Read the Docs build information Build id: 173525 Project: cyverse-visual-interactive-computing-environment Version: latest Commit: a9e78ab6ea56d4d96919d3d7d648f62c4c53fe6e Date: 2019-01-10T22:58:52.041927Z State: finished Success: True [rtd-command-info] start-time: 2019-01-10T22:58:52.550560Z, end-time: 2019-01-10T22:58:56.190544Z, duration: 3, exit-code: 0 git clone --depth 50 --no-single-branch https://github.com/CyVerse-learning-materials/Visual_Interactive_Computing_Environment.git . Cloning into '.'... [rtd-command-info] start-time: 2019-01-10T22:58:56.356819Z, end-time: 2019-01-10T22:58:56.625998Z, 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 a9e78ab Update index.rst [rtd-command-info] start-time: 2019-01-10T22:58:56.686879Z, end-time: 2019-01-10T22:58:56.705395Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-01-10T22:58:57.373215Z, end-time: 2019-01-10T22:58:59.432780Z, 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: 2019-01-10T22:58:59.495760Z, end-time: 2019-01-10T22:59:01.447385Z, duration: 1, exit-code: 0 python 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/c2/d7/90f34cb0d83a6c5631cf71dfe64cc1054598c843a92b400e55675cc2ac37/pip-18.1-py2.py3-none-any.whl (1.3MB) Installing collected packages: pip Found existing installation: pip 9.0.1 Uninstalling pip-9.0.1: Successfully uninstalled pip-9.0.1 Successfully installed pip-18.1 [rtd-command-info] start-time: 2019-01-10T22:59:01.582688Z, end-time: 2019-01-10T22:59:21.223356Z, duration: 19, exit-code: 0 python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 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https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl (154kB) Collecting pyparsing>=2.0.2 (from packaging->sphinx<1.8) Downloading https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl (59kB) Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx<1.8) Downloading https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl (510kB) Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<1.8) Downloading https://files.pythonhosted.org/packages/bc/3a/6bfd7b4b202fa33bdda8e4e3d3acc719f381fd730f9a0e7c5f34e845bd4d/MarkupSafe-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl Building wheels for collected packages: mock, pillow, commonmark Running setup.py bdist_wheel for mock: started Running setup.py bdist_wheel for mock: finished with status 'done' 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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/requirements.txt (line 1)) (1.1.0) Building wheels for collected packages: sphinx-bootstrap-theme, guzzle-sphinx-theme Running setup.py bdist_wheel for sphinx-bootstrap-theme: started Running setup.py bdist_wheel for sphinx-bootstrap-theme: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/.cache/pip/wheels/01/3c/98/f37c5ef813bb7262c17c566da10f9f7e4f6ff4b897d0a4209c Running setup.py bdist_wheel for guzzle-sphinx-theme: started Running setup.py bdist_wheel for guzzle-sphinx-theme: 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-0.6.5 sphinxcontrib-images-0.8.0 [rtd-command-info] start-time: 2019-01-10T22:59:24.806443Z, end-time: 2019-01-10T22:59:24.865567Z, 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 else: SUFFIX = source_suffix[0] 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') html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_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': 'a9e78ab6', } 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: 2019-01-10T22:59:24.928320Z, end-time: 2019-01-10T22:59:29.852205Z, duration: 4, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.7.9 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 45 source files that are out of date updating environment: 45 added, 0 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2019-01-10T22:59:36.689562Z, end-time: 2019-01-10T22:59:49.977021Z, duration: 13, 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 3.14159265-2.6-1.40.16 (TeX Live 2015/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 <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. 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Overfull \hbox (57.21007pt too wide) in paragraph at lines 719--720 [] [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] [52] Chapter 10. [53 <./cyverse_rgb2.png> <./homeicon2.png>] [54] Chapter 11. [55] [56] Chapter 12. [57] [58] Chapter 13. No file CyVerseDocumentation.ind. [59] (./CyVerseDocumentation.aux) Package rerunfilecheck Warning: File `CyVerseDocumentation.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 CyVerseDocumentation.pdf (63 pages, 8774846 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2019-01-10T22:59:50.090405Z, end-time: 2019-01-10T22:59:50.227342Z, duration: 0, exit-code: 0 makeindex -s python.ist CyVerseDocumentation.idx This is makeindex, version 2.15 [TeX Live 2015] (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: 2019-01-10T22:59:50.290867Z, end-time: 2019-01-10T23:00:03.384537Z, duration: 13, 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 3.14159265-2.6-1.40.16 (TeX Live 2015/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 <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (132.48561pt too wide) in paragraph at lines 95--96 [][] [3] [4 <./vice_diagram.png>] [5] [6] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 164--164 []\T1/phv/m/n/10 Pre-req-ui- Overfull \hbox (32.78404pt too wide) in paragraph at lines 164--164 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2--164 [][][]\T1/ptm/m/n/10 Reg-is- Underfull \hbox (badness 10000) in paragraph at lines 164--164 []\T1/ptm/m/n/10 Dis-cov-ery Underfull \hbox (badness 10000) in paragraph at lines 164--164 \T1/ptm/m/n/10 En-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 2--164 [][][]\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2--164 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2--164 \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 392--393 [][] [13 <./jupyter2-1.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 407--408 [][] Overfull \hbox (57.20068pt too wide) in paragraph at lines 414--415 [][] [14 <./jupyter2-2.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 416--417 [][] [15 <./jupyter2-3.png> <./jupyter2-4.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 440--441 [][] [16 <./jupyter2-5.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 451--452 [][] Overfull \hbox (57.20068pt too wide) in paragraph at lines 458--459 [][] [17 <./jupyter2-6.png>] [18 <./jupyter2-7.png>] Chapter 5. Overfull \hbox (57.23264pt too wide) in paragraph at lines 498--499 [][] [19] Overfull \hbox (57.20068pt too wide) in paragraph at lines 500--501 [][] [20 <./rstudio3-1.png> <./rstudio3-2.png>] Overfull \hbox (163.14012pt too wide) in paragraph at lines 511--513 []\T1/ptm/m/it/10 To use a file as an in-put... [] Overfull \hbox (174.8303pt too wide) in paragraph at lines 514--516 []\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 521--523 []\T1/ptm/m/n/10 Launch the anal-y-sis af-ter you are fin-ished se-lect-ing the in-put files (if any). Overfull \hbox (57.20068pt too wide) in paragraph at lines 521--523 [] [22 <./rstudio3-4.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 529--530 [][] [23 <./rstudio3-5.png>] Overfull \hbox (57.2051pt too wide) in paragraph at lines 536--537 [][] [24 <./rstudio3-6.png>] Overfull \hbox (57.2051pt too wide) in paragraph at lines 547--548 [][] [25 <./rstudio3-7.png>] Overfull \hbox (57.20729pt too wide) in paragraph at lines 549--550 [][] [26 <./rstudio3-8.png> <./rstud io3-9.png>] Overfull \hbox (57.20068pt too wide) in paragraph at lines 556--557 [][] [27 <./rstudio3- 10.png>] [28] Chapter 6. Overfull \hbox (57.20361pt too wide) in paragraph at lines 602--603 [][] [29] Overfull \hbox (57.20361pt too wide) in paragraph at lines 609--610 [][] [30 <./shiny1-1.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 616--617 [][] [31 <./shiny1-2.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 618--619 [][] [32 <./shiny1-3.png> <./shiny1 -4.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 625--626 [][] Overfull \hbox (57.20361pt too wide) in paragraph at lines 627--628 [][] [33 <./shiny1-5.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 634--635 [][] [34 <./shiny1-6.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 641--642 [][] [35 <./shiny1-7.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 648--649 [][] [36 <./shiny1-8.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 655--656 [][] [37 <./shiny1-9.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 657--658 [][] [38 <./shiny1-10.png> <./shin y1-11.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 664--665 [][] Overfull \hbox (57.20361pt too wide) in paragraph at lines 666--667 [][] [39 <./shiny1-12.png>] [40 <./shiny 1-13.png> <./cyverse_rgb1.png>] [41 <./homeicon1.png>] [42] Chapter 7. Overfull \hbox (57.21007pt too wide) in paragraph at lines 719--720 [] [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] [52] Chapter 10. [53 <./cyverse_rgb2.png> <./homeicon2.png>] [54] Chapter 11. [55] [56] Chapter 12. [57] [58] Chapter 13. (./CyVerseDocumentation.ind) [59] (./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 (63 pages, 8766887 bytes). Transcript written on CyVerseDocumentation.log. 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What is Ubuntu Desktop? ========================= /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. What is Ubuntu Desktop? ========================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/index.rst:19: WARNING: toctree contains reference to nonexisting document u'user_guide/quick-ubuntu-desktop' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-jupyter.rst:7: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/user_guide/quick-jupyter.rst:76: 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-jupyter.rst:76: 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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