Read the Docs build information Build id: 98108 Project: cyverse-importing-sradata-quickstart Version: latest Commit: de1137ea2eb18d1d224774d6652a2a4543c6b204 Date: 2018-04-02T21:09:56.620561Z State: finished Success: True [rtd-command-info] start-time: 2018-04-03T02:09:57.112013Z, end-time: 2018-04-03T02:09:59.004421Z, duration: 1, exit-code: 0 git clone --recursive https://github.com/CyVerse-learning-materials/importing_sradata_quickstart.git . Cloning into '.'... [rtd-command-info] start-time: 2018-04-03T02:09:59.079863Z, end-time: 2018-04-03T02:09:59.089733Z, 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 de1137e... update css to include sample data admonition, add intercom [rtd-command-info] start-time: 2018-04-03T02:09:59.159855Z, end-time: 2018-04-03T02:09:59.169070Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2018-04-03T02:09:59.269064Z, end-time: 2018-04-03T02:09:59.276139Z, duration: 0, exit-code: 0 git show-ref --tags 00671ecfa8af408e79dc6c9173d84b90154990c9 refs/tags/v1.0 [rtd-command-info] start-time: 2018-04-03T02:09:59.348537Z, end-time: 2018-04-03T02:09:59.357500Z, duration: 0, exit-code: 0 git branch -r origin/HEAD -> origin/master origin/master [rtd-command-info] start-time: 2018-04-03T02:10:00.736365Z, end-time: 2018-04-03T02:10:02.494360Z, duration: 1, exit-code: 0 python2.7 -mvirtualenv --no-site-packages --no-download New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/envs/latest/bin/python2.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/envs/latest/bin/python Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2018-04-03T02:10:02.561393Z, end-time: 2018-04-03T02:10:26.463242Z, duration: 23, exit-code: 0 python pip install --use-wheel --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/.cache/pip Pygments==2.2.0 setuptools==37.0.0 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx==1.6.5 sphinx-rtd-theme<0.3 readthedocs-sphinx-ext<0.6 Collecting Pygments==2.2.0 Downloading Pygments-2.2.0-py2.py3-none-any.whl (841kB) Collecting setuptools==37.0.0 Downloading setuptools-37.0.0-py2.py3-none-any.whl (481kB) Collecting docutils==0.13.1 Downloading docutils-0.13.1-py2-none-any.whl (537kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818kB) Collecting pillow==2.6.1 Downloading Pillow-2.6.1.tar.gz (7.3MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.10-py2.py3-none-any.whl Collecting commonmark==0.5.4 Downloading CommonMark-0.5.4.tar.gz (120kB) Collecting recommonmark==0.4.0 Downloading recommonmark-0.4.0-py2.py3-none-any.whl Collecting sphinx==1.6.5 Downloading Sphinx-1.6.5-py2.py3-none-any.whl (1.9MB) Collecting sphinx-rtd-theme<0.3 Downloading sphinx_rtd_theme-0.2.4-py2.py3-none-any.whl (1.4MB) Collecting readthedocs-sphinx-ext<0.6 Downloading readthedocs_sphinx_ext-0.5.8-py2-none-any.whl Collecting sphinxcontrib-websupport (from sphinx==1.6.5) Downloading sphinxcontrib_websupport-1.0.1-py2.py3-none-any.whl Collecting six>=1.5 (from sphinx==1.6.5) Downloading six-1.11.0-py2.py3-none-any.whl Collecting requests>=2.0.0 (from sphinx==1.6.5) Downloading requests-2.18.4-py2.py3-none-any.whl (88kB) Collecting typing; python_version < "3.5" (from sphinx==1.6.5) Downloading typing-3.6.4-py2-none-any.whl Collecting imagesize (from sphinx==1.6.5) Downloading imagesize-1.0.0-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 (from sphinx==1.6.5) Downloading Babel-2.5.3-py2.py3-none-any.whl (6.8MB) Collecting snowballstemmer>=1.1 (from sphinx==1.6.5) Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB) Collecting Jinja2>=2.3 (from sphinx==1.6.5) Downloading Jinja2-2.10-py2.py3-none-any.whl (126kB) Collecting nilsimsa>=0.3.7 (from readthedocs-sphinx-ext<0.6) Downloading nilsimsa-0.3.8.tar.gz (276kB) Collecting urllib3<1.23,>=1.21.1 (from requests>=2.0.0->sphinx==1.6.5) Downloading urllib3-1.22-py2.py3-none-any.whl (132kB) Collecting idna<2.7,>=2.5 (from requests>=2.0.0->sphinx==1.6.5) Downloading idna-2.6-py2.py3-none-any.whl (56kB) Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx==1.6.5) Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB) Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx==1.6.5) Downloading certifi-2018.1.18-py2.py3-none-any.whl (151kB) Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.6.5) Downloading pytz-2018.3-py2.py3-none-any.whl (509kB) Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.6.5) Downloading MarkupSafe-1.0.tar.gz Building wheels for collected packages: mock, pillow, commonmark, nilsimsa, MarkupSafe Running setup.py bdist_wheel for mock: started Running setup.py bdist_wheel for mock: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/.cache/pip/wheels/10/e5/4a/eed88674a2ddcf2fdddb2a00c8a2c772b24979186a4ba84d82 Running setup.py bdist_wheel for pillow: started Running setup.py bdist_wheel for pillow: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/.cache/pip/wheels/ec/e1/02/91782344499267ed189d74d0e5dae1614a1aab1f17ed2ea8eb Running setup.py bdist_wheel for commonmark: started Running setup.py bdist_wheel for commonmark: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/.cache/pip/wheels/fd/3a/ea/9ead7944d8ba3771888487ca4f6ef39bcde9fd4e986c32f442 Running setup.py bdist_wheel for nilsimsa: started Running setup.py bdist_wheel for nilsimsa: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/.cache/pip/wheels/77/f8/25/539c7b52ecbfcb7ed9b6c7189f9fdde48706c41fe529a64c9f Running setup.py bdist_wheel for MarkupSafe: started Running setup.py bdist_wheel for MarkupSafe: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/.cache/pip/wheels/88/a7/30/e39a54a87bcbe25308fa3ca64e8ddc75d9b3e5afa21ee32d57 Successfully built mock pillow commonmark nilsimsa MarkupSafe Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, sphinxcontrib-websupport, six, urllib3, idna, chardet, certifi, requests, typing, imagesize, pytz, babel, snowballstemmer, MarkupSafe, Jinja2, sphinx, sphinx-rtd-theme, nilsimsa, readthedocs-sphinx-ext Found existing installation: setuptools 28.8.0 Uninstalling setuptools-28.8.0: Successfully uninstalled setuptools-28.8.0 Successfully installed Jinja2-2.10 MarkupSafe-1.0 Pygments-2.2.0 alabaster-0.7.10 babel-2.5.3 certifi-2018.1.18 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.6 imagesize-1.0.0 mock-1.0.1 nilsimsa-0.3.8 pillow-2.6.1 pytz-2018.3 readthedocs-sphinx-ext-0.5.8 recommonmark-0.4.0 requests-2.18.4 setuptools-37.0.0 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.6.5 sphinx-rtd-theme-0.2.4 sphinxcontrib-websupport-1.0.1 typing-3.6.4 urllib3-1.22 You are using pip version 9.0.1, however version 9.0.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2018-04-03T02:10:27.035598Z, end-time: 2018-04-03T02:10:27.106902Z, 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 = 'Importing Data from SRA Quickstart' copyright = '2017, CyVerse' author = 'CyVerse' 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 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 else: SUFFIX = source_suffix[0] 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') html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = False if 'html_theme' in globals(): if html_theme in ['default']: # Allow people to bail with a hack of having an html_style if not 'html_style' in globals(): import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True else: import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' if 'http' not in settings.MEDIA_URL: websupport2_static_url = 'https://media.readthedocs.com/' else: websupport2_static_url = 'https://media.readthedocs.com/media//static' #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/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ("pdf", "//readthedocs.com/projects/cyverse-importing-sradata-quickstart/downloads/pdf/latest/"), ("htmlzip", "//readthedocs.com/projects/cyverse-importing-sradata-quickstart/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/cyverse-importing-sradata-quickstart/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-importing-sradata-quickstart', 'name': u'importing_sradata_quickstart', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/projects/cyverse-importing-sradata-quickstart/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/./', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'importing_sradata_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, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'de1137ea', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): extensions.append("readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] [rtd-command-info] start-time: 2018-04-03T02:10:27.198123Z, end-time: 2018-04-03T02:10:28.232628Z, duration: 1, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.6.5 making output directory... loading translations [en]... done building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 3 source files that are out of date updating environment: 3 added, 0 changed, 0 removed reading sources... [ 33%] Contributors_maintainers reading sources... [ 66%] License reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/License.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 33%] Contributors_maintainers writing output... [ 66%] License writing output... [100%] index generating indices... genindex writing additional pages... search copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_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, 4 warnings. [rtd-command-info] start-time: 2018-04-03T02:10:28.348796Z, end-time: 2018-04-03T02:10:29.222934Z, duration: 0, exit-code: 0 python sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json Running Sphinx v1.6.5 making output directory... loading translations [en]... done loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [json]: targets for 3 source files that are out of date updating environment: 3 added, 0 changed, 0 removed reading sources... [ 33%] Contributors_maintainers reading sources... [ 66%] License reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/License.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 33%] Contributors_maintainers writing output... [ 66%] License writing output... [100%] index generating indices... genindex writing additional pages... search copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 4 warnings. [rtd-command-info] start-time: 2018-04-03T02:10:29.320338Z, end-time: 2018-04-03T02:10:30.223116Z, duration: 0, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.6.5 making output directory... loading translations [en]... done loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 3 added, 0 changed, 0 removed reading sources... [ 33%] Contributors_maintainers reading sources... [ 66%] License reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/License.md: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... writing... done writing additional files... copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 4 warnings. [rtd-command-info] start-time: 2018-04-03T02:10:30.304007Z, end-time: 2018-04-03T02:10:31.134020Z, duration: 0, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.6.5 making output directory... loading translations [en]... done loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 3 added, 0 changed, 0 removed reading sources... [ 33%] Contributors_maintainers reading sources... [ 66%] License reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/License.md: WARNING: document isn't included in any toctree done processing CyVerseDocumentation.tex...index resolving references... writing... done copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying TeX support files... done build succeeded, 2 warnings. [rtd-command-info] start-time: 2018-04-03T02:10:31.209261Z, end-time: 2018-04-03T02:10:31.784483Z, duration: 0, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/_build/latex/CyVerseDocumentation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-qui ckstart/checkouts/latest/_build/latex/CyVerseDocumentation.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. Underfull \hbox (badness 7963) in paragraph at lines 164--164 []\T1/phv/m/n/10 Plat-form Doc-u-men-ta- Underfull \hbox (badness 10000) in paragraph at lines 164--164 []\T1/phv/m/n/10 Quick Underfull \hbox (badness 10000) in paragraph at lines 164--164 []\T1/ptm/m/n/10 Dis-cov-ery En-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 164--164 []\T1/ptm/m/n/10 Web/Point-and- Underfull \hbox (badness 10000) in paragraph at lines 2--164 [][][]\T1/ptm/m/n/10 Dis-cov-ery En-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 197--197 []\T1/phv/m/n/10 For- Underfull \hbox (badness 10000) in paragraph at lines 197--197 []\T1/ptm/m/n/10 SRA Ac-ces-sion [5] [6] Chapter 3. [7] No file CyVerseDocumentation.ind. [8] (./CyVerseDocumentation.aux) Package rerunfilecheck Warning: File `CyVerseDocumentation.out' 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 CyVerseDocumentation.pdf (12 pages, 124412 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2018-04-03T02:10:31.860220Z, end-time: 2018-04-03T02:10:31.984661Z, duration: 0, exit-code: 0 makeindex -s python.ist CyVerseDocumentation.idx This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file CyVerseDocumentation.idx...done (0 entries accepted, 0 rejected). Nothing written in CyVerseDocumentation.ind. Transcript written in CyVerseDocumentation.ilg. [rtd-command-info] start-time: 2018-04-03T02:10:32.093686Z, end-time: 2018-04-03T02:10:32.838521Z, duration: 0, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-quickstart/checkouts/latest/_build/latex/CyVerseDocumentation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/home/docs/checkouts/readthedocs.org/user_builds/cyverse-importing-sradata-qui ckstart/checkouts/latest/_build/latex/CyVerseDocumentation.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. 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[7] (./CyVerseDocumentation.ind) [8] (./CyVerseDocumentation.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on CyVerseDocumentation.pdf (12 pages, 126980 bytes). Transcript written on CyVerseDocumentation.log. 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