Installing Rstan

I’m having trouble installing rstan on my Mac OS Catalina with R version 3.6.2. I’m following the instruction on this link and I’m getting an error when I try to install RcppArmadillo. It seems like there is a problem with installing cmath. Does anyone have suggestions on what to do in this case? Thanks so much!

According to @wds15, if you download


CTRL+right click on the file, then clicking “Open” will get the installer going

it will set things up for you.

It’s still not working. I can install rstan but I get the following error:

Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.19.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
> fit <- stan(model_code = "data { vector[10] y;} parameters{real mu;} model{y~normal(mu,1);}", data = list(y = rnorm(10)))
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Core:96:
In file included from /usr/local/clang7/include/c++/v1/complex:246:
/usr/local/clang7/include/c++/v1/cmath:313:9: error: no member named 'signbit' in the global namespace
using ::signbit;
/usr/local/clang7/include/c++/v1/cmath:314:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
/usr/local/clang7/include/c++/v1/cmath:315:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'?
using ::isfinite;
In addition: Warning message:
In system(cmd, intern = !verbose) :
  running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file1456127aef68.cpp 2> file1456127aef68.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection
> pkgbuild::has_build_tools(debug = TRUE)
[1] TRUE

My Makevars file is

# clang: start
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include

SHLIB_CXXLDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
SHLIB_CXX14LDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
# clang: end

and my sessionInfo is

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages:
[1] rstan_2.19.2         ggplot2_3.2.1        StanHeaders_2.21.0-1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3         pillar_1.4.3       compiler_3.6.2     prettyunits_1.1.1 
 [5] tools_3.6.2        pkgbuild_1.0.6     lifecycle_0.1.0    tibble_2.1.3      
 [9] gtable_0.3.0       pkgconfig_2.0.3    rlang_0.4.3        cli_2.0.1         
[13] rstudioapi_0.10    parallel_3.6.2     yaml_2.2.0         loo_2.2.0         
[17] gridExtra_2.3      withr_2.1.2        dplyr_0.8.3        stats4_3.6.2      
[21] grid_3.6.2         tidyselect_0.2.5   glue_1.3.1         inline_0.3.15     
[25] R6_2.4.1           processx_3.4.1     fansi_0.4.1        purrr_0.3.2       
[29] callr_3.4.1        magrittr_1.5       scales_1.1.0       ps_1.3.0          
[33] matrixStats_0.55.0 assertthat_0.2.1   colorspace_1.4-1   lazyeval_0.2.2    
[37] munsell_0.5.0      crayon_1.3.4     

@coatless: It seems that we can get the installer to run on Catalina by pressing

CTRL+right click on the file, then clicking “Open”

but now there are other problems like the one @sunsets mentioned. Maybe something else changed with Catalina on January 1?