Read the Docs build information Build id: 285348 Project: cyverse-de-tool-integration-quickstart Version: latest Commit: 31c6a1959ccd6d6e77d06f8c966d7c6d1fff8169 Date: 2020-02-06T17:46:21.689352Z State: finished Success: True [rtd-command-info] start-time: 2020-02-06T17:46:24.472748Z, end-time: 2020-02-06T17:46:24.984194Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/DE-tool-integration-quickstart.git [rtd-command-info] start-time: 2020-02-06T17:46:25.133417Z, end-time: 2020-02-06T17:46:26.818417Z, duration: 1, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/CyVerse-learning-materials/DE-tool-integration-quickstart 90e0b47..31c6a19 master -> origin/master [rtd-command-info] start-time: 2020-02-06T17:46:27.097410Z, end-time: 2020-02-06T17:46:27.457833Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 90e0b47 removed -u option from dicker test run HEAD is now at 31c6a19 Update osg.rst [rtd-command-info] start-time: 2020-02-06T17:46:27.554010Z, end-time: 2020-02-06T17:46:27.872868Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-02-06T17:46:29.537393Z, end-time: 2020-02-06T17:46:35.272148Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv --no-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/bin/python3.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/bin/python3.7) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-02-06T17:46:35.339833Z, end-time: 2020-02-06T17:46:36.337391Z, duration: 0, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (20.0.2) [rtd-command-info] start-time: 2020-02-06T17:46:36.400384Z, end-time: 2020-02-06T17:46:39.950408Z, duration: 3, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (2.3.1) Collecting setuptools==41.0.1 Using cached setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (0.14) Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (1.0.1) Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (5.4.1) Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (0.7.12) Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (0.8.1) Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (0.5.0) Requirement already up-to-date: sphinx<2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (1.8.5) Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (0.4.3) Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (1.0.1) Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from commonmark==0.8.1) (0.18.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.8.0) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.2.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.11.1) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (20.1) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.14.0) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2.8) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2019.11.28) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (1.25.8) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/lib/python3.7/site-packages (from packaging->sphinx<2) (2.4.6) Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 45.1.0 Uninstalling setuptools-45.1.0: Successfully uninstalled setuptools-45.1.0 Successfully installed setuptools-41.0.1 [rtd-command-info] start-time: 2020-02-06T17:46:40.734061Z, end-time: 2020-02-06T17:46:41.132684Z, duration: 0, exit-code: 0 cat conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # General information about the project. import sys import os sys.path.insert(0, os.path.dirname(__file__)) from misc.cyverse_sphinx_conf import * # noqa project = 'DE-tool-integration' copyright = '2019, CyVerse' author = 'Your Name' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # 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://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//cyverse-de-tool-integration-quickstart.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//cyverse-de-tool-integration-quickstart.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//cyverse-de-tool-integration-quickstart.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'cyverse-de-tool-integration-quickstart', 'name': u'DE-tool-integration-quickstart', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-de-tool-integration-quickstart.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'proxied_api_host': '/_', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'DE-tool-integration-quickstart', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '31c6a195', } 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' [rtd-command-info] start-time: 2020-02-06T17:46:41.206522Z, end-time: 2020-02-06T17:46:45.710404Z, duration: 4, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 7 source files that are out of date updating environment: 7 added, 0 changed, 0 removed reading sources... 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[100%] slides/README /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/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-de-tool-integration-quickstart/checkouts/latest/index.rst:94: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/index.rst:170: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/interactive.rst:94: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/interactive.rst:9: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:25: WARNING: Title underline too short. **Prerequisites** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:25: WARNING: Title underline too short. **Prerequisites** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:47: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:33: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 4 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Prerequisite - Preparation/Notes - Link/Download * - CyVerse account - You will need a CyVerse account to complete this exercise - |CyVerse User Portal| * - Atmosphere Access (Optional -- for building containers remotely) - Atmosphere access is by request only - Check or request access: `CyVerse User Portal `_ * - Installation of Docker - `Docker `_ on the machine you're building containers - `Atmosphere Installation instructions `_ * - Installation of Singularity - `Singularity `_ on the machine you're building containers - `Atmosphere Installation instructions `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:60: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 3 does not contain the same number of items as row 1 (4 vs 5). .. list-table:: :header-rows: 1 * - Platform - Interface - Link - Platform Documentation - Quick Start * - Discovery Environment - Web/Point-and-click - |Discovery Environment| - |DE Manual| - |Discovery Environment Guide| * - Atmosphere - Cloud Virtual Machine - |Atmosphere| - |Atmosphere Manual| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:9: WARNING: Duplicate explicit target name: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:9: WARNING: Duplicate explicit target name: "here". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/example_directives_delete.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/slides/README.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/_static' does not exist done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 16 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2020-02-06T17:46:45.810055Z, end-time: 2020-02-06T17:46:47.989089Z, duration: 2, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 7 added, 0 changed, 0 removed reading sources... 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[100%] slides/README /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/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-de-tool-integration-quickstart/checkouts/latest/index.rst:94: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/index.rst:170: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/interactive.rst:94: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/interactive.rst:9: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:25: WARNING: Title underline too short. **Prerequisites** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:25: WARNING: Title underline too short. **Prerequisites** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:47: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:33: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 4 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Prerequisite - Preparation/Notes - Link/Download * - CyVerse account - You will need a CyVerse account to complete this exercise - |CyVerse User Portal| * - Atmosphere Access (Optional -- for building containers remotely) - Atmosphere access is by request only - Check or request access: `CyVerse User Portal `_ * - Installation of Docker - `Docker `_ on the machine you're building containers - `Atmosphere Installation instructions `_ * - Installation of Singularity - `Singularity `_ on the machine you're building containers - `Atmosphere Installation instructions `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:60: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 3 does not contain the same number of items as row 1 (4 vs 5). .. list-table:: :header-rows: 1 * - Platform - Interface - Link - Platform Documentation - Quick Start * - Discovery Environment - Web/Point-and-click - |Discovery Environment| - |DE Manual| - |Discovery Environment Guide| * - Atmosphere - Cloud Virtual Machine - |Atmosphere| - |Atmosphere Manual| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:9: WARNING: Duplicate explicit target name: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:9: WARNING: Duplicate explicit target name: "here". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/example_directives_delete.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/slides/README.md: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... osg interactive writing... done writing additional files... copying images... 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[rtd-command-info] start-time: 2020-02-06T17:46:48.120985Z, end-time: 2020-02-06T17:46:49.777749Z, duration: 1, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 7 added, 0 changed, 0 removed reading sources... [ 14%] Contributors_maintainers reading sources... [ 28%] License reading sources... [ 42%] example_directives_delete reading sources... [ 57%] index reading sources... [ 71%] interactive reading sources... [ 85%] osg reading sources... [100%] slides/README /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/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-de-tool-integration-quickstart/checkouts/latest/index.rst:94: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/index.rst:170: WARNING: Title level inconsistent: Additional information, help ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/interactive.rst:94: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/interactive.rst:9: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:25: WARNING: Title underline too short. **Prerequisites** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:25: WARNING: Title underline too short. **Prerequisites** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:47: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:33: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 4 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Prerequisite - Preparation/Notes - Link/Download * - CyVerse account - You will need a CyVerse account to complete this exercise - |CyVerse User Portal| * - Atmosphere Access (Optional -- for building containers remotely) - Atmosphere access is by request only - Check or request access: `CyVerse User Portal `_ * - Installation of Docker - `Docker `_ on the machine you're building containers - `Atmosphere Installation instructions `_ * - Installation of Singularity - `Singularity `_ on the machine you're building containers - `Atmosphere Installation instructions `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:60: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 3 does not contain the same number of items as row 1 (4 vs 5). .. list-table:: :header-rows: 1 * - Platform - Interface - Link - Platform Documentation - Quick Start * - Discovery Environment - Web/Point-and-click - |Discovery Environment| - |DE Manual| - |Discovery Environment Guide| * - Atmosphere - Cloud Virtual Machine - |Atmosphere| - |Atmosphere Manual| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:9: WARNING: Duplicate explicit target name: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:9: WARNING: Duplicate explicit target name: "here". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/example_directives_delete.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/slides/README.md: WARNING: document isn't included in any toctree done processing CyVerseDocumentation.tex...index osg interactive resolving references... writing... done copying images... [ 14%] ./img/cyverse_rgb.png copying images... [ 28%] ./img/homeicon.png copying images... [ 42%] img/add_tool_form_osg_cvmfs.png copying images... [ 57%] img/add_tool_form_osg.png copying images... [ 71%] img/add_tool_interactive_1.png copying images... [ 85%] img/add_tool_interactive_2.png copying images... [100%] img/add_tool_form.png copying TeX support files... done build succeeded, 15 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2020-02-06T17:46:52.906376Z, end-time: 2020-02-06T17:46:53.231655Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2020-02-06T17:46:53.291657Z, end-time: 2020-02-06T17:46:58.100939Z, duration: 4, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-de-tool-integration-quickstart -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. 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[3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [4] Underfull \hbox (badness 6125) in paragraph at lines 276--277 \T1/ptm/m/n/10 s-tore \T1/ptm/m/it/10 /iplant/home/upendra_35/fastq-sample-osg/ Read1.fastq \T1/ptm/m/n/10 and out-put folder in this path on Data-s-tore [5] [6] [7] [8 <./add_tool_form_osg_cvmfs.png> <./add_tool_form_osg.png>] [9] [10] Chapter 2. [11] [12] [13 <./add_tool_interactive_1.png> <./add_tool_interactive_2.png>] [14] Chapter 3. [15] [16] Chapter 4. [17] [18] Chapter 5. Overfull \vbox (1.72581pt too high) detected at line 853 [19] No file cyverse-de-tool-integration-quickstart.ind. [20 <./add_tool_form.png>] (./cyverse-de-tool-integration-quickstart.aux) Package rerunfilecheck Warning: File `cyverse-de-tool-integration-quickstart.ou t' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-de-tool-integration-quickstart.pdf (24 pages, 481546 bytes). Transcript written on cyverse-de-tool-integration-quickstart.log. Latexmk: Index file 'cyverse-de-tool-integration-quickstart.idx' was written Latexmk: Missing input file: 'cyverse-de-tool-integration-quickstart.ind' from line 'No file cyverse-de-tool-integration-quickstart.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-de-tool-integration-quickstart.pdf' Latexmk: Log file says output to 'cyverse-de-tool-integration-quickstart.pdf' Rule 'makeindex cyverse-de-tool-integration-quickstart.idx': File changes, etc: Non-existent destination files: 'cyverse-de-tool-integration-quickstart.ind' ------------ Run number 1 of rule 'makeindex cyverse-de-tool-integration-quickstart.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-de-tool-integration-quickstart.ind" "cyverse-de-tool-integration-quickstart.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-de-tool-integration-quickstart.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-de-tool-integration-quickstart.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-de-tool-integration-quickstart.ind. 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(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty 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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./cyverse-de-tool-integration-quickstart.out) (./cyverse-de-tool-integration-quickstart.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./cyverse-de-tool-integration-quickstart.toc) [1] [2] [1 <./cyverse_rgb.png> < ./homeicon.png>] [2] Chapter 1. [3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [4] Underfull \hbox (badness 6125) in paragraph at lines 276--277 \T1/ptm/m/n/10 s-tore \T1/ptm/m/it/10 /iplant/home/upendra_35/fastq-sample-osg/ Read1.fastq \T1/ptm/m/n/10 and out-put folder in this path on Data-s-tore [5] [6] [7] [8 <./add_tool_form_osg_cvmfs.png> <./add_tool_form_osg.png>] [9] [10] Chapter 2. [11] [12] [13 <./add_tool_interactive_1.png> <./add_tool_interactive_2.png>] [14] Chapter 3. [15] [16] Chapter 4. [17] [18] Chapter 5. Overfull \vbox (1.72581pt too high) detected at line 853 [19] (./cyverse-de-tool-integration-quickstart.ind) [20 <./add_tool_form.png>] (./cyverse-de-tool-integration-quickstart.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-de-tool-integration-quickstart.pdf (24 pages, 484573 bytes). Transcript written on cyverse-de-tool-integration-quickstart.log. Latexmk: Index file 'cyverse-de-tool-integration-quickstart.idx' was written Latexmk: Log file says output to 'cyverse-de-tool-integration-quickstart.pdf' Latexmk: Log file says output to 'cyverse-de-tool-integration-quickstart.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-de-tool-integration-quickstart.out' 'cyverse-de-tool-integration-quickstart.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-de-tool-integration-quickstart" "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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(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty 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[3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [4] Underfull \hbox (badness 6125) in paragraph at lines 276--277 \T1/ptm/m/n/10 s-tore \T1/ptm/m/it/10 /iplant/home/upendra_35/fastq-sample-osg/ Read1.fastq \T1/ptm/m/n/10 and out-put folder in this path on Data-s-tore [5] [6] [7] [8 <./add_tool_form_osg_cvmfs.png> <./add_tool_form_osg.png>] [9] [10] Chapter 2. [11] [12] [13 <./add_tool_interactive_1.png> <./add_tool_interactive_2.png>] [14] Chapter 3. [15] [16] Chapter 4. [17] [18] Chapter 5. Overfull \vbox (1.72581pt too high) detected at line 853 [19] (./cyverse-de-tool-integration-quickstart.ind) [20 <./add_tool_form.png>] (./cyverse-de-tool-integration-quickstart.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-de-tool-integration-quickstart.pdf (24 pages, 484573 bytes). 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