Read the Docs build information Build id: 231555 Project: cyverse-visual-interactive-computing-environment Version: latest Commit: 3ae159421f8a92116dd0c5630d2f1a0e6652486d Date: 2019-08-09T23:13:36.250324Z State: finished Success: True [rtd-command-info] start-time: 2019-08-09T23:13:36.717264Z, end-time: 2019-08-09T23:13:40.048277Z, 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: 2019-08-09T23:13:40.260943Z, end-time: 2019-08-09T23:13:40.335052Z, 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 3ae1594 Update about.rst [rtd-command-info] start-time: 2019-08-09T23:13:40.432230Z, end-time: 2019-08-09T23:13:40.454476Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-08-09T23:13:41.453463Z, end-time: 2019-08-09T23:13:44.157947Z, 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: 2019-08-09T23:13:44.247317Z, end-time: 2019-08-09T23:13:46.634366Z, 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/62/ca/94d32a6516ed197a491d17d46595ce58a83cbb2fca280414e57cd86b84dc/pip-19.2.1-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-19.2.1 [rtd-command-info] start-time: 2019-08-09T23:13:46.724091Z, end-time: 2019-08-09T23:13:58.060767Z, duration: 11, 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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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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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)) (2019.6.16) 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)) (0.17.1) 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' Created wheel for sphinx-bootstrap-theme: filename=sphinx_bootstrap_theme-0.7.1-cp27-none-any.whl size=1250224 sha256=121a9fba5b9ec463c23d364bd9185fb805ea4e771e58987e9f7fbc6900de05f3 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=2555157 sha256=a9a3db47dcfd0c815d52a8c7e23c43ac3d987e66ef2e00b1194c2145fb08d417 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: 2019-08-09T23:14:02.231735Z, end-time: 2019-08-09T23:14:02.546724Z, 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': '3ae15942', } 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: 2019-08-09T23:14:02.624957Z, end-time: 2019-08-09T23:14:08.223823Z, 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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[100%] vice_apps/examples /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} WARNING: invalid signature for autoclass (u'{{ objname }}') WARNING: don't know which module to import for autodocumenting u'{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) WARNING: invalid signature for automodule (u'{{ fullname }}') WARNING: don't know which module to import for autodocumenting u'{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_help/contact.rst:7: WARNING: Title underline too short. **Contact** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/getting_started/apptypes.rst:85: WARNING: Title underline too short. 4. 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[rtd-command-info] start-time: 2019-08-09T23:14:08.387971Z, end-time: 2019-08-09T23:14:12.303815Z, duration: 3, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia 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 [readthedocssinglehtmllocalmedia]: all documents updating environment: 46 added, 0 changed, 0 removed reading sources... [ 2%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION reading sources... [ 4%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION reading sources... [ 6%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION reading sources... [ 8%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION reading sources... 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[9] [10] [11] [12 <./cyverse_rgb4.png> <./homeicon4.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>] Chapter 5. 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Overfull \hbox (57.21007pt too wide) in paragraph at lines 731--732 [] [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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[57] [58] Chapter 12. [59] [60] Chapter 13. No file cyverse-visual-interactive-computing-environment.ind. [61] (./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 (65 page s, 8270422 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). 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[9] [10] [11] [12 <./cyverse_rgb4.png> <./homeicon4.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>] Chapter 5. 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[57] [58] Chapter 12. [59] [60] Chapter 13. (./cyverse-visual-interactive-computing-environment.ind) [61] (./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 (65 page s, 8275962 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/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_ rgb.png> <./homeicon.png> <./cyverse_rgb3.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] [8] Chapter 3. [9] [10] [11] [12 <./cyverse_rgb4.png> <./homeicon4.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>] Chapter 5. Overfull \hbox (57.23264pt too wide) in paragraph at lines 510--511 [][] [19] Overfull \hbox (57.20068pt too wide) in paragraph at lines 512--513 [][] [20 <./rstudio3-1.png> <./rstudio3-2.png>] Overfull \hbox (163.14012pt too wide) in paragraph at lines 523--525 []\T1/ptm/m/it/10 To use a file as an in-put... [] Overfull \hbox (174.8303pt too wide) in paragraph at lines 526--528 []\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 533--535 []\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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[57] [58] Chapter 12. [59] [60] Chapter 13. (./cyverse-visual-interactive-computing-environment.ind) [61] (./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 (65 page s, 8275962 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: 2019-08-09T23:15:11.036073Z, end-time: 2019-08-09T23:15:11.349373Z, 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: 2019-08-09T23:15:11.441129Z, end-time: 2019-08-09T23:15:36.428327Z, duration: 24, 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 46 source files that are out of date updating environment: 46 added, 0 changed, 0 removed reading sources... 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