Read the Docs build information Build id: 224263 Project: cyverse-container-camp-workshop-2019 Version: latest Commit: dfccc5e0a19f2b9bbe22fbe722e38bd99a0dd233 Date: 2019-07-17T01:32:44.464846Z State: finished Success: True [rtd-command-info] start-time: 2019-07-17T01:32:45.005329Z, end-time: 2019-07-17T01:32:48.856039Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/container_camp_workshop_2019.git . Cloning into '.'... [rtd-command-info] start-time: 2019-07-17T01:32:49.804500Z, end-time: 2019-07-17T01:32:50.893912Z, 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 dfccc5e Merge pull request #5 from sanjanasudarshan/master [rtd-command-info] start-time: 2019-07-17T01:32:50.977398Z, end-time: 2019-07-17T01:32:51.000128Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-07-17T01:32:52.087198Z, end-time: 2019-07-17T01:32:54.351020Z, 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 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-07-17T01:32:54.433485Z, end-time: 2019-07-17T01:32:56.682296Z, 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 pip Collecting pip Downloading https://files.pythonhosted.org/packages/5c/e0/be401c003291b56efc55aeba6a80ab790d3d4cece2778288d65323009420/pip-19.1.1-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-19.1.1 [rtd-command-info] start-time: 2019-07-17T01:32:56.769032Z, end-time: 2019-07-17T01:33:07.440452Z, duration: 10, 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==2.3.1 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<0.6 DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. 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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 mulitple 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-container-camp-workshop-2019/downloads/pdf/latest/"), ("html", "//readthedocs.com/projects/cyverse-container-camp-workshop-2019/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/cyverse-container-camp-workshop-2019/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-container-camp-workshop-2019', 'name': u'container_camp_workshop_2019', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'container_camp_workshop_2019', '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': 'dfccc5e0', } 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"] 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: 2019-07-17T01:33:12.330837Z, end-time: 2019-07-17T01:33:19.687368Z, duration: 7, 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 55 source files that are out of date updating environment: 55 added, 0 changed, 0 removed reading sources... 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[100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/biocontainers.rst:2: WARNING: Title underline too short. **Biocontainers** ================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/datascience.rst:2: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/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-container-camp-workshop-2019/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 }} 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image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/agenda.rst:2: WARNING: Duplicate explicit target name: "slides". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/main.rst:4: WARNING: Title underline too short. **Workshop Code of Conduct and Other Information** ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short. 5.0 Building your own Containers from scratch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short. 5.2 Building Singularity containers ================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:140: WARNING: Duplicate explicit target name: "user guide". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:278: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 7 supplied. .. code-block:: bash BootStrap: debootstrap OSVersion: xenial MirrorURL: http://us.archive.ubuntu.com/ubuntu/ %runscript echo "This is what happens when you run the container..." %post echo "Hello from inside the container" sed -i 's/$/ universe/' /etc/apt/sources.list apt update apt -y --allow-unauthenticated install vim build-essential wget gfortran bison libibverbs-dev libibmad-dev libibumad-dev librdmacm-dev libmlx5-dev libmlx4-dev wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz tar xvf mvapich2-2.1.tar.gz cd mvapich2-2.1 ./configure --prefix=/usr/local make -j4 make install /usr/local/bin/mpicc examples/hellow.c -o /usr/bin/hellow /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". looking for now-outdated files... none found pickling environment... done 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image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/agenda.rst:2: WARNING: Duplicate explicit target name: "slides". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/main.rst:4: WARNING: Title underline too short. **Workshop Code of Conduct and Other Information** ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short. 5.0 Building your own Containers from scratch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short. 5.2 Building Singularity containers ================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:140: WARNING: Duplicate explicit target name: "user guide". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:278: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 7 supplied. .. code-block:: bash BootStrap: debootstrap OSVersion: xenial MirrorURL: http://us.archive.ubuntu.com/ubuntu/ %runscript echo "This is what happens when you run the container..." %post echo "Hello from inside the container" sed -i 's/$/ universe/' /etc/apt/sources.list apt update apt -y --allow-unauthenticated install vim build-essential wget gfortran bison libibverbs-dev libibmad-dev libibumad-dev librdmacm-dev libmlx5-dev libmlx4-dev wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz tar xvf mvapich2-2.1.tar.gz cd mvapich2-2.1 ./configure --prefix=/usr/local make -j4 make install /usr/local/bin/mpicc examples/hellow.c -o /usr/bin/hellow /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". looking for now-outdated files... none found pickling environment... done checking consistency... 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' %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: 2019-07-17T01:33:57.031781Z, end-time: 2019-07-17T01:34:44.832208Z, duration: 47, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-container-camp-workshop-2019 -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 $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. 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[3] [4] Chapter 2. [5] Underfull \hbox (badness 5189) in paragraph at lines 2--288 [][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber- [6] Chapter 3. Underfull \hbox (badness 5802) in paragraph at lines 332--333 []|\T1/ptm/m/n/10 General in-tro-duc-tion to Underfull \hbox (badness 6675) in paragraph at lines 339--340 \T1/ptm/m/n/10 tainer tech-nol-ogy land- Underfull \hbox (badness 10000) in paragraph at lines 353--354 []|\T1/ptm/m/n/10 Introduction to Docker Underfull \hbox (badness 6412) in paragraph at lines 360--361 []|\T1/ptm/m/n/10 Lunch break (on your Underfull \hbox (badness 10000) in paragraph at lines 379--380 []|\T1/ptm/m/n/10 Docker hands-on ex-er- Underfull \hbox (badness 10000) in paragraph at lines 2--383 []|[][]\T1/ptm/m/n/10 Docker hands-on ex-er- Underfull \hbox (badness 6961) in paragraph at lines 400--401 []|\T1/ptm/m/n/10 Review Day 1 (Ques- Underfull \hbox (badness 10000) in paragraph at lines 2--421 [][][]\T1/ptm/m/n/10 Non-interactive Underfull \hbox (badness 10000) in paragraph at lines 1--441 [][][]$\T1/ptm/m/n/10 https : / / mirrorlab . 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[15] [16] Chapter 8. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [17 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [18] [19] [20] [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1041--1043 \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 [24] Overfull \vbox (11.24115pt too high) detected at line 1126 [25] LaTeX Warning: Hyper reference `docker/dockerintro:create-a-python-file-contain ing-a-function' on page 26 undefined on input line 1134. [26] [27] [28] [29] [30 <./portainer_demo.png>] [31 <./pwd.png>] [32] Chapter 9. [33] [34] [35 <./docker_image.png>] [36 <./private_registry.png>] [37] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1699--1700 [][] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1710--1711 [][] [38 <./dockerhub_create.png>] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1724--1725 [][] [39 <./dockerhub_createrepo.png>] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1728--1729 [][] [40 <./dockerhub_buildsettings.png>] [41 <./dockerhub_autobuild.png>] [42 <./cr eate_repo.png> <./create_repo2.png>] Overfull \hbox (132.49107pt too wide) in paragraph at lines 1832--1833 [][] [43] Overfull \vbox (90.47859pt too high) has occurred while \output is active [44 <./dockerhub_autobuilds.png>] [45 <./auto_build-2.1.png>] [46 <./auto_build -5.png> <./auto_build-6.png>] [47 <./auto_build-7.png>] [48 <./volumes.png>] Underfull \hbox (badness 10000) in paragraph at lines 2050--2052 \T1/ptm/b/n/10 Note: \T1/ptm/m/n/10 File lo-ca-tion on Mac OS X is a bit dif-f er-ent: [][]$https : / / timonweb . com / posts / [49] [50] [51 <./bind_mount.png>] [52 <./tmpfs.png>] [53] [54] [55] [56 <./dc-1 .png>] Chapter 10. 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[73] [74] [75] [76] Chapter 13. [77] Overfull \vbox (6.28346pt too high) detected at line 3463 [78] [79] [80] [81] [82] Chapter 14. Underfull \hbox (badness 10000) in paragraph at lines 3572--3573 \T1/ptm/m/n/10 Biocontainers for con-tainer camp by Amanda Cook-sey - [][]$http s : / / de . cyverse . org / dl / d / [83] [84] Chapter 15. Overfull \hbox (132.49107pt too wide) in paragraph at lines 3585--3586 [] [85] [86 <./dff16156a2fac35ba7650c7bae20c561e0b8d2e8.png>] [87] [88] Chapter 16. Overfull \hbox (57.21031pt too wide) in paragraph at lines 3636--3637 [] [89 <./snakemake.png>] [90] Chapter 17. [91] ! 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.3719 ...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. 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Latexmk: Index file 'cyverse-container-camp-workshop-2019.idx' was written Latexmk: Missing input file: 'cyverse-container-camp-workshop-2019.ind' from line 'No file cyverse-container-camp-workshop-2019.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Rule 'makeindex cyverse-container-camp-workshop-2019.idx': File changes, etc: Non-existent destination files: 'cyverse-container-camp-workshop-2019.ind' ------------ Run number 1 of rule 'makeindex cyverse-container-camp-workshop-2019.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-container-camp-workshop-2019.ind" "cyverse-container-camp-workshop-2019.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-container-camp-workshop-2019.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-container-camp-workshop-2019.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-container-camp-workshop-2019.ind. Transcript written in cyverse-container-camp-workshop-2019.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-container-camp-workshop-2019.aux' 'cyverse-container-camp-workshop-2019.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-container-camp-workshop-2019" "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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[3] [4] Chapter 2. [5] Underfull \hbox (badness 5189) in paragraph at lines 2--288 [][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber- [6] Chapter 3. Underfull \hbox (badness 5802) in paragraph at lines 332--333 []|\T1/ptm/m/n/10 General in-tro-duc-tion to Underfull \hbox (badness 6675) in paragraph at lines 339--340 \T1/ptm/m/n/10 tainer tech-nol-ogy land- Underfull \hbox (badness 10000) in paragraph at lines 353--354 []|\T1/ptm/m/n/10 Introduction to Docker Underfull \hbox (badness 6412) in paragraph at lines 360--361 []|\T1/ptm/m/n/10 Lunch break (on your Underfull \hbox (badness 10000) in paragraph at lines 379--380 []|\T1/ptm/m/n/10 Docker hands-on ex-er- Underfull \hbox (badness 10000) in paragraph at lines 2--383 []|[][]\T1/ptm/m/n/10 Docker hands-on ex-er- Underfull \hbox (badness 6961) in paragraph at lines 400--401 []|\T1/ptm/m/n/10 Review Day 1 (Ques- Underfull \hbox (badness 10000) in paragraph at lines 2--421 [][][]\T1/ptm/m/n/10 Non-interactive Underfull \hbox (badness 10000) in paragraph at lines 1--441 [][][]$\T1/ptm/m/n/10 https : / / mirrorlab . 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[15] [16] Chapter 8. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [17 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [18] [19] [20] [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1041--1043 \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 [24] Overfull \vbox (11.24115pt too high) detected at line 1126 [25] [26] [27] [28] [29] [30 <./portainer_demo.png>] [31 <./pwd.png>] [32] Chapter 9. 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See the inputenc package documentation for explanation. Type H for immediate help. ... l.3834 ...inxupquote{app.py}} inside the folder  — \sphinxcode{\sphinxupq... [96 <./rstudio_login.png>] [97] [98] [99 <./cyverse_rgb.png>] [100] Chapter 18. 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Latexmk: Index file 'cyverse-container-camp-workshop-2019.idx' was written Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-container-camp-workshop-2019.out' 'cyverse-container-camp-workshop-2019.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-container-camp-workshop-2019" "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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[3] [4] Chapter 2. [5] Underfull \hbox (badness 5189) in paragraph at lines 2--288 [][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber- [6] Chapter 3. 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[15] [16] Chapter 8. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [17 <./docker.png>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [18] [19] [20] [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1041--1043 \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 [24] Overfull \vbox (11.24115pt too high) detected at line 1126 [25] [26] [27] [28] [29] [30 <./portainer_demo.png>] [31 <./pwd.png>] [32] Chapter 9. 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[73] [74] [75] [76] Chapter 13. [77] Overfull \vbox (6.28346pt too high) detected at line 3463 [78] [79] [80] [81] [82] Chapter 14. Underfull \hbox (badness 10000) in paragraph at lines 3572--3573 \T1/ptm/m/n/10 Biocontainers for con-tainer camp by Amanda Cook-sey - [][]$http s : / / de . cyverse . org / dl / d / [83] [84] Chapter 15. Overfull \hbox (132.49107pt too wide) in paragraph at lines 3585--3586 [] [85] [86 <./dff16156a2fac35ba7650c7bae20c561e0b8d2e8.png>] [87] [88] Chapter 16. Overfull \hbox (57.21031pt too wide) in paragraph at lines 3636--3637 [] [89 <./snakemake.png>] [90] Chapter 17. [91] ! 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.3719 ...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.3719 ...ersion of Linux/Windows/OSX/OS9 —  well this is where Docker ... Overfull \hbox (57.21031pt too wide) in paragraph at lines 3732--3733 [][] Overfull \hbox (57.21031pt too wide) in paragraph at lines 3736--3737 [][] [92 <./jn_login.png>] Overfull \hbox (57.21031pt too wide) in paragraph at lines 3740--3741 [][] Overfull \hbox (57.21031pt too wide) in paragraph at lines 3742--3743 [][] [93 <./jn_login2.png> <./jn_login3.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.3762 ...r compose file. And there you have it  — a quick and easy way... ! 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.3762 ...ose file. And there you have it —  a quick and easy way to st... Overfull \hbox (57.21031pt too wide) in paragraph at lines 3769--3770 [][] [94 <./jn_login3.5.png>] Overfull \hbox (57.21031pt too wide) in paragraph at lines 3777--3778 [][] [95 <./rstudio_ss.png> <./rstudio_login2.png>] Overfull \hbox (57.21031pt too wide) in paragraph at lines 3783--3784 [][] ! 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.3819 ...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.3819 ...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.3834 ...inxupquote{app.py}} inside the folder  — \sphinxcode{\sphinxupq... [96 <./rstudio_login.png>] [97] [98] [99 <./cyverse_rgb.png>] [100] Chapter 18. 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Overfull \hbox (57.20361pt too wide) in paragraph at lines 4393--4394 [][] [119] Overfull \hbox (57.20361pt too wide) in paragraph at lines 4400--4401 [][] [120 <./jupyter1-1.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 4402--4403 [][] [121 <./jupyter1-2.png> <./jupyter1-3.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 4413--4414 [][] Overfull \hbox (57.20361pt too wide) in paragraph at lines 4417--4418 [][] [122 <./jupyter1-9.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 4436--4437 [][] [123 <./jupyter1-4.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 4447--4448 [][] [124 <./jupyter1-5.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 4454--4455 [][] [125 <./jupyter1-6.png>] Overfull \hbox (57.20361pt too wide) in paragraph at lines 4456--4457 [][] [126 <./jupyter1-7.png> <./jupyter1-8.png>] [127] [128] Chapter 21. [129] [130] Chapter 22. [131] [132] Chapter 23. [133] [134] Chapter 24. [135] Overfull \hbox (94.8507pt too wide) in paragraph at lines 4668--4669 [][] [136] Overfull \hbox (94.8507pt too wide) in paragraph at lines 4672--4673 [][] [137 <./static_site_docker.png> <./instructors_code.png>] [138] Chapter 25. (./cyverse-container-camp-workshop-2019.ind) [139] (./cyverse-container-camp-workshop-2019.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-container-camp-workshop-2019.pdf (143 pages, 9585158 bytes). Transcript written on cyverse-container-camp-workshop-2019.log. Latexmk: Index file 'cyverse-container-camp-workshop-2019.idx' was written Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf' Latexmk: Errors, in force_mode: so I tried finishing targets Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 [rtd-command-info] start-time: 2019-07-17T01:34:44.926392Z, end-time: 2019-07-17T01:34:45.237189Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/./_build/latex/cyverse-container-camp-workshop-2019.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/artifacts/latest/sphinx_pdf/cyverse-container-camp-workshop-2019.pdf [rtd-command-info] start-time: 2019-07-17T01:34:45.342762Z, end-time: 2019-07-17T01:35:11.564119Z, duration: 26, 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 55 source files that are out of date updating environment: 55 added, 0 changed, 0 removed reading sources... 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[100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/biocontainers.rst:2: WARNING: Title underline too short. **Biocontainers** ================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/datascience.rst:2: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/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-container-camp-workshop-2019/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 }} 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image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/agenda.rst:2: WARNING: Duplicate explicit target name: "slides". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/main.rst:4: WARNING: Title underline too short. **Workshop Code of Conduct and Other Information** ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short. 5.0 Building your own Containers from scratch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short. 5.2 Building Singularity containers ================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short. 5.2.1: Exercise (~30 minutes): Create a Singularity file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:140: WARNING: Duplicate explicit target name: "user guide". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:278: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 7 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