Read the Docs build information Build id: 771768 Project: cyverse-2021-neon-aop-workshop Version: latest Commit: df636875a5fe05320d68ecc895cb4300161626ff Date: 2021-11-12T16:08:50.648715Z State: finished Success: True [rtd-command-info] start-time: 2021-11-12T16:08:52.435497Z, end-time: 2021-11-12T16:08:55.016607Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/2021-neon-aop-workshop.git . Cloning into '.'... [rtd-command-info] start-time: 2021-11-12T16:08:55.216115Z, end-time: 2021-11-12T16:08:55.393688Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: checking out 'origin/main'. 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 df63687 Update step1.rst [rtd-command-info] start-time: 2021-11-12T16:08:55.528023Z, end-time: 2021-11-12T16:08:55.601659Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-11-12T16:08:57.038368Z, end-time: 2021-11-12T16:09:02.176888Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-11-12T16:09:02.297970Z, end-time: 2021-11-12T16:09:03.438970Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/envs/latest/lib/python3.7/site-packages (21.3.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/envs/latest/lib/python3.7/site-packages (58.5.3) [rtd-command-info] start-time: 2021-11-12T16:09:03.573563Z, end-time: 2021-11-12T16:09:11.860797Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 sphinx-rtd-theme readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx Downloading Sphinx-4.3.0-py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme Downloading sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting docutils>=0.11 Downloading docutils-0.18-py2.py3-none-any.whl (569 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting imagesize Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting babel>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/envs/latest/lib/python3.7/site-packages (from sphinx) (58.5.3) Collecting packaging Downloading packaging-21.2-py3-none-any.whl (40 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Collecting Pygments>=2.0 Downloading Pygments-2.10.0-py3-none-any.whl (1.0 MB) Collecting requests>=2.5.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting sphinxcontrib-htmlhelp>=2.0.0 Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB) Collecting sphinxcontrib-serializinghtml>=1.1.5 Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Collecting pytz>=2015.7 Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (31 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.7-py3-none-any.whl (38 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB) Collecting pyparsing<3,>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=eb9fe7683fdc5f1c4d9ca0c20542dad195d8d5b218bceea890a09a342bc154a1 Stored in directory: /tmp/pip-ephem-wheel-cache-q7i8wdnl/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=8d4e0d7335301ef9d17ca5d62412fb3208c3fc9a303bce0cf005df9e0204bbdd Stored in directory: /tmp/pip-ephem-wheel-cache-q7i8wdnl/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Successfully installed Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.7 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.2 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 snowballstemmer-2.1.0 sphinx-4.3.0 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 urllib3-1.26.7 [rtd-command-info] start-time: 2021-11-12T16:09:12.827384Z, end-time: 2021-11-12T16:09:12.896591Z, duration: 0, exit-code: 0 cat conf.py #!/usr/bin/env python3 # Version 2.1, October 2021 # -*- 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 = '2021-neon-aop-workshop' copyright = '2021, CyVerse' author = 'TL Swetnam ' version = '2.0' release = '2.0' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright ########################################################################### # 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 # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring 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://assets.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://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//cyverse-2021-neon-aop-workshop.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//cyverse-2021-neon-aop-workshop.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//cyverse-2021-neon-aop-workshop.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'cyverse-2021-neon-aop-workshop', 'name': u'2021-neon-aop-workshop', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-2021-neon-aop-workshop.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'proxied_api_host': '/_', 'github_repo': '2021-neon-aop-workshop', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'df636875', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None 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") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/cyverse-2021-neon-aop-workshop/builds/771768/' 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' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-11-12T16:09:13.034395Z, end-time: 2021-11-12T16:09:15.128236Z, duration: 2, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v4.3.0 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [html]: targets for 10 source files that are out of date updating environment: [new config] 10 added, 0 changed, 0 removed reading sources... 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[100%] step6 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/agenda.rst:42: WARNING: Unknown target name: "zoom us <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/final_step.rst:4: WARNING: Undefined substitution referenced: "CyVerse logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/final_step.rst:4: WARNING: Unknown target name: "cyverse logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/index.rst:72: WARNING: toctree contains reference to nonexisting document ' :maxdepth: 2' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/index.rst:229: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/step1.rst:59: WARNING: Title underline too short. *Walkthrough* ============ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/step1.rst:179: WARNING: Title level inconsistent: *TERMINOLOGY* +++++++++++++ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/step1.rst:187: WARNING: Title underline too short. *Walkthrough* ============ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/step1.rst:199: WARNING: Title underline too short. *Walkthrough* ============ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/step1.rst:259: WARNING: Duplicate substitution definition name: "Data Store Guide". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/step2.rst:245: WARNING: Duplicate substitution definition name: "vice_loading". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/step2.rst:227: WARNING: image file not readable: img/de/vice-loading.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/step3.rst:27: WARNING: Title underline too short. *Prerequisite* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/step4.rst:211: WARNING: At least one body element must separate transitions; adjacent transitions are not allowed. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/step5.rst:11: WARNING: Duplicate explicit target name: "github". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/final_step.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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(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/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb> Output written on cyverse-2021-neon-aop-workshop.pdf (40 pages, 1932757 bytes). Transcript written on cyverse-2021-neon-aop-workshop.log. Latexmk: Index file 'cyverse-2021-neon-aop-workshop.idx' was written Latexmk: Missing input file: 'cyverse-2021-neon-aop-workshop.ind' from line 'No file cyverse-2021-neon-aop-workshop.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-2021-neon-aop-workshop.pdf' Latexmk: Log file says output to 'cyverse-2021-neon-aop-workshop.pdf' Rule 'makeindex cyverse-2021-neon-aop-workshop.idx': File changes, etc: Non-existent destination files: 'cyverse-2021-neon-aop-workshop.ind' ------------ Run number 1 of rule 'makeindex cyverse-2021-neon-aop-workshop.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-2021-neon-aop-workshop.ind" "cyverse-2021-neon-aop-workshop.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-2021-neon-aop-workshop.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-2021-neon-aop-workshop.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-2021-neon-aop-workshop.ind. Transcript written in cyverse-2021-neon-aop-workshop.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-2021-neon-aop-workshop.aux' 'cyverse-2021-neon-aop-workshop.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-2021-neon-aop-workshop" "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] [6] Chapter 3. [7] (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qhv/m/n/10 Time Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qhv/m/n/10 (AZT Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qhv/m/n/10 Lead Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qhv/m/n/10 Per- Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qhv/m/n/10 son- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 0900- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Tyson Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qtm/m/n/10 & Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qtm/m/n/10 Brid- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 0910- Underfull \hbox (badness 10000) in paragraph at lines 500--500 [][][]\T1/qtm/m/n/10 Dis-cov-ery En-vi-ron-ment Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 0930- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Jupyter, RStu-dio, Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1030- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 In-tro to NEON Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Brid- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Down-load and Ex-plore Underfull \hbox (badness 10000) in paragraph at lines 500--500 [][][]$\T1/qtm/m/n/10 https : / / www . neonscience . org / Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qtm/m/n/10 resources / learning-[]hub / tutorials / Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1045- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1100- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Jupyter Lab Underfull \hbox (badness 5637) in paragraph at lines 500--500 \T1/qtm/m/n/10 Geospa-tial Ap-pli- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Brid- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1200- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1300- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1400- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Re-pro-ducibil-ity Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1430- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1445- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Hands-On with Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Tyson Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qtm/m/n/10 & Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qtm/m/n/10 Brid- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1645- [8] [9 <./intercom.png>] [10 <./de_architecture.png>] [11 <./data_icon.png> <./ data_window.png>] [12] [13] [14 <./apps_icon.png> <./apps_search1.png> <./analy ses_icon.png>] ! 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Type H for immediate help. ... l.2093 ...87086e249/Powered-By-CyVerse-blue}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2097 ...87086e249/Powered-By-CyVerse-blue}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2097 ...87086e249/Powered-By-CyVerse-blue}.svg}} Underfull \hbox (badness 10000) in paragraph at lines 2122--2124 []\T1/qtm/m/n/10 Your anal-y-sis will run, and when it com-pletes, it will writ e any data that Underfull \hbox (badness 10000) in paragraph at lines 2122--2124 \T1/qtm/m/n/10 you have in the WORK-ING DI-REC-TORY of the con-tainer back to t he Data Underfull \hbox (badness 10000) in paragraph at lines 2122--2124 \T1/qtm/m/n/10 Store in your Anal-y-ses folder, e.g. \T1/txtt/m/n/10 /iplant/ho me//analyses/ [31] [32] [33] [34] Chapter 4. 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Type H for immediate help. ... l.2464 \end{tabulary} (./cyverse-2021-neon-aop-workshop.ind) [36] (./cyverse-2021-neon-aop-workshop.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb> Output written on cyverse-2021-neon-aop-workshop.pdf (40 pages, 1936842 bytes). Transcript written on cyverse-2021-neon-aop-workshop.log. Latexmk: Index file 'cyverse-2021-neon-aop-workshop.idx' was written Latexmk: Log file says output to 'cyverse-2021-neon-aop-workshop.pdf' Latexmk: Log file says output to 'cyverse-2021-neon-aop-workshop.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-2021-neon-aop-workshop.out' 'cyverse-2021-neon-aop-workshop.toc' ------------ Run number 3 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-2021-neon-aop-workshop" "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/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-2021-neon-aop-workshop.out) (./cyverse-2021-neon-aop-workshop.out) (/usr/share/texmf/tex/latex/tex-gyre/t1qhv.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-2021-neon-aop-workshop.toc) [1] [2] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [1 <./cyver se_learning.png> <./homeicon.png>] [2] Chapter 1. [3] [4] Chapter 2. [5] [6] Chapter 3. [7] (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qhv/m/n/10 Time Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qhv/m/n/10 (AZT Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qhv/m/n/10 Lead Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qhv/m/n/10 Per- Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qhv/m/n/10 son- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 0900- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Tyson Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qtm/m/n/10 & Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qtm/m/n/10 Brid- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 0910- Underfull \hbox (badness 10000) in paragraph at lines 500--500 [][][]\T1/qtm/m/n/10 Dis-cov-ery En-vi-ron-ment Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 0930- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Jupyter, RStu-dio, Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1030- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 In-tro to NEON Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Brid- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Down-load and Ex-plore Underfull \hbox (badness 10000) in paragraph at lines 500--500 [][][]$\T1/qtm/m/n/10 https : / / www . neonscience . org / Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qtm/m/n/10 resources / learning-[]hub / tutorials / Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1045- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1100- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Jupyter Lab Underfull \hbox (badness 5637) in paragraph at lines 500--500 \T1/qtm/m/n/10 Geospa-tial Ap-pli- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Brid- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1200- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1300- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1400- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Re-pro-ducibil-ity Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1430- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1445- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Hands-On with Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 Tyson Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qtm/m/n/10 & Underfull \hbox (badness 10000) in paragraph at lines 500--500 \T1/qtm/m/n/10 Brid- Underfull \hbox (badness 10000) in paragraph at lines 500--500 []\T1/qtm/m/n/10 1645- [8] [9 <./intercom.png>] [10 <./de_architecture.png>] [11 <./data_icon.png> <./ data_window.png>] [12] [13] [14 <./apps_icon.png> <./apps_search1.png> <./analy ses_icon.png>] ! 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Type H for immediate help. ... l.2464 \end{tabulary} (./cyverse-2021-neon-aop-workshop.ind) [36] (./cyverse-2021-neon-aop-workshop.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb> Output written on cyverse-2021-neon-aop-workshop.pdf (40 pages, 1936842 bytes). Transcript written on cyverse-2021-neon-aop-workshop.log. Latexmk: Index file 'cyverse-2021-neon-aop-workshop.idx' was written Latexmk: Log file says output to 'cyverse-2021-neon-aop-workshop.pdf' Latexmk: Log file says output to 'cyverse-2021-neon-aop-workshop.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: 2021-11-12T16:10:02.510458Z, end-time: 2021-11-12T16:10:02.597373Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/checkouts/latest/./_build/latex/cyverse-2021-neon-aop-workshop.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-2021-neon-aop-workshop/artifacts/latest/sphinx_pdf/cyverse-2021-neon-aop-workshop.pdf [rtd-command-info] start-time: 2021-11-12T16:10:02.708453Z, end-time: 2021-11-12T16:10:49.154110Z, duration: 46, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees -D language=en . _build/epub Running Sphinx v4.3.0 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [epub]: targets for 10 source files that are out of date updating environment: 0 added, 2 changed, 0 removed reading sources... 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