Read the Docs build information Build id: 243372 Project: cyverse-jupyter-qiime2 Version: latest Commit: a383abeade4bbed866c32e15ed2b20b0e4dc0d52 Date: 2019-09-19T22:27:01.165372Z State: finished Success: True [rtd-command-info] start-time: 2019-09-19T22:27:01.656966Z, end-time: 2019-09-19T22:27:01.677710Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/jupyter_qiime2.git [rtd-command-info] start-time: 2019-09-19T22:27:01.771359Z, end-time: 2019-09-19T22:27:02.357010Z, duration: 0, exit-code: 0 git fetch origin --tags --prune --prune-tags --depth 50 From https://github.com/CyVerse-learning-materials/jupyter_qiime2 5b38732..a383abe master -> origin/master [rtd-command-info] start-time: 2019-09-19T22:27:02.580359Z, end-time: 2019-09-19T22:27:02.820675Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 5b38732 Update index.rst HEAD is now at a383abe Update index.rst [rtd-command-info] start-time: 2019-09-19T22:27:02.904700Z, end-time: 2019-09-19T22:27:02.923995Z, duration: 0, exit-code: 0 git clean -d -f -f Removing misc/__pycache__/__init__.cpython-37.pyc Removing misc/__pycache__/cyverse_sphinx_conf.cpython-37.pyc [rtd-command-info] start-time: 2019-09-19T22:27:04.048523Z, end-time: 2019-09-19T22:27:07.558188Z, 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-jupyter-qiime2/envs/latest/bin/python3.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/bin/python3.7) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-09-19T22:27:07.652774Z, end-time: 2019-09-19T22:27:08.683761Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (19.2.3) [rtd-command-info] start-time: 2019-09-19T22:27:08.772488Z, end-time: 2019-09-19T22:27:10.763782Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/.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-jupyter-qiime2/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-jupyter-qiime2/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-jupyter-qiime2/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-jupyter-qiime2/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-jupyter-qiime2/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-jupyter-qiime2/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-jupyter-qiime2/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-jupyter-qiime2/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-jupyter-qiime2/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-jupyter-qiime2/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-jupyter-qiime2/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-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from commonmark==0.8.1) (0.17.1) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.7.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.10.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.9.1) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.12.0) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from sphinx<2) (19.1) 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-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (1.25.3) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2019.9.11) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2.8) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.2) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1) Requirement already satisfied, skipping upgrade: attrs in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from packaging->sphinx<2) (19.1.0) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages (from packaging->sphinx<2) (2.4.2) [rtd-command-info] start-time: 2019-09-19T22:27:11.335078Z, end-time: 2019-09-19T22:27:11.668778Z, 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 = 'Metagenomics in QIIME 2 Using Jupyter Notebooks in VICE' copyright = '2019, 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 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-jupyter-qiime2/downloads/pdf/latest/"), ("html", "//readthedocs.com/projects/cyverse-jupyter-qiime2/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/cyverse-jupyter-qiime2/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-jupyter-qiime2', 'name': u'jupyter_qiime2', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-jupyter-qiime2.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': 'jupyter_qiime2', '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': 'a383abea', } 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: 2019-09-19T22:27:11.750438Z, end-time: 2019-09-19T22:27:15.771340Z, duration: 4, 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 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 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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-jupyter-qiime2/checkouts/latest/index.rst:10: WARNING: Title underline too short. UPDATE: Newest version QIIME-2019.7 ---- looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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/cyverse_rgb.png copying images... [100%] ./img/homeicon.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/_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. The HTML pages are in _build/html. [rtd-command-info] start-time: 2019-09-19T22:27:15.911411Z, end-time: 2019-09-19T22:27:18.055613Z, duration: 2, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 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: 3 added, 0 changed, 0 removed reading sources... [ 33%] Contributors_maintainers reading sources... [ 66%] License reading sources... [100%] index looking for now-outdated files... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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-jupyter-qiime2/checkouts/latest/index.rst:10: WARNING: Title underline too short. UPDATE: Newest version QIIME-2019.7 ---- none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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/cyverse_rgb.png copying images... [100%] ./img/homeicon.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 4 warnings. The HTML page is in _build/localmedia. [rtd-command-info] start-time: 2019-09-19T22:27:18.183578Z, end-time: 2019-09-19T22:27:19.534730Z, duration: 1, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading pickled environment... done 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 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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-jupyter-qiime2/checkouts/latest/index.rst:10: WARNING: Title underline too short. UPDATE: Newest version QIIME-2019.7 ---- looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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/cyverse_rgb.png copying images... [100%] ./img/homeicon.png copying TeX support files... done build succeeded, 3 warnings. 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). [rtd-command-info] start-time: 2019-09-19T22:27:20.813257Z, end-time: 2019-09-19T22:27:21.158619Z, 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: 2019-09-19T22:27:21.297082Z, end-time: 2019-09-19T22:27:23.880422Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-jupyter-qiime2 -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' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-jupyter-qiime2" "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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(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-jupyter-qiime2.pdf (14 pages, 148203 bytes). Transcript written on cyverse-jupyter-qiime2.log. Latexmk: Index file 'cyverse-jupyter-qiime2.idx' was written Latexmk: Missing input file: 'cyverse-jupyter-qiime2.ind' from line 'No file cyverse-jupyter-qiime2.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-jupyter-qiime2.pdf' Rule 'makeindex cyverse-jupyter-qiime2.idx': File changes, etc: Non-existent destination files: 'cyverse-jupyter-qiime2.ind' ------------ Run number 1 of rule 'makeindex cyverse-jupyter-qiime2.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-jupyter-qiime2.ind" "cyverse-jupyter-qiime2.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-jupyter-qiime2.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-jupyter-qiime2.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-jupyter-qiime2.ind. Transcript written in cyverse-jupyter-qiime2.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-jupyter-qiime2.aux' 'cyverse-jupyter-qiime2.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-jupyter-qiime2" "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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[9] (./cyverse-jupyter-qiime2.ind) [10] (./cyverse-jupyter-qiime2.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-jupyter-qiime2.pdf (14 pages, 161962 bytes). Transcript written on cyverse-jupyter-qiime2.log. Latexmk: Index file 'cyverse-jupyter-qiime2.idx' was written Latexmk: Log file says output to 'cyverse-jupyter-qiime2.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-jupyter-qiime2.out' 'cyverse-jupyter-qiime2.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-jupyter-qiime2" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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Underfull \hbox (badness 10000) in paragraph at lines 214--214 []\T1/phv/m/n/10 Learn-ing Cen-ter Underfull \hbox (badness 10000) in paragraph at lines 214--214 []\T1/ptm/m/n/10 Web/Point-and- Underfull \hbox (badness 10000) in paragraph at lines 253--253 []\T1/phv/m/n/10 In-put Overfull \hbox (3.03355pt too wide) in paragraph at lines 253--253 []\T1/phv/m/n/10 For- Overfull \hbox (1.67345pt too wide) in paragraph at lines 253--253 \T1/phv/m/n/10 mat| Underfull \hbox (badness 10000) in paragraph at lines 253--253 []\T1/ptm/m/n/10 Se- Underfull \hbox (badness 10000) in paragraph at lines 253--253 \T1/ptm/m/n/10 quenc- Underfull \hbox (badness 10000) in paragraph at lines 253--253 \T1/ptm/m/n/10 ing Overfull \hbox (8.7434pt too wide) in paragraph at lines 2--253 [][][]\T1/ptm/m/n/10 FastQ[][]| [7] [8] Chapter 4. [9] (./cyverse-jupyter-qiime2.ind) [10] (./cyverse-jupyter-qiime2.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-jupyter-qiime2.pdf (14 pages, 161962 bytes). Transcript written on cyverse-jupyter-qiime2.log. Latexmk: Index file 'cyverse-jupyter-qiime2.idx' was written Latexmk: Log file says output to 'cyverse-jupyter-qiime2.pdf' Latexmk: All targets (cyverse-jupyter-qiime2.pdf) are up-to-date [rtd-command-info] start-time: 2019-09-19T22:27:23.978065Z, end-time: 2019-09-19T22:27:24.309623Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/./_build/latex/cyverse-jupyter-qiime2.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/artifacts/latest/sphinx_pdf/cyverse-jupyter-qiime2.pdf [rtd-command-info] start-time: 2019-09-19T22:27:24.390261Z, end-time: 2019-09-19T22:27:25.818244Z, 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... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [epub]: targets for 3 source files that are out of date updating environment: 3 added, 0 changed, 0 removed reading sources... 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