I am stuck with not being able to properly install Rstan. I have read and done the instructions in github and here in discourse multiple times, reinstalled R + RStudio more than once, but it still does not work. It has been many hours already trying to repeat the same steps, and so frustrating that with previous OS it was working fine. Anyway.
I have been through the forum, tried to adjust the Makevars, but it does not work either. Any guidance much appreciated!
Here is my system info and steps I have completed.
Operating System: Mac OS, Catalina 10.15.6
Interface Version: rstan 2.19.2 ( 2.21.1 refuses to compile see below)
Compiler/Toolkit: not sure
xcode-select version 2373
R 3.6.3 (downgraded from 4.0 because it was not working)
Rstudio 1.3 (latest)
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
Clang++ installed. in R
Rcpp installed already
datate = data.frame( a = rnorm(100, 1), b = c(rep(0, 50), rep(1, 50))) library(brms) brm(bf(a~b), datate, cores = 1, chains = 4)
chain 1: Iteration: 1 / 2000 [ 0%] (Warmup)
 “Error in sampler$call_sampler(args_list[[i]]) : "
 " c++ exception (unknown reason)”
error occurred during calling the sampler; sampling not done
Then if I try to install rstanarm, I get 100s of lines with warnings and errors like this:
ibrary/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias ‘idx_t’ [-Wunused-local-typedef]
using idx_t = typename index_type<matrix_v>::type;
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias ‘idx_t’ [-Wunused-local-typedef]
using idx_t = typename index_type<matrix_d>::type;
In file included from stan_files/bernoulli.cc:3:
stan_files/bernoulli.hpp:2651:24: warning: unused typedef ‘local_scalar_t__’ [-Wunused-local-typedef]
typedef double local_scalar_t__;
R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.6 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 locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  StanHeaders_2.21.0-6 brms_2.13.5 Rcpp_126.96.36.199 loaded via a namespace (and not attached):  nlme_3.1-144 matrixStats_0.57.0 xts_0.12.1 threejs_0.3.3  rstan_2.21.2 tools_3.6.3 backports_1.1.10 R6_2.4.1  DT_0.15 colorspace_1.4-1 withr_2.3.0 tidyselect_1.1.0  gridExtra_2.3 prettyunits_1.1.1 processx_3.4.4 Brobdingnag_1.2-6  emmeans_1.5.1 curl_4.3 compiler_3.6.3 cli_2.0.2  shinyjs_2.0.0 sandwich_3.0-0 colourpicker_1.1.0 scales_1.1.1  dygraphs_188.8.131.52 mvtnorm_1.1-1 ggridges_0.5.2 callr_3.4.4  stringr_1.4.0 digest_0.6.25 base64enc_0.1-3 pkgconfig_2.0.3  htmltools_0.5.0 fastmap_1.0.1 htmlwidgets_1.5.2 rlang_0.4.7  rstudioapi_0.11 shiny_1.5.0 generics_0.0.2 zoo_1.8-8  jsonlite_1.7.1 crosstalk_184.108.40.206 gtools_3.8.2 dplyr_1.0.2  inline_0.3.16 magrittr_1.5 loo_2.3.1 bayesplot_1.7.2  Matrix_1.2-18 munsell_0.5.0 fansi_0.4.1 abind_1.4-5  lifecycle_0.2.0 stringi_1.5.3 multcomp_1.4-14 MASS_7.3-51.5  pkgbuild_1.1.0 plyr_1.8.6 grid_3.6.3 parallel_3.6.3  promises_1.1.1 crayon_1.3.4 miniUI_0.1.1.1 lattice_0.20-38  splines_3.6.3 ps_1.4.0 pillar_1.4.6 igraph_1.2.6  markdown_1.1 estimability_1.3 shinystan_2.5.0 reshape2_1.4.4  codetools_0.2-16 stats4_3.6.3 rstantools_220.127.116.1100 glue_1.4.2  V8_3.2.0 RcppParallel_5.0.2 vctrs_0.3.4 httpuv_1.5.4  gtable_0.3.0 purrr_0.3.4 assertthat_0.2.1 ggplot2_3.3.2  mime_0.9 xtable_1.8-4 coda_0.19-4 later_18.104.22.168  rsconnect_0.8.16 survival_3.1-8 tibble_3.0.3 shinythemes_1.1.2  TH.data_1.0-10 ellipsis_0.3.1 bridgesampling_1.0-0