Read the Docs build information Build id: 254772 Project: cyverse-data-store-quickstart Version: latest Commit: c143664fadc8b013126006d529b91dedc7661fe7 Date: 2019-10-30T18:20:14.506733Z State: finished Success: True [rtd-command-info] start-time: 2019-10-30T18:20:14.955379Z, end-time: 2019-10-30T18:20:14.970230Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/Data-store-quickstart.git [rtd-command-info] start-time: 2019-10-30T18:20:15.070932Z, end-time: 2019-10-30T18:20:15.636287Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/CyVerse-learning-materials/Data-store-quickstart 5f9fbce..c143664 master -> origin/master [rtd-command-info] start-time: 2019-10-30T18:20:15.869268Z, end-time: 2019-10-30T18:20:15.888489Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 5f9fbce Update index.rst HEAD is now at c143664 Update index.rst [rtd-command-info] start-time: 2019-10-30T18:20:15.970101Z, end-time: 2019-10-30T18:20:15.996109Z, duration: 0, exit-code: 0 git clean -d -f -f Removing _build/ Removing misc/__pycache__/ [rtd-command-info] start-time: 2019-10-30T18:20:17.043836Z, end-time: 2019-10-30T18:20:20.309438Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.7.1' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/bin/python3.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/bin/python3.7) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-10-30T18:20:20.402998Z, end-time: 2019-10-30T18:20:21.378751Z, duration: 0, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (19.3.1) [rtd-command-info] start-time: 2019-10-30T18:20:21.487646Z, end-time: 2019-10-30T18:20:23.414091Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-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-data-store-quickstart/envs/latest/lib/python3.7/site-packages (2.3.1) Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (41.0.1) Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-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-data-store-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-data-store-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-data-store-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-data-store-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-data-store-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-data-store-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-data-store-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-data-store-quickstart/envs/latest/lib/python3.7/site-packages (1.0.0) Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from commonmark==0.8.1) (0.18.1) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.7.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.0.0) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (19.2) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.12.0) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.10.3) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from packaging->sphinx<2) (2.4.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2019.9.11) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4) 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-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (1.25.6) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2.8) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1) [rtd-command-info] start-time: 2019-10-30T18:20:24.102110Z, end-time: 2019-10-30T18:20:24.406622Z, 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 = 'YOUR QUICKSTART NAME HERE as topic_quick_start' copyright = '2018, CyVerse' author = 'Your Name' version = '1.0' release = '1.0' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # 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", "//readthedocs.com/projects/cyverse-data-store-quickstart/downloads/pdf/latest/"), ("html", "//readthedocs.com/projects/cyverse-data-store-quickstart/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/cyverse-data-store-quickstart/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-data-store-quickstart', 'name': u'Data-store-quickstart', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-data-store-quickstart.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'Data-store-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': 'c143664f', } 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: 2019-10-30T18:20:24.498286Z, end-time: 2019-10-30T18:20:26.329505Z, 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 7 source files that are out of date updating environment: 7 added, 0 changed, 0 removed reading sources... [ 14%] Contributors_maintainers reading sources... [ 28%] License reading sources... [ 42%] README reading sources... [ 57%] example_directives_delete reading sources... [ 71%] index reading sources... [ 85%] slides/README reading sources... [100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-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-data-store-quickstart/checkouts/latest/example_directives_delete.rst:169: WARNING: Duplicate substitution definition name: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:9: WARNING: Title underline too short. **Data Store Quickstart** =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:13: WARNING: Title underline too short. Goal: Simple steps to get setup with the CyVerse Data Store ---- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:15: WARNING: Error in "toctree" directive: invalid option block. .. toctree:: :maxdepth: 2 CyVerse Discovery Environment Cyberduck Command Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:28: 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 (2 vs 3). .. 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| * - Computer, web browser, and internet access - To access the Discovery Environment (or the Data Store), you will need these things * - Cyberduck - Standalone software for upload/download to Data Store - |Download Cyberduck| * - i-commands - These are the command line tools to access the data store - | `Mac iCommands Installer 4.1.9 `_ or `Linux binaries and source `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:80: WARNING: Title underline too short. CyVerse Discovery Environment ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:95: WARNING: Enumerated list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:123: WARNING: Malformed table. +------------+------------+ | Parameter | value | +============+============+ | DNA | data.cyverse.org | +------------+------------+ | Port | 1247 | +------------+------------+ | User name | | +------------+------------+ | Zone | iplant | +------------+------------+ | Password | `_ or `Linux binaries and source `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:80: WARNING: Title underline too short. CyVerse Discovery Environment ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:95: WARNING: Enumerated list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:123: WARNING: Malformed table. +------------+------------+ | Parameter | value | +============+============+ | DNA | data.cyverse.org | +------------+------------+ | Port | 1247 | +------------+------------+ | User name | | +------------+------------+ | Zone | iplant | +------------+------------+ | Password | `_ or `Linux binaries and source `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:80: WARNING: Title underline too short. CyVerse Discovery Environment ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:95: WARNING: Enumerated list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:123: WARNING: Malformed table. +------------+------------+ | Parameter | value | +============+============+ | DNA | data.cyverse.org | +------------+------------+ | Port | 1247 | +------------+------------+ | User name | | +------------+------------+ | Zone | iplant | +------------+------------+ | Password | 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. 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(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file cyverse-data-store-quickstart.idx (./cyverse-data-store-quickstart.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) 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[3] [4] Chapter 2. [5] [6] Chapter 3. [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [8] No file cyverse-data-store-quickstart.ind. [9] (./cyverse-data-store-quickstart.aux) Package rerunfilecheck Warning: File `cyverse-data-store-quickstart.out' has ch anged. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ){/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-data-store-quickstart.pdf (13 pages, 131934 bytes). Transcript written on cyverse-data-store-quickstart.log. Latexmk: Index file 'cyverse-data-store-quickstart.idx' was written Latexmk: Missing input file: 'cyverse-data-store-quickstart.ind' from line 'No file cyverse-data-store-quickstart.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-data-store-quickstart.pdf' Rule 'makeindex cyverse-data-store-quickstart.idx': File changes, etc: Non-existent destination files: 'cyverse-data-store-quickstart.ind' ------------ Run number 1 of rule 'makeindex cyverse-data-store-quickstart.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-data-store-quickstart.ind" "cyverse-data-store-quickstart.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-data-store-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-data-store-quickstart.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-data-store-quickstart.ind. Transcript written in cyverse-data-store-quickstart.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-data-store-quickstart.aux' 'cyverse-data-store-quickstart.ind' ------------ Run number 2 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-data-store-quickstart" "CyVerseDocumentation.tex"' ------------ This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./CyVerseDocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[3] [4] Chapter 2. [5] [6] Chapter 3. [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [8] (./cyverse-data-store-quickstart.ind) [9] (./cyverse-data-store-quickstart.aux) ){/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-data-store-quickstart.pdf (13 pages, 135264 bytes). Transcript written on cyverse-data-store-quickstart.log. Latexmk: Index file 'cyverse-data-store-quickstart.idx' was written Latexmk: Log file says output to 'cyverse-data-store-quickstart.pdf' Latexmk: All targets (cyverse-data-store-quickstart.pdf) are up-to-date [rtd-command-info] start-time: 2019-10-30T18:20:33.999799Z, end-time: 2019-10-30T18:20:34.308564Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/./_build/latex/cyverse-data-store-quickstart.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/artifacts/latest/sphinx_pdf/cyverse-data-store-quickstart.pdf [rtd-command-info] start-time: 2019-10-30T18:20:34.394193Z, end-time: 2019-10-30T18:20:36.069523Z, 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 7 source files that are out of date updating environment: 7 added, 0 changed, 0 removed reading sources... 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[100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-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-data-store-quickstart/checkouts/latest/example_directives_delete.rst:169: WARNING: Duplicate substitution definition name: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:9: WARNING: Title underline too short. **Data Store Quickstart** =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:13: WARNING: Title underline too short. Goal: Simple steps to get setup with the CyVerse Data Store ---- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:15: WARNING: Error in "toctree" directive: invalid option block. .. toctree:: :maxdepth: 2 CyVerse Discovery Environment Cyberduck Command Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:28: 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 (2 vs 3). .. 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| * - Computer, web browser, and internet access - To access the Discovery Environment (or the Data Store), you will need these things * - Cyberduck - Standalone software for upload/download to Data Store - |Download Cyberduck| * - i-commands - These are the command line tools to access the data store - | `Mac iCommands Installer 4.1.9 `_ or `Linux binaries and source `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:80: WARNING: Title underline too short. CyVerse Discovery Environment ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:95: WARNING: Enumerated list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-data-store-quickstart/checkouts/latest/index.rst:123: WARNING: Malformed table. +------------+------------+ | Parameter | value | +============+============+ | DNA | data.cyverse.org | +------------+------------+ | Port | 1247 | +------------+------------+ | User name | | +------------+------------+ | Zone | iplant | +------------+------------+ | Password |