Read the Docs build information Build id: 423276 Project: cyverse-jupyter-qiime2 Version: latest Commit: e47aa7a321c2af4f25d850462fd7e4116f8cad34 Date: 2020-09-16T19:01:39.439691Z State: finished Success: True [rtd-command-info] start-time: 2020-09-16T19:15:42.299007Z, end-time: 2020-09-16T19:15:49.476955Z, duration: 7, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/jupyter_qiime2.git . Cloning into '.'... [rtd-command-info] start-time: 2020-09-16T19:15:49.783182Z, end-time: 2020-09-16T19:15:49.866248Z, 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 e47aa7a add triage issue template [rtd-command-info] start-time: 2020-09-16T19:15:49.973338Z, end-time: 2020-09-16T19:15:50.026398Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-09-16T19:15:56.313027Z, end-time: 2020-09-16T19:16:15.676906Z, duration: 19, 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-jupyter-qiime2/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-09-16T19:16:15.806996Z, end-time: 2020-09-16T19:16:16.681885Z, 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-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (20.2.3) [rtd-command-info] start-time: 2020-09-16T19:16:16.988619Z, end-time: 2020-09-16T19:16:30.558910Z, duration: 13, 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 babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting packaging Downloading packaging-20.4-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 urllib3-1.25.10-py2.py3-none-any.whl (127 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 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=07263a02bf0874c74ac7debb20cfff4f1610e0a254ec78856fcd028cdc5a7e5f Stored in directory: /tmp/pip-ephem-wheel-cache-n1ylxd9c/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=bea09a4e5da617453c2302668e09b30c3403328c6312d47cb00b3ab2cf2a5768 Stored in directory: /tmp/pip-ephem-wheel-cache-n1ylxd9c/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, snowballstemmer, six, chardet, urllib3, certifi, idna, requests, imagesize, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, pyparsing, packaging, MarkupSafe, Jinja2, 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: 2020-09-16T19:16:32.202789Z, end-time: 2020-09-16T19:16:32.314888Z, duration: 0, exit-code: 0 cat conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # General information about the project. import sys import os sys.path.insert(0, os.path.dirname(__file__)) from misc.cyverse_sphinx_conf import * # noqa project = 'Metagenomics in QIIME 2 Using Jupyter Notebooks in VICE' copyright = '2019, CyVerse' author = 'CyVerse' version = '1.0' release = '1.0' 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': [ ("pdf", "//cyverse-jupyter-qiime2.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//cyverse-jupyter-qiime2.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//cyverse-jupyter-qiime2.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'cyverse-jupyter-qiime2', 'name': u'jupyter_qiime2', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-jupyter-qiime2.readthedocs-hosted.com/en/latest/', 'analytics_code': 'UA-72224033-6', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'proxied_api_host': '/_', 'github_repo': 'jupyter_qiime2', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-72224033-6', 'global_analytics_code': 'UA-17997319-2', 'commit': 'e47aa7a3', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2020-09-16T19:16:32.645554Z, end-time: 2020-09-16T19:16:34.759797Z, duration: 2, 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 5 source files that are out of date updating environment: 5 added, 0 changed, 0 removed reading sources... [ 20%] Contributors_maintainers reading sources... [ 40%] License reading sources... [ 60%] README reading sources... [ 80%] github/ISSUE_TEMPLATE/triage-for-2-0-release reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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-jupyter-qiime2/checkouts/latest/README.rst:53: WARNING: Title underline too short. Platform(s) `````````` /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:53: WARNING: Title underline too short. Platform(s) `````````` /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:157: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:195: WARNING: Duplicate substitution definition name: "QIIME2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. README.rst:53: WARNING: Title underline too short. Platform(s) `````````` README.rst:53: WARNING: Title underline too short. Platform(s) `````````` README.rst:157: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ README.rst:195: WARNING: Duplicate substitution definition name: "QIIME2". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/github/ISSUE_TEMPLATE/triage-for-2-0-release.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 20%] Contributors_maintainers writing output... [ 40%] License writing output... [ 60%] README writing output... [ 80%] github/ISSUE_TEMPLATE/triage-for-2-0-release writing output... [100%] index generating indices... genindex writing additional pages... search copying images... [ 50%] ./img/cyverse_cmyk.png copying images... [100%] ./img/homeicon.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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, 13 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2020-09-16T19:16:35.182680Z, end-time: 2020-09-16T19:16:36.584721Z, duration: 1, 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: 5 added, 0 changed, 0 removed reading sources... [ 20%] Contributors_maintainers reading sources... [ 40%] License reading sources... [ 60%] README reading sources... [ 80%] github/ISSUE_TEMPLATE/triage-for-2-0-release reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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-jupyter-qiime2/checkouts/latest/README.rst:53: WARNING: Title underline too short. Platform(s) `````````` /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:53: WARNING: Title underline too short. Platform(s) `````````` /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:157: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:195: WARNING: Duplicate substitution definition name: "QIIME2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. README.rst:53: WARNING: Title underline too short. Platform(s) `````````` README.rst:53: WARNING: Title underline too short. Platform(s) `````````` README.rst:157: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ README.rst:195: WARNING: Duplicate substitution definition name: "QIIME2". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/github/ISSUE_TEMPLATE/triage-for-2-0-release.md: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... README writing... done writing additional files... copying images... [ 50%] ./img/cyverse_cmyk.png copying images... [100%] ./img/homeicon.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 13 warnings. The HTML page is in _build/localmedia. [rtd-command-info] start-time: 2020-09-16T19:16:37.032409Z, end-time: 2020-09-16T19:16:38.762864Z, duration: 1, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex 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 [latex]: all documents updating environment: 5 added, 0 changed, 0 removed reading sources... [ 20%] Contributors_maintainers reading sources... [ 40%] License reading sources... [ 60%] README reading sources... [ 80%] github/ISSUE_TEMPLATE/triage-for-2-0-release reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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-jupyter-qiime2/checkouts/latest/README.rst:53: WARNING: Title underline too short. Platform(s) `````````` /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:53: WARNING: Title underline too short. Platform(s) `````````` /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:157: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:195: WARNING: Duplicate substitution definition name: "QIIME2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. README.rst:53: WARNING: Title underline too short. Platform(s) `````````` README.rst:53: WARNING: Title underline too short. Platform(s) `````````` README.rst:157: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ README.rst:195: WARNING: Duplicate substitution definition name: "QIIME2". looking for now-outdated files... none found pickling environment... done checking consistency... done /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/github/ISSUE_TEMPLATE/triage-for-2-0-release.md: WARNING: document isn't included in any toctree processing CyVerseDocumentation.tex...index README resolving references... writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:195: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://de.cyverse.org/Powered-By-CyVerse-blue.svg) README.rst:195: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://de.cyverse.org/Powered-By-CyVerse-blue.svg) done copying images... [ 50%] ./img/cyverse_cmyk.png copying images... [100%] ./img/homeicon.png copying TeX support files... done build succeeded, 14 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2020-09-16T19:16:40.414896Z, end-time: 2020-09-16T19:16:40.516443Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2020-09-16T19:16:41.365308Z, end-time: 2020-09-16T19:16:50.477819Z, duration: 9, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-jupyter-qiime2 -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-jupyter-qiime2" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./CyVerseDocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file cyverse-jupyter-qiime2.idx (./cyverse-jupyter-qiime2.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] [1 <./cyverse_cmyk.png> <./homei con.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 188--188 []\T1/phv/m/n/10 Learn-ing Cen-ter Underfull \hbox (badness 10000) in paragraph at lines 188--188 []\T1/ptm/m/n/10 Web/Point-and- Underfull \hbox (badness 10000) in paragraph at lines 227--227 []\T1/phv/m/n/10 In-put Overfull \hbox (3.03355pt too wide) in paragraph at lines 227--227 []\T1/phv/m/n/10 For- Overfull \hbox (1.67345pt too wide) in paragraph at lines 227--227 \T1/phv/m/n/10 mat| Underfull \hbox (badness 10000) in paragraph at lines 227--227 []\T1/ptm/m/n/10 Se- Underfull \hbox (badness 10000) in paragraph at lines 227--227 \T1/ptm/m/n/10 quenc- Underfull \hbox (badness 10000) in paragraph at lines 227--227 \T1/ptm/m/n/10 ing Overfull \hbox (8.7434pt too wide) in paragraph at lines 2--227 [][][]\T1/ptm/m/n/10 FastQ[][]| [5] [6] Chapter 3. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.245 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.245 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [8] Chapter 4. Underfull \hbox (badness 10000) in paragraph at lines 466--466 []\T1/phv/m/n/10 Learn-ing Cen-ter Underfull \hbox (badness 10000) in paragraph at lines 466--466 []\T1/ptm/m/n/10 Web/Point-and- [9] Underfull \hbox (badness 10000) in paragraph at lines 505--505 []\T1/phv/m/n/10 In-put Overfull \hbox (3.03355pt too wide) in paragraph at lines 505--505 []\T1/phv/m/n/10 For- Overfull \hbox (1.67345pt too wide) in paragraph at lines 505--505 \T1/phv/m/n/10 mat| Underfull \hbox (badness 10000) in paragraph at lines 505--505 []\T1/ptm/m/n/10 Se- Underfull \hbox (badness 10000) in paragraph at lines 505--505 \T1/ptm/m/n/10 quenc- Underfull \hbox (badness 10000) in paragraph at lines 505--505 \T1/ptm/m/n/10 ing Overfull \hbox (8.7434pt too wide) in paragraph at lines 2--505 [][][]\T1/ptm/m/n/10 FastQ[][]| ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.523 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.523 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... [10] No file cyverse-jupyter-qiime2.ind. [11] (./cyverse-jupyter-qiime2.aux) Package rerunfilecheck Warning: File `cyverse-jupyter-qiime2.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-jupyter-qiime2.pdf (15 pages, 122995 bytes). Transcript written on cyverse-jupyter-qiime2.log. Latexmk: Index file 'cyverse-jupyter-qiime2.idx' was written Latexmk: Missing input file: 'cyverse-jupyter-qiime2.ind' from line 'No file cyverse-jupyter-qiime2.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-jupyter-qiime2.pdf' Rule 'makeindex cyverse-jupyter-qiime2.idx': File changes, etc: Non-existent destination files: 'cyverse-jupyter-qiime2.ind' ------------ Run number 1 of rule 'makeindex cyverse-jupyter-qiime2.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-jupyter-qiime2.ind" "cyverse-jupyter-qiime2.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-jupyter-qiime2.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file cyverse-jupyter-qiime2.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-jupyter-qiime2.ind. Transcript written in cyverse-jupyter-qiime2.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-jupyter-qiime2.aux' 'cyverse-jupyter-qiime2.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-jupyter-qiime2" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./CyVerseDocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file cyverse-jupyter-qiime2.idx (./cyverse-jupyter-qiime2.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./cyverse-jupyter-qiime2.out) (./cyverse-jupyter-qiime2.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./cyverse-jupyter-qiime2.toc) [1] [2] [1 <./cyverse_cmyk.png> <./homeicon.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 188--188 []\T1/phv/m/n/10 Learn-ing Cen-ter Underfull \hbox (badness 10000) in paragraph at lines 188--188 []\T1/ptm/m/n/10 Web/Point-and- Underfull \hbox (badness 10000) in paragraph at lines 227--227 []\T1/phv/m/n/10 In-put Overfull \hbox (3.03355pt too wide) in paragraph at lines 227--227 []\T1/phv/m/n/10 For- Overfull \hbox (1.67345pt too wide) in paragraph at lines 227--227 \T1/phv/m/n/10 mat| Underfull \hbox (badness 10000) in paragraph at lines 227--227 []\T1/ptm/m/n/10 Se- Underfull \hbox (badness 10000) in paragraph at lines 227--227 \T1/ptm/m/n/10 quenc- Underfull \hbox (badness 10000) in paragraph at lines 227--227 \T1/ptm/m/n/10 ing Overfull \hbox (8.7434pt too wide) in paragraph at lines 2--227 [][][]\T1/ptm/m/n/10 FastQ[][]| [5] [6] Chapter 3. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.245 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.245 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [8] Chapter 4. Underfull \hbox (badness 10000) in paragraph at lines 466--466 []\T1/phv/m/n/10 Learn-ing Cen-ter Underfull \hbox (badness 10000) in paragraph at lines 466--466 []\T1/ptm/m/n/10 Web/Point-and- [9] Underfull \hbox (badness 10000) in paragraph at lines 505--505 []\T1/phv/m/n/10 In-put Overfull \hbox (3.03355pt too wide) in paragraph at lines 505--505 []\T1/phv/m/n/10 For- Overfull \hbox (1.67345pt too wide) in paragraph at lines 505--505 \T1/phv/m/n/10 mat| Underfull \hbox (badness 10000) in paragraph at lines 505--505 []\T1/ptm/m/n/10 Se- Underfull \hbox (badness 10000) in paragraph at lines 505--505 \T1/ptm/m/n/10 quenc- Underfull \hbox (badness 10000) in paragraph at lines 505--505 \T1/ptm/m/n/10 ing Overfull \hbox (8.7434pt too wide) in paragraph at lines 2--505 [][][]\T1/ptm/m/n/10 FastQ[][]| ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.523 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.523 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... [10] (./cyverse-jupyter-qiime2.ind) [11] (./cyverse-jupyter-qiime2.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-jupyter-qiime2.pdf (15 pages, 127075 bytes). Transcript written on cyverse-jupyter-qiime2.log. Latexmk: Index file 'cyverse-jupyter-qiime2.idx' was written Latexmk: Log file says output to 'cyverse-jupyter-qiime2.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-jupyter-qiime2.out' 'cyverse-jupyter-qiime2.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-jupyter-qiime2" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./CyVerseDocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file cyverse-jupyter-qiime2.idx (./cyverse-jupyter-qiime2.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./cyverse-jupyter-qiime2.out) (./cyverse-jupyter-qiime2.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./cyverse-jupyter-qiime2.toc) [1] [2] [1 <./cyverse_cmyk.png> <./homeicon.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 188--188 []\T1/phv/m/n/10 Learn-ing Cen-ter Underfull \hbox (badness 10000) in paragraph at lines 188--188 []\T1/ptm/m/n/10 Web/Point-and- Underfull \hbox (badness 10000) in paragraph at lines 227--227 []\T1/phv/m/n/10 In-put Overfull \hbox (3.03355pt too wide) in paragraph at lines 227--227 []\T1/phv/m/n/10 For- Overfull \hbox (1.67345pt too wide) in paragraph at lines 227--227 \T1/phv/m/n/10 mat| Underfull \hbox (badness 10000) in paragraph at lines 227--227 []\T1/ptm/m/n/10 Se- Underfull \hbox (badness 10000) in paragraph at lines 227--227 \T1/ptm/m/n/10 quenc- Underfull \hbox (badness 10000) in paragraph at lines 227--227 \T1/ptm/m/n/10 ing Overfull \hbox (8.7434pt too wide) in paragraph at lines 2--227 [][][]\T1/ptm/m/n/10 FastQ[][]| [5] [6] Chapter 3. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.245 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.245 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [8] Chapter 4. Underfull \hbox (badness 10000) in paragraph at lines 466--466 []\T1/phv/m/n/10 Learn-ing Cen-ter Underfull \hbox (badness 10000) in paragraph at lines 466--466 []\T1/ptm/m/n/10 Web/Point-and- [9] Underfull \hbox (badness 10000) in paragraph at lines 505--505 []\T1/phv/m/n/10 In-put Overfull \hbox (3.03355pt too wide) in paragraph at lines 505--505 []\T1/phv/m/n/10 For- Overfull \hbox (1.67345pt too wide) in paragraph at lines 505--505 \T1/phv/m/n/10 mat| Underfull \hbox (badness 10000) in paragraph at lines 505--505 []\T1/ptm/m/n/10 Se- Underfull \hbox (badness 10000) in paragraph at lines 505--505 \T1/ptm/m/n/10 quenc- Underfull \hbox (badness 10000) in paragraph at lines 505--505 \T1/ptm/m/n/10 ing Overfull \hbox (8.7434pt too wide) in paragraph at lines 2--505 [][][]\T1/ptm/m/n/10 FastQ[][]| ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.523 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.523 ...487086e249/Powered-By-CyVerse-blue}.svg}} to log into CyVerse and v... [10] (./cyverse-jupyter-qiime2.ind) [11] (./cyverse-jupyter-qiime2.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-jupyter-qiime2.pdf (15 pages, 127075 bytes). Transcript written on cyverse-jupyter-qiime2.log. Latexmk: Index file 'cyverse-jupyter-qiime2.idx' was written Latexmk: Log file says output to 'cyverse-jupyter-qiime2.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2020-09-16T19:16:50.651157Z, end-time: 2020-09-16T19:16:50.707670Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/./_build/latex/cyverse-jupyter-qiime2.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/artifacts/latest/sphinx_pdf/cyverse-jupyter-qiime2.pdf [rtd-command-info] start-time: 2020-09-16T19:16:51.284952Z, end-time: 2020-09-16T19:16:52.861102Z, duration: 1, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub 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 [epub]: targets for 5 source files that are out of date updating environment: 5 added, 0 changed, 0 removed reading sources... [ 20%] Contributors_maintainers reading sources... [ 40%] License reading sources... [ 60%] README reading sources... [ 80%] github/ISSUE_TEMPLATE/triage-for-2-0-release reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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-jupyter-qiime2/checkouts/latest/README.rst:53: WARNING: Title underline too short. Platform(s) `````````` /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:53: WARNING: Title underline too short. Platform(s) `````````` /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:157: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/README.rst:195: WARNING: Duplicate substitution definition name: "QIIME2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. README.rst:53: WARNING: Title underline too short. Platform(s) `````````` README.rst:53: WARNING: Title underline too short. Platform(s) `````````` README.rst:157: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ README.rst:195: WARNING: Duplicate substitution definition name: "QIIME2". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/github/ISSUE_TEMPLATE/triage-for-2-0-release.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 20%] Contributors_maintainers writing output... [ 40%] License writing output... [ 60%] README writing output... [ 80%] github/ISSUE_TEMPLATE/triage-for-2-0-release writing output... [100%] index WARNING: Could not fetch remote image: https://de.cyverse.org/Powered-By-CyVerse-blue.svg [HTTPSConnectionPool(host='de.cyverse.org', port=443): Max retries exceeded with url: /Powered-By-CyVerse-blue.svg (Caused by NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))] WARNING: Could not fetch remote image: https://de.cyverse.org/Powered-By-CyVerse-blue.svg [HTTPSConnectionPool(host='de.cyverse.org', port=443): Max retries exceeded with url: /Powered-By-CyVerse-blue.svg (Caused by NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))] generating indices... genindex writing additional pages... copying images... [ 50%] ./img/cyverse_cmyk.png copying images... [100%] ./img/homeicon.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/_static' does not exist done copying extra files... done WARNING: Could not fetch remote image: https://de.cyverse.org/Powered-By-CyVerse-blue.svg [HTTPSConnectionPool(host='de.cyverse.org', port=443): Max retries exceeded with url: /Powered-By-CyVerse-blue.svg (Caused by NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))] writing mimetype file... writing META-INF/container.xml file... writing content.opf file... writing nav.xhtml file... WARNING: Could not fetch remote image: https://de.cyverse.org/Powered-By-CyVerse-blue.svg [HTTPSConnectionPool(host='de.cyverse.org', port=443): Max retries exceeded with url: /Powered-By-CyVerse-blue.svg (Caused by NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))] writing toc.ncx file... WARNING: Could not fetch remote image: https://de.cyverse.org/Powered-By-CyVerse-blue.svg [HTTPSConnectionPool(host='de.cyverse.org', port=443): Max retries exceeded with url: /Powered-By-CyVerse-blue.svg (Caused by NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))] writing MetagenomicsinQIIME2UsingJupyterNotebooksinVICE.epub file... build succeeded, 18 warnings. The ePub file is in _build/epub. [rtd-command-info] start-time: 2020-09-16T19:16:53.178150Z, end-time: 2020-09-16T19:16:53.261538Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/./_build/epub/MetagenomicsinQIIME2UsingJupyterNotebooksinVICE.epub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/artifacts/latest/sphinx_epub/cyverse-jupyter-qiime2.epub