Read the Docs build information Build id: 327940 Project: cyverse-leptin-rna-seq-lesson-dev Version: latest Commit: 5f9ee1fba043af26fa50de023e15e00c69298857 Date: 2020-05-07T21:24:36.635007Z State: finished Success: True [rtd-command-info] start-time: 2020-05-07T21:24:38.716227Z, end-time: 2020-05-07T21:24:39.737313Z, duration: 1, 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: 2020-05-07T21:24:40.090673Z, end-time: 2020-05-07T21:24:40.370209Z, 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 5f9ee1f Merge branch 'master' of https://github.com/JasonJWilliamsNY/leptin-rna-seq-lesson-dev into HEAD [rtd-command-info] start-time: 2020-05-07T21:24:40.474296Z, end-time: 2020-05-07T21:24:40.675903Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-07T21:24:41.946765Z, end-time: 2020-05-07T21:24:45.681557Z, 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/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: 2020-05-07T21:24:45.813843Z, end-time: 2020-05-07T21:24:46.607722Z, 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/cyverse-leptin-rna-seq-lesson-dev/envs/latest/lib/python3.7/site-packages (20.1) [rtd-command-info] start-time: 2020-05-07T21:24:46.757223Z, end-time: 2020-05-07T21:24:56.134569Z, duration: 9, 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-1.0.3-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.2-py2.py3-none-any.whl (39 kB) Collecting six>=1.5 Downloading six-1.14.0-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 requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting packaging Downloading packaging-20.3-py2.py3-none-any.whl (37 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 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 urllib3-1.25.9-py2.py3-none-any.whl (126 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.4.5.1-py2.py3-none-any.whl (157 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 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=c56c88fee0beac34443d03f7702b87f0f03557f4c469073137e9e73502f5a7a1 Stored in directory: /tmp/pip-ephem-wheel-cache-nsaz7624/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=491058 sha256=67fdcc71f453aec636e9de6c842ab484745fe288fd32f8a1d95a4c2d01de0087 Stored in directory: /tmp/pip-ephem-wheel-cache-nsaz7624/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, snowballstemmer, sphinxcontrib-websupport, six, pytz, babel, chardet, urllib3, certifi, idna, requests, pyparsing, packaging, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.1.3 Uninstalling setuptools-46.1.3: Successfully uninstalled setuptools-46.1.3 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.4.5.1 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.3 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.3 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.2 urllib3-1.25.9 [rtd-command-info] start-time: 2020-05-07T21:24:56.281175Z, end-time: 2020-05-07T21:24:57.616620Z, duration: 1, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r misc/requirements.txt Collecting sphinx_fontawesome Downloading sphinx_fontawesome-0.0.6.tar.gz (22 kB) 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: 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)) (20.3) 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: 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)) (1.2.2) 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)) (2.11.2) 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: 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: 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)) (2.23.0) 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: 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)) (1.14.0) 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: 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: 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)) (2.4.7) 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)) (2020.1) Requirement already satisfied: idna<3,>=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)) (2.9) 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)) (1.25.9) Requirement already satisfied: chardet<4,>=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)) (2020.4.5.1) 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' Created wheel for sphinx-fontawesome: filename=sphinx_fontawesome-0.0.6-py3-none-any.whl size=22601 sha256=9120604ca0e2f5b8ee0162111d29b86d1dd317086a2989017c34efd9dd94b87b Stored in directory: /tmp/pip-ephem-wheel-cache-tqay0b3c/wheels/c2/59/94/9f6ab8192fd4cb07ce02c27cdbf78548eae7cf63a63a4bcece Successfully built sphinx-fontawesome Installing collected packages: sphinx-fontawesome Successfully installed sphinx-fontawesome-0.0.6 [rtd-command-info] start-time: 2020-05-07T21:24:58.813261Z, end-time: 2020-05-07T21:24:59.029690Z, 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://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': [ ("html", "//cyverse-leptin-rna-seq-lesson-dev.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ], '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', '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': '5f9ee1fb', } 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: 2020-05-07T21:24:59.711701Z, end-time: 2020-05-07T21:25:09.258406Z, duration: 9, 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)) /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". /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' /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. 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/Powered-By-CyVerse-blue.png copying images... [ 20%] ./img/lesson_link_notification.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, 18 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2020-05-07T21:25:09.493025Z, end-time: 2020-05-07T21:25:18.291792Z, duration: 8, 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... [ 5%] Contributors_maintainers 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)) /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". /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' /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. 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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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 extra files... done dumping object inventory... done build succeeded, 18 warnings. The HTML page is in _build/localmedia.