Problem with R update to 4.0.2 on MacOS: stan stuck in model fit

Interfaces RStan
26

Thanks much. I’m reporting outputs here from a machine running Mohave, but I get the same behavior on a different machine I just upgraded to Catalina (and did a fresh R and RStan install on).

> Rcpp::evalCpp("1 + 1", verbose = TRUE)

Generated code for function definition: 
--------------------------------------------------------

#include <Rcpp.h>

using namespace Rcpp;

// [[Rcpp::export]]
SEXP get_value(){ return wrap( 1 + 1 ) ; }

Generated extern "C" functions 
--------------------------------------------------------


#include <Rcpp.h>
// get_value
SEXP get_value();
RcppExport SEXP sourceCpp_1_get_value() {
BEGIN_RCPP
    Rcpp::RObject rcpp_result_gen;
    Rcpp::RNGScope rcpp_rngScope_gen;
    rcpp_result_gen = Rcpp::wrap(get_value());
    return rcpp_result_gen;
END_RCPP
}

Generated R functions 
-------------------------------------------------------

`.sourceCpp_1_DLLInfo` <- dyn.load('/private/var/folders/_t/y8rbmtzj4jz0qxpl_bt_wqlw0000gp/T/Rtmpf0xuzk/sourceCpp-x86_64-apple-darwin17.0-1.0.5/sourcecpp_131e1414200d5/sourceCpp_2.so')

get_value <- Rcpp:::sourceCppFunction(function() {}, FALSE, `.sourceCpp_1_DLLInfo`, 'sourceCpp_1_get_value')

rm(`.sourceCpp_1_DLLInfo`)

Building shared library
--------------------------------------------------------

DIR: /private/var/folders/_t/y8rbmtzj4jz0qxpl_bt_wqlw0000gp/T/Rtmpf0xuzk/sourceCpp-x86_64-apple-darwin17.0-1.0.5/sourcecpp_131e1414200d5

/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o 'sourceCpp_2.so' 'file131e138e8e1d3.cpp' 
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include" -I"/private/var/folders/_t/y8rbmtzj4jz0qxpl_bt_wqlw0000gp/T/Rtmpf0xuzk/sourceCpp-x86_64-apple-darwin17.0-1.0.5" -I/usr/local/include   -fPIC  -Wall -g -O2  -c file131e138e8e1d3.cpp -o file131e138e8e1d3.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o sourceCpp_2.so file131e138e8e1d3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 2
>

And,

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2    Rcpp_1.0.5    
>

And,

> cat(readLines(file.path(Sys.getenv("HOME"), ".R", "Makevars")), sep = "\n")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/Users/jdsal/.R/Makevars': No such file or directory
>

Then following

update.packages(ask = FALSE, checkBuilt = TRUE)

I get the same hanging behavior as described above if I run the schools example.