Read the Docs build information Build id: 181588 Project: cyverse-container-camp-workshop-2019 Version: latest Commit: e625523c3de597b8e8e3a5d0f059dc25d2947be0 Date: 2019-02-07T21:36:16.932921Z State: finished Success: True [rtd-command-info] start-time: 2019-02-07T21:40:45.310912Z, end-time: 2019-02-07T21:40:45.315151Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/container_camp_workshop_2019.git [rtd-command-info] start-time: 2019-02-07T21:40:45.396582Z, end-time: 2019-02-07T21:40:45.667596Z, duration: 0, exit-code: 0 git fetch --tags --prune --prune-tags --depth 50 From https://github.com/CyVerse-learning-materials/container_camp_workshop_2019 c68e2e5..e625523 master -> origin/master [rtd-command-info] start-time: 2019-02-07T21:40:45.853854Z, end-time: 2019-02-07T21:40:45.906339Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was c68e2e5 Update breakout_session.rst HEAD is now at e625523 Update installation.rst [rtd-command-info] start-time: 2019-02-07T21:40:45.969551Z, end-time: 2019-02-07T21:40:45.987859Z, duration: 0, exit-code: 0 git clean -d -f -f Removing misc/__init__.pyc Removing misc/cyverse_sphinx_conf.pyc [rtd-command-info] start-time: 2019-02-07T21:40:46.676372Z, end-time: 2019-02-07T21:40:49.212791Z, 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-container-camp-workshop-2019/envs/latest/bin/python2.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/bin/python2.7) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-02-07T21:40:49.283905Z, end-time: 2019-02-07T21:40:49.904930Z, duration: 0, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (19.0.1) [rtd-command-info] start-time: 2019-02-07T21:40:49.966709Z, end-time: 2019-02-07T21:40:52.088240Z, duration: 2, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/.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 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6 Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (2.2.0) Collecting setuptools<40 Using cached https://files.pythonhosted.org/packages/7f/e1/820d941153923aac1d49d7fc37e17b6e73bfbd2904959fffbad77900cf92/setuptools-39.2.0-py2.py3-none-any.whl Requirement already up-to-date: docutils==0.13.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (0.13.1) Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (1.0.1) Requirement already up-to-date: pillow==2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (2.6.1) Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in 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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) (2018.11.29) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) (3.0.4) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) (2.8) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx<1.8) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from packaging->sphinx<1.8) (2.3.1) Installing collected packages: setuptools Found existing installation: setuptools 40.6.3 Uninstalling setuptools-40.6.3: Successfully uninstalled setuptools-40.6.3 Successfully installed setuptools-39.2.0 [rtd-command-info] start-time: 2019-02-07T21:40:52.149301Z, end-time: 2019-02-07T21:40:52.686929Z, duration: 0, exit-code: 0 python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/.cache/pip -r requirements.txt Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 1)) (1.7.9) Requirement already satisfied: recommonmark in 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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from packaging->sphinx->-r requirements.txt (line 1)) (2.3.1) [rtd-command-info] start-time: 2019-02-07T21:40:53.146322Z, end-time: 2019-02-07T21:40:53.207403Z, 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 = 'CyVerse Container Camp 2019: Container Technology for Scientific Research' copyright = '2019, CyVerse' author = 'CyVerse' version = '0.1.0' release = '0.1.0' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # 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[ 96%] cyverse/../img/atmo_launch1.png copying images... [ 98%] getting_started/../img/cyverse_rgb.png copying images... [100%] docker/../img/jn_ss.png copying TeX support files... done build succeeded, 33 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). 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[11] [12] Chapter 5. [13] [14] Chapter 6. [15] [16] Chapter 7. [17] [18] Chapter 8. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [19 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [20] [21] [22] ! Package inputenc Error: Unicode char ☺ (U+263A) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.787 ...to answer any of these questions yet! ☺ In this case, the client ... [23] [24] [25 <./static_site_docker.png>] Underfull \hbox (badness 10000) in paragraph at lines 860--862 \T1/pcr/m/n/10 Docker host. 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Type H for immediate help. ... l.2645 ...inxupquote{app.py}} inside the folder  — \sphinxcode{\sphinxupq... Overfull \vbox (4.47736pt too high) detected at line 2672 [73 <./rstudio_login.png>] [74] [75] [76] Chapter 10. [77 <./singularity.png>] Overfull \hbox (800.25983pt too wide) in paragraph at lines 2836--2837 [][] [78 <./singularity-2.4-flow.png>] [79] [80] [81] Overfull \vbox (1.43935pt too high) detected at line 3095 [82] [83] [84] Overfull \vbox (1.68166pt too high) detected at line 3317 [85] [86] [87] [88] [89] [90] [91] [92] Chapter 11. [93] [94] [95] [96] [97] [98] Chapter 12. 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Underfull \hbox (badness 10000) in paragraph at lines 4355--4356 []\T1/pcr/m/n/10 git clone https://github.com/CyVerse-learning-materials/ [123] Overfull \hbox (94.82553pt too wide) in paragraph at lines 4402--4403 [][] [124] [125 <./static_site_docker2.png>] [126] Chapter 18. No file CyVerseDocumentation.ind. [127] (./CyVerseDocumentation.aux) Package rerunfilecheck Warning: File `CyVerseDocumentation.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. 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 (131 pages, 6598774 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2019-02-07T21:41:17.520094Z, end-time: 2019-02-07T21:41:17.630824Z, duration: 0, exit-code: 0 makeindex -s python.ist CyVerseDocumentation.idx This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file CyVerseDocumentation.idx...done (0 entries accepted, 0 rejected). Nothing written in CyVerseDocumentation.ind. Transcript written in CyVerseDocumentation.ilg. [rtd-command-info] start-time: 2019-02-07T21:41:17.704685Z, end-time: 2019-02-07T21:41:28.868665Z, duration: 11, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/./_build/latex/CyVerseDocumentation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-worksh op-2019/checkouts/latest/./_build/latex/CyVerseDocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[11] [12] Chapter 5. [13] [14] Chapter 6. [15] [16] Chapter 7. [17] [18] Chapter 8. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [19 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [20] [21] [22] ! Package inputenc Error: Unicode char ☺ (U+263A) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.787 ...to answer any of these questions yet! ☺ In this case, the client ... [23] [24] [25 <./static_site_docker.png>] Underfull \hbox (badness 10000) in paragraph at lines 860--862 \T1/pcr/m/n/10 Docker host. However if you want to assign a fixed port then you can use \TS1/pcr/m/n/10 ``\T1/pcr/m/n/10 -p Underfull \hbox (badness 10000) in paragraph at lines 871--872 []\T1/ptm/m/n/10 If you are run-ning Docker on At-mo-sphere/Jetstream or on any other cloud, you can open [26 <./static_site_docker1.png>] [27] [28] [29] [30] [31] Underfull \hbox (badness 10000) in paragraph at lines 1221--1223 \T1/ptm/b/n/10 Note: \T1/ptm/m/n/10 When you run the \T1/pcr/m/n/10 docker bui ld \T1/ptm/m/n/10 com-mand given be-low, make sure to re-place [32] [33] [34 <./catpic-1.png>] [35] [36 <./portainer_demo.png>] [37 <./pwd.png >] [38] Chapter 9. [39] [40] [41 <./docker_image.png>] [42 <./private_registry.png>] [43] [44] Overfull \vbox (2.24004pt too high) detected at line 1720 [45 <./auto_build-1.png>] [46 <./create_repo.png>] [47 <./create_repo2.png>] [48 <./auto_build-2.png>] [49 <./auto_build-2.1.png>] [50 <./auto_build-5.png>] [51 <./auto_build-6.png>] [52 <./auto_build-7.png>] [53 <./volumes.png>] [54] [55] [56] [57 <./bind_mount.png>] [58] [59 <./tmpfs.png>] [60] [61] [62] [63 <./dc-1.png>] ! Package inputenc Error: Unicode char   (U+200A) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2490 ...your version of Linux/Windows/OSX/OS9  — well this is where D... ! Package inputenc Error: Unicode char   (U+200A) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2490 ...ersion of Linux/Windows/OSX/OS9 —  well this is where Docker ... 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Type H for immediate help. ... l.2632 ...sphinxupquote{requirements.txt}} file  — Contains python modu... ! Package inputenc Error: Unicode char   (U+200A) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2632 ...upquote{requirements.txt}} file —  Contains python modules an... ! Package inputenc Error: Unicode char   (U+200A) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.2645 ...inxupquote{app.py}} inside the folder  — \sphinxcode{\sphinxupq... Overfull \vbox (4.47736pt too high) detected at line 2672 [73 <./rstudio_login.png>] [74] [75] [76] Chapter 10. 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Overfull \hbox (57.21265pt too wide) in paragraph at lines 3918--3919 [][] [99] Overfull \hbox (57.21504pt too wide) in paragraph at lines 3937--3938 [][] [100 <./atmo-1.png>] Overfull \hbox (57.21887pt too wide) in paragraph at lines 3944--3945 [][] [101 <./atmo_cp0.png> <./atmo_cp.png>] Overfull \hbox (57.2157pt too wide) in paragraph at lines 3960--3961 [][] Overfull \hbox (57.19609pt too wide) in paragraph at lines 3967--3968 [][] [102 <./atmo_launch0.png>] Overfull \hbox (57.18947pt too wide) in paragraph at lines 3977--3978 [][] [103 <./atmo_launch1.png> <./atmo_launch.png>] Overfull \hbox (57.23364pt too wide) in paragraph at lines 3989--3990 [][] Overfull \hbox (57.21529pt too wide) in paragraph at lines 4001--4002 [][] [104 <./atmo-6.png>] Overfull \hbox (57.20352pt too wide) in paragraph at lines 4013--4014 [][] [105 <./atmo-7.png>] Overfull \hbox (57.19528pt too wide) in paragraph at lines 4020--4021 [][] [106 <./atmo-8.png> <./atmo-9.png>] [107] [108] Chapter 13. 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Underfull \hbox (badness 10000) in paragraph at lines 4355--4356 []\T1/pcr/m/n/10 git clone https://github.com/CyVerse-learning-materials/ [123] Overfull \hbox (94.82553pt too wide) in paragraph at lines 4402--4403 [][] [124] [125 <./static_site_docker2.png>] [126] Chapter 18. (./CyVerseDocumentation.ind) [127] (./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 (131 pages, 6603037 bytes). Transcript written on CyVerseDocumentation.log. 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