Read the Docs build information Build id: 274419 Project: cyverse-leptin-rna-seq-lesson-dev Version: latest Commit: 82729bf1767889d5731e559a71ec55e428424b72 Date: 2020-01-08T21:07:42.812879Z State: finished Success: True [rtd-command-info] start-time: 2020-01-08T21:11:59.118902Z, end-time: 2020-01-08T21:11:59.125861Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/JasonJWilliamsNY/leptin-rna-seq-lesson-dev.git [rtd-command-info] start-time: 2020-01-08T21:11:59.210646Z, end-time: 2020-01-08T21:11:59.648491Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/JasonJWilliamsNY/leptin-rna-seq-lesson-dev 3315ba3..82729bf master -> origin/master [rtd-command-info] start-time: 2020-01-08T21:11:59.877752Z, end-time: 2020-01-08T21:11:59.907182Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 3315ba3 add requirements file HEAD is now at 82729bf update requirments [rtd-command-info] start-time: 2020-01-08T21:12:00.134322Z, end-time: 2020-01-08T21:12:00.142113Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-01-08T21:12:01.491202Z, end-time: 2020-01-08T21:12:07.336628Z, duration: 5, 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 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/bin/python3.7) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-01-08T21:12:07.435003Z, end-time: 2020-01-08T21:12:08.258481Z, duration: 0, 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 Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (19.3.1) [rtd-command-info] start-time: 2020-01-08T21:12:08.508202Z, end-time: 2020-01-08T21:12:10.442423Z, duration: 1, 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 Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (2.3.1) 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) Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (0.14) Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (1.0.1) Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (5.4.1) Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (0.7.12) Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (0.8.1) Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (0.5.0) Requirement already up-to-date: sphinx<2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (1.8.5) Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (0.4.3) Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (1.0.1) Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from commonmark==0.8.1) (0.18.2) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from sphinx<2) (20.0) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.2.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.8.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.0.0) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.13.0) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from packaging->sphinx<2) (2.4.6) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2.8) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2019.11.28) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (1.25.7) [rtd-command-info] start-time: 2020-01-08T21:12:10.521369Z, end-time: 2020-01-08T21:12:12.159566Z, duration: 1, exit-code: 0 python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/.cache/pip -r misc/requirements.txt Collecting sphinx_fontawesome (from -r misc/requirements.txt (line 1)) Downloading https://files.pythonhosted.org/packages/e0/c5/9c14765c7f4721a7df3dc3710e3ce041b0042f91c8c75991434405657c30/sphinx_fontawesome-0.0.6.tar.gz Requirement already satisfied: Sphinx>=1.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from sphinx_fontawesome->-r misc/requirements.txt (line 1)) (1.8.5) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (2.22.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (2.0.0) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (1.13.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (20.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (2.3.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (41.0.1) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (1.1.2) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (2.10.3) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (2.8.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (0.7.12) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (1.2.0) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (0.14) Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (2.8) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (3.0.4) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (2019.11.28) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (1.25.7) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from packaging->Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (2.4.6) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (1.1.1) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->Sphinx>=1.5.0->sphinx_fontawesome->-r misc/requirements.txt (line 1)) (2019.3) Building wheels for collected packages: sphinx-fontawesome Building wheel for sphinx-fontawesome (setup.py): started Building wheel for sphinx-fontawesome (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/.cache/pip/wheels/f0/6b/0f/df5eb32ac8ef70722079fd341af3ecd726210c1b8a7d85c629 Successfully built sphinx-fontawesome Installing collected packages: sphinx-fontawesome Successfully installed sphinx-fontawesome-0.0.6 [rtd-command-info] start-time: 2020-01-08T21:12:12.756728Z, end-time: 2020-01-08T21:12:12.980237Z, 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': '82729bf1', } 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: 2020-01-08T21:12:13.083846Z, end-time: 2020-01-08T21:12:28.935104Z, duration: 15, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 19 source files that are out of date updating environment: 19 added, 0 changed, 0 removed reading sources... 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[100%] section-summary /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/example_directives_delete.rst:131: WARNING: Duplicate substitution definition name: "google". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:29: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:50: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:67: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:82: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:97: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:114: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:133: WARNING: toctree contains reference to nonexisting document ' :maxdepth: 2' defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/section-glossary.rst:17: WARNING: Document or section may not begin with a transition. defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/assets/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/example_directives_delete.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/section-glossary.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/section-n.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/section-summary.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 5%] Contributors_maintainers writing output... [ 10%] License writing output... [ 15%] README writing output... [ 21%] assets/README writing output... [ 26%] example_directives_delete writing output... [ 31%] index writing output... [ 36%] section-1 writing output... [ 42%] section-10 writing output... [ 47%] section-2 writing output... [ 52%] section-3 writing output... [ 57%] section-4 writing output... [ 63%] section-5 writing output... [ 68%] section-6 writing output... [ 73%] section-7 writing output... [ 78%] section-8 writing output... [ 84%] section-9 writing output... [ 89%] section-glossary writing output... [ 94%] section-n writing output... [100%] section-summary generating indices... genindex writing additional pages... search copying images... [ 5%] ./img/kitten_no_border.png copying images... [ 10%] ./img/kitten_w_border.png copying images... [ 15%] ./img/lesson_link_notification.png copying images... [ 21%] ./img/lab_session.png copying images... 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WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/_static' does not exist done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 33 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2020-01-08T21:12:29.060455Z, end-time: 2020-01-08T21:12:42.033994Z, duration: 12, 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... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 19 added, 0 changed, 0 removed reading sources... 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[100%] section-summary /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/example_directives_delete.rst:131: WARNING: Duplicate substitution definition name: "google". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:29: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:50: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:67: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:82: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:97: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:114: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/index.rst:133: WARNING: toctree contains reference to nonexisting document ' :maxdepth: 2' defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/section-glossary.rst:17: WARNING: Document or section may not begin with a transition. defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". defined_substitutions.txt:187: WARNING: Duplicate substitution definition name: "LINK". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/assets/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/example_directives_delete.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/section-glossary.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/section-n.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-leptin-rna-seq-lesson-dev/checkouts/latest/section-summary.rst: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... section-1 section-2 section-3 section-4 section-5 section-6 section-7 section-8 section-9 section-10 writing... done writing additional files... copying images... 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