Read the Docs build information Build id: 636254 Project: cyverse-scrna-seq Version: latest Commit: e435fe78a4108753aea79149ad48d9033eadb3df Date: 2021-05-19T01:06:02.767332Z State: finished Success: True [rtd-command-info] start-time: 2021-05-19T01:06:04.176440Z, end-time: 2021-05-19T01:06:07.934040Z, duration: 3, 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: 2021-05-19T01:06:08.056688Z, end-time: 2021-05-19T01:06:08.900582Z, 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 e435fe7 Update index.rst [rtd-command-info] start-time: 2021-05-19T01:06:09.014138Z, end-time: 2021-05-19T01:06:09.091026Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-05-19T01:06:10.359254Z, end-time: 2021-05-19T01:06:14.315734Z, duration: 3, 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: 2021-05-19T01:06:14.419156Z, end-time: 2021-05-19T01:06:15.487376Z, 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 (56.2.0) [rtd-command-info] start-time: 2021-05-19T01:06:15.606427Z, end-time: 2021-05-19T01:06:24.151563Z, 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-4.0.1-py3-none-any.whl (2.9 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 sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting babel>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting Pygments>=2.0 Downloading Pygments-2.9.0-py3-none-any.whl (1.0 MB) Collecting Jinja2<3.0,>=2.3 Downloading 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filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=d600fea45c445207b8af478b27d019832fb5010fe6c63e8cfc402bee5a90f420 Stored in directory: /tmp/pip-ephem-wheel-cache-4fy79ltr/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=6ca3ce92f83be5bd49a975f14eeeea4e69316ab4e410cfa01608c2d919548f0d Stored in directory: /tmp/pip-ephem-wheel-cache-4fy79ltr/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-4.0.1 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: 2021-05-19T01:06:24.290163Z, end-time: 2021-05-19T01:06:34.472825Z, duration: 10, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting sphinx==1.8 Downloading Sphinx-1.8.0-py2.py3-none-any.whl (3.1 MB) Collecting nbsphinx Downloading nbsphinx-0.8.5-py3-none-any.whl (24 kB) Requirement already satisfied: recommonmark in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 3)) (0.5.0) Collecting sphinxcontrib-images Downloading sphinxcontrib_images-0.9.3-py2.py3-none-any.whl (67 kB) Collecting sphinx_bootstrap_theme Downloading sphinx-bootstrap-theme-0.7.1.tar.gz (1.2 MB) Collecting guzzle_sphinx_theme==0.7.11 Downloading guzzle_sphinx_theme-0.7.11.tar.gz (2.5 MB) Requirement already satisfied: sphinx_rtd_theme in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 7)) (0.5.2) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (from sphinx==1.8->-r requirements.txt (line 1)) (2.9.0) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (from sphinx==1.8->-r requirements.txt (line 1)) (0.16) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (from sphinx==1.8->-r requirements.txt (line 1)) (20.9) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (from sphinx==1.8->-r requirements.txt (line 1)) (2.1.0) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (from sphinx==1.8->-r requirements.txt (line 1)) (2.9.1) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Requirement 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pyrsistent, sphinxcontrib-images, sphinx-bootstrap-theme Building wheel for guzzle-sphinx-theme (setup.py): started Building wheel for guzzle-sphinx-theme (setup.py): finished with status 'done' Created wheel for guzzle-sphinx-theme: filename=guzzle_sphinx_theme-0.7.11-py3-none-any.whl size=2555155 sha256=67141554d18f34c859a5037ce2a957331231afed7e4a116da9daefc38121d90b Stored in directory: /tmp/pip-ephem-wheel-cache-118y2w4t/wheels/5c/d1/84/25697025762e126f3a2eba16cae45f22432fe99669b05df5c0 Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=7992 sha256=213ce98b762a969f422e47f443aecdb2930f7ad53f780c28cdb10f0727af54d7 Stored in directory: /tmp/pip-ephem-wheel-cache-118y2w4t/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp37-cp37m-linux_x86_64.whl size=115334 sha256=3de71d8c248e379f89857ac3fec40c3e51370cce950c23a3bb80270390d32781 Stored in directory: /tmp/pip-ephem-wheel-cache-118y2w4t/wheels/a5/52/bf/71258a1d7b3c8cbe1ee53f9314c6f65f20385481eaee573cc5 Building wheel for sphinxcontrib-images (setup.py): started Building wheel for sphinxcontrib-images (setup.py): finished with status 'done' Created wheel for sphinxcontrib-images: filename=sphinxcontrib_images-0.8.0-py3-none-any.whl size=63617 sha256=5d3f3366b0bd601eb8c366da04e30ed1df85422aafa8109ed91f60ce6ea01ba8 Stored in directory: /tmp/pip-ephem-wheel-cache-118y2w4t/wheels/38/92/c8/ad9fb1ccdccf8ff3d2cdaf05aaad2e1db3917dd37ed7eead59 Building wheel for sphinx-bootstrap-theme (setup.py): started Building wheel for sphinx-bootstrap-theme (setup.py): finished with status 'done' Created wheel for sphinx-bootstrap-theme: filename=sphinx_bootstrap_theme-0.7.1-py3-none-any.whl size=1250222 sha256=16c5f69599e49f5c3e2cad8daf7889eadceaab548b596fe11ae4e6db1a998905 Stored in directory: /tmp/pip-ephem-wheel-cache-118y2w4t/wheels/08/be/f3/01d145bc6faf769e37d9fb6f1d2f078bc8cd9725c9d883699c Successfully built guzzle-sphinx-theme pandocfilters pyrsistent sphinxcontrib-images sphinx-bootstrap-theme Installing collected packages: zipp, typing-extensions, ipython-genutils, traitlets, six, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, python-dateutil, jupyter-core, jsonschema, webencodings, nest-asyncio, nbformat, jupyter-client, async-generator, testpath, sphinxcontrib-websupport, pandocfilters, nbclient, mistune, jupyterlab-pygments, entrypoints, defusedxml, bleach, sphinx, nbconvert, sphinxcontrib-images, sphinx-bootstrap-theme, nbsphinx, guzzle-sphinx-theme Attempting uninstall: sphinx Found existing installation: Sphinx 4.0.1 Uninstalling Sphinx-4.0.1: Successfully uninstalled Sphinx-4.0.1 Successfully installed async-generator-1.10 attrs-21.2.0 bleach-3.3.0 defusedxml-0.7.1 entrypoints-0.3 guzzle-sphinx-theme-0.7.11 importlib-metadata-4.0.1 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-client-6.1.12 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 mistune-0.8.4 nbclient-0.5.3 nbconvert-6.0.7 nbformat-5.1.3 nbsphinx-0.8.5 nest-asyncio-1.5.1 pandocfilters-1.4.3 pyrsistent-0.17.3 python-dateutil-2.8.1 pyzmq-22.0.3 six-1.16.0 sphinx-1.8.0 sphinx-bootstrap-theme-0.7.1 sphinxcontrib-images-0.8.0 sphinxcontrib-websupport-1.2.4 testpath-0.5.0 tornado-6.1 traitlets-5.0.5 typing-extensions-3.10.0.0 webencodings-0.5.1 zipp-3.4.1 [rtd-command-info] start-time: 2021-05-19T01:06:35.265652Z, end-time: 2021-05-19T01:06:35.329943Z, 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': 'e435fe78', } # 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/636254/' 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: 2021-05-19T01:06:35.431651Z, end-time: 2021-05-19T01:06:38.227257Z, duration: 2, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v1.8.0 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [html]: targets for 37 source files that are out of date updating environment: 37 added, 0 changed, 0 removed reading sources... 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maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/buildenv/lib/python3.7/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} WARNING: invalid signature for autoclass ('{{ objname }}') WARNING: don't know which module to import for autodocumenting '{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) WARNING: invalid signature for automodule ('{{ fullname }}') WARNING: don't know which module to import for autodocumenting '{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) /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:152: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/step1-1.rst:77: WARNING: Duplicate substitution definition name: "rstudio_demo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/step1-1.rst:82: WARNING: Duplicate substitution definition name: "access_analysis". looking for now-outdated files... none found pickling environment... done checking consistency... 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[100%] step5 generating indices... genindex writing additional pages... search copying images... [ 12%] ./img/cyverse_learning.png copying images... [ 25%] ./img/homeicon.png copying images... [ 37%] ./img/Powered-By-CyVerse-blue.png copying images... [ 50%] ./img/kitten_no_border.png copying images... [ 62%] ./img/kitten_w_border.png copying images... [ 75%] ./img/intercom.png copying images... [ 87%] ./img/quicklaunch.png copying images... [100%] ./img/rstudio_demo_app.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 48 warnings. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-05-19T01:06:38.391355Z, end-time: 2021-05-19T01:06:39.255992Z, duration: 0, exit-code: 0 python -m sphinx -T -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v1.8.0 loading translations [en]... done making output directory... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found pickling environment... done preparing documents... done assembling single document... step1-1 step5 writing... done writing additional files... copying images... [ 16%] ./img/cyverse_learning.png copying images... [ 33%] ./img/homeicon.png copying images... [ 50%] ./img/quicklaunch.png copying images... [ 66%] ./img/rstudio_demo_app.png copying images... [ 83%] ./img/intercom.png copying images... [100%] ./img/Powered-By-CyVerse-blue.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/_static' does not exist done copying extra files... done dumping object inventory... done build succeeded, 1 warning. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-05-19T01:06:39.404513Z, end-time: 2021-05-19T01:06:40.219039Z, duration: 0, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.8.0 loading translations [en]... done making output directory... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found pickling environment... done processing CyVerseDocumentation.tex...index step1-1 step5 resolving references... writing... done copying images... [ 16%] ./img/cyverse_learning.png copying images... [ 33%] ./img/homeicon.png copying images... [ 50%] ./img/quicklaunch.png copying images... [ 66%] ./img/rstudio_demo_app.png copying images... [ 83%] ./img/intercom.png copying images... [100%] ./img/Powered-By-CyVerse-blue.png copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages/sphinx/builders/latex/__init__.py:201: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. if toctrees[0].get('maxdepth') > 0: WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2021-05-19T01:06:41.224054Z, end-time: 2021-05-19T01:06:41.297896Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2021-05-19T01:06:41.420079Z, end-time: 2021-05-19T01:06:45.845666Z, duration: 4, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-scrna-seq -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. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-scrna-seq" "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. (./sphinxmanual.cls Document Class: sphinxmanual 2017/03/26 v1.6 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/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-scrna-seq.idx (./cyverse-scrna-seq.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)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] [1 <./cyverse_learning.png> <./h omeicon.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. Overfull \hbox (132.48178pt too wide) in paragraph at lines 2--169 [][][][][][] [5] Overfull \hbox (207.76201pt too wide) in paragraph at lines 2--185 [][][][][][] [6 <./quicklaunch.png> <./rstudio_demo_app.png>] Overfull \hbox (7.96182pt too wide) in paragraph at lines 208--208 []\T1/ptm/m/it/10 Healthy.gz| [7 <./intercom.png>] [8] Chapter 3. [9 <./Powered-By-CyVerse-blue.png>] No file cyverse-scrna-seq.ind. [10] (./cyverse-scrna-seq.aux) Package rerunfilecheck Warning: File `cyverse-scrna-seq.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 cyverse-scrna-seq.pdf (14 pages, 719973 bytes). Transcript written on cyverse-scrna-seq.log. Latexmk: Index file 'cyverse-scrna-seq.idx' was written Latexmk: Missing input file: 'cyverse-scrna-seq.ind' from line 'No file cyverse-scrna-seq.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-scrna-seq.pdf' Rule 'makeindex cyverse-scrna-seq.idx': File changes, etc: Non-existent destination files: 'cyverse-scrna-seq.ind' ------------ Run number 1 of rule 'makeindex cyverse-scrna-seq.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-scrna-seq.ind" "cyverse-scrna-seq.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-scrna-seq.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-scrna-seq.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-scrna-seq.ind. Transcript written in cyverse-scrna-seq.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-scrna-seq.aux' 'cyverse-scrna-seq.ind' ------------ Run number 2 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. (./sphinxmanual.cls Document Class: sphinxmanual 2017/03/26 v1.6 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty 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(/usr/share/texlive/texmf-dist/tex/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-scrna-seq.idx (./cyverse-scrna-seq.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)) (./cyverse-scrna-seq.out) (./cyverse-scrna-seq.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./cyverse-scrna-seq.toc) [1] [2] [1 <./cyverse_learning.png> <./homeicon.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. Overfull \hbox (132.48178pt too wide) in paragraph at lines 2--169 [][][][][][] [5] Overfull \hbox (207.76201pt too wide) in paragraph at lines 2--185 [][][][][][] [6 <./quicklaunch.png> <./rstudio_demo_app.png>] Overfull \hbox (7.96182pt too wide) in paragraph at lines 208--208 []\T1/ptm/m/it/10 Healthy.gz| [7 <./intercom.png>] [8] Chapter 3. [9 <./Powered-By-CyVerse-blue.png>] (./cyverse-scrna-seq.ind) [10] (./cyverse-scrna-seq.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-scrna-seq.pdf (14 pages, 724200 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. Overfull \hbox (132.48178pt too wide) in paragraph at lines 2--169 [][][][][][] [5] Overfull \hbox (207.76201pt too wide) in paragraph at lines 2--185 [][][][][][] [6 <./quicklaunch.png> <./rstudio_demo_app.png>] Overfull \hbox (7.96182pt too wide) in paragraph at lines 208--208 []\T1/ptm/m/it/10 Healthy.gz| [7 <./intercom.png>] [8] Chapter 3. [9 <./Powered-By-CyVerse-blue.png>] (./cyverse-scrna-seq.ind) [10] (./cyverse-scrna-seq.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-scrna-seq.pdf (14 pages, 724200 bytes). Transcript written on cyverse-scrna-seq.log. 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