R crashes when trying out example(stan_model...)

General
1

Hello,

I have tried to install and use rstan on my Windows 10 computer. I am using RStudio Version 1.4.1106 with R version 4.1.0. I was following the description on GitHub (RStan Getting Started · stan-dev/rstan Wiki · GitHub). However, when I try out the example, R always crashes.

This is what I did. First, I removed rstan and cleared RData.

remove.packages("rstan")
if (file.exists(".RData")) file.remove(".RData")

Then, I closed RStudio and opened it up again to install rstan with the following command, producing the following output:

> install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE)

Installing package into ‘C:/Users/Oswin/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/bin/windows/contrib/4.1/rstan_2.21.5.zip'
Content type 'application/zip' length 5268817 bytes (5.0 MB)
downloaded 5.0 MB

package ‘rstan’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Oswin\AppData\Local\Temp\RtmpQPqyZr\downloaded_packages

To try out my installation, I used:

example(stan_model, package = "rstan", run.dontrun = TRUE)

This runs for a bit and then R crashes:

R_crash
R_crash1555×1236 123 KB

Does anyone have an idea what is going wrong here?

2

Sorry for the delay in getting to this! I just need to check some config details to see where the issue might be coming from.

Can you post the outputs from the following R commands:

readLines("~/.Renviron")
readLines("~/.Rprofile")
readLines("~/.R/Makevars.win")
Sys.getenv("PATH")
3

One more: Sys.getenv("RTOOLS40_HOME")

4

Hey,

Thanks for your replies. I had to adapt the paths a bit, I hope these are the files that you were looking for:


> readLines("C:/Program Files/R/R-4.1.0/src/library/windlgs/src/Makevars.win")
[1] "PKG_LIBS=$(GRAPHAPP_LIB)"
> readLines("C:/Program Files/R/R-4.1.0/library/base/help/Renviron.html")
[1] "<html><head><meta http-equiv='refresh' content='0; url=../html/Startup.html'></head></html>"
> readLines("C:/Program Files/R/R-4.1.0/library/base/R/Rprofile")
  [1] "### This is the system Rprofile file. It is always run on startup."                                                           
  [2] "### Additional commands can be placed in site or user Rprofile files"                                                         
  [3] "### (see ?Rprofile)."                                                                                                         
  [4] ""                                                                                                                             
  [5] "### Copyright (C) 1995-2020 The R Core Team"                                                                                  
  [6] ""                                                                                                                             
  [7] "### Notice that it is a bad idea to use this file as a template for"                                                          
  [8] "### personal startup files, since things will be executed twice and in"                                                       
  [9] "### the wrong environment (user profiles are run in .GlobalEnv)."                                                             
 [10] ""                                                                                                                             
 [11] ".GlobalEnv <- globalenv()"                                                                                                    
 [12] "attach(NULL, name = \"Autoloads\")"                                                                                           
 [13] ".AutoloadEnv <- as.environment(2)"                                                                                            
 [14] "assign(\".Autoloaded\", NULL, envir = .AutoloadEnv)"                                                                          
 [15] "T <- TRUE"                                                                                                                    
 [16] "F <- FALSE"                                                                                                                   
 [17] "R.version <- structure(R.Version(), class = \"simple.list\")"                                                                 
 [18] "version <- R.version            # for S compatibility"                                                                        
 [19] ""                                                                                                                             
 [20] "## for backwards compatibility only"                                                                                          
 [21] "R.version.string <- R.version$version.string"                                                                                 
 [22] ""                                                                                                                             
 [23] "## NOTA BENE: options() for non-base package functionality are in places like"                                                
 [24] "##            --------- ../utils/R/zzz.R"                                                                                     
 [25] ""                                                                                                                             
 [26] "options(keep.source = interactive())"                                                                                         
 [27] "options(warn = 0)"                                                                                                            
 [28] "# options(repos = c(CRAN=\"@CRAN@\"))"                                                                                        
 [29] "# options(BIOC = \"http://www.bioconductor.org\")"                                                                            
 [30] ""                                                                                                                             
 [31] "## setting from an env variable added in 4.0.2"                                                                               
 [32] "local({to <- as.integer(Sys.getenv(\"R_DEFAULT_INTERNET_TIMEOUT\", 60))"                                                      
 [33] "    if (is.na(to) || to <= 0) to <- 60L"                                                                                      
 [34] "    options(timeout = to)"                                                                                                    
 [35] "})"                                                                                                                           
 [36] "options(encoding = \"native.enc\")"                                                                                           
 [37] "options(show.error.messages = TRUE)"                                                                                          
 [38] "## keep in sync with PrintDefaults() in  ../../main/print.c :"                                                                
 [39] "options(scipen = 0)"                                                                                                          
 [40] "options(max.print = 99999)# max. #{entries} in internal printMatrix()"                                                        
 [41] "options(add.smooth = TRUE)# currently only used in 'plot.lm'"                                                                 
 [42] ""                                                                                                                             
 [43] "if(isFALSE(as.logical(Sys.getenv(\"_R_OPTIONS_STRINGS_AS_FACTORS_\","                                                         
 [44] "                                 \"FALSE\")))) {"                                                                             
 [45] "    options(stringsAsFactors = FALSE)"                                                                                        
 [46] "} else {"                                                                                                                     
 [47] "    options(stringsAsFactors = TRUE)"                                                                                         
 [48] "}"                                                                                                                            
 [49] ""                                                                                                                             
 [50] "if(!interactive() && is.null(getOption(\"showErrorCalls\")))"                                                                 
 [51] "    options(showErrorCalls = TRUE)"                                                                                           
 [52] ""                                                                                                                             
 [53] "local({dp <- Sys.getenv(\"R_DEFAULT_PACKAGES\")"                                                                              
 [54] "       if(identical(dp, \"\")) ## it fact methods is done first"                                                              
 [55] "           dp <- c(\"datasets\", \"utils\", \"grDevices\", \"graphics\","                                                     
 [56] "                   \"stats\", \"methods\")"                                                                                   
 [57] "       else if(identical(dp, \"NULL\")) dp <- character(0)"                                                                   
 [58] "       else dp <- strsplit(dp, \",\")[[1]]"                                                                                   
 [59] "       dp <- sub(\"[[:blank:]]*([[:alnum:]]+)\", \"\\\\1\", dp) # strip whitespace"                                           
 [60] "       options(defaultPackages = dp)"                                                                                         
 [61] "    })"                                                                                                                       
 [62] ""                                                                                                                             
 [63] "## Expand R_LIBS_* environment variables."                                                                                    
 [64] "Sys.setenv(R_LIBS_SITE ="                                                                                                     
 [65] "           .expand_R_libs_env_var(Sys.getenv(\"R_LIBS_SITE\")))"                                                              
 [66] "Sys.setenv(R_LIBS_USER ="                                                                                                     
 [67] "           .expand_R_libs_env_var(Sys.getenv(\"R_LIBS_USER\")))"                                                              
 [68] ""                                                                                                                             
 [69] "local({"                                                                                                                      
 [70] "    if(nzchar(tl <- Sys.getenv(\"R_SESSION_TIME_LIMIT_CPU\")))"                                                               
 [71] "        setSessionTimeLimit(cpu = tl)"                                                                                        
 [72] "    if(nzchar(tl <- Sys.getenv(\"R_SESSION_TIME_LIMIT_ELAPSED\")))"                                                           
 [73] "        setSessionTimeLimit(elapsed = tl)"                                                                                    
 [74] "})"                                                                                                                           
 [75] ""                                                                                                                             
 [76] ".First.sys <- function()"                                                                                                     
 [77] "{"                                                                                                                            
 [78] "    for(pkg in getOption(\"defaultPackages\")) {"                                                                             
 [79] "        res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE,"                                                          
 [80] "                       character.only = TRUE)"                                                                                
 [81] "        if(!res)"                                                                                                             
 [82] "            warning(gettextf('package %s in options(\"defaultPackages\") was not found', sQuote(pkg)),"                       
 [83] "                    call. = FALSE, domain = NA)"                                                                              
 [84] "    }"                                                                                                                        
 [85] "}"                                                                                                                            
 [86] ""                                                                                                                             
 [87] "## called at C level in the startup process prior to .First.sys"                                                              
 [88] ".OptRequireMethods <- function()"                                                                                             
 [89] "{"                                                                                                                            
 [90] "    pkg <- \"methods\" # done this way to avoid R CMD check warning"                                                          
 [91] "    if(pkg %in% getOption(\"defaultPackages\"))"                                                                              
 [92] "        if(!require(pkg, quietly = TRUE, warn.conflicts = FALSE,"                                                             
 [93] "                    character.only = TRUE))"                                                                                  
 [94] "            warning('package \"methods\" in options(\"defaultPackages\") was not found',"                                     
 [95] "                    call. = FALSE)"                                                                                           
 [96] "}"                                                                                                                            
 [97] ""                                                                                                                             
 [98] "if(nzchar(Sys.getenv(\"R_BATCH\"))) {"                                                                                        
 [99] "    .Last.sys <- function()"                                                                                                  
[100] "    {"                                                                                                                        
[101] "        cat(\"> proc.time()\\n\")"                                                                                            
[102] "        print(proc.time())"                                                                                                   
[103] "    }"                                                                                                                        
[104] "    ## avoid passing on to spawned R processes"                                                                               
[105] "    ## A system has been reported without Sys.unsetenv, so try this"                                                          
[106] "    try(Sys.setenv(R_BATCH=\"\"))"                                                                                            
[107] "}"                                                                                                                            
[108] ""                                                                                                                             
[109] "local({"                                                                                                                      
[110] "    if(nzchar(rv <- Sys.getenv(\"_R_RNG_VERSION_\")))"                                                                        
[111] "        suppressWarnings(RNGversion(rv))"                                                                                     
[112] "})"                                                                                                                           
[113] ""                                                                                                                             
[114] ".sys.timezone <- NA_character_"                                                                                               
[115] "###-*- R -*-"                                                                                                                 
[116] ""                                                                                                                             
[117] "## this will break if R is on a network share"                                                                                
[118] ".Library <- file.path(chartr(\"\\\\\", \"/\", R.home()), \"library\")"                                                        
[119] ".Library.site <- Sys.getenv(\"R_LIBS_SITE\")"                                                                                 
[120] ".Library.site <- if(!nzchar(.Library.site)) file.path(R.home(), \"site-library\") else unlist(strsplit(.Library.site, \";\"))"
[121] ".Library.site <- .Library.site[file.exists(.Library.site)]"                                                                   
[122] ""                                                                                                                             
[123] "if(!nzchar(Sys.getenv(\"R_LIBS_USER\")))"                                                                                     
[124] "    Sys.setenv(R_LIBS_USER="                                                                                                  
[125] "               file.path(Sys.getenv(\"R_USER\"), \"R\","                                                                      
[126] "                         \"win-library\","                                                                                    
[127] "                         paste(R.version$major,"                                                                              
[128] "                               sub(\"\\\\..*$\", \"\", R.version$minor),"                                                     
[129] "                               sep=\".\")"                                                                                    
[130] "                         ))"                                                                                                  
[131] ""                                                                                                                             
[132] "invisible(.libPaths(c(unlist(strsplit(Sys.getenv(\"R_LIBS\"), \";\")),"                                                       
[133] "                      unlist(strsplit(Sys.getenv(\"R_LIBS_USER\"), \";\"))"                                                   
[134] "                      )))"                                                                                                    
[135] ""                                                                                                                             
[136] "local({"                                                                                                                      
[137] "    popath <- Sys.getenv(\"R_TRANSLATIONS\", \"\")"                                                                           
[138] "    if(!nzchar(popath)) {"                                                                                                    
[139] "        paths <- file.path(.libPaths(), \"translations\", \"DESCRIPTION\")"                                                   
[140] "        popath <- dirname(paths[file.exists(paths)][1])"                                                                      
[141] "    }"                                                                                                                        
[142] "    bindtextdomain(\"R\", popath)"                                                                                            
[143] "    bindtextdomain(\"R-base\", popath)"                                                                                       
[144] "    bindtextdomain(\"RGui\", popath)"                                                                                         
[145] "    assign(\".popath\", popath, .BaseNamespaceEnv)"                                                                           
[146] "})"                                                                                                                           
[147] ""                                                                                                                             
[148] "if(nzchar(Sys.getenv(\"R_PAPERSIZE\"))) {"                                                                                    
[149] "    options(papersize = Sys.getenv(\"R_PAPERSIZE\"))"                                                                         
[150] "} else {"                                                                                                                     
[151] "    if(grepl(\"(canada|united.states)\", Sys.getlocale(\"LC_MONETARY\"),"                                                     
[152] "             ignore.case = TRUE)) options(papersize = \"letter\")"                                                            
[153] "    else options(papersize = \"a4\")"                                                                                         
[154] "}"                                                                                                                            
[155] ""                                                                                                                             
[156] "options(pager = if(length(grep(\"--ess\", commandArgs()))) \"console\" else \"internal\","                                    
[157] "        useFancyQuotes = (.Platform$GUI == \"Rgui\"),"                                                                        
[158] "        pdfviewer = Sys.getenv(\"R_PDFVIEWER\", file.path(R.home(\"bin\"), \"open.exe\")))"                                   
[159] ""                                                                                                                             
[160] "if(.Platform$GUI == \"Rgui\")"                                                                                                
[161] "    Sys.setenv(GFORTRAN_STDOUT_UNIT = \"-1\", GFORTRAN_STDERR_UNIT = \"-1\")"                                                 
[162] ""                                                                                                                             
[163] "local({"                                                                                                                      
[164] "    br <- Sys.getenv(\"R_BROWSER\", NA_character_)"                                                                           
[165] "    if(!is.na(br)) options(browser = br)"                                                                                     
[166] "    tests_startup <- Sys.getenv(\"R_TESTS\")"                                                                                 
[167] "    if(nzchar(tests_startup)) source(tests_startup)"                                                                          
[168] "    ca_cert <- Sys.getenv(\"CURL_CA_BUNDLE\", NA_character_)"                                                                 
[169] "    if(!is.na(ca_cert) &&"                                                                                                    
[170] "       file.exists(ca_path <- file.path(R.home(\"etc\"), \"curl-ca-bundle.crt\")))"                                           
[171] "        Sys.setenv(CURL_CA_BUNDLE = ca_path)"                                                                                 
[172] "})"                                                                                                                           
> readLines("C:/Program Files/R/R-4.1.0/src/library/windlgs/src/Makevars.win")
[1] "PKG_LIBS=$(GRAPHAPP_LIB)"
> Sys.getenv("PATH")
[1] "C:\\Program Files\\R\\R-4.1.0\\bin\\x64;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Windows\\System32\\OpenSSH\\;C:\\Program Files\\NVIDIA Corporation\\NVIDIA NvDLISR;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\WINDOWS\\System32\\OpenSSH\\;C:\\Program Files\\MATLAB\\R2020b\\bin;C:\\Users\\Oswin\\AppData\\Local\\Programs\\Python\\Python39;C:\\Users\\Oswin\\AppData\\Local\\Programs\\Julia-1.6.1\\bin;C:\\Users\\Oswin\\AppData\\Local\\Programs\\Python\\Python39\\Scripts;C:\\Program Files\\dotnet\\;C:\\Program Files\\Docker\\Docker\\resources\\bin;C:\\ProgramData\\DockerDesktop\\version-bin;C:\\Users\\Oswin\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\Oswin\\AppData\\Roaming\\Python\\Python38\\Scripts;C:\\Users\\Oswin\\AppData\\Roaming\\Python\\Python38\\site-packages;C:\\Users\\Oswin\\AppData\\Local\\Programs\\MiKTeX\\miktex\\bin\\x64\\;C:\\Program Files\\Inkscape\\bin;;C:\\Program Files\\JetBrains\\PyCharm Community Edition 2021.1.2\\bin;"
> Sys.getenv("RTOOLS40_HOME")
[1] "C:\\Program Files\\rtools40"
5

Ah no, I needed you to run the code as-is without adapting any paths

Even if it returns an error that no file exists, that’s also helpful for me to know

6

Oh, okay, sorry, all the readLines give me errors then:

> readLines("~/.Renviron")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/Oswin/Documents/.Renviron': No such file or directory
> readLines("~/.Rprofile")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/Oswin/Documents/.Rprofile': No such file or directory
> readLines("~/.R/Makevars.win")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/Oswin/Documents/.R/Makevars.win': No such file or directory
> Sys.getenv("PATH")
[1] "C:\\Program Files\\R\\R-4.1.0\\bin\\x64;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Windows\\System32\\OpenSSH\\;C:\\Program Files\\NVIDIA Corporation\\NVIDIA NvDLISR;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\WINDOWS\\System32\\OpenSSH\\;C:\\Program Files\\MATLAB\\R2020b\\bin;C:\\Users\\Oswin\\AppData\\Local\\Programs\\Python\\Python39;C:\\Users\\Oswin\\AppData\\Local\\Programs\\Julia-1.6.1\\bin;C:\\Users\\Oswin\\AppData\\Local\\Programs\\Python\\Python39\\Scripts;C:\\Program Files\\dotnet\\;C:\\Program Files\\Docker\\Docker\\resources\\bin;C:\\ProgramData\\DockerDesktop\\version-bin;C:\\Users\\Oswin\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\Oswin\\AppData\\Roaming\\Python\\Python38\\Scripts;C:\\Users\\Oswin\\AppData\\Roaming\\Python\\Python38\\site-packages;C:\\Users\\Oswin\\AppData\\Local\\Programs\\MiKTeX\\miktex\\bin\\x64\\;C:\\Program Files\\Inkscape\\bin;;C:\\Program Files\\JetBrains\\PyCharm Community Edition 2021.1.2\\bin;"
> Sys.getenv("RTOOLS40_HOME")
[1] "C:\\Program Files\\rtools40"
7

Ah it looks like you’ve missed a step when installing RTools. Can you complete the installation steps at the RTools4 download page: Using Rtools4 on Windows, specifically the " Putting Rtools on the PATH" section

8

I have done the “Putting Rtools on the PATH” section, however, this only changes the Renviron one and not the Rprofile or the Makevars.win output:

> readLines("~/.Renviron")
[1] "PATH=\"${RTOOLS40_HOME}\\usr\\bin;${PATH}\""
> readLines("~/.Rprofile")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/Oswin/Documents/.Rprofile': No such file or directory
> readLines("~/.R/Makevars.win")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/Oswin/Documents/.R/Makevars.win': No such file or directory
> Sys.getenv("PATH")
[1] "C:\\Program Files\\rtools40\\usr\\bin;C:\\Program Files\\R\\R-4.1.0\\bin\\x64;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Windows\\System32\\OpenSSH\\;C:\\Program Files\\NVIDIA Corporation\\NVIDIA NvDLISR;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\WINDOWS\\System32\\OpenSSH\\;C:\\Program Files\\MATLAB\\R2020b\\bin;C:\\Users\\Oswin\\AppData\\Local\\Programs\\Python\\Python39;C:\\Users\\Oswin\\AppData\\Local\\Programs\\Julia-1.6.1\\bin;C:\\Users\\Oswin\\AppData\\Local\\Programs\\Python\\Python39\\Scripts;C:\\Program Files\\dotnet\\;C:\\Program Files\\Docker\\Docker\\resources\\bin;C:\\ProgramData\\DockerDesktop\\version-bin;C:\\Users\\Oswin\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\Oswin\\AppData\\Roaming\\Python\\Python38\\Scripts;C:\\Users\\Oswin\\AppData\\Roaming\\Python\\Python38\\site-packages;C:\\Users\\Oswin\\AppData\\Local\\Programs\\MiKTeX\\miktex\\bin\\x64\\;C:\\Program Files\\Inkscape\\bin;;C:\\Program Files\\JetBrains\\PyCharm Community Edition 2021.1.2\\bin;"
> Sys.getenv("RTOOLS40_HOME")
[1] "C:\\Program Files\\rtools40"
9

Yep that’s fine, can you try the example model again?

10

I completely restarted R, then I used:

> example(stan_model, package = "rstan", run.dontrun = TRUE)
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.21.5, 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)
Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file

It still crashed at the same spot.

11

The next step is to try reinstalling rstan and StanHeaders from source.

Can you restart R and then run:

remove.packages(c("StanHeaders", "rstan"))
remove.packages(c("StanHeaders", "rstan"), type = "source")

Then if the install completes successfully, try the example model again

12

Yes, now it works. Thanks so much for your help!

1 Like