Read the Docs build information Build id: 254874 Project: cyverse-visual-interactive-computing-environment Version: latest Commit: 1d3d59e3d24278fb4879bd60fdc67e2e73bb9765 Date: 2019-10-30T21:00:34.143090Z State: finished Success: True [rtd-command-info] start-time: 2019-10-30T21:00:34.664431Z, end-time: 2019-10-30T21:00:34.674840Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/Visual_Interactive_Computing_Environment.git [rtd-command-info] start-time: 2019-10-30T21:00:34.766272Z, end-time: 2019-10-30T21:00:35.258178Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/CyVerse-learning-materials/Visual_Interactive_Computing_Environment 4333d08..1d3d59e master -> origin/master [rtd-command-info] start-time: 2019-10-30T21:00:35.471474Z, end-time: 2019-10-30T21:00:35.503927Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 4333d08 Update index.rst HEAD is now at 1d3d59e Update quick-jupyter.rst [rtd-command-info] start-time: 2019-10-30T21:00:35.603963Z, end-time: 2019-10-30T21:00:35.627961Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-10-30T21:00:36.749289Z, end-time: 2019-10-30T21:00:39.752293Z, duration: 3, exit-code: 0 python2.7 -mvirtualenv --no-site-packages --no-download New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python2.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python2.7) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-10-30T21:00:39.846933Z, end-time: 2019-10-30T21:00:40.749595Z, duration: 0, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.cache/pip pip DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (19.3.1) [rtd-command-info] start-time: 2019-10-30T21:00:40.918076Z, end-time: 2019-10-30T21:00:43.077286Z, duration: 2, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (2.3.1) Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (41.0.1) Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (0.14) Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (1.0.1) Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (5.4.1) Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (0.7.12) Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (0.8.1) Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (0.5.0) Requirement already up-to-date: sphinx<2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (1.8.5) Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (0.4.3) Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (1.0.0) Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from commonmark==0.8.1) (0.18.1) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<2) (19.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<2) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<2) (2.7.0) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<2) (2.10.3) Requirement already satisfied, skipping upgrade: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<2) (3.7.4.1) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<2) (1.1.0) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx<2) (1.12.0) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from packaging->sphinx<2) (2.4.2) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<2) (1.25.6) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<2) (2019.9.11) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<2) (2.8) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1) [rtd-command-info] start-time: 2019-10-30T21:00:43.154070Z, end-time: 2019-10-30T21:00:43.950357Z, duration: 0, exit-code: 0 python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.cache/pip -r requirements.txt DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 1)) (1.8.5) Requirement already satisfied: recommonmark in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 2)) (0.5.0) Requirement already satisfied: sphinxcontrib-images in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 3)) (0.8.0) Requirement already satisfied: sphinx_bootstrap_theme in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 4)) (0.7.1) Requirement already satisfied: guzzle_sphinx_theme==0.7.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 5)) (0.7.11) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.7.12) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.0.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.3.1) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.1.2) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (19.2) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.7.0) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.22.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (41.0.1) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.14) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.10.3) Requirement already satisfied: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (3.7.4.1) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.1.0) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.12.0) Requirement already satisfied: commonmark>=0.7.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from recommonmark->-r requirements.txt (line 2)) (0.8.1) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from packaging->sphinx->-r requirements.txt (line 1)) (2.4.2) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx->-r requirements.txt (line 1)) (2019.3) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (1.25.6) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2019.9.11) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (3.0.4) Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2.8) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx->-r requirements.txt (line 1)) (1.1.1) Requirement already satisfied: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from commonmark>=0.7.3->recommonmark->-r requirements.txt (line 2)) (0.18.1) [rtd-command-info] start-time: 2019-10-30T21:00:44.598615Z, end-time: 2019-10-30T21:00:44.903029Z, 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 = '2018, CyVerse' author = 'CyVerse' version = '1.0' release = '1.0' 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 # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//readthedocs.com/projects/cyverse-visual-interactive-computing-environment/downloads/pdf/latest/"), ("html", "//readthedocs.com/projects/cyverse-visual-interactive-computing-environment/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/cyverse-visual-interactive-computing-environment/downloads/epub/latest/"), ], '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': '', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'Visual_Interactive_Computing_Environment', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '1d3d59e3', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' [rtd-command-info] start-time: 2019-10-30T21:00:45.004987Z, end-time: 2019-10-30T21:00:50.645577Z, duration: 5, 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 48 source files that are out of date updating environment: 48 added, 0 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2019-10-30T21:01:19.175412Z, end-time: 2019-10-30T21:01:19.487896Z, 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: 2019-10-30T21:01:19.580173Z, end-time: 2019-10-30T21:02:07.900818Z, duration: 48, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-visual-interactive-computing-environment -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. 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(/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> <./cyverse_cmyk1.png> <./homeicon3.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (132.49107pt too wide) in paragraph at lines 104--105 [][] [3] [4 <./vice_diagram.png>] [5] [6] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 173--173 []\T1/phv/m/n/10 Pre-req-ui- Overfull \hbox (32.78404pt too wide) in paragraph at lines 173--173 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2--173 [][][]\T1/ptm/m/n/10 Reg-is- Underfull \hbox (badness 10000) in paragraph at lines 173--173 []\T1/ptm/m/n/10 Dis-cov-ery Underfull \hbox (badness 10000) in paragraph at lines 173--173 \T1/ptm/m/n/10 En-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 2--173 [][][]\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2--173 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2--173 \T1/ptm/m/n/10 User (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [7 <./cyverse_rgb3.p ng>] [8] Chapter 3. [9] [10] [11] [12 <./cyverse_rgb4.png>] Chapter 4. Overfull \hbox (57.20068pt too wide) in paragraph at lines 404--405 [][] [13 <./jupyter2-1.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 419--420 [][] Overfull \hbox (57.20068pt too wide) in paragraph at lines 426--427 [][] [14 <./jupyter2-2.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 428--429 [][] [15 <./jupyter2-3.png> <./jupyter2-4.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 452--453 [][] [16 <./jupyter2-5.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 463--464 [][] Overfull \hbox (57.20068pt too wide) in paragraph at lines 470--471 [][] [17 <./jupyter2-6.png>] [18 <./jupyter2-7.png>] [19 <./homeicon4.png>] [20] Chapter 5. Overfull \hbox (57.23264pt too wide) in paragraph at lines 517--518 [][] [21] Overfull \hbox (57.20068pt too wide) in paragraph at lines 519--520 [][] [22 <./rstudio3-1.png> <./rstudio3-2.png>] Overfull \hbox (163.14012pt too wide) in paragraph at lines 530--532 []\T1/ptm/m/it/10 To use a file as an in-put... [] Overfull \hbox (174.8303pt too wide) in paragraph at lines 533--535 []\T1/ptm/m/it/10 To use a folder as an in-put... [] [23 <./rstudio3-3.png>] Underfull \hbox (badness 10000) in paragraph at lines 540--542 []\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). 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[55] Overfull \vbox (9.16396pt too high) has occurred while \output is active [56 <./add-tools.png>] Overfull \hbox (94.8507pt too wide) in paragraph at lines 1018--1019 [][] [57] [58 <./do_not_pass.png> <./cyverse_rgb5.png> <./homeicon5.png>] Chapter 12. 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[61] [62] Chapter 14. [63] [64] Chapter 15. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [65] [66] [67] [68] Chapter 16. No file cyverse-visual-interactive-computing-environment.ind. [69] (./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 (73 page s, 10720079 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: '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' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-visual-interactive-computing-environment.ind" "cyverse-visual-interactive-computing-environment.idx"' ------------ Latexmk: applying rule 'makeindex 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). 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[55] Overfull \vbox (9.16396pt too high) has occurred while \output is active [56 <./add-tools.png>] Overfull \hbox (94.8507pt too wide) in paragraph at lines 1018--1019 [][] [57] [58 <./do_not_pass.png> <./cyverse_rgb5.png> <./homeicon5.png>] Chapter 12. 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[61] [62] Chapter 14. [63] [64] Chapter 15. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [65] [66] [67] [68] Chapter 16. (./cyverse-visual-interactive-computing-environment.ind) [69] (./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 (73 page s, 10725872 bytes). Transcript written on cyverse-visual-interactive-computing-environment.log. Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written 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' ------------ ------------ 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/generic/oberdiek/gettitlestring.sty)) (./cyverse-visual-interactive-computing-environment.out) (./cyverse-visual-interactive-computing-environment.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-visual-interactive-computing-environment.toc) [1] [2] [1 <./cyverse_ cmyk.png> <./homeicon.png> <./cyverse_cmyk1.png> <./homeicon3.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (132.49107pt too wide) in paragraph at lines 104--105 [][] [3] [4 <./vice_diagram.png>] [5] [6] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 173--173 []\T1/phv/m/n/10 Pre-req-ui- Overfull \hbox (32.78404pt too wide) in paragraph at lines 173--173 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2--173 [][][]\T1/ptm/m/n/10 Reg-is- Underfull \hbox (badness 10000) in paragraph at lines 173--173 []\T1/ptm/m/n/10 Dis-cov-ery Underfull \hbox (badness 10000) in paragraph at lines 173--173 \T1/ptm/m/n/10 En-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 2--173 [][][]\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2--173 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2--173 \T1/ptm/m/n/10 User (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [7 <./cyverse_rgb3.p ng>] [8] Chapter 3. [9] [10] [11] [12 <./cyverse_rgb4.png>] Chapter 4. Overfull \hbox (57.20068pt too wide) in paragraph at lines 404--405 [][] [13 <./jupyter2-1.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 419--420 [][] Overfull \hbox (57.20068pt too wide) in paragraph at lines 426--427 [][] [14 <./jupyter2-2.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 428--429 [][] [15 <./jupyter2-3.png> <./jupyter2-4.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 452--453 [][] [16 <./jupyter2-5.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 463--464 [][] Overfull \hbox (57.20068pt too wide) in paragraph at lines 470--471 [][] [17 <./jupyter2-6.png>] [18 <./jupyter2-7.png>] [19 <./homeicon4.png>] [20] Chapter 5. Overfull \hbox (57.23264pt too wide) in paragraph at lines 517--518 [][] [21] Overfull \hbox (57.20068pt too wide) in paragraph at lines 519--520 [][] [22 <./rstudio3-1.png> <./rstudio3-2.png>] Overfull \hbox (163.14012pt too wide) in paragraph at lines 530--532 []\T1/ptm/m/it/10 To use a file as an in-put... [] Overfull \hbox (174.8303pt too wide) in paragraph at lines 533--535 []\T1/ptm/m/it/10 To use a folder as an in-put... [] [23 <./rstudio3-3.png>] Underfull \hbox (badness 10000) in paragraph at lines 540--542 []\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). Overfull \hbox (57.20068pt too wide) in paragraph at lines 540--542 [] [24 <./rstudio3-4.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 548--549 [][] [25 <./rstudio3-5.png>] Overfull \hbox (57.2051pt too wide) in paragraph at lines 555--556 [][] [26 <./rstudio3-6.png>] Overfull \hbox (57.2051pt too wide) in paragraph at lines 566--567 [][] [27 <./rstudio3-7.png>] Overfull \hbox (57.20729pt too wide) in paragraph at lines 568--569 [][] [28 <./rstudio3-8.png> <./rstudio3-9.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 575--576 [][] [29 <./rstudio3-10.png>] [30] Chapter 6. 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[55] Overfull \vbox (9.16396pt too high) has occurred while \output is active [56 <./add-tools.png>] Overfull \hbox (94.8507pt too wide) in paragraph at lines 1018--1019 [][] [57] [58 <./do_not_pass.png> <./cyverse_rgb5.png> <./homeicon5.png>] Chapter 12. 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[61] [62] Chapter 14. [63] [64] Chapter 15. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [65] [66] [67] [68] Chapter 16. (./cyverse-visual-interactive-computing-environment.ind) [69] (./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 (73 page s, 10725872 bytes). Transcript written on cyverse-visual-interactive-computing-environment.log. Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written 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: All targets (cyverse-visual-interactive-computing-environment.pdf) are up-to-date [rtd-command-info] start-time: 2019-10-30T21:02:08.031140Z, end-time: 2019-10-30T21:02:08.351198Z, 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: 2019-10-30T21:02:08.441681Z, end-time: 2019-10-30T21:02:29.885046Z, duration: 21, 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... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [epub]: targets for 48 source files that are out of date updating environment: 48 added, 0 changed, 0 removed reading sources... 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