Read the Docs build information Build id: 585699 Project: mdolab-pygeo Version: latest Commit: 17cb3fcf49497f185bad118d39849bf91c2753e7 Date: 2021-03-10T14:36:46.444333Z State: finished Success: True [rtd-command-info] start-time: 2021-03-10T14:37:52.334238Z, end-time: 2021-03-10T14:37:55.384567Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/mdolab/pygeo.git . Cloning into '.'... [rtd-command-info] start-time: 2021-03-10T14:37:55.671195Z, end-time: 2021-03-10T14:37:55.962429Z, 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 17cb3fc Delete .travis.yml [rtd-command-info] start-time: 2021-03-10T14:37:56.084841Z, end-time: 2021-03-10T14:37:56.168058Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-03-10T14:37:57.310878Z, end-time: 2021-03-10T14:38:01.584772Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-03-10T14:38:01.724377Z, end-time: 2021-03-10T14:38:03.399207Z, 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/mdolab-pygeo/envs/latest/lib/python3.7/site-packages (21.0.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/envs/latest/lib/python3.7/site-packages (54.1.1) [rtd-command-info] start-time: 2021-03-10T14:38:03.590001Z, end-time: 2021-03-10T14:38:12.694609Z, duration: 9, 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<2 sphinx-rtd-theme<0.5 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 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Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/envs/latest/lib/python3.7/site-packages (from sphinx<2) (54.1.1) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux2010_x86_64.whl (33 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.3-py2.py3-none-any.whl (137 kB) 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) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=5a603f97b07e8e2c38be90875f3928b0954960d3124926c471464ab4d284e611 Stored in directory: /tmp/pip-ephem-wheel-cache-0tt5amyq/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=5e189425816840086702f1c2be470ea894c58b221a34a1e16ebc0894ecc62bf5 Stored in directory: /tmp/pip-ephem-wheel-cache-0tt5amyq/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, 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-2.8.1 alabaster-0.7.12 babel-2.9.0 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-2.1.3 recommonmark-0.5.0 requests-2.25.1 six-1.15.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.3 [rtd-command-info] start-time: 2021-03-10T14:38:12.879715Z, end-time: 2021-03-10T14:38:15.794235Z, duration: 2, 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) Collecting sphinx_mdolab_theme Downloading sphinx_mdolab_theme-1.1.0-py3-none-any.whl (21 kB) Requirement already satisfied: sphinx>=1.6.5 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/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-pygeo/envs/latest/lib/python3.7/site-packages (from numpydoc->-r doc/requirements.txt (line 1)) (2.11.3) Requirement already satisfied: MarkupSafe>=0.23 in 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doc/conf.py from sphinx_mdolab_theme.config import * # -- Path setup -------------------------------------------------------------- # 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. import os import sys sys.path.insert(0, os.path.abspath("../")) sys.path.insert(0, os.path.abspath("../../")) # -- Project information ----------------------------------------------------- project = u"pyGeo" # -- General configuration ----------------------------------------------------- # Built-in Sphinx extensions are already contained in the imported variable # here we add external extensions, which must also be added to requirements.txt # so that RTD can import and use them extensions.extend(["numpydoc"]) # mock import for autodoc autodoc_mock_imports = ["numpy", "mpi4py", "scipy", "pyspline"] ########################################################################### # 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/"), ("stable", "/en/stable/"), ], 'downloads': [ ("pdf", "//mdolab-pygeo.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//mdolab-pygeo.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//mdolab-pygeo.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'mdolab-pygeo', 'name': u'pygeo', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://mdolab-pygeo.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': 'pygeo', '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': '17cb3fcf', } # 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/mdolab-pygeo/builds/585699/' 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: 2021-03-10T14:38:17.034145Z, end-time: 2021-03-10T14:38:22.754576Z, duration: 5, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees-html -D language=en . _build/html Running Sphinx v3.5.2 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [html]: targets for 6 source files that are out of date updating environment: [new config] 6 added, 0 changed, 0 removed reading sources... [ 16%] DVConstraints reading sources... [ 33%] DVGeometry reading sources... [ 50%] index reading sources... [ 66%] pyBlock reading sources... [ 83%] pyGeo reading sources... [100%] pyNetwork looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 16%] DVConstraints writing output... [ 33%] DVGeometry writing output... [ 50%] index writing output... [ 66%] pyBlock writing output... [ 83%] pyGeo writing output... [100%] pyNetwork generating indices... genindex done highlighting module code... [ 20%] pygeo.DVConstraints highlighting module code... [ 40%] pygeo.DVGeometry highlighting module code... [ 60%] pygeo.pyBlock highlighting module code... [ 80%] pygeo.pyGeo highlighting module code... [100%] pygeo.pyNetwork writing additional pages... search done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1 warning. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-03-10T14:38:22.911435Z, end-time: 2021-03-10T14:38:27.477595Z, duration: 4, exit-code: 0 python -m sphinx -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v3.5.2 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 6 added, 0 changed, 0 removed reading sources... [ 16%] DVConstraints reading sources... 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[rtd-command-info] start-time: 2021-03-10T14:38:27.642315Z, end-time: 2021-03-10T14:38:32.123633Z, duration: 4, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.5.2 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [new config] 6 added, 0 changed, 0 removed reading sources... [ 16%] DVConstraints reading sources... [ 33%] DVGeometry reading sources... [ 50%] index reading sources... [ 66%] pyBlock reading sources... [ 83%] pyGeo reading sources... [100%] pyNetwork looking for now-outdated files... none found pickling environment... done checking consistency... done processing pygeo.tex... index DVConstraints DVGeometry pyNetwork pyGeo pyBlock resolving references... done writing... done copying TeX support files... copying TeX support files... done build succeeded, 1 warning. 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). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/checkouts/latest/doc/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2021-03-10T14:38:32.358911Z, end-time: 2021-03-10T14:38:32.438214Z, 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: 2021-03-10T14:38:32.556378Z, end-time: 2021-03-10T14:38:34.959269Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=mdolab-pygeo -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. 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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) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (./sphinxhighlight.sty) 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[25] [26] [27] ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2765 \item {} \begin{description} [28] [29] [30] [31] Underfull \hbox (badness 10000) in paragraph at lines 3210--3210 []\T1/ptm/m/it/10 directory\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-clude-Lo-cal=Tru e\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-clude-Global=True\T1/ptm/m/n/10 , \T1/ptm/ m/it/10 pointSet=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 call- [32] [33] [34] [35] LaTeX Warning: Hyper reference `DVGeometry:pygeo.DVGeometry.addPointSet' on pag e 36 undefined on input line 3710. [36] [37] [38] Chapter 3. [39] [40] Chapter 4. [41] [42] [43] [44] Chapter 5. 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Latexmk: Index file 'mdolab-pygeo.idx' was written Latexmk: Missing input file: 'mdolab-pygeo.ind' from line 'No file mdolab-pygeo.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'mdolab-pygeo.pdf' Rule 'makeindex mdolab-pygeo.idx': File changes, etc: Non-existent destination files: 'mdolab-pygeo.ind' ------------ Run number 1 of rule 'makeindex mdolab-pygeo.idx' ------------ ------------ Running 'makeindex -s python.ist -o "mdolab-pygeo.ind" "mdolab-pygeo.idx"' ------------ Latexmk: applying rule 'makeindex mdolab-pygeo.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-pygeo.idx....done (100 entries accepted, 0 rejected). Sorting entries....done (716 comparisons). Generating output file mdolab-pygeo.ind....done (151 lines written, 0 warnings). Output written in mdolab-pygeo.ind. Transcript written in mdolab-pygeo.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'mdolab-pygeo.aux' 'mdolab-pygeo.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="mdolab-pygeo" "pygeo.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 (./pygeo.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'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb> Output written on mdolab-pygeo.pdf (54 pages, 289765 bytes). Transcript written on mdolab-pygeo.log. Latexmk: Index file 'mdolab-pygeo.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'mdolab-pygeo.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'mdolab-pygeo.aux' 'mdolab-pygeo.out' 'mdolab-pygeo.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="mdolab-pygeo" "pygeo.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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