Read the Docs build information Build id: 803131 Project: cyverse-visual-interactive-computing-environment Version: latest Commit: 8795a5d7af7ba75f718a6667134cfc0e2c5863e3 Date: 2021-12-16T19:51:55.323926Z State: finished Success: True [rtd-command-info] start-time: 2021-12-16T19:51:56.844729Z, end-time: 2021-12-16T19:52:07.883548Z, duration: 11, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/Visual_Interactive_Computing_Environment.git . Cloning into '.'... [rtd-command-info] start-time: 2021-12-16T19:52:08.039247Z, end-time: 2021-12-16T19:52:08.418816Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: checking out 'origin/main'. 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 8795a5d Update quick-cloudshell.rst [rtd-command-info] start-time: 2021-12-16T19:52:08.681613Z, end-time: 2021-12-16T19:52:08.747051Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-12-16T19:52:09.843780Z, end-time: 2021-12-16T19:52:13.809657Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-12-16T19:52:13.919954Z, end-time: 2021-12-16T19:52:15.634973Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (21.3.1) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 59.6.0 Uninstalling setuptools-59.6.0: Successfully uninstalled setuptools-59.6.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2021-12-16T19:52:15.764073Z, end-time: 2021-12-16T19:52:25.323499Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' 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-1.8.6-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<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting docutils>=0.11 Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting requests>=2.0.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting Pygments>=2.0 Downloading Pygments-2.10.0-py3-none-any.whl (1.0 MB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) Collecting imagesize Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx<2) (58.2.0) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting pytz>=2015.7 Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (31 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.9-py3-none-any.whl (39 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) Collecting pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.6-py3-none-any.whl (97 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 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=23772 sha256=735370372fc77cd1b942782a4a186157a2236914cb548934cf8e2a01d777e798 Stored in directory: /tmp/pip-ephem-wheel-cache-pjd3et_2/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 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=491070 sha256=de66f725faafc192725231cc5e706bcdbe03e98cb4f1f1758c2097dbbbbd0ed8 Stored in directory: /tmp/pip-ephem-wheel-cache-pjd3et_2/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Successfully installed Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.9 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.6 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.7 [rtd-command-info] start-time: 2021-12-16T19:52:25.446285Z, end-time: 2021-12-16T19:52:28.317147Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting sphinx==3.4.3 Downloading Sphinx-3.4.3-py3-none-any.whl (2.9 MB) Collecting docutils<0.17 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) Collecting sphinx_rtd_theme==0.5.1 Downloading sphinx_rtd_theme-0.5.1-py2.py3-none-any.whl (2.8 MB) Collecting readthedocs-sphinx-search==0.1.0rc3 Downloading readthedocs_sphinx_search-0.1.0rc3-py3-none-any.whl (25 kB) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r requirements.txt (line 1)) (2.9.1) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r requirements.txt (line 1)) (3.0.3) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r requirements.txt (line 1)) (2.2.0) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r requirements.txt (line 1)) (2.26.0) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r requirements.txt (line 1)) (1.1.5) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r requirements.txt (line 1)) (0.7.12) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r requirements.txt (line 1)) (2.10.0) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r requirements.txt (line 1)) (1.3.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r requirements.txt (line 1)) (21.3) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r requirements.txt (line 1)) (58.2.0) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx==3.4.3->-r requirements.txt (line 1)) (2021.3) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx==3.4.3->-r requirements.txt (line 1)) (2.0.1) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx==3.4.3->-r requirements.txt (line 1)) (3.3) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx==3.4.3->-r requirements.txt (line 1)) (1.26.7) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx==3.4.3->-r requirements.txt (line 1)) (2021.10.8) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx==3.4.3->-r requirements.txt (line 1)) (2.0.9) Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python3.7/site-packages (from packaging->sphinx==3.4.3->-r requirements.txt (line 1)) (3.0.6) Installing collected packages: sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, docutils, sphinx, sphinx-rtd-theme, readthedocs-sphinx-search Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed docutils-0.16 readthedocs-sphinx-search-0.1.0rc3 sphinx-3.4.3 sphinx-rtd-theme-0.5.1 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 [rtd-command-info] start-time: 2021-12-16T19:52:29.462194Z, end-time: 2021-12-16T19:52:29.529853Z, 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 = 'Visual Interactive Computing Environment' copyright = '2021, CyVerse' author = 'CyVerse' version = '2.1' version = '2.1' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright exclude_patterns = ['README.md', 'License.md', 'Contributors_maintainers.md'] ########################################################################### # 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 # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring 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/"), ("main", "/en/main/"), ], 'downloads': [ ("pdf", "//learning.cyverse.org/_/downloads/vice/en/latest/pdf/"), ("html", "//learning.cyverse.org/_/downloads/vice/en/latest/htmlzip/"), ("epub", "//learning.cyverse.org/_/downloads/vice/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'cyverse-visual-interactive-computing-environment', 'name': u'Visual_Interactive_Computing_Environment', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/projects/vice/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': 'Visual_Interactive_Computing_Environment', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', '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': '8795a5d7', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None 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") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/cyverse-visual-interactive-computing-environment/builds/803131/' 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: 2021-12-16T19:52:29.682826Z, end-time: 2021-12-16T19:52:32.889910Z, duration: 3, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v3.4.3 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [html]: targets for 19 source files that are out of date updating environment: [new config] 19 added, 0 changed, 0 removed reading sources... 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[100%] getting_help/../img/homeicon.png copying TeX support files... copying TeX support files... done build succeeded, 111 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). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2021-12-16T19:52:50.660092Z, end-time: 2021-12-16T19:52:50.726642Z, 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'} . 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LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.583 ...th=700\sphinxpxdimen]{{app_loading3}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.583 ...th=700\sphinxpxdimen]{{app_loading3}.gif} [19 <./jupyter2-23.png>] [20 <./jupyter2-33.png>] Underfull \hbox (badness 10000) in paragraph at lines 621--622 []\T1/ptm/m/n/10 Navigate to \T1/pcr/m/n/10 /shared/cyverse_training/platform_g uides/discovery_environment/ [21 <./jupyter2-43.png> <./jupyter2-53.png>] [22 <./jupyter2-63.png>] [23 <./ju pyter2-73.png> <./jupyter2-83.png>] [24] Chapter 6. [25 <./rstudio3-1.png>] [26 <./rstudio3-2.png>] Overfull \hbox (169.61896pt too wide) in paragraph at lines 693--695 []\T1/ptm/m/it/10 Use quick launch to in-put ex-am-ple data... [] Underfull \hbox (badness 10000) in paragraph at lines 700--702 []\T1/ptm/m/n/10 Launch the anal-y-sis af-ter you are fin-ished se-lect-ing the in-put files (if any). [27 <./rstudio3-3.png> <./rstudio3-4.png>] [28 <./rstudio3-5.png> <./rstudio3-6 .png>] [29 <./rstudio3-7.png>] [30 <./rstudio3-8.png> <./rstudio3-9.png>] [31 <./rstudio3-10.png>] [32] Chapter 7. [33 <./vice-share-1.png>] [34 <./vice-share-2.png> <./vice-share-3.png>] [35 <./vice-share-6.png>] [36 <./vice-share-7.png>] [37 <./create_quick_launch. png> <./create_quick_launch_dialog.png>] [38 <./use_quick_launch.png> <./cyvers e_learning.png> <./homeicon.png>] Chapter 8. [39 <./flow_new.png>] [40] Chapter 9. [41] [42] Chapter 10. [43] [44 <./cyverse_learning5.png> <./homeicon5.png>] Chapter 11. [45] [46] Chapter 12. [47] [48] Chapter 13. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! 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LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} [49 <./cyverse_learning1.png> <./homeicon1.png>] [50] Chapter 14. [51] [52] Chapter 15. [53] [54] Chapter 16. [55] [56] [57] [58] Chapter 17. LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426. LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426. ! Package pdftex.def Error: File `./img/intercom.png' not found: using draft se tting. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.1426 ...=25\sphinxpxdimen]{{./img/intercom}.png} on the lower right\sphinx... No file cyverse-visual-interactive-computing-environment.ind. [59] (./cyverse-visual-interactive-computing-environment.aux) Package rerunfilecheck Warning: File `cyverse-visual-interactive-computing-envi ronment.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-visual-interactive-computing-environment.pdf (63 page s, 9170609 bytes). Transcript written on cyverse-visual-interactive-computing-environment.log. Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written Latexmk: Missing input file: '{./img/intercom}.png' from line 'LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426.' Latexmk: Missing input file: '{./img/intercom}.png' from line 'LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426.' Latexmk: Missing input file: 'cyverse-visual-interactive-computing-environment.ind' from line 'No file cyverse-visual-interactive-computing-environment.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf' Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf' Rule 'makeindex cyverse-visual-interactive-computing-environment.idx': File changes, etc: Non-existent destination files: 'cyverse-visual-interactive-computing-environment.ind' ------------ Run number 1 of rule 'makeindex cyverse-visual-interactive-computing-environment.idx' ------------ Latexmk: applying rule 'makeindex cyverse-visual-interactive-computing-environment.idx'... ------------ Running 'makeindex -s python.ist -o "cyverse-visual-interactive-computing-environment.ind" "cyverse-visual-interactive-computing-environment.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-visual-interactive-computing-environment.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-visual-interactive-computing-environment.ind. Transcript written in cyverse-visual-interactive-computing-environment.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-visual-interactive-computing-environment.aux' 'cyverse-visual-interactive-computing-environment.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-visual-interactive-computing-environment" "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. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 192--192 []\T1/phv/m/n/10 Pre-req-ui- Overfull \hbox (32.78404pt too wide) in paragraph at lines 192--192 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2--192 [][][]\T1/ptm/m/n/10 Reg-is- Underfull \hbox (badness 10000) in paragraph at lines 192--192 []\T1/ptm/m/n/10 Dis-cov-ery Underfull \hbox (badness 10000) in paragraph at lines 192--192 \T1/ptm/m/n/10 En-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 2--192 [][][]\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2--192 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2--192 \T1/ptm/m/n/10 User [5] [6] Chapter 3. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. 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LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} [49 <./cyverse_learning1.png> <./homeicon1.png>] [50] Chapter 14. [51] [52] Chapter 15. [53] [54] Chapter 16. [55] [56] [57] [58] Chapter 17. LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426. LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426. ! Package pdftex.def Error: File `./img/intercom.png' not found: using draft se tting. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.1426 ...=25\sphinxpxdimen]{{./img/intercom}.png} on the lower right\sphinx... (./cyverse-visual-interactive-computing-environment.ind) [59] (./cyverse-visual-interactive-computing-environment.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-visual-interactive-computing-environment.pdf (63 page s, 9175136 bytes). Transcript written on cyverse-visual-interactive-computing-environment.log. Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written Latexmk: Missing input file: '{./img/intercom}.png' from line 'LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426.' Latexmk: Missing input file: '{./img/intercom}.png' from line 'LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426.' Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf' Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-visual-interactive-computing-environment.out' 'cyverse-visual-interactive-computing-environment.toc' ------------ Run number 3 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-visual-interactive-computing-environment" "CyVerseDocumentation.tex"' ------------ 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. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 192--192 []\T1/phv/m/n/10 Pre-req-ui- Overfull \hbox (32.78404pt too wide) in paragraph at lines 192--192 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2--192 [][][]\T1/ptm/m/n/10 Reg-is- Underfull \hbox (badness 10000) in paragraph at lines 192--192 []\T1/ptm/m/n/10 Dis-cov-ery Underfull \hbox (badness 10000) in paragraph at lines 192--192 \T1/ptm/m/n/10 En-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 2--192 [][][]\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2--192 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2--192 \T1/ptm/m/n/10 User [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.222 ...b780d2e24bf25e74/Verse-latest-blue}.svg}} \sphinxhref{https://de.cy... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.222 ...b780d2e24bf25e74/Verse-latest-blue}.svg}} \sphinxhref{https://de.cy... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.222 ...6499fa51/Datascience-latest-orange}.svg}} ) ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.222 ...6499fa51/Datascience-latest-orange}.svg}} ) [7] [8] [9 <./homeicon4.png>] [10] Chapter 4. [11 <./cloudshell-03.png>] [12 <./cloudshell-13.png>] [13 <./cloudshell-23.png> ] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14 <./cloudshell- 33.png>] [15] [16] Chapter 5. [17 <./jupyter2-03.png>] [18 <./jupyter2-13.png>] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.583 ...th=700\sphinxpxdimen]{{app_loading3}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.583 ...th=700\sphinxpxdimen]{{app_loading3}.gif} [19 <./jupyter2-23.png>] [20 <./jupyter2-33.png>] Underfull \hbox (badness 10000) in paragraph at lines 621--622 []\T1/ptm/m/n/10 Navigate to \T1/pcr/m/n/10 /shared/cyverse_training/platform_g uides/discovery_environment/ [21 <./jupyter2-43.png> <./jupyter2-53.png>] [22 <./jupyter2-63.png>] [23 <./ju pyter2-73.png> <./jupyter2-83.png>] [24] Chapter 6. [25 <./rstudio3-1.png>] [26 <./rstudio3-2.png>] Overfull \hbox (169.61896pt too wide) in paragraph at lines 693--695 []\T1/ptm/m/it/10 Use quick launch to in-put ex-am-ple data... [] Underfull \hbox (badness 10000) in paragraph at lines 700--702 []\T1/ptm/m/n/10 Launch the anal-y-sis af-ter you are fin-ished se-lect-ing the in-put files (if any). [27 <./rstudio3-3.png> <./rstudio3-4.png>] [28 <./rstudio3-5.png> <./rstudio3-6 .png>] [29 <./rstudio3-7.png>] [30 <./rstudio3-8.png> <./rstudio3-9.png>] [31 <./rstudio3-10.png>] [32] Chapter 7. [33 <./vice-share-1.png>] [34 <./vice-share-2.png> <./vice-share-3.png>] [35 <./vice-share-6.png>] [36 <./vice-share-7.png>] [37 <./create_quick_launch. png> <./create_quick_launch_dialog.png>] [38 <./use_quick_launch.png> <./cyvers e_learning.png> <./homeicon.png>] Chapter 8. [39 <./flow_new.png>] [40] Chapter 9. [41] [42] Chapter 10. [43] [44 <./cyverse_learning5.png> <./homeicon5.png>] Chapter 11. [45] [46] Chapter 12. [47] [48] Chapter 13. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! 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LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1151 \end{tabulary} [49 <./cyverse_learning1.png> <./homeicon1.png>] [50] Chapter 14. [51] [52] Chapter 15. [53] [54] Chapter 16. [55] [56] [57] [58] Chapter 17. LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426. LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426. ! Package pdftex.def Error: File `./img/intercom.png' not found: using draft se tting. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.1426 ...=25\sphinxpxdimen]{{./img/intercom}.png} on the lower right\sphinx... (./cyverse-visual-interactive-computing-environment.ind) [59] (./cyverse-visual-interactive-computing-environment.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-visual-interactive-computing-environment.pdf (63 page s, 9175136 bytes). Transcript written on cyverse-visual-interactive-computing-environment.log. Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written Latexmk: Missing input file: '{./img/intercom}.png' from line 'LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426.' Latexmk: Missing input file: '{./img/intercom}.png' from line 'LaTeX Warning: File `{./img/intercom}.png' not found on input line 1426.' Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf' Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf' Latexmk: Errors, in force_mode: so I tried finishing targets Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 [rtd-command-info] start-time: 2021-12-16T19:53:37.561855Z, end-time: 2021-12-16T19:53:37.651128Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/./_build/latex/cyverse-visual-interactive-computing-environment.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/artifacts/latest/sphinx_pdf/cyverse-visual-interactive-computing-environment.pdf [rtd-command-info] start-time: 2021-12-16T19:53:37.765072Z, end-time: 2021-12-16T19:53:50.607270Z, duration: 12, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees -D language=en . _build/epub Running Sphinx v3.4.3 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [epub]: targets for 19 source files that are out of date updating environment: [config changed ('source_parsers')] 19 added, 0 changed, 0 removed reading sources... 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