Read the Docs build information Build id: 254827 Project: cyverse-visual-interactive-computing-environment Version: latest Commit: 57654f40b96237c7f04245e6c0f795bcd73e081e Date: 2019-10-30T20:31:54.953934Z State: finished Success: True [rtd-command-info] start-time: 2019-10-30T20:31:55.454581Z, end-time: 2019-10-30T20:31:59.880061Z, 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: 2019-10-30T20:32:00.164616Z, end-time: 2019-10-30T20:32:01.288312Z, duration: 1, 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 57654f4 Update index.rst [rtd-command-info] start-time: 2019-10-30T20:32:01.456193Z, end-time: 2019-10-30T20:32:01.483310Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-10-30T20:32:02.649082Z, end-time: 2019-10-30T20:32:05.565977Z, 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: 2019-10-30T20:32:05.921073Z, end-time: 2019-10-30T20:32:08.083047Z, 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 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. Collecting pip Downloading https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl (1.4MB) Installing collected packages: pip Found existing installation: pip 19.1.1 Uninstalling pip-19.1.1: Successfully uninstalled pip-19.1.1 Successfully installed pip-19.3.1 [rtd-command-info] start-time: 2019-10-30T20:32:08.690354Z, end-time: 2019-10-30T20:32:18.904305Z, 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==41.0.1 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. 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python_version < "3.5" Downloading https://files.pythonhosted.org/packages/22/30/64ca29543375759dc589ade14a6cd36382abf2bec17d67de8481bc9814d7/typing-3.7.4.1-py2-none-any.whl Collecting packaging Downloading https://files.pythonhosted.org/packages/cf/94/9672c2d4b126e74c4496c6b3c58a8b51d6419267be9e70660ba23374c875/packaging-19.2-py2.py3-none-any.whl Collecting imagesize Downloading https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl Collecting six>=1.5 Downloading https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl Collecting pytz>=2015.7 Downloading https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl (509kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading https://files.pythonhosted.org/packages/e0/da/55f51ea951e1b7c63a579c09dd7db825bb730ec1fe9c0180fc77bfb31448/urllib3-1.25.6-py2.py3-none-any.whl (125kB) Collecting certifi>=2017.4.17 Downloading https://files.pythonhosted.org/packages/18/b0/8146a4f8dd402f60744fa380bc73ca47303cccf8b9190fd16a827281eac2/certifi-2019.9.11-py2.py3-none-any.whl (154kB) Collecting chardet<3.1.0,>=3.0.2 Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB) Collecting idna<2.9,>=2.5 Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB) Collecting MarkupSafe>=0.23 Downloading https://files.pythonhosted.org/packages/fb/40/f3adb7cf24a8012813c5edb20329eb22d5d8e2a0ecf73d21d6b85865da11/MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl Collecting pyparsing>=2.0.2 Downloading https://files.pythonhosted.org/packages/11/fa/0160cd525c62d7abd076a070ff02b2b94de589f1a9789774f17d7c54058e/pyparsing-2.4.2-py2.py3-none-any.whl (65kB) 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-cp27-none-any.whl size=23756 sha256=7f6a9dfcfc4f0e016d39df13a75cac41720e5b7ee9b25f8ea38feed6459e67c7 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.1-cp27-none-any.whl size=501929 sha256=25874f9feab8d6299d31375b136100dc8a24c67e3d6c8993eb38f05d42b8ccea Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.cache/pip/wheels/74/bc/50/ae030267a192919b289f84661cfeb5573cf383841c543e8696 Successfully built mock future Installing collected packages: Pygments, docutils, mock, pillow, alabaster, future, commonmark, snowballstemmer, sphinxcontrib-websupport, pytz, babel, urllib3, certifi, chardet, idna, requests, MarkupSafe, Jinja2, typing, pyparsing, six, packaging, imagesize, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Successfully installed Jinja2-2.10.3 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.7.0 certifi-2019.9.11 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.1 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.2 pillow-5.4.1 pyparsing-2.4.2 pytz-2019.3 readthedocs-sphinx-ext-1.0.0 recommonmark-0.5.0 requests-2.22.0 six-1.12.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 typing-3.7.4.1 urllib3-1.25.6 [rtd-command-info] start-time: 2019-10-30T20:32:18.989316Z, end-time: 2019-10-30T20:32:22.201722Z, duration: 3, 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. 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 https://files.pythonhosted.org/packages/19/09/da51642f401be838476d5f02fb6b382600f731cdbcbf0579d431f2be3378/sphinxcontrib_images-0.8.0-py2-none-any.whl (65kB) Collecting sphinx_bootstrap_theme 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 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)) (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 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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: 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: 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) 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-cp27-none-any.whl size=1250223 sha256=ada3c661482af9aaff8c0821a51e8bf9b65c644eda00150a05086a4db34a9fcf 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' Created wheel for guzzle-sphinx-theme: filename=guzzle_sphinx_theme-0.7.11-cp27-none-any.whl size=2555156 sha256=3c5db8aee7abde18c932b540ad609c3e2d623672c95c1002cfd15107b8897445 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: 2019-10-30T20:32:22.907249Z, end-time: 2019-10-30T20:32:23.216415Z, 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': '57654f40', } 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: 2019-10-30T20:32:23.295290Z, end-time: 2019-10-30T20:32:28.813627Z, 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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' %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: 2019-10-30T20:32:57.199014Z, end-time: 2019-10-30T20:33:43.085624Z, duration: 45, 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. 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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, 10577395 bytes). Transcript written on cyverse-visual-interactive-computing-environment.log. Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written Latexmk: Missing input file: '{./img/cyverse_cymk}.png' from line 'LaTeX Warning: File `{./img/cyverse_cymk}.png' not found on input line 83.' 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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[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, 10583268 bytes). Transcript written on cyverse-visual-interactive-computing-environment.log. Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written Latexmk: Missing input file: '{./img/cyverse_cymk}.png' from line 'LaTeX Warning: File `{./img/cyverse_cymk}.png' not found on input line 83.' 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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, 10583268 bytes). Transcript written on cyverse-visual-interactive-computing-environment.log. Latexmk: Index file 'cyverse-visual-interactive-computing-environment.idx' was written Latexmk: Missing input file: '{./img/cyverse_cymk}.png' from line 'LaTeX Warning: File `{./img/cyverse_cymk}.png' not found on input line 83.' Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf' Latexmk: Log file says output to 'cyverse-visual-interactive-computing-environment.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2019-10-30T20:33:43.196674Z, end-time: 2019-10-30T20:33:43.513670Z, 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: 2019-10-30T20:33:43.594042Z, end-time: 2019-10-30T20:34:12.900518Z, duration: 29, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [epub]: targets for 48 source files that are out of date updating environment: 48 added, 0 changed, 0 removed reading sources... 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Complete and Save Outputs =========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-jupyter.rst:75: WARNING: Title underline too short. 6. Complete and Save Outputs =========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:8: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:66: WARNING: Title underline too short. 6. Complete your analysis ======================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-rstudio.rst:66: WARNING: Title underline too short. 6. 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