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Dev package version failing to install #927

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micahwiesner67 opened this issue Jan 14, 2025 · 4 comments
Open

Dev package version failing to install #927

micahwiesner67 opened this issue Jan 14, 2025 · 4 comments

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@micahwiesner67
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micahwiesner67 commented Jan 14, 2025 •
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Summary:
When attempting to install the dev version of this package remotes::install_gitub("epiforecasts/EpiNow2") the C compiler does not complete compilation and 'spins' endlessly. Note: remotes::install_github() defaults to the latest commit on the 'main' branch. I believe this commit is 439cf62.

Reproducible Steps:
To re-create this issue, I attempted to install to a rocker image (geospatial) using the install_github function from the remotes package.
image

After running the above build, I receive massive strings of compilation warnings / errors and the install doesn't complete.

image

install.packages("EpiNow2") appears to be stable.
@jamesmbaazam
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Hi @micahwiesner67, Sorry to hear you're having installation issues. Could you share some system specs to help with diagnosing the issue? It installs fine for me on my computer.

> packageVersion("EpiNow2")
Error in packageVersion("EpiNow2") : there is no package called ‘EpiNow2’
> remotes::install_github("epiforecasts/EpiNow2")
Using GitHub PAT from the git credential store.
Downloading GitHub repo epiforecasts/EpiNow2@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                 
2: CRAN packages only                  
3: None                                
4: Rcpp     (1.0.13-1 -> 1.0.14) [CRAN]
5: processx (3.8.4    -> 3.8.5 ) [CRAN]
6: QuickJSR (1.4.0    -> 1.5.1 ) [CRAN]
7: inline   (0.3.20   -> 0.3.21) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────
   checking for file ‘/private/var/folders/vr/dn4r1_zj417drd1zr9301trw0000gp/T/Rtmplwwmnb/remotes1ca43bd75b8✔  checking for file ‘/private/var/folders/vr/dn4r1_zj417drd1zr9301trw0000gp/T/Rtmplwwmnb/remotes1ca43bd75b88/epiforecasts-EpiNow2-439cf62/DESCRIPTION’ (453ms)
─  preparing ‘EpiNow2’: (3.2s)
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts (3.1s)
─  checking for empty or unneeded directories
─  building ‘EpiNow2_1.6.1.9000.tar.gz’
   
Installing package into ‘/Users/lshja16/Library/R/arm64/4.4/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘EpiNow2’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
using C++17
using SDK: ‘’


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -D_HAS_AUTO_PTR_ETC=0 -I'/Users/lshja16/Library/R/arm64/4.4/library/BH/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/rstan/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include' -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp    -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseCore:61:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from RcppExports.cpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseLU:35:
/Users/lshja16/Library/R/arm64/4.4/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]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Users/lshja16/Library/R/arm64/4.4/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]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from RcppExports.cpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: 
      variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from RcppExports.cpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
5 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -D_HAS_AUTO_PTR_ETC=0 -I'/Users/lshja16/Library/R/arm64/4.4/library/BH/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/rstan/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include' -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp    -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_dist_fit.cc -o stanExports_dist_fit.o
In file included from stanExports_dist_fit.cc:5:
In file included from ./stanExports_dist_fit.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseCore:61:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from stanExports_dist_fit.cc:5:
In file included from ./stanExports_dist_fit.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseLU:35:
/Users/lshja16/Library/R/arm64/4.4/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]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Users/lshja16/Library/R/arm64/4.4/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]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from stanExports_dist_fit.cc:5:
In file included from ./stanExports_dist_fit.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 
      'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   47 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_dist_fit.cc:5:
In file included from ./stanExports_dist_fit.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 
      'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   70 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_dist_fit.cc:5:
In file included from ./stanExports_dist_fit.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: 
      variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from stanExports_dist_fit.cc:5:
In file included from ./stanExports_dist_fit.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from stanExports_dist_fit.cc:5:
In file included from ./stanExports_dist_fit.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim.hpp:11:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/constraint.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun.hpp:125:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_1F0.hpp:32:25: warning: 
      unused variable 'function' [-Wunused-variable]
   32 |   constexpr const char* function = "hypergeometric_1f0";
      |                         ^~~~~~~~
In file included from stanExports_dist_fit.cc:5:
In file included from ./stanExports_dist_fit.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: 
      variable 'ret' set but not used [-Wunused-but-set-variable]
 1252 |     int ret = stan::services::error_codes::CONFIG;
      |         ^
In file included from stanExports_dist_fit.cc:5:
In file included from ./stanExports_dist_fit.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/model_header.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:7:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:516:22: warning: 
      unused variable 'rows' [-Wunused-variable]
  516 |   const Eigen::Index rows = row_idx.ns_.size();
      |                      ^~~~
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:517:22: warning: 
      unused variable 'cols' [-Wunused-variable]
  517 |   const Eigen::Index cols = col_idx.ns_.size();
      |                      ^~~~
11 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -D_HAS_AUTO_PTR_ETC=0 -I'/Users/lshja16/Library/R/arm64/4.4/library/BH/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/rstan/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include' -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp    -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_estimate_infections.cc -o stanExports_estimate_infections.o
In file included from stanExports_estimate_infections.cc:5:
In file included from ./stanExports_estimate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseCore:61:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from stanExports_estimate_infections.cc:5:
In file included from ./stanExports_estimate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseLU:35:
/Users/lshja16/Library/R/arm64/4.4/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]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Users/lshja16/Library/R/arm64/4.4/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]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from stanExports_estimate_infections.cc:5:
In file included from ./stanExports_estimate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 
      'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   47 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_estimate_infections.cc:5:
In file included from ./stanExports_estimate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 
      'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   70 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_estimate_infections.cc:5:
In file included from ./stanExports_estimate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: 
      variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from stanExports_estimate_infections.cc:5:
In file included from ./stanExports_estimate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from stanExports_estimate_infections.cc:5:
In file included from ./stanExports_estimate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim.hpp:11:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/constraint.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun.hpp:125:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_1F0.hpp:32:25: warning: 
      unused variable 'function' [-Wunused-variable]
   32 |   constexpr const char* function = "hypergeometric_1f0";
      |                         ^~~~~~~~
In file included from stanExports_estimate_infections.cc:5:
In file included from ./stanExports_estimate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: 
      variable 'ret' set but not used [-Wunused-but-set-variable]
 1252 |     int ret = stan::services::error_codes::CONFIG;
      |         ^
In file included from stanExports_estimate_infections.cc:5:
In file included from ./stanExports_estimate_infections.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/model_header.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:7:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:516:22: warning: 
      unused variable 'rows' [-Wunused-variable]
  516 |   const Eigen::Index rows = row_idx.ns_.size();
      |                      ^~~~
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:517:22: warning: 
      unused variable 'cols' [-Wunused-variable]
  517 |   const Eigen::Index cols = col_idx.ns_.size();
      |                      ^~~~
In file included from stanExports_estimate_infections.cc:5:
./stanExports_estimate_infections.h:6269:18: warning: variable 'rescaled_rho' set but
      not used [-Wunused-but-set-variable]
 6269 |           double rescaled_rho = std::numeric_limits<double>::quiet_NaN();
      |                  ^
12 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -D_HAS_AUTO_PTR_ETC=0 -I'/Users/lshja16/Library/R/arm64/4.4/library/BH/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/rstan/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include' -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp    -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_estimate_secondary.cc -o stanExports_estimate_secondary.o
In file included from stanExports_estimate_secondary.cc:5:
In file included from ./stanExports_estimate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseCore:61:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from stanExports_estimate_secondary.cc:5:
In file included from ./stanExports_estimate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseLU:35:
/Users/lshja16/Library/R/arm64/4.4/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]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Users/lshja16/Library/R/arm64/4.4/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]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from stanExports_estimate_secondary.cc:5:
In file included from ./stanExports_estimate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 
      'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   47 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_estimate_secondary.cc:5:
In file included from ./stanExports_estimate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 
      'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   70 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_estimate_secondary.cc:5:
In file included from ./stanExports_estimate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: 
      variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from stanExports_estimate_secondary.cc:5:
In file included from ./stanExports_estimate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from stanExports_estimate_secondary.cc:5:
In file included from ./stanExports_estimate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim.hpp:11:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/constraint.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun.hpp:125:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_1F0.hpp:32:25: warning: 
      unused variable 'function' [-Wunused-variable]
   32 |   constexpr const char* function = "hypergeometric_1f0";
      |                         ^~~~~~~~
In file included from stanExports_estimate_secondary.cc:5:
In file included from ./stanExports_estimate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: 
      variable 'ret' set but not used [-Wunused-but-set-variable]
 1252 |     int ret = stan::services::error_codes::CONFIG;
      |         ^
In file included from stanExports_estimate_secondary.cc:5:
In file included from ./stanExports_estimate_secondary.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/model_header.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:7:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:516:22: warning: 
      unused variable 'rows' [-Wunused-variable]
  516 |   const Eigen::Index rows = row_idx.ns_.size();
      |                      ^~~~
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:517:22: warning: 
      unused variable 'cols' [-Wunused-variable]
  517 |   const Eigen::Index cols = col_idx.ns_.size();
      |                      ^~~~
11 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -D_HAS_AUTO_PTR_ETC=0 -I'/Users/lshja16/Library/R/arm64/4.4/library/BH/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/rstan/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include' -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp    -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_estimate_truncation.cc -o stanExports_estimate_truncation.o
In file included from stanExports_estimate_truncation.cc:5:
In file included from ./stanExports_estimate_truncation.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseCore:61:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from stanExports_estimate_truncation.cc:5:
In file included from ./stanExports_estimate_truncation.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseLU:35:
/Users/lshja16/Library/R/arm64/4.4/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]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Users/lshja16/Library/R/arm64/4.4/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]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from stanExports_estimate_truncation.cc:5:
In file included from ./stanExports_estimate_truncation.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 
      'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   47 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_estimate_truncation.cc:5:
In file included from ./stanExports_estimate_truncation.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 
      'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   70 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_estimate_truncation.cc:5:
In file included from ./stanExports_estimate_truncation.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: 
      variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from stanExports_estimate_truncation.cc:5:
In file included from ./stanExports_estimate_truncation.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from stanExports_estimate_truncation.cc:5:
In file included from ./stanExports_estimate_truncation.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim.hpp:11:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/constraint.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun.hpp:125:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_1F0.hpp:32:25: warning: 
      unused variable 'function' [-Wunused-variable]
   32 |   constexpr const char* function = "hypergeometric_1f0";
      |                         ^~~~~~~~
In file included from stanExports_estimate_truncation.cc:5:
In file included from ./stanExports_estimate_truncation.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: 
      variable 'ret' set but not used [-Wunused-but-set-variable]
 1252 |     int ret = stan::services::error_codes::CONFIG;
      |         ^
In file included from stanExports_estimate_truncation.cc:5:
In file included from ./stanExports_estimate_truncation.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/model_header.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:7:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:516:22: warning: 
      unused variable 'rows' [-Wunused-variable]
  516 |   const Eigen::Index rows = row_idx.ns_.size();
      |                      ^~~~
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:517:22: warning: 
      unused variable 'cols' [-Wunused-variable]
  517 |   const Eigen::Index cols = col_idx.ns_.size();
      |                      ^~~~
11 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -D_HAS_AUTO_PTR_ETC=0 -I'/Users/lshja16/Library/R/arm64/4.4/library/BH/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/rstan/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include' -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp    -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_simulate_infections.cc -o stanExports_simulate_infections.o
In file included from stanExports_simulate_infections.cc:5:
In file included from ./stanExports_simulate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseCore:61:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from stanExports_simulate_infections.cc:5:
In file included from ./stanExports_simulate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseLU:35:
/Users/lshja16/Library/R/arm64/4.4/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]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Users/lshja16/Library/R/arm64/4.4/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]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from stanExports_simulate_infections.cc:5:
In file included from ./stanExports_simulate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 
      'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   47 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_simulate_infections.cc:5:
In file included from ./stanExports_simulate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 
      'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   70 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_simulate_infections.cc:5:
In file included from ./stanExports_simulate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: 
      variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from stanExports_simulate_infections.cc:5:
In file included from ./stanExports_simulate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from stanExports_simulate_infections.cc:5:
In file included from ./stanExports_simulate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim.hpp:11:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/constraint.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun.hpp:125:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_1F0.hpp:32:25: warning: 
      unused variable 'function' [-Wunused-variable]
   32 |   constexpr const char* function = "hypergeometric_1f0";
      |                         ^~~~~~~~
In file included from stanExports_simulate_infections.cc:5:
In file included from ./stanExports_simulate_infections.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: 
      variable 'ret' set but not used [-Wunused-but-set-variable]
 1252 |     int ret = stan::services::error_codes::CONFIG;
      |         ^
In file included from stanExports_simulate_infections.cc:5:
In file included from ./stanExports_simulate_infections.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/model_header.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:7:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:516:22: warning: 
      unused variable 'rows' [-Wunused-variable]
  516 |   const Eigen::Index rows = row_idx.ns_.size();
      |                      ^~~~
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:517:22: warning: 
      unused variable 'cols' [-Wunused-variable]
  517 |   const Eigen::Index cols = col_idx.ns_.size();
      |                      ^~~~
11 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -D_HAS_AUTO_PTR_ETC=0 -I'/Users/lshja16/Library/R/arm64/4.4/library/BH/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/rstan/include' -I'/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include' -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp    -I'/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_simulate_secondary.cc -o stanExports_simulate_secondary.o
In file included from stanExports_simulate_secondary.cc:5:
In file included from ./stanExports_simulate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseCore:61:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from stanExports_simulate_secondary.cc:5:
In file included from ./stanExports_simulate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/Eigen/SparseLU:35:
/Users/lshja16/Library/R/arm64/4.4/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]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Users/lshja16/Library/R/arm64/4.4/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]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from stanExports_simulate_secondary.cc:5:
In file included from ./stanExports_simulate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 
      'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   47 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_simulate_secondary.cc:5:
In file included from ./stanExports_simulate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:21:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 
      'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   70 |       virtual std::streamsize xsputn(const char_type* s, const int n) {
      |                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:276:22: note: 
      hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch
      at 2nd parameter ('streamsize' (aka 'long') vs 'const int')
  276 |   virtual streamsize xsputn(const char_type* __s, streamsize __n);
      |                      ^
In file included from stanExports_simulate_secondary.cc:5:
In file included from ./stanExports_simulate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: 
      variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from stanExports_simulate_secondary.cc:5:
In file included from ./stanExports_simulate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Users/lshja16/Library/R/arm64/4.4/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: 
      variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from stanExports_simulate_secondary.cc:5:
In file included from ./stanExports_simulate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim.hpp:11:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/constraint.hpp:4:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun.hpp:125:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_1F0.hpp:32:25: warning: 
      unused variable 'function' [-Wunused-variable]
   32 |   constexpr const char* function = "hypergeometric_1f0";
      |                         ^~~~~~~~
In file included from stanExports_simulate_secondary.cc:5:
In file included from ./stanExports_simulate_secondary.h:23:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/rstaninc.hpp:4:
/Users/lshja16/Library/R/arm64/4.4/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: 
      variable 'ret' set but not used [-Wunused-but-set-variable]
 1252 |     int ret = stan::services::error_codes::CONFIG;
      |         ^
In file included from stanExports_simulate_secondary.cc:5:
In file included from ./stanExports_simulate_secondary.h:25:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/model_header.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing.hpp:13:
In file included from /Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:7:
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:516:22: warning: 
      unused variable 'rows' [-Wunused-variable]
  516 |   const Eigen::Index rows = row_idx.ns_.size();
      |                      ^~~~
/Users/lshja16/Library/R/arm64/4.4/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:517:22: warning: 
      unused variable 'cols' [-Wunused-variable]
  517 |   const Eigen::Index cols = col_idx.ns_.size();
      |                      ^~~~
11 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -L/opt/homebrew/opt/libomp/lib -lomp -o EpiNow2.so RcppExports.o stanExports_dist_fit.o stanExports_estimate_infections.o stanExports_estimate_secondary.o stanExports_estimate_truncation.o stanExports_simulate_infections.o stanExports_simulate_secondary.o -L/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/lib/ -Wl,-rpath,/Users/lshja16/Library/R/arm64/4.4/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: ignoring duplicate libraries: '-ltbb', '-ltbbmalloc'
installing to /Users/lshja16/Library/R/arm64/4.4/library/00LOCK-EpiNow2/00new/EpiNow2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EpiNow2)
> Sys.time()
[1] "2025-01-15 12:08:46 GMT"

@jamesmbaazam
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@micahwiesner67 Could you check if you can successfully install and run an rstan model?

install.packages("rstan", repos = c('https://stan-dev.r-universe.dev', getOption("repos")))

library(rstan)
example(stan_model, package = "rstan", run.dontrun = TRUE)

If this works, the model will sample without errors.

@micahwiesner67
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I should have clarified this issue is when installing into linux. Specifically we are installing into a WSL system.

@sbfnk
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sbfnk commented Jan 15, 2025

Is this a new problem (i.e. did it work before), or is this the first time you install the development version?

If new, is it linked to a recent version of the package, i.e. does remotes::install_gitub("epiforecasts/[email protected]") (or e.g. v1.6.0, or v1.5.0) show the same issues?

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@sbfnk @micahwiesner67 @jamesmbaazam