# RStan installation on Mac

**URL:** <https://discourse.mc-stan.org/t/rstan-installation-on-mac/15821>\
**Category:** Interfaces\
**Tags:** rstan\
**Created:** [June 10, 2020, 3:44pm UTC](https://discourse.mc-stan.org/t/rstan-installation-on-mac/15821 "2020-06-10T15:44:25Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![brophyj](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/brophyj/32/9922_2.png) [@brophyj](https://discourse.mc-stan.org/u/brophyj)\
**Post date:** [June 10, 2020, 3:44pm UTC](https://discourse.mc-stan.org/t/rstan-installation-on-mac/15821/1 "2020-06-10T15:44:25Z")

</div>

Novice Rstan user. Updated to R4.0 and re-installed Rstan according to web instructions.  
Rcpp installed no problem  
\*\* testing if installed package keeps a record of temporary installation path

- DONE (Rcpp)  
Did notice warnings with rstan  
R\> install.packages(“rstan”, type = “source”)  
trying URL ‘[https://cran.rstudio.com/src/contrib/rstan\_2.19.3.tar.gz](https://cran.rstudio.com/src/contrib/rstan_2.19.3.tar.gz)’

Content type ‘application/x-gzip’ length 922337 bytes (900 KB)

==================================================

downloaded 900 KB

- installing _source_ package ‘rstan’ …

\*\* package ‘rstan’ successfully unpacked and MD5 sums checked

\*\* using staged installation  
\*\* libs

In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:535:  
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]  
#pragma clang diagnostic pop  
^

Simple program no longer runs

```
R> model_string <- "
+ data {
+ // Number of data points
+ int n1;
+ int n2;
+ // Number of successes
+ int y1[n1];
+ int y2[n2];
+ }
+ 
+ parameters {
+ real<lower=0, upper=1> theta1;
+ real<lower=0, upper=1> theta2;
+ }
+ 
+ model {  
+ theta1 ~ beta(1, 1);
+ theta2 ~ beta(1, 1);
+ y1 ~ bernoulli(theta1);
+ y2 ~ bernoulli(theta2); 
+ }
+ 
+ generated quantities {
+ }
+ "
R> y1 <- c(0, 1, 0, 0, 0, 0, 1, 0, 0, 0)
R> y2 <- c(0, 0, 1, 1, 1, 0, 1, 1, 1, 0)
R> data_list <- list(y1 = y1, y2 = y2, n1 = length(y1), n2 = length(y2))
R> 
R> library(rstan)
Loading required package: StanHeaders
Loading required package: ggplot2
Keep up to date with changes at https://www.tidyverse.org/blog/
rstan (Version 2.19.3, 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)
R> ###### This is maybe unnecessary
R> options(mc.cores = parallel::detectCores())
R> rstan_options(auto_write = TRUE)
R> # Compiling and producing posterior samples from the model.
R> stan_samples <- stan(model_code = model_string, data = data_list)
starting worker pid=54113 on localhost:11391 at 11:24:08.911
starting worker pid=54111 on localhost:11391 at 11:24:08.911
starting worker pid=54112 on localhost:11391 at 11:24:08.911
starting worker pid=54110 on localhost:11391 at 11:24:08.911
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Execution halted
Execution halted
Execution halted
Execution halted
Error in makePSOCKcluster(names = spec, ...) : 
  Cluster setup failed. 4 of 4 workers failed to connect.

```

SessionInfo

```
R> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[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_2.19.3 ggplot2_3.3.1 StanHeaders_2.21.0-3

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.12 pillar_1.4.4 compiler_4.0.0 prettyunits_1.1.1 tools_4.0.0 digest_0.6.25     
 [7] packrat_0.5.0 pkgbuild_1.0.8 lubridate_1.7.8 evaluate_0.14 lifecycle_0.2.0 tibble_3.0.1      
[13] gtable_0.3.0 lattice_0.20-41 pkgconfig_2.0.3 rlang_0.4.6 Matrix_1.2-18 cli_2.0.2         
[19] rstudioapi_0.11 parallel_4.0.0 yaml_2.2.1 xfun_0.14 loo_2.2.0 gridExtra_2.3     
[25] withr_2.2.0 dplyr_0.8.5 knitr_1.28 generics_0.0.2 vctrs_0.3.1 stats4_4.0.0      
[31] grid_4.0.0 tidyselect_1.1.0 glue_1.4.1 inline_0.3.15 R6_2.4.1 processx_3.4.2    
[37] fansi_0.4.1 rmarkdown_2.1 callr_3.4.3 purrr_0.3.4 magrittr_1.5 codetools_0.2-16  
[43] matrixStats_0.56.0 ps_1.3.3 scales_1.1.1 ellipsis_0.3.1 htmltools_0.4.0 assertthat_0.2.1  
[49] colorspace_1.4-1 munsell_0.5.0 crayon_1.3.4  

```

Thank you

---

<div class="post-metadata">

**Author:** ![torkar](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/torkar/32/1355_2.png) [@torkar](https://discourse.mc-stan.org/u/torkar)\
**Post date:** [June 10, 2020, 3:58pm UTC](https://discourse.mc-stan.org/t/rstan-installation-on-mac/15821/2 "2020-06-10T15:58:05Z")

</div>

Welcome to the community!

Add this to `~/.Rprofile`

```
## WORKAROUND: https://github.com/rstudio/rstudio/issues/6692
## Revert to 'sequential' setup of PSOCK cluster in RStudio Console on macOS and R 4.0.0
if (Sys.getenv("RSTUDIO") == "1" && !nzchar(Sys.getenv("RSTUDIO_TERM")) && 
    Sys.info()["sysname"] == "Darwin") {
  parallel:::setDefaultClusterOptions(setup_strategy = "sequential")
}                   

```

---

<div class="post-metadata">

**Author:** ![brophyj](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/brophyj/32/9922_2.png) [@brophyj](https://discourse.mc-stan.org/u/brophyj)\
**Post date:** [June 10, 2020, 4:48pm UTC](https://discourse.mc-stan.org/t/rstan-installation-on-mac/15821/3 "2020-06-10T16:48:41Z")

</div>

Changes made and it now works.  
Thank you!

---

<div class="post-metadata">

**Author:** ![torkar](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/torkar/32/1355_2.png) [@torkar](https://discourse.mc-stan.org/u/torkar)\
**Post date:** [June 10, 2020, 5:19pm UTC](https://discourse.mc-stan.org/t/rstan-installation-on-mac/15821/4 "2020-06-10T17:19:09Z")

</div>

May the chains mix well!