Read the Docs build information Build id: 425726 Project: cyverse-de-tool-integration-quickstart Version: latest Commit: a23a7a35ec972d307b2feafa94d37fabe4aeb575 Date: 2020-09-18T16:10:47.786387Z State: finished Success: True [rtd-command-info] start-time: 2020-09-18T16:10:49.996985Z, end-time: 2020-09-18T16:10:50.745881Z, duration: 0, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/DE-tool-integration-quickstart.git . Cloning into '.'... [rtd-command-info] start-time: 2020-09-18T16:10:51.539066Z, end-time: 2020-09-18T16:10:51.622829Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at a23a7a3 add triage issue template [rtd-command-info] start-time: 2020-09-18T16:10:52.212165Z, end-time: 2020-09-18T16:10:52.268972Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-09-18T16:10:54.410625Z, end-time: 2020-09-18T16:10:58.323765Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv 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 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-09-18T16:10:58.895359Z, end-time: 2020-09-18T16:10:59.579053Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 (20.2.3) [rtd-command-info] start-time: 2020-09-18T16:11:00.163717Z, end-time: 2020-09-18T16:11:08.736090Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 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.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 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 Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.10-py2.py3-none-any.whl (127 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 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=23754 sha256=877b16e128585abd9c88304bd15af037bcb505d954922edccaadc85a4fdc8291 Stored in directory: /tmp/pip-ephem-wheel-cache-9t1sg0rp/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b 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=25e8d5304ef83bc5804539eaa14a14f7d981f4f0fd3cc1b6285f9953189148ee Stored in directory: /tmp/pip-ephem-wheel-cache-9t1sg0rp/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, MarkupSafe, Jinja2, pytz, babel, six, certifi, urllib3, idna, chardet, requests, pyparsing, packaging, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, snowballstemmer, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 50.3.0 Uninstalling setuptools-50.3.0: Successfully uninstalled setuptools-50.3.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 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 urllib3-1.25.10 [rtd-command-info] start-time: 2020-09-18T16:11:10.214441Z, end-time: 2020-09-18T16:11:10.289664Z, 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 = '2020, 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://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//cyverse-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': 'UA-72224033-6', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'proxied_api_host': '/_', '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, 'docsearch_disabled': False, 'user_analytics_code': 'UA-72224033-6', 'global_analytics_code': 'UA-17997319-2', 'commit': 'a23a7a35', } 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: 2020-09-18T16:11:10.565246Z, end-time: 2020-09-18T16:11:11.859994Z, duration: 1, 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 8 source files that are out of date updating environment: 8 added, 0 changed, 0 removed reading sources... 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FYI:: **What is the OpenScienceGrid?** A national, distributed computing partnership for data-intensive research **What is an OSG Tool?** Any software/tool that can be run in the command line interface without the need to open ports /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: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". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png 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/.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-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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FYI:: **What is the OpenScienceGrid?** A national, distributed computing partnership for data-intensive research **What is an OSG Tool?** Any software/tool that can be run in the command line interface without the need to open ports /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: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". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png 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/.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-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: 2020-09-18T16:11:13.901403Z, end-time: 2020-09-18T16:11:15.010764Z, 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... building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 8 added, 0 changed, 0 removed reading sources... [ 12%] .github/ISSUE_TEMPLATE/triage-for-2-0-release reading sources... [ 25%] Contributors_maintainers reading sources... [ 37%] License reading sources... [ 50%] example_directives_delete reading sources... [ 62%] index reading sources... [ 75%] interactive reading sources... [ 87%] 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/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png /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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png /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". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:16: WARNING: Unknown directive type "FYI". .. FYI:: **What is the OpenScienceGrid?** A national, distributed computing partnership for data-intensive research **What is an OSG Tool?** Any software/tool that can be run in the command line interface without the need to open ports /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: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". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png 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/.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-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... 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' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2020-09-18T16:11:17.168217Z, end-time: 2020-09-18T16:11:20.340850Z, duration: 3, 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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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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Package pdftex.def Error: File `./img/cyverse_learning.png' not found: using draft setting. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.82 ...inxpxdimen]{{./img/cyverse_learning}.png}} ^^M (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) LaTeX Warning: File `{./img/cyverse_learning}.png' not found on input line 2. ! Package pdftex.def Error: File `./img/cyverse_learning.png' not found: using draft setting. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.91 ...inxpxdimen]{{./img/cyverse_learning}.png}} ^^M [1 <./homeicon.png>] [2] Chapter 1. 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Type H for immediate help. ... l.593 ...nxpxdimen]{{./img/cyverse_learning}.png}} ^^M [9 <./add_tool_form_osg.png> <./intercom.png>] [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 1003 [19] (./cyverse-de-tool-integration-quickstart.ind) [20 <./add_tool_form.png>] [21] (./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 (25 pages, 450759 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: '{./img/cyverse_learning}.png' from line 'LaTeX Warning: File `{./img/cyverse_learning}.png' not found on input line 2.' Latexmk: Missing input file: '{./img/cyverse_learning}.png' from line 'LaTeX Warning: File `{./img/cyverse_learning}.png' not found on input line 2.' Latexmk: Missing input file: '{./img/cyverse_learning}.png' from line 'LaTeX Warning: File `{./img/cyverse_learning}.png' not found on input line 2.' 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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Latexmk: Log file says output to 'cyverse-de-tool-integration-quickstart.pdf' Latexmk: Log file says output to 'cyverse-de-tool-integration-quickstart.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: 2020-09-18T16:11:20.537289Z, end-time: 2020-09-18T16:11:20.593621Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/./_build/latex/cyverse-de-tool-integration-quickstart.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/artifacts/latest/sphinx_pdf/cyverse-de-tool-integration-quickstart.pdf [rtd-command-info] start-time: 2020-09-18T16:11:20.999057Z, end-time: 2020-09-18T16:11:22.220121Z, duration: 1, 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 8 source files that are out of date updating environment: 8 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/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png /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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png /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". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de-tool-integration-quickstart/checkouts/latest/osg.rst:16: WARNING: Unknown directive type "FYI". .. FYI:: **What is the OpenScienceGrid?** A national, distributed computing partnership for data-intensive research **What is an OSG Tool?** Any software/tool that can be run in the command line interface without the need to open ports /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: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". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png 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/.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-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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