Read the Docs build information Build id: 348585 Project: cyverse-visual-interactive-computing-environment Version: latest Commit: 7df7dfbca0a642e45739b93efeb73bbedc655f68 Date: 2020-06-23T13:32:34.606908Z State: finished Success: True [rtd-command-info] start-time: 2020-06-23T13:32:39.263853Z, end-time: 2020-06-23T13:32:42.485190Z, duration: 3, 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: 2020-06-23T13:32:42.778735Z, end-time: 2020-06-23T13:32:43.595718Z, 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 7df7dfb Update quick-jupyter.rst [rtd-command-info] start-time: 2020-06-23T13:32:44.114819Z, end-time: 2020-06-23T13:32:44.322984Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-06-23T13:32:46.347430Z, end-time: 2020-06-23T13:32:56.929963Z, duration: 10, exit-code: 0 python2.7 -mvirtualenv 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: 2020-06-23T13:32:57.040240Z, end-time: 2020-06-23T13:32:57.803867Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support 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 (20.1.1) [rtd-command-info] start-time: 2020-06-23T13:32:57.963917Z, end-time: 2020-06-23T13:33:06.993685Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py2-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp27-cp27mu-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting typing; python_version < "3.5" Downloading typing-3.7.4.1-py2-none-any.whl (26 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl (39 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl (24 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 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-py2-none-any.whl size=23755 sha256=5c940257f3d9a3a64abbd5b6a669c1ee13d5e86531c956ab7a42b44c238ee7cc Stored in directory: /tmp/pip-ephem-wheel-cache-fAGfir/wheels/ad/62/e0/a06cc957652749e64c7904e899eca3ecb2ec47c60d52653660 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-py2-none-any.whl size=502566 sha256=98ba874b1c0488949ab693c84dc2a69d9075830550433958684b9d4442bc13d2 Stored in directory: /tmp/pip-ephem-wheel-cache-fAGfir/wheels/5f/11/0c/aad680baf5ef4fbcbab992c9f03e1130357e0c173a4fdabfff Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, imagesize, typing, MarkupSafe, Jinja2, certifi, urllib3, idna, chardet, requests, six, pyparsing, packaging, snowballstemmer, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 44.1.1 Uninstalling setuptools-44.1.1: Successfully uninstalled setuptools-44.1.1 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 typing-3.7.4.1 urllib3-1.25.9 [rtd-command-info] start-time: 2020-06-23T13:33:07.135137Z, end-time: 2020-06-23T13:33:09.806128Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support 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 Downloading sphinxcontrib_images-0.9.2-py2.py3-none-any.whl (63 kB) Collecting sphinx_bootstrap_theme Downloading sphinx-bootstrap-theme-0.7.1.tar.gz (1.2 MB) Collecting guzzle_sphinx_theme==0.7.11 Downloading guzzle_sphinx_theme-0.7.11.tar.gz (2.5 MB) 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)) (2.8.0) 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)) (1.2.0) 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: 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)) (2.11.2) 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)) (2.24.0) 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)) (20.4) 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: 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: 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: 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)) (1.15.0) 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: 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>=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)) (2020.1) 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: 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)) (1.25.9) 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)) (2020.6.20) Requirement already satisfied: idna<3,>=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)) (2.9) Requirement already satisfied: chardet<4,>=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: 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)) (2.4.7) 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)) (0.18.2) 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' Created wheel for sphinx-bootstrap-theme: filename=sphinx_bootstrap_theme-0.7.1-py2-none-any.whl size=1250222 sha256=ad75cea5557198e4be6c559fdcf92884169919d75d3feb22c59f7ceb3bc76c08 Stored in directory: /tmp/pip-ephem-wheel-cache-f0GgMa/wheels/95/93/4e/ce6bc27771a672df0da2021feb26f922e8a74bacdeb9195838 Building wheel for guzzle-sphinx-theme (setup.py): started Building wheel for guzzle-sphinx-theme (setup.py): finished with status 'done' Created wheel for guzzle-sphinx-theme: filename=guzzle_sphinx_theme-0.7.11-py2-none-any.whl size=2555155 sha256=11238be91cee96362b8d3490cf59b0e741084948f4800efd2a8e3bad317946cd Stored in directory: /tmp/pip-ephem-wheel-cache-f0GgMa/wheels/9d/61/03/c574afdc16ce34de1d382f4d4cdb1eb624fafabe9e0a6988c2 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-0.9.2 [rtd-command-info] start-time: 2020-06-23T13:33:11.488784Z, end-time: 2020-06-23T13:33:11.705295Z, 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://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//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': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-72224033-6', 'global_analytics_code': 'UA-17997319-2', 'commit': '7df7dfbc', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' [rtd-command-info] start-time: 2020-06-23T13:33:11.966402Z, end-time: 2020-06-23T13:33:16.763692Z, duration: 4, 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: 2020-06-23T13:42:20.657895Z, end-time: 2020-06-23T13:42:20.866308Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2020-06-23T13:42:20.991737Z, end-time: 2020-06-23T13:43:05.835410Z, duration: 44, 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. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-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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Overfull \hbox (57.21684pt too wide) in paragraph at lines 843--844 [][] [49 <./flow_new.png>] [50] Chapter 9. [51] [52] Chapter 10. [53] [54 <./add-tool.png>] Overfull \hbox (94.8507pt too wide) in paragraph at lines 1051--1052 [][] [55] [56 <./do_not_pass.png> <./cyverse_cmyk1.png> <./homeicon5.png>] Chapter 11. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. [57 <./cyverse_learning1.png> <./homeicon2.png>] [58] Chapter 12. [59] [60] Chapter 13. [61] [62] Chapter 14. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [63] [64] [65] [66] Chapter 15. No file cyverse-visual-interactive-computing-environment.ind. [67] (./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 (71 page s, 10903084 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). 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/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file cyverse-visual-interactive-computing-environment.idx (./cyverse-visual-interactive-computing-environment.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./cyverse-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_ learning.png> <./homeicon.png> <./cyverse_learning2.png> <./homeicon3.png>] [2] Chapter 1. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [63] [64] [65] [66] Chapter 15. (./cyverse-visual-interactive-computing-environment.ind) [67] (./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 (71 page s, 10907797 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' ------------ 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/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_ learning.png> <./homeicon.png> <./cyverse_learning2.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 108--109 [][] [3] [4 <./vice_diagram.png>] [5] [6] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 177--177 []\T1/phv/m/n/10 Pre-req-ui- Overfull \hbox (32.78404pt too wide) in paragraph at lines 177--177 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2--177 [][][]\T1/ptm/m/n/10 Reg-is- Underfull \hbox (badness 10000) in paragraph at lines 177--177 []\T1/ptm/m/n/10 Dis-cov-ery Underfull \hbox (badness 10000) in paragraph at lines 177--177 \T1/ptm/m/n/10 En-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 2--177 [][][]\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2--177 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2--177 \T1/ptm/m/n/10 User (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [7] [8] Chapter 3. [9] [10] [11 <./homeicon4.png>] [12] Chapter 4. Overfull \hbox (57.20068pt too wide) in paragraph at lines 408--409 [][] [13 <./jupyter2-1.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 423--424 [][] Overfull \hbox (57.20068pt too wide) in paragraph at lines 430--431 [][] [14 <./jupyter2-2.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 432--433 [][] [15 <./jupyter2-3.png> <./jupyter2-4.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 456--457 [][] [16 <./jupyter2-5.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 467--468 [][] Overfull \hbox (57.20068pt too wide) in paragraph at lines 474--475 [][] [17 <./jupyter2-6.png>] [18 <./jupyter2-7.png>] Chapter 5. Overfull \hbox (57.23264pt too wide) in paragraph at lines 519--520 [][] [19] Overfull \hbox (57.20068pt too wide) in paragraph at lines 521--522 [][] [20 <./rstudio3-1.png> <./rstudio3-2.png>] Overfull \hbox (163.14012pt too wide) in paragraph at lines 532--534 []\T1/ptm/m/it/10 To use a file as an in-put... [] Overfull \hbox (174.8303pt too wide) in paragraph at lines 535--537 []\T1/ptm/m/it/10 To use a folder as an in-put... [] [21 <./rstudio3-3.png>] Underfull \hbox (badness 10000) in paragraph at lines 542--544 []\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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Overfull \hbox (94.8507pt too wide) in paragraph at lines 740--741 [][] Overfull \hbox (94.8507pt too wide) in paragraph at lines 742--743 [][] [41 <./vice-share-1.png>] Overfull \hbox (94.8507pt too wide) in paragraph at lines 744--745 [][] Overfull \hbox (94.8507pt too wide) in paragraph at lines 746--747 [][] [42 <./vice-share-2.png> <./vice-share-3.png>] Overfull \hbox (94.8507pt too wide) in paragraph at lines 748--749 [][] Overfull \hbox (94.8507pt too wide) in paragraph at lines 752--753 [][] [43 <./vice-share-4.png> <./vice-share-5.png>] Overfull \hbox (94.8507pt too wide) in paragraph at lines 754--755 [][] Overfull \hbox (94.8507pt too wide) in paragraph at lines 756--757 [][] [44 <./vice-share-6.png>] Overfull \hbox (12.04185pt too wide) in paragraph at lines 790--791 [][] [45 <./vice-share-7.png>] [46 <./create_quick_launch.png> <./create_quick_launc h_dialog.png>] [47 <./use_quick_launch.png> <./cyverse_cmyk.png> <./homeicon1.p ng>] [48] Chapter 8. Overfull \hbox (57.21684pt too wide) in paragraph at lines 843--844 [][] [49 <./flow_new.png>] [50] Chapter 9. [51] [52] Chapter 10. [53] [54 <./add-tool.png>] Overfull \hbox (94.8507pt too wide) in paragraph at lines 1051--1052 [][] [55] [56 <./do_not_pass.png> <./cyverse_cmyk1.png> <./homeicon5.png>] Chapter 11. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. Package hyperref Warning: Suppressing empty link on input line 2. [57 <./cyverse_learning1.png> <./homeicon2.png>] [58] Chapter 12. [59] [60] Chapter 13. [61] [62] Chapter 14. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [63] [64] [65] [66] Chapter 15. (./cyverse-visual-interactive-computing-environment.ind) [67] (./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 (71 page s, 10907797 bytes). Transcript written on cyverse-visual-interactive-computing-environment.log. 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