Read the Docs build information Build id: 274404 Project: cyverse-leptin-rna-seq-lesson-dev Version: latest Commit: f10b4357dcaa2789598968f5a6f00ddf3a92b791 Date: 2020-01-08T20:46:14.200965Z State: finished Success: False [rtd-command-info] start-time: 2020-01-08T20:50:35.218223Z, end-time: 2020-01-08T20:50:36.105191Z, duration: 0, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/JasonJWilliamsNY/leptin-rna-seq-lesson-dev.git . Cloning into '.'... [rtd-command-info] start-time: 2020-01-08T20:50:36.326866Z, end-time: 2020-01-08T20:50:36.456656Z, 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 f10b435 initial lesson draft [rtd-command-info] start-time: 2020-01-08T20:50:36.532226Z, end-time: 2020-01-08T20:50:36.542804Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-01-08T20:50:37.925489Z, end-time: 2020-01-08T20:50:42.177477Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-01-08T20:50:42.279283Z, end-time: 2020-01-08T20:50:44.691796Z, duration: 2, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/.cache/pip pip Collecting pip Downloading https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl (1.4MB) Installing collected packages: pip Found existing installation: pip 19.1.1 Uninstalling pip-19.1.1: Successfully uninstalled pip-19.1.1 Successfully installed pip-19.3.1 [rtd-command-info] start-time: 2020-01-08T20:50:44.769773Z, end-time: 2020-01-08T20:50:56.323459Z, duration: 11, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/.cache/pip 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 https://files.pythonhosted.org/packages/13/e5/6d710c9cf96c31ac82657bcfb441df328b22df8564d58d0c4cd62612674c/Pygments-2.3.1-py2.py3-none-any.whl (849kB) Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (41.0.1) Collecting docutils==0.14 Downloading https://files.pythonhosted.org/packages/36/fa/08e9e6e0e3cbd1d362c3bbee8d01d0aedb2155c4ac112b19ef3cae8eed8d/docutils-0.14-py3-none-any.whl (543kB) Collecting mock==1.0.1 Downloading https://files.pythonhosted.org/packages/a2/52/7edcd94f0afb721a2d559a5b9aae8af4f8f2c79bc63fdbe8a8a6c9b23bbe/mock-1.0.1.tar.gz (818kB) Collecting pillow==5.4.1 Downloading https://files.pythonhosted.org/packages/ae/2a/0a0ab2833e5270664fb5fae590717f867ac6319b124160c09f1d3291de28/Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl 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readthedocs-sphinx-ext<1.1 Downloading https://files.pythonhosted.org/packages/8a/b5/73b740dc7182b4f458de18ab54adaf5698ace3a723569c5e2a748130a314/readthedocs_sphinx_ext-1.0.1-py2.py3-none-any.whl Collecting future Downloading https://files.pythonhosted.org/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz (829kB) Collecting Jinja2>=2.3 Downloading https://files.pythonhosted.org/packages/65/e0/eb35e762802015cab1ccee04e8a277b03f1d8e53da3ec3106882ec42558b/Jinja2-2.10.3-py2.py3-none-any.whl (125kB) Collecting imagesize Downloading https://files.pythonhosted.org/packages/31/b2/b5522a0c8d11e4aff83f8342f3f0dea68c2fb25aa44403e420587f0ce204/imagesize-1.2.0-py2.py3-none-any.whl Collecting snowballstemmer>=1.1 Downloading https://files.pythonhosted.org/packages/7d/4b/cdf1113a0e88b641893b814e9c36f69a6fda28cd88b62c7f0d858cde3166/snowballstemmer-2.0.0-py2.py3-none-any.whl (97kB) Collecting babel!=2.0,>=1.3 Downloading https://files.pythonhosted.org/packages/15/a1/522dccd23e5d2e47aed4b6a16795b8213e3272c7506e625f2425ad025a19/Babel-2.8.0-py2.py3-none-any.whl (8.6MB) Collecting sphinxcontrib-websupport Downloading https://files.pythonhosted.org/packages/2a/59/d64bda9b7480a84a3569be4dde267c0f6675b255ba63b4c8e84469940457/sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl Collecting packaging Downloading https://files.pythonhosted.org/packages/d8/5b/3098db49a61ccc8583ffead6aedc226f08ff56dc03106b6ec54451e27a30/packaging-20.0-py2.py3-none-any.whl Collecting requests>=2.0.0 Downloading https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl (57kB) Collecting six>=1.5 Downloading https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl Collecting MarkupSafe>=0.23 Downloading https://files.pythonhosted.org/packages/98/7b/ff284bd8c80654e471b769062a9b43cc5d03e7a615048d96f4619df8d420/MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl Collecting pytz>=2015.7 Downloading https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl (509kB) Collecting pyparsing>=2.0.2 Downloading https://files.pythonhosted.org/packages/5d/bc/1e58593167fade7b544bfe9502a26dc860940a79ab306e651e7f13be68c2/pyparsing-2.4.6-py2.py3-none-any.whl (67kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading https://files.pythonhosted.org/packages/b4/40/a9837291310ee1ccc242ceb6ebfd9eb21539649f193a7c8c86ba15b98539/urllib3-1.25.7-py2.py3-none-any.whl (125kB) Collecting chardet<3.1.0,>=3.0.2 Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB) Collecting certifi>=2017.4.17 Downloading https://files.pythonhosted.org/packages/b9/63/df50cac98ea0d5b006c55a399c3bf1db9da7b5a24de7890bc9cfd5dd9e99/certifi-2019.11.28-py2.py3-none-any.whl (156kB) Collecting idna<2.9,>=2.5 Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB) 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-cp37-none-any.whl size=23754 sha256=f5909d0b39962d45f2a42476f822c79121ff671fbb0c4369c0850329650fcadc Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6 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-cp37-none-any.whl size=491057 sha256=5b6aea1f8ac8d95918bea31faaca7f338fc9d14823cfa3ab3e1f8d6ec3d17a36 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/.cache/pip/wheels/8b/99/a0/81daf51dcd359a9377b110a8a886b3895921802d2fc1b2397e Successfully built mock future Installing collected packages: Pygments, docutils, mock, pillow, alabaster, future, commonmark, MarkupSafe, Jinja2, imagesize, snowballstemmer, pytz, babel, sphinxcontrib-websupport, six, pyparsing, packaging, urllib3, chardet, certifi, idna, requests, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Successfully installed Jinja2-2.10.3 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.8 imagesize-1.2.0 mock-1.0.1 packaging-20.0 pillow-5.4.1 pyparsing-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.22.0 six-1.13.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.7 [rtd-command-info] start-time: 2020-01-08T20:50:56.899094Z, end-time: 2020-01-08T20:50:57.131022Z, duration: 0, exit-code: 0 cat conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # General information about the project. import sys import os from recommonmark.parser import CommonMarkParser from recommonmark.transform import AutoStructify import sphinx_fontawesome sys.path.insert(0, os.path.dirname(__file__)) rst_prolog = sphinx_fontawesome.prolog from misc.sphinx_conf import * # noqa project = 'RNA-Seq analysis of Mouse Leptin Gene' copyright = '2019, Genomics Education Alliance' author = 'your_name' version = '1.0' release = '1.0' html_logo = './img/GEA_logo.png' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'cyverse-leptin-rna-seq-lesson-dev', 'name': u'leptin-rna-seq-lesson-dev', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-leptin-rna-seq-lesson-dev.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'proxied_api_host': 'https://readthedocs.com', 'github_user': 'JasonJWilliamsNY', 'github_repo': 'leptin-rna-seq-lesson-dev', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'f10b4357', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' [rtd-command-info] start-time: 2020-01-08T20:50:57.213405Z, end-time: 2020-01-08T20:50:57.801636Z, duration: 0, exit-code: 2 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file execfile_(filename, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_ exec_(code, _globals) File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/conf.py", line 10, in import sphinx_fontawesome ModuleNotFoundError: No module named 'sphinx_fontawesome' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/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/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 201, in __init__ self.config = Config.read(self.confdir, confoverrides or {}, self.tags) File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 203, in read namespace = eval_config_file(filename, tags) File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 380, in eval_config_file raise ConfigError(msg % traceback.format_exc()) sphinx.errors.ConfigError: There is a programmable error in your configuration file: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file execfile_(filename, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_ exec_(code, _globals) File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/conf.py", line 10, in import sphinx_fontawesome ModuleNotFoundError: No module named 'sphinx_fontawesome' Configuration error: There is a programmable error in your configuration file: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file execfile_(filename, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_ exec_(code, _globals) File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/conf.py", line 10, in import sphinx_fontawesome ModuleNotFoundError: No module named 'sphinx_fontawesome'