# Problems getting Stan to run after upgrading to R 4.0.2

**URL:** <https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896>\
**Category:** RStan\
**Created:** [September 7, 2020, 1:03pm UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896 "2020-09-07T13:03:54Z")\
**Posts on this page:** 20\
**Page:** 1

<div class="post-metadata">

**Author:** ![Chris\_Dalton](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/chris_dalton/32/9283_2.png) [@Chris\_Dalton](https://discourse.mc-stan.org/u/Chris_Dalton)\
**Post date:** [September 7, 2020, 1:03pm UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/1 "2020-09-07T13:03:54Z")

</div>

2020-09-06T14:00:00Z  
Hello  
This seems to be a common problem but the threads are long and difficult to follow. Can’t get Stan to run now after multiple re-installs of R and R studio.  
Tried fiddling with the makevars.win file; this is what I have in it now in the makevars file:

```
CXX14=$(BINPREF)g++ -O2 -march=native -mtune=native”

```

and I’ve tried

```
Sys.setenv(BINPREF = "C:/RBuildTools/4.0/mingw64/bin/g++.exe")

```

as my Rtools directory downloaded as RBuildTools. I keep getting this error message:

```
Error in compileCode(f, code, language = language, verbose = verbose) : 
  sh: C:/Rtools/mingw_64/bin/g++: No such file or directorymake: *** [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:229: file123061c3410a.o] Error 127
In addition: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  '-E' not found
Error in sink(type = "output") : invalid connection

```

Thanks for any advice.  
regards  
Chris

- Windows 10
- RStan 2.21.2
- R 4.0.2
- RStudio 1.3.1073

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 7, 2020, 1:41pm UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/2 "2020-09-07T13:41:16Z")

</div>

Hi Chris,

With RTools 4, you don’t want to be setting the CXX14 variable or the BINPREF variable, you also don’t want to use `-march=native`, since that can cause crashes.

The first step is to reset your Makevars to some ‘safe’ but optimised settings:

```
cat("CXX14FLAGS += -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2",file = "~/.R/Makevars.win", sep = "\n", append = FALSE)

```

Can you run that and then run the example model:

```
library(rstan)
example(stan_model,run.dontrun=TRUE,verbose=TRUE)

```

And post any line(s) that start with `error:`?

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 7, 2020, 1:45pm UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/3 "2020-09-07T13:45:20Z")

</div>

Also, small world! I finished my Biostats masters through Sydney uni last year

---

<div class="post-metadata">

**Author:** ![Chris\_Dalton](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/chris_dalton/32/9283_2.png) [@Chris\_Dalton](https://discourse.mc-stan.org/u/Chris_Dalton)\
**Post date:** [September 8, 2020, 4:09am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/4 "2020-09-08T04:09:25Z")

</div>

Thanks very much for your reply.  
The error message I got now is

```
Error in compileCode(f, code, language = language, verbose = verbose) : 
  sh: C:/Rtools/mingw_64/bin/g++: No such file or directorymake: *** [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:229: file1fc42e38522.o] Error 127
In addition: Warning messages:
1: In find.package(package, lib.loc, verbose = verbose) :
  package ‘base’ found more than once, using the first from
  “C:/PROGRA~1/R/R-40~1.2/library/base”,
  “C:/Program Files/R/R-4.0.2/library/base”
2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/RBUILD~1/4.0/usr/mingw_/bin/g++' not found

```

I finished the MBiostats last semester at Sydney Uni.  
Are you Sydney based (if it’s not an inappropriate question on a public forum)?  
Regards  
Chris

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 8, 2020, 5:43am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/5 "2020-09-08T05:43:46Z")

</div>

No, I’m over in Perth. But always good to see more Australians on the forums!

This line:

```
sh: C:/Rtools/mingw_64/bin/g++

```

Indicates that R is looking for the old Rtools installation. What output do you get from the following:

```
Sys.getenv("PATH")
Sys.getenv("BINPREF")
readLines("~/.R/Makevars.win")
readLines("~/.Renviron")

```

---

<div class="post-metadata">

**Author:** ![Chris\_Dalton](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/chris_dalton/32/9283_2.png) [@Chris\_Dalton](https://discourse.mc-stan.org/u/Chris_Dalton)\
**Post date:** [September 8, 2020, 6:47am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/6 "2020-09-08T06:47:19Z")

</div>

Thanks  
I get this with that request

```
 Sys.getenv("PATH")
[1] "C:\\RBuildTools\\4.0\\usr\\bin;C:\\Program Files\\R\\R-4.0.2\\bin\\x64;C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath_target_289689671;C:\\Perl64\\site\\bin;C:\\Perl64\\bin;c:\\Rtools\\bin;c:\\Rtools\\mingw_32\\bin;C:\\Windows\\System32;C:\\Windows;C:\\Windows\\System32\\wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0;C:\\Windows\\System32\\OpenSSH;C:\\Program Files\\Intel\\WiFi\\bin;C:\\Program Files\\Common Files\\Intel\\WirelessCommon;C:\\Program Files (x86)\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Program Files\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Users\\dalto\\AppData\\Local\\Microsoft\\WindowsApps"
> Sys.getenv("BINPREF")
[1] "C:/Rtools/mingw_$(WIN)/bin/"
> readLines("~/.R/Makevars.win")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/dalto/Documents/.R/Makevars.win': No such file or directory
> readLines("~/.Renviron")
[1] "PATH=\"${RTOOLS40_HOME}\\usr\\bin;${PATH}\""

```

Something to do with RTools and RBuildTools?  
Regards  
Chris

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 8, 2020, 6:56am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/7 "2020-09-08T06:56:12Z")

</div>

It looks like the BINPREF variable is being set to the old RTools installation, which tells R where to look for the compilers. I think you probably have an `.Rprofile` file in your home directory that’s setting the `BINPREF` variable on startup.

If you don’t need any other settings in the file, you can just delete it via:

```
unlist("~/.Rprofile")

```

Otherwise just open the file in a text editor and remove the line mentioning `BINPREF`.

After deleting/editing the `.Rprofile` file, restart R and try your model again.

Additionally, you’re missing out on some compiler optimisations by not setting up a Makevars file. You can run the following to setup a Makevars:

```
cat("CXX14FLAGS += -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2",file = "~/.R/Makevars.win", sep = "\n", append = FALSE)

```

---

<div class="post-metadata">

**Author:** ![Chris\_Dalton](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/chris_dalton/32/9283_2.png) [@Chris\_Dalton](https://discourse.mc-stan.org/u/Chris_Dalton)\
**Post date:** [September 8, 2020, 7:24am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/8 "2020-09-08T07:24:23Z")

</div>

Now I seem to have some other problems!  
1.RStudio keeps aborting the session when I try to open a file.  
2.When using

```
cat("CXX14FLAGS += -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2",file = "~/.R/Makevars.win", sep = "\n", append = FALSE)

```

I get

```
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file 'C:/Users/dalto/Documents/.R/Makevars.win': No such file or directory

```

My makevars file is here

```
"C:\Users\dalto\Documents\R\win-library\4.0\rstantools\include\sys\Makevars.win"

```

and contains

```
cat("CXX14FLAGS += -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2",file = "~/.R/Makevars.win", sep = "\n", append = FALSE)

```

3.When running a stan program I get

```
Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/RBUILD~1/4.0/usr/mingw_/bin/g++' not found

```

4.Running

```
library(rstan)
example(stan_model,run.dontrun=TRUE,verbose=TRUE)

```

I get

```
Warning messages:
1: In find.package(package, lib.loc, verbose = verbose) :
  package ‘base’ found more than once, using the first from
  “C:/PROGRA~1/R/R-40~1.2/library/base”,
  “C:/Program Files/R/R-4.0.2/library/base”
2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/RBUILD~1/4.0/usr/mingw_/bin/g++' not found

```

Sorry about this! Stan used to work well before I upgraded R and RStudio!  
Regards  
Chris

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 8, 2020, 7:35am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/9 "2020-09-08T07:35:19Z")

</div>

For the makevars file, you need to have it in your Documents folder, in a folder named ‘.R’

So you need to create a folder:

```
C:/Users/dalto/Documents/.R/

```

And then inside that folder create a file called `Makevars.win` which contains:

```
CXX14FLAGS += -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2

```

The `cat(...)` command was just to automatically create that file and it’s contents (not sure why it didn’t work), you don’t want to have the actual `cat(...)` command in there.

As for the models, those warnings are all safe to ignore (the `g++` one will be fixed in the next release). Do the models all compile and sample without issue?

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 8, 2020, 7:38am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/10 "2020-09-08T07:38:02Z")

</div>

As another check, would you be able to post the output from:

```
devtools::session_info("rstan")

```

---

<div class="post-metadata">

**Author:** ![Chris\_Dalton](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/chris_dalton/32/9283_2.png) [@Chris\_Dalton](https://discourse.mc-stan.org/u/Chris_Dalton)\
**Post date:** [September 8, 2020, 8:38am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/11 "2020-09-08T08:38:51Z")

</div>

This is the output from

```
devtools::session_info("rstan")

```

```
Session info -----------------------------------------------------------------------------------------------------------------
 setting value                       
 version R version 4.0.2 (2020-06-22)
 os Windows 10 x64              
 system x86_64, mingw32             
 ui RStudio                     
 language (EN)                        
 collate English_Australia.1252      
 ctype English_Australia.1252      
 tz Australia/Sydney            
 date 2020-09-08                  

- Packages ---------------------------------------------------------------------------------------------------------------------
 ! package * version date lib source                         
   assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)                 
   backports 1.1.9 2020-08-24 [1] CRAN (R 4.0.2)                 
   BH 1.72.0-3 2020-01-08 [1] CRAN (R 4.0.0)                 
   callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.2)                 
   checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.2)                 
   cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2)                 
   colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2)                 
   crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)                 
   curl 4.3 2019-12-02 [1] CRAN (R 4.0.2)                 
   desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)                 
   digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2)                 
   ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)                 
   evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.2)                 
   fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)                 
   farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2)                 
   ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)                 
   glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)                 
   gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2)                 
   gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)                 
   inline 0.3.15 2020-09-07 [1] Github (bgoodri/inline@21105c7)
   isoband 0.2.2 2020-06-20 [1] CRAN (R 4.0.2)                 
   jsonlite 1.7.0 2020-06-25 [1] CRAN (R 4.0.2)                 
   labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)                 
   lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.2)                 
   lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)                 
   loo 2.3.1 2020-07-14 [1] CRAN (R 4.0.2)                 
   magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)                 
   MASS 7.3-51.6 2020-04-26 [2] CRAN (R 4.0.2)                 
   Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.0.2)                 
   matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.2)                 
   mgcv 1.8-31 2019-11-09 [2] CRAN (R 4.0.2)                 
   munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)                 
   nlme 3.1-148 2020-05-24 [2] CRAN (R 4.0.2)                 
   pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)                 
   pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)                 
   pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)                 
   pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)                 
   praise 1.0.0 2015-08-11 [1] CRAN (R 4.0.2)                 
   prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)                 
   processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)                 
   ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2)                 
   R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)                 
   RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)                 
   Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)                 
   RcppEigen 0.3.3.7.0 2019-11-16 [1] CRAN (R 4.0.2)                 
 D RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.2)                 
   rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)                 
   rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)                 
   rstan * 2.21.2 2020-07-27 [1] CRAN (R 4.0.2)                 
   rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2)                 
   scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)                 
   StanHeaders * 2.21.0-6 2020-08-16 [1] CRAN (R 4.0.2)                 
   testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2)                 
   tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)                 
   utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.2)                 
   V8 3.2.0 2020-06-19 [1] CRAN (R 4.0.2)                 
   vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2)                 
   viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.2)                 
   withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2)                 

[1] C:/Users/dalto/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.2/library

 D -- DLL MD5 mismatch, broken installation.

```

and running a stan model I still get

```
Warning messages:
1: In find.package(package, lib.loc, verbose = verbose) :
  package ‘base’ found more than once, using the first from
  “C:/PROGRA~1/R/R-40~1.2/library/base”,
  “C:/Program Files/R/R-4.0.2/library/base”
2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/RBUILD~1/4.0/usr/mingw_/bin/g++' not found

```

Thanks again for your help!

---

<div class="post-metadata">

**Author:** ![Chris\_Dalton](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/chris_dalton/32/9283_2.png) [@Chris\_Dalton](https://discourse.mc-stan.org/u/Chris_Dalton)\
**Post date:** [September 8, 2020, 8:42am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/12 "2020-09-08T08:42:54Z")

</div>

But the models do compile and sample now with only this message!

```
Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/RBUILD~1/4.0/usr/mingw_/bin/g++' not found

```

Thanks!

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 8, 2020, 9:03am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/13 "2020-09-08T09:03:21Z")

</div>

Great, all of those warnings are safe to ignore, so you’re good to go

---

<div class="post-metadata">

**Author:** ![royworth](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/royworth/32/6202_2.png) [@royworth](https://discourse.mc-stan.org/u/royworth)\
**Post date:** [September 8, 2020, 5:20pm UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/14 "2020-09-08T17:20:11Z")

</div>

For posterity, I thought I’d mention within this thread that I had every issue _exactly_ as listed and tested by Chris above. Unfortunately, after following all of the suggestions, I still couldn’t get the example model to compile.

However, after going through these instructions and then _also_ adding to my makevars file the line:

`CXX14 = C:/Rtools40/mingw64/bin/g++`

…everything worked out.

My makevars.win file now reads:

```
CXX14FLAGS += -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2
CXX14 = C:/Rtools40/mingw64/bin/g++

```

I took this advice from an older comment by @bgoodri here: [G++ Compile Error With R Package](https://discourse.mc-stan.org/t/g-compile-error-with-r-package/10628/13)

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 9, 2020, 12:11am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/15 "2020-09-09T00:11:26Z")

</div>

Hi Roy,

Just to check some reasons for why it wasn’t working initially (in case it’s a new issue I need to be aware of), can you post the outputs from:

```
Sys.getenv("BINPREF")
Sys.getenv("PATH")
Sys.which("make")
readLines("~/.Renviron")
readLines("~/.Rprofile")

```

---

<div class="post-metadata">

**Author:** ![royworth](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/royworth/32/6202_2.png) [@royworth](https://discourse.mc-stan.org/u/royworth)\
**Post date:** [September 9, 2020, 8:42am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/16 "2020-09-09T08:42:30Z")

</div>

Hi Andrew,

Thanks for the follow up. I admit I have little idea what is going on here and I was a little afraid I might unintentionally lead someone astray. Here is what I get running those commands:

```
> Sys.getenv("BINPREF")
[1] "C:/Rtools/mingw_$(WIN)/bin/"

> Sys.getenv("PATH")
[1] "C:\\rtools40\\usr\\bin;C:\\Program Files\\R\\R-4.0.2\\bin\\x64;C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath_target_325312;C:\\Windows\\System32;C:\\Windows;C:\\Windows\\System32\\wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0;C:\\Program Files (x86)\\Windows Live\\Shared;C:\\Program Files\\Git\\cmd;C:\\Windows\\System32\\OpenSSH;C:\\Program Files\\McAfee\\Solidcore\\Tools\\GatherInfo;C:\\Program Files\\McAfee\\Solidcore\\Tools\\ScAnalyzer;C:\\Program Files\\McAfee\\Solidcore;C:\\Program Files\\McAfee\\Solidcore\\Tools\\ScGetCerts;C:\\Users\\rmartin\\AppData\\Local\\Microsoft\\WindowsApps"

> Sys.which("make")
                              make 
"C:\\rtools40\\usr\\bin\\make.exe" 

> readLines("~/.Renviron")
[1] "PATH=\"${RTOOLS40_HOME}\\usr\\bin;${PATH}\""

> readLines("~/.Rprofile")
[1] "Sys.setenv(BINPREF = \"C:/Rtools/mingw_$(WIN)/bin/\")"

```

Also, not sure if relevant, but I run Stan on an intel Xeon workstation (2 processors), which is maybe different from the average user. In the past, I _think_ I’ve needed to fiddle a bit with the makevars settings relative to the usual recommendations for those settings, but unfortunately I forget the details. For example, I’m not sure if that was because of the Xeon setup, or just the general ‘march=native’ issues.

Finally, in case it helps, here is the output of errors I get when I run

```
library(rstan)
example(stan_model,run.dontrun=TRUE,verbose=TRUE)

```

without adding the

`CXX14 = C:/Rtools40/mingw64/bin/g++`

to the makevars.win file.

```
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) : 
  sh: C:/Rtools/mingw_64/bin/g++: No such file or directorymake: *** [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:229: file9ce4183c6852.o] Error 127
In addition: Warning messages:
1: In find.package(package, lib.loc, verbose = verbose) :
  package ‘base’ found more than once, using the first from
  “C:/PROGRA~1/R/R-40~1.2/library/base”,
  “C:/Program Files/R/R-4.0.2/library/base”
2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/rtools40/usr/mingw_/bin/g++' not found

```

Thanks again,

Roy

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 9, 2020, 9:02am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/17 "2020-09-09T09:02:18Z")

</div>

Hi Roy,

That’s an easy fix thankfully! You were getting those errors because you’ve set the `BINPREF` variable in your `.Rprofile` file.

If you follow the instructions I posted above to delete the file, you won’t need to set the CXX14 variable.

Cheers  
Andrew

---

<div class="post-metadata">

**Author:** ![royworth](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/royworth/32/6202_2.png) [@royworth](https://discourse.mc-stan.org/u/royworth)\
**Post date:** [September 9, 2020, 9:18am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/18 "2020-09-09T09:18:01Z")

</div>

Ohhhh OK! I actually _thought_ I did the delete the .Rprofile by running `unlist("~/.Rprofile")`, but I’ll fiddle around and try it again.Great to know what the underlying issue was, in any case!

-Roy

---

<div class="post-metadata">

**Author:** ![Namurava](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/namurava/32/9144_2.png) [@Namurava](https://discourse.mc-stan.org/u/Namurava)\
**Post date:** [September 25, 2020, 10:53pm UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/19 "2020-09-25T22:53:44Z")

</div>

I had the same issue from above, and after switching withr to 2.2.0 and running:

```
example(stan_model,run.dontrun=TRUE,verbose=TRUE)

```

Warning messages:  
1: In find.package(package, lib.loc, verbose = verbose) :  
package ‘base’ found more than once, using the first from  
“C:/Users/NMURAV~1/DOCUME~1/R/R-40~1.2/library/base”,  
“C:/Users/nmuravskaya/Documents/R/R-4.0.2/library/base”  
2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :  
‘C:/RBUILD~1/4.0/usr/mingw\_/bin/g++’ not found

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 26, 2020, 2:21am UTC](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896/20 "2020-09-26T02:21:11Z")

</div>

Hi Namurava,

None of those are errors that imply that the fitting failed. Were there any other errors or did the model finish running?

[Next page](https://discourse.mc-stan.org/t/problems-getting-stan-to-run-after-upgrading-to-r-4-0-2/17896.md?page=2)