Read the Docs build information Build id: 198591 Project: cyverse-visual-interactive-computing-environment Version: latest Commit: 47524823a7552a5803a1aac0cddad17c079f9510 Date: 2019-04-05T05:42:21.644770Z State: finished Success: True [rtd-command-info] start-time: 2019-04-05T05:42:22.200561Z, end-time: 2019-04-05T05:42:26.475449Z, duration: 4, 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: 2019-04-05T05:42:26.637012Z, end-time: 2019-04-05T05:42:27.292287Z, 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 4752482 Fix merge conflict [rtd-command-info] start-time: 2019-04-05T05:42:27.353928Z, end-time: 2019-04-05T05:42:27.373508Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-04-05T05:42:28.043224Z, end-time: 2019-04-05T05:42:30.103419Z, duration: 2, 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 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: 2019-04-05T05:42:30.193831Z, end-time: 2019-04-05T05:42:32.511103Z, 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 pip Collecting pip Downloading https://files.pythonhosted.org/packages/d8/f3/413bab4ff08e1fc4828dfc59996d721917df8e8583ea85385d51125dceff/pip-19.0.3-py2.py3-none-any.whl (1.4MB) Installing collected packages: pip Found existing installation: pip 18.1 Uninstalling pip-18.1: Successfully uninstalled pip-18.1 Successfully installed pip-19.0.3 [rtd-command-info] start-time: 2019-04-05T05:42:32.571526Z, end-time: 2019-04-05T05:42:43.045206Z, duration: 10, 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 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<0.6 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. 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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) Collecting sphinxcontrib-images (from -r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/19/09/da51642f401be838476d5f02fb6b382600f731cdbcbf0579d431f2be3378/sphinxcontrib_images-0.8.0-py2-none-any.whl (65kB) Collecting sphinx_bootstrap_theme (from -r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/a9/b8/ebcd1a7c579eb85929bbfd54617c5c484ba8cd78e4d3499d749e64b5ad3b/sphinx-bootstrap-theme-0.7.1.tar.gz (1.2MB) Collecting guzzle_sphinx_theme==0.7.11 (from -r requirements.txt (line 5)) Downloading https://files.pythonhosted.org/packages/f4/7d/aed8cd5e4ca52bb8550d2c33fcbb8d6dbd5c2cf5e1694202d2135b374eba/guzzle_sphinx_theme-0.7.11.tar.gz (2.5MB) 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)) (1.2.1) 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)) (1.1.0) 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)) (2.6.0) 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)) (2.21.0) 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)) (40.9.0) 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: 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)) (19.0) 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) 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)) (3.6.6) 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: pytz>=0a 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)) (2018.9) Requirement already satisfied: urllib3<1.25,>=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)) (1.24.1) 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)) (2019.3.9) 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: 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)) (2.3.1) 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)) (0.17.1) Building wheels for collected packages: sphinx-bootstrap-theme, guzzle-sphinx-theme Building wheel for sphinx-bootstrap-theme (setup.py): started Building wheel for sphinx-bootstrap-theme (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.cache/pip/wheels/71/28/10/e04d1ab1110dbde7f436dd159ed5ee35113f66536df6d99a79 Building wheel for guzzle-sphinx-theme (setup.py): started Building wheel for guzzle-sphinx-theme (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.cache/pip/wheels/6e/68/e9/4626607977db13794bfaf48afab2cf05487bb4d3612c09dcee Successfully built sphinx-bootstrap-theme guzzle-sphinx-theme Installing collected packages: sphinxcontrib-images, sphinx-bootstrap-theme, guzzle-sphinx-theme Successfully installed guzzle-sphinx-theme-0.7.11 sphinx-bootstrap-theme-0.7.1 sphinxcontrib-images-0.8.0 [rtd-command-info] start-time: 2019-04-05T05:42:46.583331Z, end-time: 2019-04-05T05:42:46.636992Z, 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 mulitple 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/"), ("htmlzip", "//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': '47524823', } 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"] [rtd-command-info] start-time: 2019-04-05T05:42:46.697092Z, end-time: 2019-04-05T05:42:51.932634Z, 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 46 source files that are out of date updating environment: 46 added, 0 changed, 0 removed reading sources... 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(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 CyVerseDocumentation.pdf (65 pages, 8268948 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2019-04-05T05:43:11.520089Z, end-time: 2019-04-05T05:43:11.632004Z, duration: 0, exit-code: 0 makeindex -s python.ist CyVerseDocumentation.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 CyVerseDocumentation.idx...done (0 entries accepted, 0 rejected). Nothing written in CyVerseDocumentation.ind. Transcript written in CyVerseDocumentation.ilg. [rtd-command-info] start-time: 2019-04-05T05:43:11.708865Z, end-time: 2019-04-05T05:43:23.727458Z, duration: 12, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/./_build/latex/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 (/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-co mputing-environment/checkouts/latest/./_build/latex/CyVerseDocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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Overfull \hbox (57.21007pt too wide) in paragraph at lines 729--730 [] [43] Overfull \vbox (136.57585pt too high) has occurred while \output is active [44 <./flow.png>] [45] [46] Chapter 8. [47] [48] Chapter 9. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [49] [50] [51] Overfull \vbox (9.16396pt too high) has occurred while \output is active [52 <./add-tools.png>] [53] [54 <./cyverse_rgb5.png> <./homeicon5.png>] Chapter 10. 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(./CyVerseDocumentation.ind) [61] (./CyVerseDocumentation.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on CyVerseDocumentation.pdf (65 pages, 8274763 bytes). Transcript written on CyVerseDocumentation.log. 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