Read the Docs build information Build id: 532282 Project: cyverse-foss Version: foss-2019-spring Commit: d79992bbfbf236bc7957b5459618ab1b2bbf578c Date: 2021-01-15T04:16:53.218310Z State: finished Success: True [rtd-command-info] start-time: 2021-01-15T04:16:54.862297Z, end-time: 2021-01-15T04:16:59.756690Z, duration: 4, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:CyVerse-learning-materials/foss.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2021-01-15T04:17:00.266643Z, end-time: 2021-01-15T04:17:00.767818Z, duration: 0, exit-code: 0 git checkout --force origin/foss-2019-spring Note: checking out 'origin/foss-2019-spring'. 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 d79992b Adding FOSS 2019 Spring [rtd-command-info] start-time: 2021-01-15T04:17:00.962088Z, end-time: 2021-01-15T04:17:01.019477Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-01-15T04:17:02.771966Z, end-time: 2021-01-15T04:17:07.104068Z, duration: 4, 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-foss/envs/foss-2019-spring/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2019-spring/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-01-15T04:17:07.275050Z, end-time: 2021-01-15T04:17:08.893044Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2019-spring/lib/python3.7/site-packages (20.3.3) [rtd-command-info] start-time: 2021-01-15T04:17:09.100586Z, end-time: 2021-01-15T04:17:18.707336Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.2-py2.py3-none-any.whl (11 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting six Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting Jinja2>=2.9 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting Pygments>=2.0 Downloading Pygments-2.7.4-py3-none-any.whl (950 kB) Collecting pytz>=2015.7 Downloading pytz-2020.5-py2.py3-none-any.whl (510 kB) Collecting requests Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.2-py2.py3-none-any.whl (136 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting packaging Downloading packaging-20.8-py2.py3-none-any.whl (39 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 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=23755 sha256=37fdb8efb8bb3da44a1c025588b5325bdf4658f5929cf048a7ad141fad30cf3e Stored in directory: /tmp/pip-ephem-wheel-cache-hakrr4t9/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=491059 sha256=d3868aba4aaa26184dcbd238b90189b91c25033084fad00f822d3399986e53a3 Stored in directory: /tmp/pip-ephem-wheel-cache-hakrr4t9/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Attempting uninstall: setuptools Found existing installation: setuptools 51.1.2 Uninstalling setuptools-51.1.2: Successfully uninstalled setuptools-51.1.2 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.4 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.8 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.5 readthedocs-sphinx-ext-2.1.2 recommonmark-0.5.0 requests-2.25.1 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2 [rtd-command-info] start-time: 2021-01-15T04:17:20.406544Z, end-time: 2021-01-15T04:17:20.479681Z, duration: 0, exit-code: 0 cat conf.py #!/usr/bin/env python3 # Version 2.0, May 2020 # -*- 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 Learning Institute Foundational Open Science Skills 2019' copyright = '2021, CyVerse' author = 'CyVerse' version = '2019-spring' release = '2019-spring' epub_title = 'CyVerse Learning Institute Foundations of Open Science Skills 2019' epub_author = 'Ramona L. Walls, Tyson L. Swetnam, Amanda Cooksey, Meghan Balk' epub_publisher = 'CyVerse' epub_copyright = 'CC0 - Open Source' ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "foss-2019-spring", 'version_slug': "foss-2019-spring", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'cyverse-foss', 'name': u'foss', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-foss.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': 'foss', 'github_version': 'foss-2019-spring', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'foss-2019-spring', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'foss-2019-spring', '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': 'd79992bb', } # 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") 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: 2021-01-15T04:17:20.794751Z, end-time: 2021-01-15T04:17:26.885739Z, duration: 6, exit-code: 0 python sphinx-build -T -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 41 source files that are out of date updating environment: 41 added, 0 changed, 0 removed reading sources... 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[100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2019-spring/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/biocontainers.rst:181: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:449: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 3 supplied. .. code-block:: bash -v /home/username/your_data_folder:/data:ro /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:578: WARNING: Error in "code-block" directive: 1 argument(s) required, 0 supplied. .. code-block:: $ docker inspect jupytertest /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:417: WARNING: Unknown target name: "see here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:498: WARNING: Duplicate explicit target name: "dockerfile". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:554: WARNING: Duplicate explicit target name: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:591: WARNING: Duplicate explicit target name: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:470: WARNING: Duplicate target name, cannot be used as a unique reference: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:471: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeronatmo.rst:10: WARNING: Title underline too short. Launching a Docker app on Atmosphere --------------------------------- cyverse_rst_defined_substitutions.txt:36: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:21: WARNING: Title underline too short. **Virtual Machines on Atmosphere or Jetstream** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:65: WARNING: The "list-table" directive is empty; content required. .. list-table:: :header-rows: 1 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:9: WARNING: Duplicate explicit target name: "image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:110: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:518: WARNING: Duplicate substitution definition name: "CyVerse_logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:522: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:408: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:511: WARNING: image file not readable: CyVerse/../img/notebook_terminal.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:9: WARNING: Title underline too short. **CyVerse Data Store** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:77: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:77: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:112: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:112: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:10: WARNING: Title underline too short. **Discovery Environment** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:24: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:24: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:55: WARNING: Title underline too short. Analyses Window ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:55: WARNING: Title underline too short. Analyses Window ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:173: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:173: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:204: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:204: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:113: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:164: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:3: WARNING: Undefined substitution referenced: "CyVerse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:3: WARNING: Unknown target name: "cyverse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/vice.rst:66: WARNING: Title underline too short. *Specific instructions for launching VICE applications* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/vice.rst:103: WARNING: Title underline too short. |vice-share-7| ---- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/FAIR.rst:45: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:9: WARNING: Title underline too short. **Data Management Plans (DMP)** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:30: WARNING: Title underline too short. Elements of a good DMP ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:84: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:84: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:9: WARNING: Title underline too short. **Data Management Overview** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:14: WARNING: Title underline too short. Why should you care about data management? ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:68: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:68: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:94: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:163: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:163: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:9: WARNING: Title underline too short. **Before you arrive** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:18: WARNING: Title underline too short. **About FOSS** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:29: WARNING: Title underline too short. **FOSS Camp Goes Green** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:29: WARNING: Title underline too short. **FOSS Camp Goes Green** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:34: WARNING: Title underline too short. **Who should attend?** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:34: WARNING: Title underline too short. **Who should attend?** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:39: WARNING: Title underline too short. **Workshop level** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/agenda.rst:9: WARNING: Duplicate explicit target name: "lesson". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/agenda.rst:288: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/glossary.rst:9: WARNING: Title underline too short. **Glossary & Acronyms** ^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:10: WARNING: Title underline too short. **FOSS 2019 Introduction** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:13: WARNING: Title underline too short. Welcome and staff introductions =========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:26: WARNING: Title overline & underline mismatch. ---- Course Overview ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/open_sci_lab.rst:10: WARNING: Title underline too short. **Open Science Lab** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:2: WARNING: Title overline too short. ***** DEPRECATED: Visit `FOSS-2020 `_ for current pages ***** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:9: WARNING: Title underline too short. CyVerse Learning Institute - Foundational Open Science Skills (FOSS) 2019 ------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:162: WARNING: Undefined substitution referenced: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:42: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:9: WARNING: Title underline too short. **Other Cyberinfrastructure Projects** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:12: WARNING: Title underline too short. **National Groups** ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:42: WARNING: Title underline too short. **National Science Foundation** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:10: WARNING: Title underline too short. **Research Cyberinfrastructure associated with CyVerse** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:17: WARNING: Title underline too short. **XSEDE** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:30: WARNING: Title underline too short. **Jetstream** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:44: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 3 supplied. .. code:: R ```{R, echo=FALSE} ``` ```{bash, echo=FALSE} ``` ```{python, echo=FALSE} ``` 4. Run the code block /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:65: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 2 supplied. .. code:: install.package(c("workflowr","drake"), dependencies=TRUE) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:86: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "CyverseLogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "LearningCenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "cyverselogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "learningcenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:26: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R setwd(path) getwd() #see what working directory you're in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:35: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:39: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:117: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:176: WARNING: Unknown directive type "code-blocl". .. code-blocl:: R #both do the same thing: require("package") #loads dependencies; will give a warning if it is in conflict with another package (e.g., masks) #can overwrite masked functions using "::" (e.g., package::function) library("package") #will give an error if in conflict with other packages or has missing dependencies /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:214: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.character() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:220: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.numeric() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:226: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.integer() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:231: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R as.factor() #creates groupings within dataset /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:306: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R d <- c(d, "a) str(d) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:334: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hi <- data.frame(numbers = 1:26, letters, c("hey", "you")) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:340: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hola <- data.frame(1:26, letters, words = "hey", "you") /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:360: WARNING: Unknown directive type "code-black". .. code-black:: R hello[1:5, 2] hello$letters[1:5] /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:451: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 8 supplied. .. code-block:: R p <- subset(cats, cats$weight <= 3) p q <- cats[cats$weight <= 3,] q cats$likes_string == 1 cats[cats$likes_string == TRUE,] cats[c(1,3),] cats[colnames(cats) == "weight"] cats[cats$weight >= 2 & cats$weight <= 5] cats[cats$likes_string != 0,] #not equal to cats[!(is.na(cats$weight))] #is not /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:490: WARNING: Missing matching underline for section title overline. -------------- **Fix or improve this documentation:** - On Github: |Github Repo Link| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:494: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:496: WARNING: Error in "image" directive: no content permitted. image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:496: WARNING: Substitution definition "R Console" empty or invalid. .. |R Console| image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:55: WARNING: Undefined substitution referenced: "R Console". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:128: WARNING: Content block expected for the "admonition" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:508: WARNING: Content block expected for the "hint" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:941: WARNING: Missing matching underline for section title overline. ------------- **Fix or improve this documentation:** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:946: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:820: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:18: WARNING: Title underline too short. *Some things to remember* ------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:33: WARNING: Title underline too short. *Other popular alternatives* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:33: WARNING: Title underline too short. *Other popular alternatives* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:57: WARNING: Block quote ends without a blank line; unexpected unindent. cyverse_rst_defined_substitutions.txt:122: WARNING: image file not readable: software_essentials/./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Title underline too short. **Continuous Integration** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:29: WARNING: Title underline too short. **Travis CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:47: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:47: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:54: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:82: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:82: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:18: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:35: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "mint". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:28: WARNING: Title underline too short. **Git ready** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:38: WARNING: Title underline too short. **Command line versus User Interfaces** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:47: WARNING: Title underline too short. **Git cheat sheet** ~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:47: WARNING: Title underline too short. **Git cheat sheet** ~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:92: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:70: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 7 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Basic Snapshots - Command - Description * - - ``git status`` - Check status of the repository * - - ``git add [file-name.txt]`` - Add a file to "the staging area" * - - ``git add -A`` - Add all new and changed files to "the staging area" * - - ``git commit -m "[brief commit message]"`` - Commit changes to "the staging area" * - - ``git rm -r [file-name.txt]`` - Remove a file (or folder) * - -`git push` - Push changes to remote repository (remembered branch) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:215: WARNING: Title underline too short. **Your first Repository** ~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:230: WARNING: Title underline too short. **Issue Tracking** ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:230: WARNING: Title underline too short. **Issue Tracking** ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:207: WARNING: Unknown target name: "travis". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:24: WARNING: Title underline too short. *Some things to remember* ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:27: WARNING: Title underline too short. *ReadTheDocs* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:9: WARNING: Duplicate explicit target name: "github pages". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- looking for now-outdated files... none 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[100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2019-spring/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/biocontainers.rst:181: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:449: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 3 supplied. .. code-block:: bash -v /home/username/your_data_folder:/data:ro /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:578: WARNING: Error in "code-block" directive: 1 argument(s) required, 0 supplied. .. code-block:: $ docker inspect jupytertest /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:417: WARNING: Unknown target name: "see here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:498: WARNING: Duplicate explicit target name: "dockerfile". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:554: WARNING: Duplicate explicit target name: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:591: WARNING: Duplicate explicit target name: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:470: WARNING: Duplicate target name, cannot be used as a unique reference: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:471: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeronatmo.rst:10: WARNING: Title underline too short. Launching a Docker app on Atmosphere --------------------------------- cyverse_rst_defined_substitutions.txt:36: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:21: WARNING: Title underline too short. **Virtual Machines on Atmosphere or Jetstream** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:65: WARNING: The "list-table" directive is empty; content required. .. list-table:: :header-rows: 1 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:9: WARNING: Duplicate explicit target name: "image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:110: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:518: WARNING: Duplicate substitution definition name: "CyVerse_logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:522: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:408: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:511: WARNING: image file not readable: CyVerse/../img/notebook_terminal.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:9: WARNING: Title underline too short. **CyVerse Data Store** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:77: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:77: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:112: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:112: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:10: WARNING: Title underline too short. **Discovery Environment** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:24: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:24: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:55: WARNING: Title underline too short. Analyses Window ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:55: WARNING: Title underline too short. Analyses Window ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:173: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:173: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:204: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:204: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:113: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:164: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:3: WARNING: Undefined substitution referenced: "CyVerse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:3: WARNING: Unknown target name: "cyverse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/vice.rst:66: WARNING: Title underline too short. *Specific instructions for launching VICE applications* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/vice.rst:103: WARNING: Title underline too short. |vice-share-7| ---- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/FAIR.rst:45: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:9: WARNING: Title underline too short. **Data Management Plans (DMP)** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:30: WARNING: Title underline too short. Elements of a good DMP ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:84: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:84: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:9: WARNING: Title underline too short. **Data Management Overview** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:14: WARNING: Title underline too short. Why should you care about data management? ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:68: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:68: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:94: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:163: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:163: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:9: WARNING: Title underline too short. **Before you arrive** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:18: WARNING: Title underline too short. **About FOSS** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:29: WARNING: Title underline too short. **FOSS Camp Goes Green** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:29: WARNING: Title underline too short. **FOSS Camp Goes Green** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:34: WARNING: Title underline too short. **Who should attend?** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:34: WARNING: Title underline too short. **Who should attend?** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:39: WARNING: Title underline too short. **Workshop level** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/agenda.rst:9: WARNING: Duplicate explicit target name: "lesson". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/agenda.rst:288: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/glossary.rst:9: WARNING: Title underline too short. **Glossary & Acronyms** ^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:10: WARNING: Title underline too short. **FOSS 2019 Introduction** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:13: WARNING: Title underline too short. Welcome and staff introductions =========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:26: WARNING: Title overline & underline mismatch. ---- Course Overview ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/open_sci_lab.rst:10: WARNING: Title underline too short. **Open Science Lab** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:2: WARNING: Title overline too short. ***** DEPRECATED: Visit `FOSS-2020 `_ for current pages ***** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:9: WARNING: Title underline too short. CyVerse Learning Institute - Foundational Open Science Skills (FOSS) 2019 ------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:162: WARNING: Undefined substitution referenced: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:42: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:9: WARNING: Title underline too short. **Other Cyberinfrastructure Projects** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:12: WARNING: Title underline too short. **National Groups** ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:42: WARNING: Title underline too short. **National Science Foundation** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:10: WARNING: Title underline too short. **Research Cyberinfrastructure associated with CyVerse** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:17: WARNING: Title underline too short. **XSEDE** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:30: WARNING: Title underline too short. **Jetstream** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:44: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 3 supplied. .. code:: R ```{R, echo=FALSE} ``` ```{bash, echo=FALSE} ``` ```{python, echo=FALSE} ``` 4. Run the code block /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:65: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 2 supplied. .. code:: install.package(c("workflowr","drake"), dependencies=TRUE) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:86: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "CyverseLogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "LearningCenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "cyverselogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "learningcenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:26: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R setwd(path) getwd() #see what working directory you're in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:35: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:39: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:117: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:176: WARNING: Unknown directive type "code-blocl". .. code-blocl:: R #both do the same thing: require("package") #loads dependencies; will give a warning if it is in conflict with another package (e.g., masks) #can overwrite masked functions using "::" (e.g., package::function) library("package") #will give an error if in conflict with other packages or has missing dependencies /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:214: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.character() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:220: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.numeric() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:226: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.integer() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:231: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R as.factor() #creates groupings within dataset /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:306: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R d <- c(d, "a) str(d) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:334: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hi <- data.frame(numbers = 1:26, letters, c("hey", "you")) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:340: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hola <- data.frame(1:26, letters, words = "hey", "you") /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:360: WARNING: Unknown directive type "code-black". .. code-black:: R hello[1:5, 2] hello$letters[1:5] /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:451: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 8 supplied. .. code-block:: R p <- subset(cats, cats$weight <= 3) p q <- cats[cats$weight <= 3,] q cats$likes_string == 1 cats[cats$likes_string == TRUE,] cats[c(1,3),] cats[colnames(cats) == "weight"] cats[cats$weight >= 2 & cats$weight <= 5] cats[cats$likes_string != 0,] #not equal to cats[!(is.na(cats$weight))] #is not /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:490: WARNING: Missing matching underline for section title overline. -------------- **Fix or improve this documentation:** - On Github: |Github Repo Link| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:494: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:496: WARNING: Error in "image" directive: no content permitted. image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:496: WARNING: Substitution definition "R Console" empty or invalid. .. |R Console| image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:55: WARNING: Undefined substitution referenced: "R Console". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:128: WARNING: Content block expected for the "admonition" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:508: WARNING: Content block expected for the "hint" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:941: WARNING: Missing matching underline for section title overline. ------------- **Fix or improve this documentation:** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:946: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:820: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:18: WARNING: Title underline too short. *Some things to remember* ------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:33: WARNING: Title underline too short. *Other popular alternatives* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:33: WARNING: Title underline too short. *Other popular alternatives* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:57: WARNING: Block quote ends without a blank line; unexpected unindent. cyverse_rst_defined_substitutions.txt:122: WARNING: image file not readable: software_essentials/./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Title underline too short. **Continuous Integration** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:29: WARNING: Title underline too short. **Travis CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:47: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:47: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:54: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:82: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:82: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:18: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:35: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "mint". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:28: WARNING: Title underline too short. **Git ready** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:38: WARNING: Title underline too short. **Command line versus User Interfaces** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:47: WARNING: Title underline too short. **Git cheat sheet** ~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:47: WARNING: Title underline too short. **Git cheat sheet** ~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:92: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:70: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 7 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Basic Snapshots - Command - Description * - - ``git status`` - Check status of the repository * - - ``git add [file-name.txt]`` - Add a file to "the staging area" * - - ``git add -A`` - Add all new and changed files to "the staging area" * - - ``git commit -m "[brief commit message]"`` - Commit changes to "the staging area" * - - ``git rm -r [file-name.txt]`` - Remove a file (or folder) * - -`git push` - Push changes to remote repository (remembered branch) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:215: WARNING: Title underline too short. **Your first Repository** ~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:230: WARNING: Title underline too short. **Issue Tracking** ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:230: WARNING: Title underline too short. **Issue Tracking** ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:207: WARNING: Unknown target name: "travis". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:24: WARNING: Title underline too short. *Some things to remember* ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:27: WARNING: Title underline too short. *ReadTheDocs* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:9: WARNING: Duplicate explicit target name: "github pages". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerhandson.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/example_directives_delete.rst: WARNING: 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[100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2019-spring/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/biocontainers.rst:181: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:449: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 3 supplied. .. code-block:: bash -v /home/username/your_data_folder:/data:ro /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:578: WARNING: Error in "code-block" directive: 1 argument(s) required, 0 supplied. .. code-block:: $ docker inspect jupytertest /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:417: WARNING: Unknown target name: "see here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:498: WARNING: Duplicate explicit target name: "dockerfile". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:554: WARNING: Duplicate explicit target name: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:591: WARNING: Duplicate explicit target name: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:470: WARNING: Duplicate target name, cannot be used as a unique reference: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:471: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeronatmo.rst:10: WARNING: Title underline too short. Launching a Docker app on Atmosphere --------------------------------- cyverse_rst_defined_substitutions.txt:36: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:21: WARNING: Title underline too short. **Virtual Machines on Atmosphere or Jetstream** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:65: WARNING: The "list-table" directive is empty; content required. .. list-table:: :header-rows: 1 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:9: WARNING: Duplicate explicit target name: "image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:110: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:518: WARNING: Duplicate substitution definition name: "CyVerse_logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:522: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:408: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:511: WARNING: image file not readable: CyVerse/../img/notebook_terminal.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:9: WARNING: Title underline too short. **CyVerse Data Store** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:77: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:77: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:112: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:112: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:10: WARNING: Title underline too short. **Discovery Environment** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:24: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:24: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:55: WARNING: Title underline too short. Analyses Window ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:55: WARNING: Title underline too short. Analyses Window ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:173: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:173: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:204: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:204: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:113: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:164: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:3: WARNING: Undefined substitution referenced: "CyVerse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:3: WARNING: Unknown target name: "cyverse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/vice.rst:66: WARNING: Title underline too short. *Specific instructions for launching VICE applications* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/vice.rst:103: WARNING: Title underline too short. |vice-share-7| ---- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/FAIR.rst:45: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:9: WARNING: Title underline too short. **Data Management Plans (DMP)** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:30: WARNING: Title underline too short. Elements of a good DMP ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:84: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:84: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:9: WARNING: Title underline too short. **Data Management Overview** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:14: WARNING: Title underline too short. Why should you care about data management? ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:68: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:68: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:94: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:163: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:163: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:9: WARNING: Title underline too short. **Before you arrive** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:18: WARNING: Title underline too short. **About FOSS** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:29: WARNING: Title underline too short. **FOSS Camp Goes Green** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:29: WARNING: Title underline too short. **FOSS Camp Goes Green** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:34: WARNING: Title underline too short. **Who should attend?** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:34: WARNING: Title underline too short. **Who should attend?** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:39: WARNING: Title underline too short. **Workshop level** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/agenda.rst:9: WARNING: Duplicate explicit target name: "lesson". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/agenda.rst:288: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/glossary.rst:9: WARNING: Title underline too short. **Glossary & Acronyms** ^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:10: WARNING: Title underline too short. **FOSS 2019 Introduction** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:13: WARNING: Title underline too short. Welcome and staff introductions =========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:26: WARNING: Title overline & underline mismatch. ---- Course Overview ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/open_sci_lab.rst:10: WARNING: Title underline too short. **Open Science Lab** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:2: WARNING: Title overline too short. ***** DEPRECATED: Visit `FOSS-2020 `_ for current pages ***** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:9: WARNING: Title underline too short. CyVerse Learning Institute - Foundational Open Science Skills (FOSS) 2019 ------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:162: WARNING: Undefined substitution referenced: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:42: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:9: WARNING: Title underline too short. **Other Cyberinfrastructure Projects** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:12: WARNING: Title underline too short. **National Groups** ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:42: WARNING: Title underline too short. **National Science Foundation** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:10: WARNING: Title underline too short. **Research Cyberinfrastructure associated with CyVerse** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:17: WARNING: Title underline too short. **XSEDE** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:30: WARNING: Title underline too short. **Jetstream** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:44: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 3 supplied. .. code:: R ```{R, echo=FALSE} ``` ```{bash, echo=FALSE} ``` ```{python, echo=FALSE} ``` 4. Run the code block /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:65: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 2 supplied. .. code:: install.package(c("workflowr","drake"), dependencies=TRUE) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:86: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "CyverseLogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "LearningCenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "cyverselogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "learningcenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:26: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R setwd(path) getwd() #see what working directory you're in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:35: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:39: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:117: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:176: WARNING: Unknown directive type "code-blocl". .. code-blocl:: R #both do the same thing: require("package") #loads dependencies; will give a warning if it is in conflict with another package (e.g., masks) #can overwrite masked functions using "::" (e.g., package::function) library("package") #will give an error if in conflict with other packages or has missing dependencies /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:214: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.character() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:220: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.numeric() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:226: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.integer() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:231: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R as.factor() #creates groupings within dataset /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:306: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R d <- c(d, "a) str(d) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:334: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hi <- data.frame(numbers = 1:26, letters, c("hey", "you")) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:340: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hola <- data.frame(1:26, letters, words = "hey", "you") /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:360: WARNING: Unknown directive type "code-black". .. code-black:: R hello[1:5, 2] hello$letters[1:5] /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:451: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 8 supplied. .. code-block:: R p <- subset(cats, cats$weight <= 3) p q <- cats[cats$weight <= 3,] q cats$likes_string == 1 cats[cats$likes_string == TRUE,] cats[c(1,3),] cats[colnames(cats) == "weight"] cats[cats$weight >= 2 & cats$weight <= 5] cats[cats$likes_string != 0,] #not equal to cats[!(is.na(cats$weight))] #is not /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:490: WARNING: Missing matching underline for section title overline. -------------- **Fix or improve this documentation:** - On Github: |Github Repo Link| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:494: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:496: WARNING: Error in "image" directive: no content permitted. image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:496: WARNING: Substitution definition "R Console" empty or invalid. .. |R Console| image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:55: WARNING: Undefined substitution referenced: "R Console". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:128: WARNING: Content block expected for the "admonition" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:508: WARNING: Content block expected for the "hint" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:941: WARNING: Missing matching underline for section title overline. ------------- **Fix or improve this documentation:** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:946: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:820: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:18: WARNING: Title underline too short. *Some things to remember* ------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:33: WARNING: Title underline too short. *Other popular alternatives* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:33: WARNING: Title underline too short. *Other popular alternatives* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:57: WARNING: Block quote ends without a blank line; unexpected unindent. cyverse_rst_defined_substitutions.txt:122: WARNING: image file not readable: software_essentials/./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Title underline too short. **Continuous Integration** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:29: WARNING: Title underline too short. **Travis CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:47: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:47: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:54: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:82: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:82: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:18: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:35: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "mint". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:28: WARNING: Title underline too short. **Git ready** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:38: WARNING: Title underline too short. **Command line versus User Interfaces** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:47: WARNING: Title underline too short. **Git cheat sheet** ~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:47: WARNING: Title underline too short. **Git cheat sheet** ~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:92: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:70: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 7 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Basic Snapshots - Command - Description * - - ``git status`` - Check status of the repository * - - ``git add [file-name.txt]`` - Add a file to "the staging area" * - - ``git add -A`` - Add all new and changed files to "the staging area" * - - ``git commit -m "[brief commit message]"`` - Commit changes to "the staging area" * - - ``git rm -r [file-name.txt]`` - Remove a file (or folder) * - -`git push` - Push changes to remote repository (remembered branch) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:215: WARNING: Title underline too short. **Your first Repository** ~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:230: WARNING: Title underline too short. **Issue Tracking** ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:230: WARNING: Title underline too short. **Issue Tracking** ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:207: WARNING: Unknown target name: "travis". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:24: WARNING: Title underline too short. *Some things to remember* ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:27: WARNING: Title underline too short. *ReadTheDocs* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:9: WARNING: Duplicate explicit target name: "github pages". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- looking for now-outdated files... none 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[3] [4] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5 <./cyverse_cmyk3. png> <./homeicon3.png>] [6 <./cyverse_globe_cmyk.png> <./Learningcenter_DkBlue1 .png>] Underfull \hbox (badness 5189) in paragraph at lines 2--343 [][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber- [7] [8] [9 <./cyverse_cmyk4.png> <./homeicon5.png>] Overfull \hbox (221.13737pt too wide) in paragraph at lines 495--495 [] Underfull \hbox (badness 10000) in paragraph at lines 495--495 [10] [11] Underfull \hbox (badness 7649) in paragraph at lines 711--712 \T1/ptm/m/n/10 overview of the day's Underfull \hbox (badness 5403) in paragraph at lines 730--731 \T1/ptm/m/n/10 roles (Michael Man-del, Underfull \hbox (badness 6412) in paragraph at lines 737--738 []|\T1/ptm/m/n/10 Lunch break (on your Underfull \hbox (badness 10000) in paragraph at lines 742--743 []|\T1/ptm/m/n/10 Tools for col-lab-o-ra-tion Underfull \hbox (badness 10000) in paragraph at lines 754--755 []|\T1/ptm/m/n/10 Tools for col-lab-o-ra-tion Underfull \hbox (badness 10000) in paragraph at lines 756--758 []|[][]\T1/ptm/m/n/10 Team Com-mu-ni-ca-tion: Underfull \hbox (badness 5787) in paragraph at lines 756--758 \T1/ptm/m/n/10 Slack, Git-ter, Zen-Hub, Underfull \hbox (badness 10000) in paragraph at lines 761--762 []|\T1/ptm/m/n/10 Tools for col-lab-o-ra-tion Underfull \hbox (badness 10000) in paragraph at lines 763--765 \T1/ptm/m/n/10 At-las-sian Con-flu-ence, Underfull \hbox (badness 10000) in paragraph at lines 768--769 []|\T1/ptm/m/n/10 Wrap-up, Dis-cus-sion, Underfull \hbox (badness 10000) in paragraph at lines 794--795 []|\T1/ptm/m/n/10 Introduction to Bash: Underfull \hbox (badness 10000) in paragraph at lines 830--831 []|\T1/ptm/m/n/10 RStudio with Ver-sion Underfull \hbox (badness 10000) in paragraph at lines 837--838 []|\T1/ptm/m/n/10 Wrap-up, Dis-cus-sion, Underfull \hbox (badness 10000) in paragraph at lines 865--866 []|\T1/ptm/m/n/10 Introduction to Cy- Underfull \hbox (badness 10000) in paragraph at lines 901--902 []|\T1/ptm/m/n/10 Introduction to VICE Underfull \hbox (badness 10000) in paragraph at lines 922--924 []|[][]\T1/ptm/m/n/10 Using Cy-Verse At-mo- Underfull \hbox (badness 10000) in paragraph at lines 927--928 []|\T1/ptm/m/n/10 Wrap-up, Dis-cus-sion, [12] Underfull \hbox (badness 10000) in paragraph at lines 991--992 []|\T1/ptm/m/n/10 DMPs con-tin-ued (if Underfull \hbox (badness 10000) in paragraph at lines 1017--1018 []|\T1/ptm/m/n/10 Wrap-up, Dis-cus-sion, Underfull \hbox (badness 5147) in paragraph at lines 1052--1053 []|[][]\T1/ptm/m/n/10 Docker Con-tain-ers Git- Underfull \hbox (badness 10000) in paragraph at lines 1071--1072 []|\T1/ptm/m/n/10 Creating DE apps Underfull \hbox (badness 10000) in paragraph at lines 1080--1082 []|\T1/ptm/m/n/10 Coffee shop closes at Underfull \hbox (badness 10000) in paragraph at lines 1085--1086 []|\T1/ptm/m/n/10 Collaborative ex-er-cise [13] Underfull \hbox (badness 10000) in paragraph at lines 1106--1108 []|\T1/ptm/m/n/10 Everyone briefly de- Underfull \hbox (badness 10000) in paragraph at lines 1111--1112 []|\T1/ptm/m/n/10 Wrap-up, Eval-u-a-tions, [14] [15] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [16] [17] [18 <./cyverse_cmyk6.png> <./homeicon7.png>] [19] Underfull \hbox (badness 10000) in paragraph at lines 1570--1570 []\T1/pcr/m/n/10 git config --global user.name "Cy Underfull \hbox (badness 10000) in paragraph at lines 1570--1570 []\T1/pcr/m/n/10 git config --global user.email Underfull \hbox (badness 10000) in paragraph at lines 1570--1570 []\T1/pcr/m/n/10 git clone ssh://git@github.com/ Underfull \hbox (badness 10000) in paragraph at lines 1657--1657 []\T1/phv/m/n/10 Branch-ing & Underfull \hbox (badness 10000) in paragraph at lines 1657--1657 []\T1/pcr/m/n/10 git push origin --delete [branch Underfull \hbox (badness 10000) in paragraph at lines 1657--1657 []\T1/pcr/m/n/10 git checkout -b [branch name] Underfull \hbox (badness 10000) in paragraph at lines 1657--1657 []\T1/pcr/m/n/10 git merge [source branch] [target [20] Underfull \hbox (badness 10000) in paragraph at lines 1714--1714 []\T1/phv/m/n/10 Shar-ing & Underfull \hbox (badness 10000) in paragraph at lines 1714--1714 \T1/phv/m/n/10 Up-dat-ing Underfull \hbox (badness 10000) in paragraph at lines 1714--1714 []\T1/ptm/m/n/10 Pull changes from re-mote Underfull \hbox (badness 10000) in paragraph at lines 1714--1714 []\T1/pcr/m/n/10 git remote add origin ssh://git@github. 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[153] [154] Chapter 4. [155] [156] Chapter 5. No file cyverse-foss.ind. [157 <./intercom.png>] (./cyverse-foss.aux) Package rerunfilecheck Warning: File `cyverse-foss.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}{/usr/share/texmf/fonts/enc/dvips/cm-super/cm-s uper-ts1.enc}< /usr/share/texmf/fonts/type1/public/cm-super/sfbx1000.pfb> Output written on cyverse-foss.pdf (161 pages, 10803457 bytes). Transcript written on cyverse-foss.log. Latexmk: Index file 'cyverse-foss.idx' was written Latexmk: Missing input file: '{software_essentials/./img/intercom}.png' from line 'LaTeX Warning: File `{software_essentials/./img/intercom}.png' not found on inp' Latexmk: Missing input file: '{software_essentials/./img/intercom}.png' from line 'LaTeX Warning: File `{software_essentials/./img/intercom}.png' not found on input line 1999.' Latexmk: Missing input file: '{CyVerse/../img/notebook_terminal}.png' from line 'LaTeX Warning: File `{CyVerse/../img/notebook_terminal}.png' not found on input' Latexmk: Missing input file: '{CyVerse/../img/notebook_terminal}.png' from line 'LaTeX Warning: File `{CyVerse/../img/notebook_terminal}.png' not found on input line 5313.' Latexmk: Missing input file: 'cyverse-foss.ind' from line 'No file cyverse-foss.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-foss.pdf' Rule 'makeindex cyverse-foss.idx': File changes, etc: Non-existent destination files: 'cyverse-foss.ind' ------------ Run number 1 of rule 'makeindex cyverse-foss.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-foss.ind" "cyverse-foss.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-foss.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-foss.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-foss.ind. Transcript written in cyverse-foss.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-foss.aux' 'cyverse-foss.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-foss" "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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[153] [154] Chapter 4. [155] [156] Chapter 5. (./cyverse-foss.ind) [157 <./intercom.png>] (./cyverse-foss.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips/cm-super/cm-s uper-ts1.enc}< /usr/share/texmf/fonts/type1/public/cm-super/sfbx1000.pfb> Output written on cyverse-foss.pdf (161 pages, 10805644 bytes). Transcript written on cyverse-foss.log. Latexmk: Index file 'cyverse-foss.idx' was written Latexmk: Missing input file: '{software_essentials/./img/intercom}.png' from line 'LaTeX Warning: File `{software_essentials/./img/intercom}.png' not found on inp' Latexmk: Missing input file: '{software_essentials/./img/intercom}.png' from line 'LaTeX Warning: File `{software_essentials/./img/intercom}.png' not found on input line 1999.' Latexmk: Missing input file: '{CyVerse/../img/notebook_terminal}.png' from line 'LaTeX Warning: File `{CyVerse/../img/notebook_terminal}.png' not found on input' Latexmk: Missing input file: '{CyVerse/../img/notebook_terminal}.png' from line 'LaTeX Warning: File `{CyVerse/../img/notebook_terminal}.png' not found on input line 5313.' Latexmk: Log file says output to 'cyverse-foss.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-foss.out' 'cyverse-foss.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-foss" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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[153] [154] Chapter 4. [155] [156] Chapter 5. (./cyverse-foss.ind) [157 <./intercom.png>] (./cyverse-foss.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips/cm-super/cm-s uper-ts1.enc}< /usr/share/texmf/fonts/type1/public/cm-super/sfbx1000.pfb> Output written on cyverse-foss.pdf (161 pages, 10805644 bytes). Transcript written on cyverse-foss.log. Latexmk: Index file 'cyverse-foss.idx' was written Latexmk: Missing input file: '{software_essentials/./img/intercom}.png' from line 'LaTeX Warning: File `{software_essentials/./img/intercom}.png' not found on inp' Latexmk: Missing input file: '{software_essentials/./img/intercom}.png' from line 'LaTeX Warning: File `{software_essentials/./img/intercom}.png' not found on input line 1999.' 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Latexmk: Log file says output to 'cyverse-foss.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2021-01-15T04:18:25.231847Z, end-time: 2021-01-15T04:18:25.287855Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/./_build/latex/cyverse-foss.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/artifacts/foss-2019-spring/sphinx_pdf/cyverse-foss.pdf [rtd-command-info] start-time: 2021-01-15T04:18:25.396949Z, end-time: 2021-01-15T04:18:32.946529Z, duration: 7, 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 41 source files that are out of date updating environment: 41 added, 0 changed, 0 removed reading sources... 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[100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2019-spring/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/biocontainers.rst:181: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:449: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 3 supplied. .. code-block:: bash -v /home/username/your_data_folder:/data:ro /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:578: WARNING: Error in "code-block" directive: 1 argument(s) required, 0 supplied. .. code-block:: $ docker inspect jupytertest /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeradvanced.rst:417: WARNING: Unknown target name: "see here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:498: WARNING: Duplicate explicit target name: "dockerfile". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:554: WARNING: Duplicate explicit target name: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:591: WARNING: Duplicate explicit target name: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:470: WARNING: Duplicate target name, cannot be used as a unique reference: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockerintro.rst:471: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Containers/dockeronatmo.rst:10: WARNING: Title underline too short. Launching a Docker app on Atmosphere --------------------------------- cyverse_rst_defined_substitutions.txt:36: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:21: WARNING: Title underline too short. **Virtual Machines on Atmosphere or Jetstream** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:65: WARNING: The "list-table" directive is empty; content required. .. list-table:: :header-rows: 1 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:9: WARNING: Duplicate explicit target name: "image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:110: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:518: WARNING: Duplicate substitution definition name: "CyVerse_logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:522: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:408: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/atmo.rst:511: WARNING: image file not readable: CyVerse/../img/notebook_terminal.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:9: WARNING: Title underline too short. **CyVerse Data Store** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:77: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:77: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:112: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/data_store.rst:112: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:10: WARNING: Title underline too short. **Discovery Environment** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:24: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:24: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:55: WARNING: Title underline too short. Analyses Window ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/de.rst:55: WARNING: Title underline too short. Analyses Window ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:173: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:173: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:204: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/intro_to_cyverse.rst:204: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:113: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:164: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:3: WARNING: Undefined substitution referenced: "CyVerse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/tool_integration_app_building_DE.rst:3: WARNING: Unknown target name: "cyverse". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/vice.rst:66: WARNING: Title underline too short. *Specific instructions for launching VICE applications* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/CyVerse/vice.rst:103: WARNING: Title underline too short. |vice-share-7| ---- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/FAIR.rst:45: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:9: WARNING: Title underline too short. **Data Management Plans (DMP)** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:30: WARNING: Title underline too short. Elements of a good DMP ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:84: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/dmp.rst:84: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:9: WARNING: Title underline too short. **Data Management Overview** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:14: WARNING: Title underline too short. Why should you care about data management? ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:68: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:68: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:94: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:163: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/Data_management/overview.rst:163: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:9: WARNING: Title underline too short. **Before you arrive** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:18: WARNING: Title underline too short. **About FOSS** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:29: WARNING: Title underline too short. **FOSS Camp Goes Green** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:29: WARNING: Title underline too short. **FOSS Camp Goes Green** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:34: WARNING: Title underline too short. **Who should attend?** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:34: WARNING: Title underline too short. **Who should attend?** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/before/main.rst:39: WARNING: Title underline too short. **Workshop level** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/agenda.rst:9: WARNING: Duplicate explicit target name: "lesson". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/agenda.rst:288: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/glossary.rst:9: WARNING: Title underline too short. **Glossary & Acronyms** ^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:10: WARNING: Title underline too short. **FOSS 2019 Introduction** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:13: WARNING: Title underline too short. Welcome and staff introductions =========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/intro.rst:26: WARNING: Title overline & underline mismatch. ---- Course Overview ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/getting_started/open_sci_lab.rst:10: WARNING: Title underline too short. **Open Science Lab** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:2: WARNING: Title overline too short. ***** DEPRECATED: Visit `FOSS-2020 `_ for current pages ***** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:9: WARNING: Title underline too short. CyVerse Learning Institute - Foundational Open Science Skills (FOSS) 2019 ------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:162: WARNING: Undefined substitution referenced: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/index.rst:42: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:9: WARNING: Title underline too short. **Other Cyberinfrastructure Projects** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:12: WARNING: Title underline too short. **National Groups** ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:42: WARNING: Title underline too short. **National Science Foundation** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:10: WARNING: Title underline too short. **Research Cyberinfrastructure associated with CyVerse** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:17: WARNING: Title underline too short. **XSEDE** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:30: WARNING: Title underline too short. **Jetstream** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/moving_on/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:44: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 3 supplied. .. code:: R ```{R, echo=FALSE} ``` ```{bash, echo=FALSE} ``` ```{python, echo=FALSE} ``` 4. Run the code block /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:65: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 2 supplied. .. code:: install.package(c("workflowr","drake"), dependencies=TRUE) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:86: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "CyverseLogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "LearningCenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "cyverselogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "learningcenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:26: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R setwd(path) getwd() #see what working directory you're in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:35: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:39: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:117: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:176: WARNING: Unknown directive type "code-blocl". .. code-blocl:: R #both do the same thing: require("package") #loads dependencies; will give a warning if it is in conflict with another package (e.g., masks) #can overwrite masked functions using "::" (e.g., package::function) library("package") #will give an error if in conflict with other packages or has missing dependencies /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:214: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.character() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:220: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.numeric() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:226: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.integer() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:231: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R as.factor() #creates groupings within dataset /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:306: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R d <- c(d, "a) str(d) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:334: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hi <- data.frame(numbers = 1:26, letters, c("hey", "you")) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:340: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hola <- data.frame(1:26, letters, words = "hey", "you") /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:360: WARNING: Unknown directive type "code-black". .. code-black:: R hello[1:5, 2] hello$letters[1:5] /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:451: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 8 supplied. .. code-block:: R p <- subset(cats, cats$weight <= 3) p q <- cats[cats$weight <= 3,] q cats$likes_string == 1 cats[cats$likes_string == TRUE,] cats[c(1,3),] cats[colnames(cats) == "weight"] cats[cats$weight >= 2 & cats$weight <= 5] cats[cats$likes_string != 0,] #not equal to cats[!(is.na(cats$weight))] #is not /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:490: WARNING: Missing matching underline for section title overline. -------------- **Fix or improve this documentation:** - On Github: |Github Repo Link| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:494: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:496: WARNING: Error in "image" directive: no content permitted. image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:496: WARNING: Substitution definition "R Console" empty or invalid. .. |R Console| image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/R_Studio.rst:55: WARNING: Undefined substitution referenced: "R Console". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:128: WARNING: Content block expected for the "admonition" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:508: WARNING: Content block expected for the "hint" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:941: WARNING: Missing matching underline for section title overline. ------------- **Fix or improve this documentation:** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:946: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/commandline.rst:820: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:18: WARNING: Title underline too short. *Some things to remember* ------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:33: WARNING: Title underline too short. *Other popular alternatives* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:33: WARNING: Title underline too short. *Other popular alternatives* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/communication.rst:57: WARNING: Block quote ends without a blank line; unexpected unindent. cyverse_rst_defined_substitutions.txt:122: WARNING: image file not readable: software_essentials/./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Title underline too short. **Continuous Integration** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:29: WARNING: Title underline too short. **Travis CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:47: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:47: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:54: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:82: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/continuous_integration.rst:82: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:18: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:35: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "mint". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:28: WARNING: Title underline too short. **Git ready** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:38: WARNING: Title underline too short. **Command line versus User Interfaces** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:47: WARNING: Title underline too short. **Git cheat sheet** ~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:47: WARNING: Title underline too short. **Git cheat sheet** ~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:92: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:70: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 7 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Basic Snapshots - Command - Description * - - ``git status`` - Check status of the repository * - - ``git add [file-name.txt]`` - Add a file to "the staging area" * - - ``git add -A`` - Add all new and changed files to "the staging area" * - - ``git commit -m "[brief commit message]"`` - Commit changes to "the staging area" * - - ``git rm -r [file-name.txt]`` - Remove a file (or folder) * - -`git push` - Push changes to remote repository (remembered branch) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:215: WARNING: Title underline too short. **Your first Repository** ~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:230: WARNING: Title underline too short. **Issue Tracking** ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:230: WARNING: Title underline too short. **Issue Tracking** ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/version_control.rst:207: WARNING: Unknown target name: "travis". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:24: WARNING: Title underline too short. *Some things to remember* ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:27: WARNING: Title underline too short. *ReadTheDocs* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:9: WARNING: Duplicate explicit target name: "github pages". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2019-spring/software_essentials/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- looking for now-outdated files... none 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