Read the Docs build information Build id: 424719 Project: institute-for-disease-modeling-emod-hiv Version: latest Commit: ef9fd0048712b2cffd849fb38932ce56452a50c6 Date: 2020-09-17T20:47:51.378767Z State: finished Success: False [rtd-command-info] start-time: 2020-09-17T20:47:55.850697Z, end-time: 2020-09-17T20:48:08.845528Z, duration: 12, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/Documentation.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2020-09-17T20:48:09.360507Z, end-time: 2020-09-17T20:48:09.812685Z, 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 ef9fd004 Merge pull request #1152 from JSchripsema-IDM/rtd_w_lauren [rtd-command-info] start-time: 2020-09-17T20:48:09.360507Z, end-time: 2020-09-17T20:48:09.812685Z, 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 ef9fd004 Merge pull request #1152 from JSchripsema-IDM/rtd_w_lauren [rtd-command-info] start-time: 2020-09-17T20:48:15.230416Z, end-time: 2020-09-17T20:48:15.310932Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-09-17T20:48:21.541081Z, end-time: 2020-09-17T20:48:25.438975Z, 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/institute-for-disease-modeling-emod-hiv/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-09-17T20:48:25.682395Z, end-time: 2020-09-17T20:48:26.370748Z, 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/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (20.2.3) [rtd-command-info] start-time: 2020-09-17T20:48:26.638515Z, end-time: 2020-09-17T20:48:34.708541Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 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 idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 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=424281f66548154b3ed5b52e008a0c4d2f828a41d50e1140510a9bd78b6a0afa Stored in directory: /tmp/pip-ephem-wheel-cache-vs6gk3s9/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=51f6a87b97c5cf82afb485385faed46af0d1d05fd91261756a92215aad8149e3 Stored in directory: /tmp/pip-ephem-wheel-cache-vs6gk3s9/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, pytz, babel, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, chardet, urllib3, idna, certifi, requests, MarkupSafe, Jinja2, snowballstemmer, pyparsing, packaging, imagesize, 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-2.3.1 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: 2020-09-17T20:48:35.226940Z, end-time: 2020-09-17T20:48:40.218245Z, duration: 4, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting sphinx-rtd-theme~=0.5.0 Downloading sphinx_rtd_theme-0.5.0-py2.py3-none-any.whl (10.8 MB) Collecting sphinxcontrib-napoleon~=0.7 Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinx~=3.2.0 Downloading Sphinx-3.2.1-py3-none-any.whl (2.9 MB) Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting numpy~=1.19.1 Downloading numpy-1.19.2-cp37-cp37m-manylinux2010_x86_64.whl (14.5 MB) Collecting numpydoc~=1.0.0 Downloading numpydoc-1.0.0-py3-none-any.whl (47 kB) Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r requirements.txt (line 2)) (1.15.0) Collecting pockets>=0.3 Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (1.1.4) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.3.1) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.8.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.0.0) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.24.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (0.7.12) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (20.4) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (41.0.1) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (0.14) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.11.2) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (1.2.0) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.0->-r requirements.txt (line 3)) (2020.1) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (1.25.10) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (2020.6.20) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (2.10) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (3.0.4) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from packaging->sphinx~=3.2.0->-r requirements.txt (line 3)) (2.4.7) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.0->-r requirements.txt (line 3)) (1.1.1) Installing collected packages: sphinxcontrib-qthelp, sphinxcontrib-applehelp, sphinxcontrib-htmlhelp, sphinxcontrib-jsmath, sphinxcontrib-devhelp, sphinx, sphinx-rtd-theme, pockets, sphinxcontrib-napoleon, plantweb, numpy, numpydoc Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed numpy-1.19.2 numpydoc-1.0.0 plantweb-1.2.1 pockets-0.9.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-qthelp-1.0.3