Read the Docs build information Build id: 629221 Project: cyverse-scrna-seq Version: latest Commit: b1d23b8c6e0068a8233debe6b7a40ae917f28557 Date: 2021-05-08T21:09:45.468017Z State: finished Success: True [rtd-command-info] start-time: 2021-05-08T21:09:47.009686Z, end-time: 2021-05-08T21:09:48.652841Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:CyVerse-learning-materials/scRNA-seq.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2021-05-08T21:09:48.831309Z, end-time: 2021-05-08T21:09:48.919363Z, 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 b1d23b8 typo corrections [rtd-command-info] start-time: 2021-05-08T21:09:49.043305Z, end-time: 2021-05-08T21:09:49.110610Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-05-08T21:09:50.047240Z, end-time: 2021-05-08T21:09:54.131329Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-05-08T21:09:54.249316Z, end-time: 2021-05-08T21:09:55.352661Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (21.1.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (56.1.0) [rtd-command-info] start-time: 2021-05-08T21:09:55.503720Z, end-time: 2021-05-08T21:10:04.307083Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 sphinx-rtd-theme readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting 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 Downloading Sphinx-3.5.4-py3-none-any.whl (2.8 MB) Collecting sphinx-rtd-theme Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting Pygments>=2.0 Downloading Pygments-2.9.0-py3-none-any.whl (1.0 MB) Collecting requests>=2.5.0 Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (from sphinx) (56.1.0) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Collecting babel>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Collecting docutils>=0.11 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux2010_x86_64.whl (33 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.4-py2.py3-none-any.whl (153 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=cbc4ddbd13c1db17e417dae40cf774f40569e13772cd2bb590299d9afe4e27e1 Stored in directory: /tmp/pip-ephem-wheel-cache-dolydtx2/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=be66dcb78591c8e8af454fc78c424aef7dbf57484f3d4125b141a966d352dae7 Stored in directory: /tmp/pip-ephem-wheel-cache-dolydtx2/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.9.0 alabaster-0.7.12 babel-2.9.1 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.16 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 snowballstemmer-2.1.0 sphinx-3.5.4 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.4 urllib3-1.26.4 [rtd-command-info] start-time: 2021-05-08T21:10:05.160004Z, end-time: 2021-05-08T21:10:05.230701Z, duration: 0, exit-code: 0 cat conf.py #!/usr/bin/env python3 # Version 2.0, May 2020 # -*- coding: utf-8 -*- # # General information about the project. import sys import os sys.path.insert(0, os.path.dirname(__file__)) from misc.cyverse_sphinx_conf import * # noqa project = 'Single-cell analysis using CyVerse' copyright = '2020, CyVerse' author = 'CyVerse' version = '2.0' release = '2.0' 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 # # Note: this file should't rely on extra depencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring 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-scrna-seq.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//cyverse-scrna-seq.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//cyverse-scrna-seq.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'cyverse-scrna-seq', 'name': u'scRNA-seq', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-scrna-seq.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'proxied_api_host': '/_', 'github_repo': 'scRNA-seq', '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': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'b1d23b8c', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/cyverse-scrna-seq/builds/629221/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-05-08T21:10:05.335335Z, end-time: 2021-05-08T21:10:06.855462Z, duration: 1, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v3.5.4 loading translations [en]... done making output directory... done /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:74: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead. app.add_stylesheet('cyverse.css') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:75: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead. app.add_stylesheet('detail-expand.css') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:76: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead. app.add_stylesheet('question-answer.css') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:78: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead. app.add_javascript('cyverse.js') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:79: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead. app.add_javascript('detail-expand.js') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:80: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead. app.add_javascript('question-answer.js') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:81: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead. app.add_javascript('intercom-script-for-learning.js') WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [html]: targets for 9 source files that are out of date updating environment: [new config] 9 added, 0 changed, 0 removed reading sources... [ 11%] example_directives_delete reading sources... [ 22%] final_step reading sources... [ 33%] index reading sources... [ 44%] step1 reading sources... [ 55%] step1-1 reading sources... [ 66%] step2 reading sources... [ 77%] step3 reading sources... [ 88%] step4 reading sources... [100%] step5 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/final_step.rst:4: WARNING: Undefined substitution referenced: "CyVerse logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/final_step.rst:4: WARNING: Unknown target name: "cyverse logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/index.rst:43: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/index.rst:45: WARNING: toctree contains reference to nonexisting document ' :maxdepth: 2' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/index.rst:173: WARNING: Explicit markup ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/example_directives_delete.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/final_step.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 11%] example_directives_delete writing output... [ 22%] final_step writing output... [ 33%] index writing output... [ 44%] step1 writing output... [ 55%] step1-1 writing output... [ 66%] step2 writing output... [ 77%] step3 writing output... [ 88%] step4 writing output... [100%] step5 generating indices... genindex done writing additional pages... search done copying images... [ 16%] img/cyverse_learning.png copying images... [ 33%] img/homeicon.png copying images... [ 50%] img/intercom.png copying images... [ 66%] img/Powered-By-CyVerse-blue.png copying images... [ 83%] img/kitten_no_border.png copying images... [100%] img/kitten_w_border.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 8 warnings. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-05-08T21:10:07.010990Z, end-time: 2021-05-08T21:10:08.268345Z, duration: 1, exit-code: 0 python -m sphinx -T -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v3.5.4 loading translations [en]... done making output directory... done /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:74: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead. app.add_stylesheet('cyverse.css') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:75: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead. app.add_stylesheet('detail-expand.css') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:76: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead. app.add_stylesheet('question-answer.css') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:78: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead. app.add_javascript('cyverse.js') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:79: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead. app.add_javascript('detail-expand.js') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:80: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead. app.add_javascript('question-answer.js') /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py:81: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead. app.add_javascript('intercom-script-for-learning.js') WARNING: html_static_path entry '_static' does not exist loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [config changed ('source_parsers')] 9 added, 0 changed, 0 removed reading sources... [ 11%] example_directives_delete reading sources... 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. [5] [6 <./intercom.png> <./Powered-By-CyVerse-blue.png>] [7] [8] [9] [10] Chapter 3. [11] (./cyverse-scrna-seq.ind) [12] (./cyverse-scrna-seq.aux) ){/usr/share/texl ive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-scrna-seq.pdf (16 pages, 216570 bytes). Transcript written on cyverse-scrna-seq.log. Latexmk: Index file 'cyverse-scrna-seq.idx' was written Latexmk: Log file says output to 'cyverse-scrna-seq.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-scrna-seq.out' 'cyverse-scrna-seq.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-scrna-seq" "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/psnfss/ts1ptm.fd) [3] [4] Chapter 2. [5] [6 <./intercom.png> <./Powered-By-CyVerse-blue.png>] [7] [8] [9] [10] Chapter 3. [11] (./cyverse-scrna-seq.ind) [12] (./cyverse-scrna-seq.aux) ){/usr/share/texl ive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-scrna-seq.pdf (16 pages, 216570 bytes). Transcript written on cyverse-scrna-seq.log. 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