# Problem running RStan in RStudio

**URL:** <https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236>\
**Category:** General\
**Created:** [September 28, 2020, 7:05pm UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236 "2020-09-28T19:05:25Z")\
**Posts on this page:** 12\
**Page:** 1

<div class="post-metadata">

**Author:** ![Paul\_Vanags](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/paul_vanags/32/4452_2.png) [@Paul\_Vanags](https://discourse.mc-stan.org/u/Paul_Vanags)\
**Post date:** [September 28, 2020, 7:05pm UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/1 "2020-09-28T19:05:25Z")

</div>

HI - I’m new to Stan and working through a course on Bayesian modelling.

When I run this code;  
library(rethinking)  
data(Wines2012)  
d \<- Wines2012

dat\_list \<- list(S = standardize(d$score),  
jid = as.integer(d$judge),  
wid = as.integer(d$wine))

m1 \<- ulam(alist(  
S ~ dnorm( mu , sigma ),  
mu \<- a[jid] + w[wid],  
a[jid] ~ dnorm(0,0.5),  
w[wid] ~ dnorm(0,0.5),  
sigma ~ dexp(1)), data=dat\_list , chains=4 , cores=4)

I get this issue;  
The NEXT version of Stan will not be able to pre-process your Stan program.  
Please open an issue at

> **[stan-dev/stanc3](https://github.com/stan-dev/stanc3/issues)**
>
> The Stan transpiler (from Stan to C++ and beyond). - stan-dev/stanc3

  
if you can share or at least describe your Stan program. This will help ensure that Stan  
continues to work on your Stan programs in the future. Thank you!  
This message can be avoided by wrapping your function call inside suppressMessages().  
Error in file(con, “r”) : cannot open the connection  
In addition: Warning messages:  
1: In file.remove(c(unprocessed, processed)) :  
cannot remove file ‘C:\Users\BEN10~~1\AppData\Local\Temp\RtmpS6E4Od\file21504f9e6cf2.stan’, reason ‘No such file or directory’  
2: In system(cmd, intern = !verbose) :  
running command ‘C:/PROGRA~~1/R/R-40~1.2/bin/x64/R CMD SHLIB file2150102d7cbc.cpp 2\> file2150102d7cbc.cpp.err.txt’ had status 1  
3: In file(con, “r”) :  
cannot open file ‘file2150102d7cbc.cpp.err.txt’: No such file or directory  
Error in sink(type = “output”) : invalid connection

I’m running R Studio  
Version 1.3.959  
© 2009-2020 RStudio, PBC  
“Middlemist Red” (3a09be39, 2020-05-18) for Windows  
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.6 Chrome/69.0.3497.128 Safari/537.36

Stan version 2.21.0

UPDATE: I updated RStan to 2.21.2 latest version but it still generates an error…

Error in file(con, “r”) : cannot open the connection  
In addition: Warning messages:  
1: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :  
‘C:/rtools40/usr/mingw\_/bin/g++’ not found  
2: In system(cmd, intern = !verbose) :  
running command ‘C:/PROGRA ~~1/R/R-40~~ 1.2/bin/x64/R CMD SHLIB file550c6614374a.cpp 2\> file550c6614374a.cpp.err.txt’ had status 1  
3: In file(con, “r”) :  
cannot open file ‘file550c6614374a.cpp.err.txt’: No such file or directory  
Error in sink(type = “output”) : invalid connection

---

<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:** [September 28, 2020, 7:41pm UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/2 "2020-09-28T19:41:16Z")

</div>

@andrjohns might be able to help you since you’re on a Windows machine. I believe I’ve seen this several times on this forum. @andrjohns, do you have one page with your knowledge encoded somewhere? :)

---

<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 29, 2020, 1:14am UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/3 "2020-09-29T01:14:11Z")

</div>

Thanks Richard! All I mainly look for is:

- inline/StanHeaders/rstan out of date
- RTools4 not added to the PATH (via .Renviron)
- R configured to use RTools 3.5 with R4.0 (via BINPREF)

Paul - Can I get a bit more information about your system? What output do you get from:

```
Sys.getenv("PATH")
Sys.getenv("BINPREF")
readLines("~/.R/Makevars.win")
readLines("~/.Rprofile")
readLines("~/.Renviron")
devtools::session_info("rstan")

```

---

<div class="post-metadata">

**Author:** ![Paul\_Vanags](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/paul_vanags/32/4452_2.png) [@Paul\_Vanags](https://discourse.mc-stan.org/u/Paul_Vanags)\
**Post date:** [September 29, 2020, 6:24am UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/4 "2020-09-29T06:24:04Z")

</div>

Hi @andrjohns ! Thanks for your reply…

I get this…

Sys.getenv(“PATH”)  
[1] “C:\rtools40\usr\bin;C:\Program Files\R\R-4.0.2\bin\x64;C:\ProgramData\Oracle\Java\javapath;C:\Program Files\Common Files\microsoft shared\Windows Live;C:\Program Files (x86)\Common Files\Microsoft Shared\Windows Live;C:\Windows\System32;C:\Windows;C:\Windows\System32\wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x86;C:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x64;C:\Program Files (x86)\Windows Live\Shared;C:\Windows\System32\OpenSSH;C:\Program Files\Git\cmd;C:\Users\Ben 10\AppData\Local\Microsoft\WindowsApps”

> Sys.getenv(“BINPREF”)  
> [1] “”  
> 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/Ben 10/Documents/.R/Makevars.win’: 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/Ben 10/Documents/.Rprofile’: No such file or directory  
> readLines(“~/.Renviron”)  
> [1] “PATH="{RTOOLS40\_HOME}\\usr\\bin;{PATH}"”  
> 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\_United Kingdom.1252  
ctype English\_United Kingdom.1252  
tz Europe/London  
date 2020-09-29

- Packages -------------------------------------------------------------------------------  
! package \* version date lib source  
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)  
backports 1.1.8 2020-06-17 [1] CRAN (R 4.0.0)  
BH 1.72.0-3 2020-01-08 [1] CRAN (R 4.0.0)  
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)  
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.2)  
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)  
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)  
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)  
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)  
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)  
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)  
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)  
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)  
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)  
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)  
ggplot2 \* 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)  
glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.2)  
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)  
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)  
inline 0.3.15 2020-09-28 [1] local  
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 4.0.0)  
loo 2.3.0 2020-07-07 [1] CRAN (R 4.0.2)  
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)  
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 4.0.0)  
nlme 3.1-148 2020-05-24 [2] CRAN (R 4.0.2)  
pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.0)  
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.0)  
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)  
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)  
praise 1.0.0 2015-08-11 [1] CRAN (R 4.0.0)  
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)  
processx 3.4.3 2020-07-05 [1] CRAN (R 4.0.2)  
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.2)  
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)  
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 4.0.0)  
D RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.2)  
rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.0)  
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)  
rstan \* 2.21.2 2020-07-27 [1] CRAN (R 4.0.2)  
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)  
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)  
StanHeaders \* 2.21.0-5 2020-06-09 [1] CRAN (R 4.0.2)  
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)  
tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.0)  
utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.0)  
V8 3.2.0 2020-06-19 [1] CRAN (R 4.0.2)  
vctrs 0.3.1 2020-06-05 [1] CRAN (R 4.0.2)  
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.0)  
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)

[1] C:/Users/Ben 10/Documents/R/win-library/4.0  
[2] C:/Program Files/R/R-4.0.2/library

D – DLL MD5 mismatch, broken installation.

---

<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 29, 2020, 6:27am UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/5 "2020-09-29T06:27:58Z")

</div>

Thanks Paul! Your `inline` and `StanHeaders` packages are both out of date, which can cause the errors that you’re seeing (each for different reasons). Try updating these packages and running your model again

---

<div class="post-metadata">

**Author:** ![Paul\_Vanags](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/paul_vanags/32/4452_2.png) [@Paul\_Vanags](https://discourse.mc-stan.org/u/Paul_Vanags)\
**Post date:** [September 29, 2020, 7:21am UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/6 "2020-09-29T07:21:24Z")

</div>

OK - that seemed to go a bit better, but still not fully woking:

make cmd is  
make -f “C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf” -f “C:/PROGRA~1/R/R-40~1.2/share/make/winshlib.mk” CXX=’(CXX14) (CXX14STD)’ CXXFLAGS=’(CXX14FLAGS)' CXXPICFLAGS='(CXX14PICFLAGS)’ SHLIB\_LDFLAGS=’(SHLIB\_CXX14LDFLAGS)' SHLIB\_LD='(SHLIB\_CXX14LD)’ SHLIB=“file20d4364a7140.dll” WIN=64 TCLBIN=64 OBJECTS=“file20d4364a7140.o”

make would use  
“C:/rtools40/mingw64/bin/“g++ -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.2/include” -DNDEBUG -I"C:/Users/Ben 10/Documents/R/win-library/4.0/Rcpp/include/” -I"C:/Users/Ben 10/Documents/R/win-library/4.0/RcppEigen/include/" -I"C:/Users/Ben 10/Documents/R/win-library/4.0/RcppEigen/include/unsupported" -I"C:/Users/Ben 10/Documents/R/win-library/4.0/BH/include" -I"C:/Users/Ben 10/Documents/R/win-library/4.0/StanHeaders/include/src/" -I"C:/Users/Ben 10/Documents/R/win-library/4.0/StanHeaders/include/" -I"C:/Users/Ben 10/Documents/R/win-library/4.0/RcppParallel/include/" -I"C:/Users/Ben 10/Documents/R/win-library/4.0/rstan/include" -DEIGEN\_NO\_DEBUG -DBOOST\_DISABLE\_ASSERTS -DBOOST\_PENDING\_INTEGER\_LOG2\_HPP -DSTAN\_THREADS -DBOOST\_NO\_AUTO\_PTR -include “C:/Users/Ben 10/Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp” -std=c++1y -include C:/Users/Ben 10/Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp -I “C:/Users/Ben 10/Documents/R/win-library/4.0/StanHeaders/include” -I “C:/Users/Ben 10/Documents/R/win-library/4.0/RcppEigen/include” -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file20d4364a7140.cpp -o file20d4364a7140.o  
if test “zfile20d4364a7140.o” != “z”; then   
if test -e “file20d4364a7140-win.def”; then   
echo “C:/rtools40/mingw64/bin/“g++ -shared -s -static-libgcc -o file20d4364a7140.dll file20d4364a7140-win.def file20d4364a7140.o “C:/Users/Ben 10/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a” -L"C:/Users/Ben 10/Documents/R/win-library/4.0/StanHeaders/libs/x64” -lStanHeaders -L"C:/Users/Ben 10/Documents/R/win-library/4.0/RcppParallel/lib/x64” -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ;   
“C:/rtools40/mingw64/bin/“g++ -shared -s -static-libgcc -o file20d4364a7140.dll file20d4364a7140-win.def file20d4364a7140.o “C:/Users/Ben 10/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a” -L"C:/Users/Ben 10/Documents/R/win-library/4.0/StanHeaders/libs/x64” -lStanHeaders -L"C:/Users/Ben 10/Documents/R/win-library/4.0/RcppParallel/lib/x64” -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ;   
else   
echo EXPORTS \> tmp.def;   
“C:/rtools40/mingw64/bin/“nm file20d4364a7140.o | sed -n ‘s/^.\* [BCDRT] / /p’ | sed -e ‘/[.]refptr[.]/d’ -e ‘/[.]weak[.]/d’ | sed 's/[^][^]\*/”&”/g’ \>\> tmp.def;   
echo “C:/rtools40/mingw64/bin/“g++ -shared -s -static-libgcc -o file20d4364a7140.dll tmp.def file20d4364a7140.o “C:/Users/Ben 10/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a” -L"C:/Users/Ben 10/Documents/R/win-library/4.0/StanHeaders/libs/x64” -lStanHeaders -L"C:/Users/Ben 10/Documents/R/win-library/4.0/RcppParallel/lib/x64” -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ;   
“C:/rtools40/mingw64/bin/“g++ -shared -s -static-libgcc -o file20d4364a7140.dll tmp.def file20d4364a7140.o “C:/Users/Ben 10/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a” -L"C:/Users/Ben 10/Documents/R/win-library/4.0/StanHeaders/libs/x64” -lStanHeaders -L"C:/Users/Ben 10/Documents/R/win-library/4.0/RcppParallel/lib/x64” -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ;   
rm -f tmp.def;   
fi   
fi  
Error in compileCode(f, code, language = language, verbose = verbose) :  
g++.exe: error: 10/Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directorymake: \*\*\* [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:229: file20d4364a7140.o] Error 1  
In addition: Warning message:  
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :  
‘C:/rtools40/usr/mingw\_/bin/g++’ not found  
Error in sink(type = “output”) : invalid connection

---

<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 29, 2020, 7:29am UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/7 "2020-09-29T07:29:10Z")

</div>

Thanks Paul. That error implies that your StanHeaders package is still out of date. You can check this by running:

```
packageVersion("StanHeaders")

```

Where the output should be:

```
[1] ‘2.21.0.6’

```

(I suspect that you’ll be on `2.21.0.5`)

---

<div class="post-metadata">

**Author:** ![Paul\_Vanags](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/paul_vanags/32/4452_2.png) [@Paul\_Vanags](https://discourse.mc-stan.org/u/Paul_Vanags)\
**Post date:** [September 29, 2020, 7:30am UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/8 "2020-09-29T07:30:16Z")

</div>

> [@andrjohns](#):
>
> `packageVersion("StanHeaders")`

Hmm, nope…

packageVersion(“StanHeaders”)  
[1] ‘2.21.0.6’

---

<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 29, 2020, 7:33am UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/9 "2020-09-29T07:33:02Z")

</div>

Odd! The next thing to try would be to restart R, and then reinstall StanHeaders & RStan from source:

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

```

To speed up the install, make sure you set the number of cores to use for compilation with:

```
Sys.setenv(MAKEFLAGS="-jC")

```

Where C is the number of cores in your computer

---

<div class="post-metadata">

**Author:** ![Paul\_Vanags](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/paul_vanags/32/4452_2.png) [@Paul\_Vanags](https://discourse.mc-stan.org/u/Paul_Vanags)\
**Post date:** [September 29, 2020, 7:43am UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/10 "2020-09-29T07:43:10Z")

</div>

> [@andrjohns](#):
>
> `install.packages(c("StanHeaders","rstan"), type="source")`

OK - doing that now - it takes ages! (I only have 2 cores), let you know when done!

---

<div class="post-metadata">

**Author:** ![Paul\_Vanags](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/paul_vanags/32/4452_2.png) [@Paul\_Vanags](https://discourse.mc-stan.org/u/Paul_Vanags)\
**Post date:** [September 29, 2020, 7:51am UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/11 "2020-09-29T07:51:56Z")

</div>

The model has run! Yippee!!  
I did get this warning message though…  
Warning message:  
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :  
‘C:/rtools40/usr/mingw\_/bin/g++’ not found

Is that anything to worry about??

---

<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 29, 2020, 7:59am UTC](https://discourse.mc-stan.org/t/problem-running-rstan-in-rstudio/18236/12 "2020-09-29T07:59:55Z")

</div>

Great! That warning is safe to ignore and should be removed in the next release