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Unable to install epidemics on MacBook #63

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jamesmbaazam opened this issue Jun 5, 2023 · 9 comments · Fixed by #88
Closed

Unable to install epidemics on MacBook #63

jamesmbaazam opened this issue Jun 5, 2023 · 9 comments · Fixed by #88
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@jamesmbaazam
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I am unable to install this package on my Apple Mac with M2 chip. Here is a reprex

pak::pak("epiverse-trace/epidemics")
#> ℹ Loading metadata database
#> ✔ Loading metadata database ... done
#> 
#> 
#> → Will install 1 package.
#> → Will download 1 package with unknown size.
#> + epidemics   0.0.0.9000 👷🏾🔧 ⬇ (GitHub: e8ae6a6)
#> ℹ Getting 1 pkg with unknown size
#> ✔ Got epidemics 0.0.0.9000 (source) (221.57 kB)
#> ℹ Packaging epidemics 0.0.0.9000
#> ✔ Packaged epidemics 0.0.0.9000 (1.9s)
#> ℹ Building epidemics 0.0.0.9000
#> ✖ Failed to build epidemics 0.0.0.9000
#> Error: ! error in pak subprocess
#> Caused by error in `stop_task_build(state, worker)`:
#> ! Failed to build source package 'epidemics'
#> Full installation output:
#> * installing *source* package ‘epidemics’ ...
#> staged installation is only possible with locking
#> ** using non-staged installation
#> ** libs
#> using C++ compiler: ‘Homebrew clang version 16.0.3’
#> using SDK: ‘MacOSX13.3.sdk’
#> /opt/homebrew/bin/ccache /opt/homebrew/opt/llvm/bin/clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp   -I../inst/include -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:540:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:2:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/LU:47:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:3:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:3:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:4:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/QR:15:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Householder:27:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:4:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/QR:48:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:5:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SVD:48:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:6:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Geometry:58:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:7:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
#>       Index count = 0;
#>             ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:27:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:31:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:33:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
#>   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
#>         ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
#>   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
#>         ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:32:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:33:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:44:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:239:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
#>   int count = 0;
#>       ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#>     #pragma clang diagnostic pop
#>                              ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:367:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_difference_op<double> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations]
#>   typedef typename std::result_of<T>::type type1;
#>                         ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_difference_op<double> (const double &, const double &)>' requested here
#>   typedef typename result_of<
#>                    ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1, 0>>, const Eigen::Array<double, -1, 1, 0>>>' requested here
#> template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
#>                                                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<CwiseBinaryOp<scalar_difference_op<double, double>, const CwiseNullaryOp<scalar_constant_op<double>, const Array<double, -1, 1, 0, -1, 1>>, const Array<double, -1, 1, 0, -1, 1>>>' required here
#>   : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type
#>                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1, 0>>, const Eigen::Array<double, -1, 1, 0>, Eigen::Dense>' requested here
#>   public CwiseBinaryOpImpl<
#>          ^
#> ../inst/include/intervention.h:33:35: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1, 0>>, const Eigen::Array<double, -1, 1, 0>>' requested here
#>       cm.array().colwise() * (1.0 - contact_reduction);
#>                                   ^
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__type_traits/result_of.h:24:34: note: 'result_of<Eigen::internal::scalar_difference_op<double> (const double &, const double &)>' has been explicitly marked deprecated here
#> template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
#>                                  ^
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:808:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#> #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
#>                                         ^
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:781:49: note: expanded from macro '_LIBCPP_DEPRECATED'
#> #      define _LIBCPP_DEPRECATED __attribute__((deprecated))
#>                                                 ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:367:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_product_op<double> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations]
#>   typedef typename std::result_of<T>::type type1;
#>                         ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_product_op<double> (const double &, const double &)>' requested here
#>   typedef typename result_of<
#>                    ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, -1, 0>>, const Eigen::Replicate<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1, 0>>, const Eigen::Array<double, -1, 1, 0>>, 1, -1>>>' requested here
#> template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
#>                                                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<CwiseBinaryOp<scalar_product_op<double, double>, const ArrayWrapper<const Matrix<double, -1, -1, 0, -1, -1>>, const Replicate<CwiseBinaryOp<scalar_difference_op<double, double>, const CwiseNullaryOp<scalar_constant_op<double>, const Array<double, -1, 1, 0, -1, 1>>, const Array<double, -1, 1, 0, -1, 1>>, 1, -1>>>' required here
#>   : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type
#>                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_product_op<double>, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, -1, 0>>, const Eigen::Replicate<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1, 0>>, const Eigen::Array<double, -1, 1, 0>>, 1, -1>, Eigen::Dense>' requested here
#>   public CwiseBinaryOpImpl<
#>          ^
#> ../inst/include/intervention.h:33:28: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, -1, 0>>, const Eigen::Replicate<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1, 0>>, const Eigen::Array<double, -1, 1, 0>>, 1, -1>>' requested here
#>       cm.array().colwise() * (1.0 - contact_reduction);
#>                            ^
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__type_traits/result_of.h:24:34: note: 'result_of<Eigen::internal::scalar_product_op<double> (const double &, const double &)>' has been explicitly marked deprecated here
#> template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
#>                                  ^
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:808:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#> #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
#>                                         ^
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:781:49: note: expanded from macro '_LIBCPP_DEPRECATED'
#> #      define _LIBCPP_DEPRECATED __attribute__((deprecated))
#>                                                 ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/quantity.hpp:29:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/conversion.hpp:17:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/conversion_impl.hpp:20:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/heterogeneous_system.hpp:34:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token]
#> #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
#>          ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
#>      <boost/typeof/incr_registration_group.hpp>
#>             ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/quantity.hpp:29:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/conversion.hpp:17:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/conversion_impl.hpp:20:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/heterogeneous_system.hpp:35:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/dimension.hpp:21:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token]
#> #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
#>          ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
#>      <boost/typeof/incr_registration_group.hpp>
#>             ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/quantity.hpp:29:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/conversion.hpp:17:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/conversion_impl.hpp:20:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/heterogeneous_system.hpp:35:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/dimension.hpp:21:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/dimension_list.hpp:131:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token]
#> #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
#>          ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
#>      <boost/typeof/incr_registration_group.hpp>
#>             ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/quantity.hpp:29:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/conversion.hpp:17:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/conversion_impl.hpp:20:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/heterogeneous_system.hpp:39:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/linear_algebra.hpp:20:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token]
#> #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
#>          ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
#>      <boost/typeof/incr_registration_group.hpp>
#>             ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/quantity.hpp:29:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/conversion.hpp:17:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/conversion_impl.hpp:20:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/heterogeneous_system.hpp:40:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/unscale.hpp:28:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token]
#> #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
#>          ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
#>      <boost/typeof/incr_registration_group.hpp>
#>             ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/quantity.hpp:29:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/conversion.hpp:17:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/conversion_impl.hpp:20:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token]
#> #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
#>          ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
#>      <boost/typeof/incr_registration_group.hpp>
#>             ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/quantity.hpp:29:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/conversion.hpp:17:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/detail/conversion_impl.hpp:21:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token]
#> #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
#>          ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
#>      <boost/typeof/incr_registration_group.hpp>
#>             ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token]
#> #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
#>          ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
#>      <boost/typeof/incr_registration_group.hpp>
#>             ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:63:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/multi_array_algebra.hpp:22:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/multi_array.hpp:34:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/multi_array/multi_array_ref.hpp:32:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:45:24: error: no member named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
#>             using std::unary_function;
#>                   ~~~~~^~~~~~~~~~~~~~
#>                        __unary_function
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
#> using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
#> ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:63:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/multi_array_algebra.hpp:22:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/multi_array.hpp:34:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/multi_array/multi_array_ref.hpp:32:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:46:24: error: no member named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
#>             using std::binary_function;
#>                   ~~~~~^~~~~~~~~~~~~~~
#>                        __binary_function
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
#> using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
#> ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:19:
#> In file included from ../inst/include/epidemic_default.h:13:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint.hpp:63:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/numeric/odeint/algebra/multi_array_algebra.hpp:22:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/multi_array.hpp:34:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/multi_array/multi_array_ref.hpp:32:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:180:45: error: no template named 'unary_function' in namespace 'boost::functional::detail'; did you mean '__unary_function'?
#>         : public boost::functional::detail::unary_function<typename unary_traits<Predicate>::argument_type,bool>
#>                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
#>                                             __unary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:45:24: note: '__unary_function' declared here
#>             using std::unary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:214:45: error: no template named 'binary_function' in namespace 'boost::functional::detail'; did you mean '__binary_function'?
#>         : public boost::functional::detail::binary_function<
#>                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
#>                                             __binary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:46:24: note: '__binary_function' declared here
#>             using std::binary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:252:45: error: no template named 'unary_function' in namespace 'boost::functional::detail'; did you mean '__unary_function'?
#>         : public boost::functional::detail::unary_function<
#>                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
#>                                             __unary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:45:24: note: '__unary_function' declared here
#>             using std::unary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:299:45: error: no template named 'unary_function' in namespace 'boost::functional::detail'; did you mean '__unary_function'?
#>         : public boost::functional::detail::unary_function<
#>                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
#>                                             __unary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:45:24: note: '__unary_function' declared here
#>             using std::unary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:345:57: error: no template named 'unary_function' in namespace 'boost::functional::detail'; did you mean '__unary_function'?
#>     class mem_fun_t : public boost::functional::detail::unary_function<T*, S>
#>                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
#>                                                         __unary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:45:24: note: '__unary_function' declared here
#>             using std::unary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:361:58: error: no template named 'binary_function' in namespace 'boost::functional::detail'; did you mean '__binary_function'?
#>     class mem_fun1_t : public boost::functional::detail::binary_function<T*, A, S>
#>                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
#>                                                          __binary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:46:24: note: '__binary_function' declared here
#>             using std::binary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:377:63: error: no template named 'unary_function' in namespace 'boost::functional::detail'; did you mean '__unary_function'?
#>     class const_mem_fun_t : public boost::functional::detail::unary_function<const T*, S>
#>                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
#>                                                               __unary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:45:24: note: '__unary_function' declared here
#>             using std::unary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:393:64: error: no template named 'binary_function' in namespace 'boost::functional::detail'; did you mean '__binary_function'?
#>     class const_mem_fun1_t : public boost::functional::detail::binary_function<const T*, A, S>
#>                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
#>                                                                __binary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:46:24: note: '__binary_function' declared here
#>             using std::binary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:438:61: error: no template named 'unary_function' in namespace 'boost::functional::detail'; did you mean '__unary_function'?
#>     class mem_fun_ref_t : public boost::functional::detail::unary_function<T&, S>
#>                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
#>                                                             __unary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:45:24: note: '__unary_function' declared here
#>             using std::unary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:454:62: error: no template named 'binary_function' in namespace 'boost::functional::detail'; did you mean '__binary_function'?
#>     class mem_fun1_ref_t : public boost::functional::detail::binary_function<T&, A, S>
#>                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
#>                                                              __binary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:46:24: note: '__binary_function' declared here
#>             using std::binary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:470:67: error: no template named 'unary_function' in namespace 'boost::functional::detail'; did you mean '__unary_function'?
#>     class const_mem_fun_ref_t : public boost::functional::detail::unary_function<const T&, S>
#>                                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
#>                                                                   __unary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:45:24: note: '__unary_function' declared here
#>             using std::unary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:487:68: error: no template named 'binary_function' in namespace 'boost::functional::detail'; did you mean '__binary_function'?
#>     class const_mem_fun1_ref_t : public boost::functional::detail::binary_function<const T&, A, S>
#>                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
#>                                                                    __binary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:46:24: note: '__binary_function' declared here
#>             using std::binary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:533:73: error: no template named 'unary_function' in namespace 'boost::functional::detail'; did you mean '__unary_function'?
#>     class pointer_to_unary_function : public boost::functional::detail::unary_function<Arg,Result>
#>                                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
#>                                                                         __unary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:45:24: note: '__unary_function' declared here
#>             using std::unary_function;
#>                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:557:74: error: no template named 'binary_function' in namespace 'boost::functional::detail'; did you mean '__binary_function'?
#>     class pointer_to_binary_function : public boost::functional::detail::binary_function<Arg1,Arg2,Result>
#>                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
#>                                                                          __binary_function
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/functional.hpp:46:24: note: '__binary_function' declared here
#>             using std::binary_function;
#>                        ^
#> In file included from RcppExports.cpp:4:
#> In file included from ./../inst/include/epidemics.h:15:
#> In file included from ../inst/include/ode_tools.h:11:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:367:
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_opposite_op<double> (const double &)>' is deprecated [-Wdeprecated-declarations]
#>   typedef typename std::result_of<T>::type type1;
#>                         ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:21:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_opposite_op<double> (const double &)>' requested here
#>   typedef typename result_of<
#>                    ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseUnaryOp<Eigen::internal::scalar_opposite_op<double>, const Eigen::Array<double, -1, 1, 0>>>' requested here
#> template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
#>                                                        ^
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:95:22: note: in instantiation of default argument for 'generic_xpr_base<CwiseUnaryOp<scalar_opposite_op<double>, const Array<double, -1, 1, 0, -1, 1>>>' required here
#>   : public internal::generic_xpr_base<CwiseUnaryOp<UnaryOp, XprType> >::type
#>                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:55:29: note: in instantiation of template class 'Eigen::CwiseUnaryOpImpl<Eigen::internal::scalar_opposite_op<double>, const Eigen::Array<double, -1, 1, 0>, Eigen::Dense>' requested here
#> class CwiseUnaryOp : public CwiseUnaryOpImpl<UnaryOp, XprType, typename internal::traits<XprType>::StorageKind>, internal::no_assignment_operator
#>                             ^
#> ../inst/include/epidemic_default.h:67:19: note: in instantiation of template class 'Eigen::CwiseUnaryOp<Eigen::internal::scalar_opposite_op<double>, const Eigen::Array<double, -1, 1, 0>>' requested here
#>     dxdt.col(0) = -sToE - sToV;  // -β*S*contacts*I - ν*S
#>                   ^
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__type_traits/result_of.h:24:34: note: 'result_of<Eigen::internal::scalar_opposite_op<double> (const double &)>' has been explicitly marked deprecated here
#> template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
#>                                  ^
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:808:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#> #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
#>                                         ^
#> /opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:781:49: note: expanded from macro '_LIBCPP_DEPRECATED'
#> #      define _LIBCPP_DEPRECATED __attribute__((deprecated))
#>                                                 ^
#> 33 warnings and 16 errors generated.
#> make: *** [RcppExports.o] Error 1
#> ERROR: compilation failed for package ‘epidemics’
#> * removing ‘/private/var/folders/vr/dn4r1_zj417drd1zr9301trw0000gp/T/RtmpbKwOQS/pkg-lib96a67b352889/epidemics’
Created on 2023-06-05 with [reprex v2.0.2](https://reprex.tidyverse.org/)
@jamesmbaazam
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Here's my session info:

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

@pratikunterwegs
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Thanks - I'll take a look to see whether throwing the current state on to Rhub flags any problems, that might help diagnose the issue.

@pratikunterwegs pratikunterwegs added the Discussion Issues kept open for discussions in the comments label Jun 6, 2023
@pratikunterwegs pratikunterwegs added Stale Stale issues that have been open for some time and are not likely to be tackled. and removed Discussion Issues kept open for discussions in the comments labels Jun 21, 2023
@jamesmbaazam
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jamesmbaazam commented Aug 3, 2023 •
edited
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This issue has been fixed here stan-dev/cmdstanr#790 as it was more broadly an issue with my computer not being able to install packages from source because of a broken toolchain. Hope this helps someone else later on.

The issue can be closed now.

@pratikunterwegs
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Thanks for following up @jamesmbaazam - I'll re-add the Discussion tag and add a 'known-issue' tag as well, and keep this open for future reference.

@pratikunterwegs pratikunterwegs added Discussion Issues kept open for discussions in the comments known-issue and removed Stale Stale issues that have been open for some time and are not likely to be tackled. labels Aug 3, 2023
@pratikunterwegs pratikunterwegs pinned this issue Aug 3, 2023
@jamesmbaazam
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jamesmbaazam commented Aug 3, 2023 •
edited
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It might also help to set up an installation wiki OR point to those in other places, for example, rstan. I was contacted by someone last week about installing this package on Windows and it turned out their issue was that {rtools} wasn't on their path.

@pratikunterwegs
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Do you mean installing {epidemics} on Windows?

I would rather do docs as code and include installation instructions in the Readme or in a vignette.

@jamesmbaazam
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jamesmbaazam commented Aug 3, 2023 •
edited
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Do you mean installing {epidemics} on Windows?

Yes

I would rather do docs as code and include installation instructions in the Readme or in a vignette.

That should be fine too. Was only providing one suggestion.

@pratikunterwegs
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Thanks, I'll open an issue for this. Would you or the person who asked about Windows installation be able to provide a reprex or more details about the Rtools issue? Or any other issues that I could cover in the installation guide?

@pratikunterwegs pratikunterwegs mentioned this issue Aug 3, 2023
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@jamesmbaazam
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That was Hikaru. I doubt the issue can be reprex'd as it was a path issue and has been resolved. More broadly, the instruction for Windows users should be for them to ensure they have {Rtools} installed and added to the system path. Something along the lines of the instruction in the rstan wiki.

pratikunterwegs added a commit that referenced this issue Aug 11, 2023
@pratikunterwegs
Add installation notes, fixes #63, fixes #78
2fc8021
@pratikunterwegs pratikunterwegs mentioned this issue Aug 11, 2023
Merged
pratikunterwegs added a commit that referenced this issue Aug 14, 2023
@pratikunterwegs
Add installation notes, fixes #63, fixes #78
8644186
@pratikunterwegs pratikunterwegs unpinned this issue Aug 15, 2023
@pratikunterwegs pratikunterwegs mentioned this issue Oct 5, 2023
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@jamesmbaazam jamesmbaazam mentioned this issue Oct 5, 2023
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Add installation notes, fixes #63, fixes #78 epiverse-trace/epidemics
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@pratikunterwegs @jamesmbaazam