8b5372401445e0cf6be4f Date: 2020-10-08T21:53:26.126361Z State: finished Success: False [rtd-command-info] start-time: 2020-10-08T21:53:28.186298Z, end-time: 2020-10-08T21:53:35.272470Z, duration: 7, 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: 2020-10-08T21:53:36.119182Z, end-time: 2020-10-08T21:53:36.661297Z, duration: 0, 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 c1856ac v0.6.2 (#35) [rtd-command-info] start-time: 2020-10-08T21:53:37.015525Z, end-time: 2020-10-08T21:53:37.066540Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-10-08T21:53:40.910367Z, end-time: 2020-10-08T21:53:44.899198Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv 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: 2020-10-08T21:53:45.290751Z, end-time: 2020-10-08T21:53:45.950442Z, 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 (20.2.3) [rtd-command-info] start-time: 2020-10-08T21:53:46.308191Z, end-time: 2020-10-08T21:53:54.044657Z, duration: 7, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 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-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting Pygments>=2.0 Downloading Pygments-2.7.1-py3-none-any.whl (944 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.10-py2.py3-none-any.whl (127 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-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=edea475867d519808ff8a579de34ee5467836bd0b170a184b0b6f8fac018b486 Stored in directory: /tmp/pip-ephem-wheel-cache-41ytc57q/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=491059 sha256=42bb3fb5e1454bb2b87c0171df18c3295842a823b3301035dd1c4705d40d7f02 Stored in directory: /tmp/pip-ephem-wheel-cache-41ytc57q/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, idna, chardet, urllib3, certifi, requests, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, MarkupSafe, Jinja2, pytz, babel, snowballstemmer, Pygments, imagesize, pyparsing, six, packaging, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 50.3.0 Uninstalling setuptools-50.3.0: Successfully uninstalled setuptools-50.3.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 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-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 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 urllib3-1.25.10 [rtd-command-info] start-time: 2020-10-08T21:53:54.208615Z, end-time: 2020-10-08T21:54:05.214919Z, duration: 11, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting numpy Downloading numpy-1.19.2-cp37-cp37m-manylinux2010_x86_64.whl (14.5 MB) Collecting pandas Downloading pandas-1.1.3-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB) Collecting scipy Downloading scipy-1.5.2-cp37-cp37m-manylinux1_x86_64.whl (25.9 MB) Collecting matplotlib<3.1.3 Downloading matplotlib-3.1.2-cp37-cp37m-manylinux1_x86_64.whl (13.1 MB) Collecting seaborn Downloading seaborn-0.11.0-py3-none-any.whl (283 kB) Collecting xlrd>=1.0.0 Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB) Collecting tqdm Downloading tqdm-4.50.2-py2.py3-none-any.whl (70 kB) Collecting python-dateutil>=2.7.3 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 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)) (2020.1) Collecting cycler>=0.10 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 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<3.1.3->-r requirements.txt (line 4)) (2.4.7) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.2.0-cp37-cp37m-manylinux1_x86_64.whl (88 kB) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from python-dateutil>=2.7.3->pandas->-r requirements.txt (line 2)) (1.15.0) Installing collected packages: numpy, python-dateutil, pandas, scipy, cycler, kiwisolver, matplotlib, seaborn, xlrd, tqdm Successfully installed cycler-0.10.0 kiwisolver-1.2.0 matplotlib-3.1.2 numpy-1.19.2 pandas-1.1.3 python-dateutil-2.8.1 scipy-1.5.2 seaborn-0.11.0 tqdm-4.50.2 xlrd-1.2.0 [rtd-command-info] start-time: 2020-10-08T21:54:06.811662Z, end-time: 2020-10-08T21:54:09.162389Z, 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-0.6.2-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-0.6.2-py3.7.egg Copying methylcheck-0.6.2-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Adding methylcheck 0.6.2 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-0.6.2-py3.7.egg Processing dependencies for methylcheck==0.6.2 Searching for statsmodels Reading https://pypi.org/simple/statsmodels/ Downloading https://files.pythonhosted.org/packages/ff/68/ca52fc6a114141f13dfaee340fc355e2825753f1cbe3702a13a5046e16de/statsmodels-0.12.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=9ada3ddf13e60a5728304e6ca176e6ad8ca83b80c85db593087d853c5c6d4a98 Best match: statsmodels 0.12.0 Processing statsmodels-0.12.0-cp37-cp37m-manylinux1_x86_64.whl Installing statsmodels-0.12.0-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-0.12.0-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt Adding statsmodels 0.12.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/statsmodels-0.12.0-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==4.50.2 Best match: tqdm 4.50.2 Adding tqdm 4.50.2 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/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages Searching for numpy==1.19.2 Best match: numpy 1.19.2 Adding numpy 1.19.2 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==1.5.2 Best match: scipy 1.5.2 Adding scipy 1.5.2 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 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==2.4.7 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 kiwisolver==1.2.0 Best match: kiwisolver 1.2.0 Adding kiwisolver 1.2.0 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 pytz==2020.1 Best match: pytz 2020.1 Adding pytz 2020.1 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 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==0.6.2 [rtd-command-info] start-time: 2020-10-08T21:54:11.316923Z, end-time: 2020-10-08T21:54:11.385766Z, 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/"), ], 'downloads': [ ("pdf", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylcheck', 'name': u'methylcheck', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://life-epigenetics-methylcheck.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'FOXOBioScience', 'proxied_api_host': '/_', 'github_repo': 'methylcheck', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'c1856ac8', } 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: 2020-10-08T21:54:11.597361Z, end-time: 2020-10-08T21:54:12.133740Z, duration: 0, exit-code: 2 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 Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/registry.py", line 472, in load_extension mod = __import__(extname, None, None, ['setup']) ModuleNotFoundError: No module named 'sphinxcontrib.apidoc' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 303, in build_main args.tags, args.verbosity, args.jobs, args.keep_going) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 228, in __init__ self.setup_extension(extension) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 449, in setup_extension self.registry.load_extension(self, extname) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/registry.py", line 475, in load_extension raise ExtensionError(__('Could not import extension %s') % extname, err) sphinx.errors.ExtensionError: Could not import extension sphinxcontrib.apidoc (exception: No module named 'sphinxcontrib.apidoc') Extension error: Could not import extension sphinxcontrib.apidoc (exception: No module named 'sphinxcontrib.apidoc')