Stan compiling error

Hi,
I have a problem with compiling rstan after I updated new macOS operating system. I ran the 8-school example code on getting-started-with-rstan and got the error:

Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from file25277b5520e.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:8:
In file included from /usr/local/clang4/bin/../include/c++/v1/cstdlib:86:
/
In addition: Warning messages:
1: In readLines(file, warn = TRUE) :
  incomplete final line found on '/Users/yang/Documents/RProgramming/8schools.stan'
2: In system(cmd, intern = !verbose) :
  running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file25277b5520e.cpp 2> file25277b5520e.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection

For traceback, the stan file is:

// saved as 8schools.stan
data {
  int<lower=0> J;         // number of schools 
  real y[J];              // estimated treatment effects
  real<lower=0> sigma[J]; // standard error of effect estimates 
}
parameters {
  real mu;                // population treatment effect
  real<lower=0> tau;      // standard deviation in treatment effects
  vector[J] eta;          // unscaled deviation from mu by school
}
transformed parameters {
  vector[J] theta = mu + tau * eta;        // school treatment effects
}
model {
  target += normal_lpdf(eta | 0, 1);       // prior log-density
  target += normal_lpdf(y | theta, sigma); // log-likelihood
}

And the R code is:

schools_dat <- list(J = 8, 
                    y = c(28,  8, -3,  7, -1,  1, 18, 12),
                    sigma = c(15, 10, 16, 11,  9, 11, 10, 18))
fit <- stan(file = '8schools.stan', data = schools_dat)
print(fit)
plot(fit)

Can anyone help me out here? Thanks!!!

Operating system: macOS Mojave 10.14
R version 3.5.1

Try first doing

file.rename("~/.R/Makevars", "~/.R/old_Makevars")
2 Likes

I’m sorry. It returns FALSE with the warning message:

Warning message:
In file.rename("~/.R/Makevars", "~/.R/old_Makevars") :
  cannot rename file '/Users/yang/.R/Makevars' to '/Users/yang/.R/old_Makevars', reason 'Permission denied'

OK. I don’t know why you wouldn’t be able to write to your own home directory. Try

file.edit("~/.R/Makevars")

and deleting everything in it.

Yea. It works. Thank you so much.

I’ve just run into the same problem, but am unable to rename the Makevars file or delete the contents of the existing file. Any idea what causes this?

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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    
[5] datasets  methods   base     

other attached packages:
 [1] raster_2.6-7       bindrcpp_0.2.2    
 [3] ggridges_0.5.1     tidybayes_1.0.1   
 [5] rstan_2.18.2       StanHeaders_2.18.0
 [7] tigris_0.7         forcats_0.3.0     
 [9] stringr_1.3.1      dplyr_0.7.6       
[11] purrr_0.2.5        readr_1.1.1       
[13] tidyr_0.8.1        tibble_1.4.2      
[15] ggplot2_3.0.0      tidyverse_1.2.1   
[17] sf_0.6-3           spdep_0.7-9       
[19] spData_0.2.9.4     Matrix_1.2-14     
[21] sp_1.3-1          

loaded via a namespace (and not attached):
 [1] nlme_3.1-137             
 [2] matrixStats_0.54.0       
 [3] lubridate_1.7.4          
 [4] gmodels_2.18.1           
 [5] httr_1.3.1               
 [6] LaplacesDemon_16.1.1     
 [7] tools_3.5.1              
 [8] backports_1.1.2          
 [9] rgdal_1.3-4              
[10] R6_2.2.2                 
[11] DBI_1.0.0                
[12] lazyeval_0.2.1           
[13] colorspace_1.3-2         
[14] withr_2.1.2              
[15] tidyselect_0.2.4         
[16] gridExtra_2.3            
[17] prettyunits_1.0.2        
[18] processx_3.2.0           
[19] compiler_3.5.1           
[20] cli_1.0.1                
[21] rvest_0.3.2              
[22] arrayhelpers_1.0-20160527
[23] expm_0.999-3             
[24] xml2_1.2.0               
[25] scales_1.0.0             
[26] classInt_0.2-3           
[27] mvtnorm_1.0-8            
[28] callr_3.0.0              
[29] rappdirs_0.3.1           
[30] foreign_0.8-70           
[31] rethinking_1.59          
[32] base64enc_0.1-3          
[33] pkgconfig_2.0.2          
[34] rlang_0.2.2              
[35] readxl_1.1.0             
[36] rstudioapi_0.7           
[37] svUnit_0.7-12            
[38] bindr_0.1.1              
[39] jsonlite_1.5             
[40] gtools_3.8.1             
[41] inline_0.3.15            
[42] magrittr_1.5             
[43] loo_2.0.0                
[44] Rcpp_0.12.19             
[45] munsell_0.5.0            
[46] stringi_1.2.4            
[47] yaml_2.2.0               
[48] MASS_7.3-50              
[49] ggstance_0.3.1           
[50] pkgbuild_1.0.2           
[51] plyr_1.8.4               
[52] grid_3.5.1               
[53] maptools_0.9-4           
[54] parallel_3.5.1           
[55] gdata_2.18.0             
[56] crayon_1.3.4             
[57] deldir_0.1-15            
[58] lattice_0.20-35          
[59] haven_1.1.2              
[60] splines_3.5.1            
[61] hms_0.4.2                
[62] ps_1.1.0                 
[63] pillar_1.3.0             
[64] uuid_0.1-2               
[65] boot_1.3-20              
[66] stats4_3.5.1             
[67] LearnBayes_2.15.1        
[68] glue_1.3.0               
[69] modelr_0.1.2             
[70] cellranger_1.1.0         
[71] gtable_0.2.0             
[72] assertthat_0.2.0         
[73] broom_0.5.0              
[74] e1071_1.7-0              
[75] coda_0.19-2              
[76] class_7.3-14             
[77] units_0.6-1

Never mind - I figured it out by looking at this post