Read the Docs build information Build id: 433872 Project: mdolab-idwarp Version: latest Commit: 1ebf0fc60700b963ef4340bbeccb5824bbe17f98 Date: 2020-09-27T18:38:55.067361Z State: finished Success: True [rtd-command-info] start-time: 2020-09-27T18:38:56.772928Z, end-time: 2020-09-27T18:38:58.066309Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/mdolab/idwarp.git . Cloning into '.'... [rtd-command-info] start-time: 2020-09-27T18:38:58.413553Z, end-time: 2020-09-27T18:38:58.519956Z, 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 1ebf0fc Update .travis.yml [rtd-command-info] start-time: 2020-09-27T18:38:58.626456Z, end-time: 2020-09-27T18:38:58.680491Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-09-27T18:38:59.774952Z, end-time: 2020-09-27T18:39:03.623261Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-09-27T18:39:03.753682Z, end-time: 2020-09-27T18:39:04.432603Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (20.2.3) [rtd-command-info] start-time: 2020-09-27T18:39:04.728218Z, end-time: 2020-09-27T18:39:13.066476Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 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Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting Pygments>=2.0 Downloading Pygments-2.7.1-py3-none-any.whl (944 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.10-py2.py3-none-any.whl (127 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 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=23754 sha256=5cc6ae6e45720b48b48cbecd4debaaf11405108a3c4fcdeb91704764b3c732cd Stored in directory: /tmp/pip-ephem-wheel-cache-y2g2waf_/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b 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=aafdebddb1fd19d991911242613ad10bab61651005fc10e84c74a2a8d42da59e Stored in directory: /tmp/pip-ephem-wheel-cache-y2g2waf_/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, pyparsing, packaging, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, imagesize, snowballstemmer, certifi, chardet, urllib3, idna, requests, Pygments, MarkupSafe, Jinja2, pytz, babel, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 50.3.0 Uninstalling setuptools-50.3.0: Successfully uninstalled setuptools-50.3.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.10 [rtd-command-info] start-time: 2020-09-27T18:39:13.202495Z, end-time: 2020-09-27T18:39:14.058551Z, duration: 0, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r doc/requirements.txt Collecting numpydoc Downloading numpydoc-1.1.0-py3-none-any.whl (47 kB) Requirement already satisfied: sphinx>=1.6.5 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from numpydoc->-r doc/requirements.txt (line 1)) (1.8.5) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from numpydoc->-r doc/requirements.txt (line 1)) (2.11.2) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2.24.0) Requirement already satisfied: packaging in 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/home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (1.2.0) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2.8.0) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (1.15.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (0.7.12) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (41.0.1) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2.0.0) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->numpydoc->-r doc/requirements.txt (line 1)) (1.1.1) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (3.0.4) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2020.6.20) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (1.25.10) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2.10) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from packaging->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2.4.7) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (1.1.4) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2020.1) Installing collected packages: numpydoc Successfully installed numpydoc-1.1.0 [rtd-command-info] start-time: 2020-09-27T18:39:15.494284Z, end-time: 2020-09-27T18:39:15.565898Z, duration: 0, exit-code: 0 cat doc/conf.py # -*- coding: utf-8 -*- # # IDWarp documentation build configuration file, created by # sphinx-quickstart on Thu Jul 9 16:26:28 2015. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. import sys import os # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. sys.path.insert(0, os.path.abspath('../')) # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'numpydoc'] # mock import for autodoc autodoc_mock_imports = ['numpy', 'mpi4py', 'petsc4py'] numpydoc_show_class_members = False # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix of source filenames. source_suffix = '.rst' # The master toctree document. master_doc = 'index' # General information about the project. project = u'IDWarp' copyright = u'2020, MDO Lab' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. exclude_patterns = ['_build'] # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. html_theme_path = ['themes'] html_theme = 'sphinx_rtd_theme' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css', # override wide tables in RTD theme ], } ########################################################################### # 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://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/"), ("stable", "/en/stable/"), ], 'downloads': [ ("pdf", "//mdolab-idwarp.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//mdolab-idwarp.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//mdolab-idwarp.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'mdolab-idwarp', 'name': u'idwarp', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://mdolab-idwarp.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/doc/', 'api_host': 'https://readthedocs.com', 'github_user': 'mdolab', 'proxied_api_host': '/_', 'github_repo': 'idwarp', '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': '1ebf0fc6', } 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' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2020-09-27T18:39:15.881413Z, end-time: 2020-09-27T18:39:17.423975Z, duration: 1, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 7 source files that are out of date updating environment: 7 added, 0 changed, 0 removed reading sources... [ 14%] API reading sources... [ 28%] MultiUSMesh reading sources... [ 42%] USMesh reading sources... [ 57%] building reading sources... [ 71%] index reading sources... [ 85%] options reading sources... [100%] tutorial looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 14%] API writing output... [ 28%] MultiUSMesh writing output... [ 42%] USMesh writing output... [ 57%] building writing output... [ 71%] index writing output... [ 85%] options writing output... [100%] tutorial generating indices... genindex highlighting module code... [ 50%] idwarp.MultiUnstructuredMesh highlighting module code... [100%] idwarp.UnstructuredMesh writing additional pages... search copying static files... 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. The HTML pages are in _build/html. [rtd-command-info] start-time: 2020-09-27T18:39:17.552090Z, end-time: 2020-09-27T18:39:18.815513Z, duration: 1, 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... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 7 added, 0 changed, 0 removed reading sources... [ 14%] API reading sources... [ 28%] MultiUSMesh reading sources... [ 42%] USMesh reading sources... [ 57%] building reading sources... [ 71%] index reading sources... [ 85%] options reading sources... [100%] tutorial looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... building tutorial options API USMesh MultiUSMesh writing... done writing additional files... copying static files... done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia. [rtd-command-info] start-time: 2020-09-27T18:39:18.948604Z, end-time: 2020-09-27T18:39:20.148261Z, 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... building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 7 added, 0 changed, 0 removed reading sources... [ 14%] API reading sources... [ 28%] MultiUSMesh reading sources... [ 42%] USMesh reading sources... [ 57%] building reading sources... [ 71%] index reading sources... [ 85%] options reading sources... [100%] tutorial looking for now-outdated files... none found pickling environment... done checking consistency... done processing IDWarp.tex...index building tutorial options API USMesh MultiUSMesh resolving references... writing... done 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). [rtd-command-info] start-time: 2020-09-27T18:39:20.378447Z, end-time: 2020-09-27T18:39:20.434621Z, 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: 2020-09-27T18:39:20.541986Z, end-time: 2020-09-27T18:39:21.941259Z, duration: 1, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=mdolab-idwarp -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="mdolab-idwarp" "IDWarp.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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[11] Underfull \hbox (badness 5893) in paragraph at lines 666--666 []\T1/ptm/m/it/10 dXv=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 solverVec=True\T1/pt m/m/n/10 , \T1/ptm/m/it/10 dof-S-tart=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dofEnd= 10\T1/ptm/m/n/10 , \T1/ptm/m/it/10 h=1e-06\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ran- dom- [12] [13] [14] [15] [16] Chapter 5. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [17] [18] Chapter 6. No file mdolab-idwarp.ind. [19] (./mdolab-idwarp.aux) Package rerunfilecheck Warning: File `mdolab-idwarp.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. 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 mdolab-idwarp.pdf (23 pages, 138258 bytes). Transcript written on mdolab-idwarp.log. Latexmk: Index file 'mdolab-idwarp.idx' was written Latexmk: Missing input file: 'mdolab-idwarp.ind' from line 'No file mdolab-idwarp.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'mdolab-idwarp.pdf' Rule 'makeindex mdolab-idwarp.idx': File changes, etc: Non-existent destination files: 'mdolab-idwarp.ind' ------------ Run number 1 of rule 'makeindex mdolab-idwarp.idx' ------------ ------------ Running 'makeindex -s python.ist -o "mdolab-idwarp.ind" "mdolab-idwarp.idx"' ------------ Latexmk: applying rule 'makeindex mdolab-idwarp.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 mdolab-idwarp.idx....done (28 entries accepted, 0 rejected). Sorting entries....done (160 comparisons). Generating output file mdolab-idwarp.ind....done (70 lines written, 0 warnings). Output written in mdolab-idwarp.ind. 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Latexmk: Index file 'mdolab-idwarp.idx' was written Latexmk: Log file says output to 'mdolab-idwarp.pdf' Latexmk: All targets (mdolab-idwarp.pdf) are up-to-date [rtd-command-info] start-time: 2020-09-27T18:39:22.183361Z, end-time: 2020-09-27T18:39:22.233739Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/checkouts/latest/doc/_build/latex/mdolab-idwarp.pdf /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/artifacts/latest/sphinx_pdf/mdolab-idwarp.pdf [rtd-command-info] start-time: 2020-09-27T18:39:23.006269Z, end-time: 2020-09-27T18:39:24.270684Z, duration: 1, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [epub]: targets for 7 source files that are out of date updating environment: 7 added, 0 changed, 0 removed reading sources... [ 14%] API reading sources... [ 28%] MultiUSMesh reading sources... [ 42%] USMesh reading sources... [ 57%] building reading sources... [ 71%] index reading sources... [ 85%] options reading sources... [100%] tutorial looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 14%] API writing output... [ 28%] MultiUSMesh writing output... [ 42%] USMesh writing output... [ 57%] building writing output... [ 71%] index writing output... [ 85%] options writing output... [100%] tutorial generating indices... genindex writing additional pages... copying static files... done copying extra files... done WARNING: conf value "version" should not be empty for EPUB3 writing mimetype file... writing META-INF/container.xml file... writing content.opf file... writing nav.xhtml file... writing toc.ncx file... writing IDWarp.epub file... build succeeded, 1 warning. The ePub file is in _build/epub. [rtd-command-info] start-time: 2020-09-27T18:39:24.712984Z, end-time: 2020-09-27T18:39:24.766656Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/checkouts/latest/doc/_build/epub/IDWarp.epub /home/docs/checkouts/readthedocs.org/user_builds/mdolab-idwarp/artifacts/latest/sphinx_epub/mdolab-idwarp.epub