Read the Docs build information Build id: 2872700 Project: institute-for-disease-modeling-laser-measles Version: latest Commit: b28a63a8041a2498a70df80f8b6daacec02434a9 Date: 2025-03-12T00:56:25.123008Z State: finished Success: True [rtd-command-info] start-time: 2025-03-12T00:56:26.153912Z, end-time: 2025-03-12T00:56:26.671181Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser-measles.git . Cloning into '.'... [rtd-command-info] start-time: 2025-03-12T00:56:26.754164Z, end-time: 2025-03-12T00:56:27.602135Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main From https://github.com/InstituteforDiseaseModeling/laser-measles * [new tag] v0.5.0 -> v0.5.0 [rtd-command-info] start-time: 2025-03-12T00:56:27.719166Z, end-time: 2025-03-12T00:56:27.799581Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. 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 switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at b28a63a 💬 fix typo [rtd-command-info] start-time: 2025-03-12T00:56:27.865681Z, end-time: 2025-03-12T00:56:27.903580Z, duration: 0, exit-code: 0 cat .readthedocs.yml # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details version: 2 sphinx: configuration: docs/conf.py formats: all build: os: ubuntu-22.04 tools: python: "3.12" python: install: - requirements: docs/requirements.txt - method: pip path: . # Optionally build your docs in additional formats such as PDF and ePub # formats: # - pdf # - epub [rtd-command-info] start-time: 2025-03-12T00:56:32.136027Z, end-time: 2025-03-12T00:56:32.190736Z, duration: 0, exit-code: 0 asdf global python 3.12.7 [rtd-command-info] start-time: 2025-03-12T00:56:32.515976Z, end-time: 2025-03-12T00:56:33.458174Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.7.final.0-64 in 670ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2025-03-12T00:56:33.556664Z, end-time: 2025-03-12T00:56:44.459162Z, duration: 10, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: pip in 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alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.2 Pygments-2.19.1 alabaster-1.0.0 babel-2.17.0 certifi-2025.1.31 charset-normalizer-3.4.1 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.2 requests-2.32.3 roman-numerals-py-3.1.0 snowballstemmer-2.2.0 sphinx-8.2.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.3.0 [rtd-command-info] start-time: 2025-03-12T00:56:54.521536Z, end-time: 2025-03-12T00:56:56.612558Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: sphinx>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages (from -r 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Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Processing /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting click (from laser-measles==0.5.0) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7e/d4/7ebdbd03970677812aac39c869717059dbb71a4cfc033ca6e5221787892c/click-8.1.8-py3-none-any.whl (98 kB) Collecting laser-core==0.1.1 (from laser-measles==0.5.0) Downloading 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0:00:00 Collecting numpy<2.0.0,>=1.26.4 (from laser-core==0.1.1->laser-measles==0.5.0) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/0f/50/de23fde84e45f5c4fda2488c759b69990fd4512387a8632860f3ac9cd225/numpy-1.26.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.0/18.0 MB 14.5 MB/s eta 0:00:00 Collecting numba~=0.59.1 (from laser-core==0.1.1->laser-measles==0.5.0) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/47/ab/ef2605f0463889ea8934feb84ac71c3b3c562bd25bb0fda690ba46ee2fbe/numba-0.59.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.7/3.7 MB 14.8 MB/s eta 0:00:00 Collecting polars (from laser-core==0.1.1->laser-measles==0.5.0) Downloading 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https://packages.idmod.org/api/pypi/pypi-production/packages/packages/38/0d/84200ed6a871ce386ddc82904bfadc0c6b28b0c0ec78176871a4679e40b3/pillow-11.1.0-cp312-cp312-manylinux_2_28_x86_64.whl (4.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 13.7 MB/s eta 0:00:00 Collecting pyparsing>=2.3.1 (from matplotlib->laser-core==0.1.1->laser-measles==0.5.0) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1c/a7/c8a2d361bf89c0d9577c934ebb7421b25dc84bf3a8e3ac0a40aed9acc547/pyparsing-3.2.1-py3-none-any.whl (107 kB) Collecting iniconfig (from pytest->laser-core==0.1.1->laser-measles==0.5.0) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ef/a6/62565a6e1cf69e10f5727360368e451d4b7f58beeac6173dc9db836a5b46/iniconfig-2.0.0-py3-none-any.whl (5.9 kB) Collecting pluggy<2,>=1.5 (from pytest->laser-core==0.1.1->laser-measles==0.5.0) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/88/5f/e351af9a41f866ac3f1fac4ca0613908d9a41741cfcf2228f4ad853b697d/pluggy-1.5.0-py3-none-any.whl (20 kB) Building wheels for collected packages: laser-measles Building wheel for laser-measles (pyproject.toml): started Building wheel for laser-measles (pyproject.toml): finished with status 'done' Created wheel for laser-measles: filename=laser_measles-0.5.0-py3-none-any.whl size=4439818 sha256=4c3afd4b02900ccb837e47246d555e1cb64275a2c70dd89d2332b7162dca2045 Stored in directory: /tmp/pip-ephem-wheel-cache-qaug4n76/wheels/62/3a/36/ef67797e01da7b9b6a2f5625cf489f3ab1d1bec0d42e59cb70 Successfully built laser-measles Installing collected packages: pytz, tzdata, tqdm, six, pyproj, pyparsing, polars, pluggy, pillow, numpy, llvmlite, kiwisolver, iniconfig, fonttools, cycler, click, shapely, python-dateutil, pytest, pyogrio, numba, contourpy, pandas, matplotlib, laser-core, geopandas, laser-measles Successfully installed click-8.1.8 contourpy-1.3.1 cycler-0.12.1 fonttools-4.56.0 geopandas-1.0.1 iniconfig-2.0.0 kiwisolver-1.4.8 laser-core-0.1.1 laser-measles-0.5.0 llvmlite-0.42.0 matplotlib-3.10.1 numba-0.59.1 numpy-1.26.4 pandas-2.2.3 pillow-11.1.0 pluggy-1.5.0 polars-1.24.0 pyogrio-0.10.0 pyparsing-3.2.1 pyproj-3.7.1 pytest-8.3.5 python-dateutil-2.9.0.post0 pytz-2025.1 shapely-2.0.7 six-1.17.0 tqdm-4.67.1 tzdata-2025.1 [rtd-command-info] start-time: 2025-03-12T00:57:37.677853Z, end-time: 2025-03-12T00:57:37.718890Z, duration: 0, exit-code: 0 cat docs/conf.py extensions = [ "sphinx.ext.autodoc", "sphinx.ext.autosummary", "sphinx.ext.coverage", "sphinx.ext.doctest", "sphinx.ext.extlinks", "sphinx.ext.ifconfig", "sphinx.ext.napoleon", "sphinx.ext.todo", "sphinx.ext.viewcode", ] source_suffix = {".rst": "restructuredtext"} master_doc = "index" project = "laser_measles" year = "2024" author = "Institute for Disease Modeling" copyright = f"{year}, Bill & Melinda Gates Foundation" version = release = "0.5.0" pygments_style = "trac" templates_path = ["."] extlinks = { "issue": ("https://github.com/InstituteforDiseaseModeling/laser-measles/issues/%s", "#%s"), "pr": ("https://github.com/InstituteforDiseaseModeling/laser-measles/pull/%s", "PR #%s"), } html_theme = "sphinx_rtd_theme" html_theme_options = { # "githuburl": "https://github.com/InstituteforDiseaseModeling/laser-measles/", } html_use_smartypants = True html_last_updated_fmt = "%b %d, %Y" html_split_index = False html_short_title = f"{project}-{version}" # Napoleon settings (Napolean converts Google-style docstrings to reStructuredText) napoleon_google_docstring = True napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_include_private_with_doc = False napoleon_include_special_with_doc = True napoleon_use_admonition_for_examples = False napoleon_use_admonition_for_notes = False napoleon_use_admonition_for_references = False napoleon_use_ivar = True # from Cookiecutter template, False is the default napoleon_use_param = False # from Cookiecutter template, True is the default napoleon_use_rtype = False # from Cookiecutter template, True is the default napoleon_preprocess_types = False napoleon_type_aliases = None napoleon_attr_annotations = True mathjax3_config = {"TeX": {"Macros": {"small": ["{\\scriptstyle #1}", 1]}}} # Prevent the following warning: # sphinx/builders/linkcheck.py:86: RemovedInSphinx80Warning: The default value for 'linkcheck_report_timeouts_as_broken' will change to False in Sphinx 8, meaning that request timeouts will be reported with a new 'timeout' status, instead of as 'broken'. This is intended to provide more detail as to the failure mode. See https://github.com/sphinx-doc/sphinx/issues/11868 for details. # warnings.warn(deprecation_msg, RemovedInSphinx80Warning, stacklevel=1) linkcheck_report_timeouts_as_broken = False [rtd-command-info] start-time: 2025-03-12T00:57:37.791402Z, end-time: 2025-03-12T00:57:56.582030Z, duration: 18, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.2.3 loading translations [en]... done making output directory... done [autosummary] generating autosummary for: authors.rst, changelog.rst, contributing.rst, index.rst, installation.rst, readme.rst, reference/laser_measles.generic.rst, reference/laser_measles.nigeria.rst, reference/laser_measles.rst, reference/modules.rst, usage.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 11 source files that are out of date updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] authors reading sources... [ 18%] changelog reading sources... [ 27%] contributing reading sources... [ 36%] index reading sources... [ 45%] installation reading sources... [ 55%] readme reading sources... [ 64%] reference/laser_measles reading sources... [ 73%] reference/laser_measles.generic reading sources... [ 82%] reference/laser_measles.nigeria reading sources... [ 91%] reference/modules reading sources... [100%] usage looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/html/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/html/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/html/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/html/_static/js/versions.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 9%] authors writing output... [ 18%] changelog writing output... [ 27%] contributing writing output... [ 36%] index writing output... [ 45%] installation writing output... [ 55%] readme writing output... [ 64%] reference/laser_measles writing output... [ 73%] reference/laser_measles.generic writing output... [ 82%] reference/laser_measles.nigeria writing output... [ 91%] reference/modules writing output... [100%] usage generating indices... genindex py-modindex done highlighting module code... [ 7%] laser_measles.antibodies highlighting module code... [ 13%] laser_measles.births highlighting module code... [ 20%] laser_measles.core highlighting module code... [ 27%] laser_measles.generic.metapop highlighting module code... [ 33%] laser_measles.generic.params highlighting module code... [ 40%] laser_measles.incubation highlighting module code... [ 47%] laser_measles.infection highlighting module code... [ 53%] laser_measles.model highlighting module code... [ 60%] laser_measles.mortality highlighting module code... [ 67%] laser_measles.nigeria.metapop highlighting module code... [ 73%] laser_measles.nigeria.params highlighting module code... [ 80%] laser_measles.routine highlighting module code... [ 87%] laser_measles.susceptibility highlighting module code... [ 93%] laser_measles.transmission highlighting module code... [100%] laser_measles.utils writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2025-03-12T00:57:56.648782Z, end-time: 2025-03-12T00:58:07.517268Z, duration: 10, exit-code: 0 python -m sphinx -T -b singlehtml -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v8.2.3 loading translations [en]... done making output directory... done loading pickled environment... The configuration has changed (2 options: 'html_permalinks_icon', 'jquery_use_sri') done [autosummary] generating autosummary for: authors.rst, changelog.rst, contributing.rst, index.rst, installation.rst, readme.rst, reference/laser_measles.generic.rst, reference/laser_measles.nigeria.rst, reference/laser_measles.rst, reference/modules.rst, usage.rst building [mo]: targets for 0 po files that are out of date writing output... building [singlehtml]: all documents updating environment: 0 added, 0 changed, 0 removed reading sources... looking for now-outdated files... none found preparing documents... done copying assets... copying static files... 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Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/js/versions.js copying static files: done copying extra files... copying extra files: done dumping object inventory... done build succeeded. The HTML page is in ../_readthedocs/htmlzip. [rtd-command-info] start-time: 2025-03-12T00:58:08.093375Z, end-time: 2025-03-12T00:58:21.130111Z, duration: 13, exit-code: 0 python -m sphinx -T -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v8.2.3 loading translations [en]... done making output directory... done loading pickled environment... The configuration has changed (2 options: 'html_permalinks_icon', 'jquery_use_sri') done [autosummary] generating autosummary for: authors.rst, changelog.rst, contributing.rst, index.rst, installation.rst, readme.rst, reference/laser_measles.generic.rst, reference/laser_measles.nigeria.rst, reference/laser_measles.rst, reference/modules.rst, usage.rst building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed reading sources... looking for now-outdated files... none found preparing documents... done copying assets... copying TeX support files... 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The LaTeX files are in ../_readthedocs/pdf. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2025-03-12T00:58:21.192940Z, end-time: 2025-03-12T00:58:21.232339Z, 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: 2025-03-12T00:58:21.316696Z, end-time: 2025-03-12T00:58:25.090004Z, duration: 3, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-laser-measles -interaction=nonstopmode Use of uninitialized value in concatenation (.) or string at (eval 10) line 1. Use of uninitialized value in concatenation (.) or string at (eval 10) line 2. Use of uninitialized value in concatenation (.) or string at (eval 10) line 3. Use of uninitialized value in concatenation (.) or string at (eval 10) line 4. Subroutine makeglo redefined at (eval 11) line 7. Use of uninitialized value in concatenation (.) or string at (eval 11) line 1. Use of uninitialized value in concatenation (.) or string at (eval 11) line 2. 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Rerun to get cross-references right. Package rerunfilecheck Warning: File `institute-for-disease-modeling-laser-meas les.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb> Output written on institute-for-disease-modeling-laser-measles.pdf (49 pages, 2 56802 bytes). Transcript written on institute-for-disease-modeling-laser-measles.log. Latexmk: Index file 'institute-for-disease-modeling-laser-measles.idx' was written Latexmk: Missing input file 'institute-for-disease-modeling-laser-measles.ind' (or dependence on it) from following: 'No file institute-for-disease-modeling-laser-measles.ind.' Latexmk: References changed. 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Latexmk: Log file says output to 'institute-for-disease-modeling-laser-measles.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-laser-measles.pdf' Latexmk: List of undefined refs and citations: Reference `reference/laser_measles.generic:module-laser_measles.generic' on page 45 undefined on input line 4679 Reference `reference/laser_measles.generic:module-laser_measles.generic.metapop' on page 45 undefined on input line 4680 Reference `reference/laser_measles.generic:module-laser_measles.generic.model' on page 45 undefined on input line 4681 Reference `reference/laser_measles.generic:module-laser_measles.generic.params' on page 45 undefined on input line 4682 Reference `reference/laser_measles.nigeria:module-laser_measles.nigeria' on page 45 undefined on input line 4687 Reference `reference/laser_measles.nigeria:module-laser_measles.nigeria.lgas' on page 45 undefined on input line 4688 Reference `reference/laser_measles.nigeria:module-laser_measles.nigeria.metapop' on page 45 undefined on input line 4689 Reference `reference/laser_measles.nigeria:module-laser_measles.nigeria.model' on page 45 undefined on input line 4690 Reference `reference/laser_measles.nigeria:module-laser_measles.nigeria.params' on page 45 undefined on input line 4691 Reference `reference/laser_measles:module-laser_measles' on page 45 undefined on input line 4674 Reference `reference/laser_measles:module-laser_measles.antibodies' on page 45 undefined on input line 4675 Reference `reference/laser_measles:module-laser_measles.births' on page 45 undefined on input line 4676 Reference `reference/laser_measles:module-laser_measles.cli' on page 45 undefined on input line 4677 Reference `reference/laser_measles:module-laser_measles.core' on page 45 undefined on input line 4678 Reference `reference/laser_measles:module-laser_measles.incubation' on page 45 undefined on input line 4683 Reference `reference/laser_measles:module-laser_measles.infection' on page 45 undefined on input line 4684 Reference `reference/laser_measles:module-laser_measles.model' on page 45 undefined on input line 4685 Reference `reference/laser_measles:module-laser_measles.mortality' on page 45 undefined on input line 4686 Reference `reference/laser_measles:module-laser_measles.routine' on page 45 undefined on input line 4692 Reference `reference/laser_measles:module-laser_measles.susceptibility' on page 45 undefined on input line 4693 Reference `reference/laser_measles:module-laser_measles.transmission' on page 45 undefined on input line 4694 Reference `reference/laser_measles:module-laser_measles.utils' on page 45 undefined on input line 4695 Rule 'makeindex institute-for-disease-modeling-laser-measles.idx': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-laser-measles.idx' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-laser-measles.idx' ------------ Latexmk: Examining 'institute-for-disease-modeling-laser-measles.log' === TeX engine is 'pdfTeX' Latexmk: applying rule 'makeindex institute-for-disease-modeling-laser-measles.idx'... ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-laser-measles.ind" "institute-for-disease-modeling-laser-measles.idx"' ------------ This is makeindex, version 2.15 [TeX Live 2022/dev] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-laser-measles.idx....done (156 entries accepted, 0 rejected). Sorting entries....done (1192 comparisons). Generating output file institute-for-disease-modeling-laser-measles.ind....done (269 lines written, 0 warnings). Output written in institute-for-disease-modeling-laser-measles.ind. Transcript written in institute-for-disease-modeling-laser-measles.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-laser-measles.aux' 'institute-for-disease-modeling-laser-measles.ind' 'institute-for-disease-modeling-laser-measles.out' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-laser-measles" "laser_measles.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb> Output written on institute-for-disease-modeling-laser-measles.pdf (53 pages, 2 75803 bytes). Transcript written on institute-for-disease-modeling-laser-measles.log. Latexmk: Index file 'institute-for-disease-modeling-laser-measles.idx' was written Latexmk: References changed. 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