Error when Configuring RStan C++ toolchain

aschmidt · September 8, 2020, 12:14pm

Hello! I am a new user to RStan and I ran into an issue when configuring the C++ toolchain and subsequent loading of the RStan package.

I am using Windows 10, R x64 v.4.0.2 and RStudio v.1.3.1073. I followed these instructions to the letter in R and RStudio: https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started. Below are the commands I used an abbreviated version of the output highlighting the error.

> install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE)
ERROR: compilation failed for package 'jsonlite'
* removing 'C:/Users/Allison/Documents/R/win-library/4.0/jsonlite'
Warning in install.packages :
  installation of package ‘jsonlite’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\Allison\AppData\Local\Temp\RtmpAnUOQm\downloaded_packages’
> pkgbuild::has_build_tools(debug = TRUE)
>library("rstan") 
Loading required package: StanHeaders
Loading required package: ggplot2
Error: package or namespace load failed for ‘rstan’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘jsonlite’

Any insights on would be helpful.
Thank you!
Allison

rok_cesnovar · September 8, 2020, 12:22pm

Can you try running:

writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")

and restart the R ression and then try installing rstan again.

aschmidt · September 8, 2020, 2:09pm

Still the same error.
Error: package or namespace load failed for ‘rstan’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘jsonlite’

rok_cesnovar · September 8, 2020, 2:19pm

Can you run

install.packages(“jsonlite”)

aschmidt · September 8, 2020, 3:21pm

This is what I get when I try installing just the jsonlite package.

ERROR: compilation failed for package ‘jsonlite’

removing ‘C:/Users/Allison/Documents/R/win-library/4.0/jsonlite’

The downloaded source packages are in
‘C:\Users\Allison\AppData\Local\Temp\Rtmpu2NfgF\downloaded_packages’
Warning message:
In install.packages(“jsonlite”) :
installation of package ‘jsonlite’ had non-zero exit status

aschmidt · September 8, 2020, 3:22pm

Here is the complete output in case it helps.

install.packages(“jsonlite”)
Installing package into ‘C:/Users/Allison/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
— Please select a CRAN mirror for use in this session —

There is a binary version available but the source version is later:
binary source needs_compilation
jsonlite 1.7.0 1.7.1 TRUE

installing the source package ‘jsonlite’

trying URL ‘https://cran.case.edu/src/contrib/jsonlite_1.7.1.tar.gz’
Content type ‘application/x-gzip’ length 1057786 bytes (1.0 MB)
downloaded 1.0 MB

installing source package ‘jsonlite’ …
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
C:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c base64.c -o base64.o
C:/Rtools/mingw_32/bin/gcc: not found
make: *** [base64.o] Error 127
ERROR: compilation failed for package ‘jsonlite’

removing ‘C:/Users/Allison/Documents/R/win-library/4.0/jsonlite’

The downloaded source packages are in
‘C:\Users\Allison\AppData\Local\Temp\Rtmpu2NfgF\downloaded_packages’
Warning message:
In install.packages(“jsonlite”) :
installation of package ‘jsonlite’ had non-zero exit status

rok_cesnovar · September 8, 2020, 3:33pm

What does Sys.getenv(“RTOOLS40_HOME”) return?

aschmidt · September 8, 2020, 3:33pm

Sys.getenv(“RTOOLS40_HOME”)
[1] “”

rok_cesnovar · September 8, 2020, 4:36pm

Oh ok, in this case you do not have RTools 4.0 installed.

See: https://cran.r-project.org/bin/windows/Rtools/

aschmidt · September 8, 2020, 4:51pm

I followed the instructions to the link you sent and I get a compilation error for the jsonlite package.

Sys.which(“make”)
make
“C:\rtools40\usr\bin\make.exe”
install.packages(“jsonlite”, type = “source”)
Installing package into ‘C:/Users/Allison/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
trying URL ‘https://cran.rstudio.com/src/contrib/jsonlite_1.7.1.tar.gz’
Content type ‘application/x-gzip’ length 1057786 bytes (1.0 MB)
downloaded 1.0 MB

installing source package ‘jsonlite’ …
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
C:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c base64.c -o base64.o
sh: C:/Rtools/mingw_32/bin/gcc: No such file or directory
make: *** [C:/PROGRA~1/R/R-40~1.2/etc/i386/Makeconf:222: base64.o] Error 127
ERROR: compilation failed for package ‘jsonlite’

removing ‘C:/Users/Allison/Documents/R/win-library/4.0/jsonlite’
Warning in install.packages :
installation of package ‘jsonlite’ had non-zero exit status

The downloaded source packages are in
‘C:\Users\Allison\AppData\Local\Temp\RtmpyI6z2r\downloaded_packages’

andrjohns · September 9, 2020, 12:13am

Hi Allison,

That means that R is still configured to look for the old RTools installation. To help figure out what needs to be changed, can you post the outputs from:

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

aschmidt · September 12, 2020, 1:32pm

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:\Rtools\bin;c:\Rtools\mingw_64\bin;C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Program Files (x86)\Common Files\Intel\Shared Libraries\redist\ia32\mpirt;C:\Program Files (x86)\Common Files\Intel\Shared Libraries\redist\ia32\compiler;C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS Client\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\Intel® Management Engine Components\DAL;C:\Program Files\Intel\Intel® Management Engine Components\IPT;C:\Program Files (x86)\Intel\Intel® Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel® Management Engine Components\IPT;C:\Program Files (x86)\Intel\OpenCL SDK\3.0\bin\x86;C:\Program Files (x86)\Intel\OpenCL SDK\3.0\bin\x64;C:\Program Files (x86)\Toshiba\Bluetooth Toshiba Stack\sys\;C:\Program Files (x86)\Toshiba\Bluetooth Toshiba Stack\sys\x64\;C:\MATLAB701\bin\win32;C:\Program Files\MATLAB\R2017b\runtime\win64;C:\Program Files\MATLAB\R2017b\bin;C:\Program Files (x86)\Kensington\TrackballWorks;C:\WINDOWS\System32\OpenSSH\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;%USERPROFILE%\AppData\Local\Microsoft\WindowsApps;”

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

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

readLines("~/.R/Makevars.win")
[1] “”
[2] “CXX14FLAGS=-O3 -mtune=native -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2”
[3] “”
[4] “CXX14FLAGS=-O3 -mtune=native -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2”
[5] “”
[6] “CXX14FLAGS=-O3 -mtune=native -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2”
[7] “”
[8] “CXX14FLAGS=-O3 -mtune=native -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2”

andrjohns · September 13, 2020, 1:28pm

Great! Three steps to take here:

In your Documents folder there will a file called .Rprofile, delete that
In your Documents folder there will be a .R folder, in that will be a Makevars.win file. Open that in a text editor and delete all but one of the CXX14FLAGS lines
Restart R and try your model again

Laura_Verbeek · March 2, 2021, 11:09am

Hi There!

I have a similar problem. I have R version 4.0.4 with Rstudio version 1.4.1106 (both updated today). I have been trying to get the installation from source to work, but I keep getting the same error messages. I have already done all the steps from this thread, including numerous steps from other threads to get jsonlite to install. I get the following error message:

install.packages(“jsonlite”, type = “source”)
Installing package into ‘C:/Users/laura/OneDrive/Documenten/R/win-library/4.0’
(as ‘lib’ is unspecified)
trying URL ‘http://cran.rstudio.com/src/contrib/jsonlite_1.7.2.tar.gz’
Content type ‘application/x-gzip’ length 421716 bytes (411 KB)
downloaded 411 KB

installing source package ‘jsonlite’ …
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
C:/rtools40/usr/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-40~1.4/include" -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c base64.c -o base64.o
sh: C:/rtools40/usr/mingw_32/bin/gcc: No such file or directory
make: *** [C:/PROGRA~1/R/R-40~1.4/etc/i386/Makeconf:222: base64.o] Error 127
ERROR: compilation failed for package ‘jsonlite’

removing ‘C:/Users/laura/OneDrive/Documenten/R/win-library/4.0/jsonlite’
restoring previous ‘C:/Users/laura/OneDrive/Documenten/R/win-library/4.0/jsonlite’
Warning in install.packages :
installation of package ‘jsonlite’ had non-zero exit status

The downloaded source packages are in
‘C:\Users\laura\AppData\Local\Temp\Rtmpctpahf\downloaded_packages’

Laura_Verbeek · March 2, 2021, 11:10am

Btw, my output to the code metioned above is as following:

Sys.getenv(“BINPREF”)
[1] “C:/rtools40/usr/mingw_$(WIN)/bin/”

Sys.getenv(“PATH”)
[1] “C:\rtools40\usr\bin;C:\Program Files\R\R-4.0.4\bin\x64;C:\Python27\Lib\site-packages\PyQt4;C:\Windows\System32;C:\Windows;C:\Windows\System32\wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\Windows\System32\OpenSSH;C:\Program Files (x86)\Intel\Intel® Management Engine Components\DAL;C:\Program Files\Intel\Intel® Management Engine Components\DAL;C:\Program Files\MATLAB\R2019a\bin;C:\Python27;C:\Python27\DLLs;C:\Python27\Scripts;C:\Python27\gnuplot\binary;C:\Program Files (x86)\pythonxy\SciTE-3.5.1-4;C:\Program Files (x86)\pythonxy\console;C:\Users\laura\AppData\Roaming\TinyTeX\bin\win32;C:\Users\laura\AppData\Local\Microsoft\WindowsApps;C:\Users\laura\AppData\Local\Programs\MiKTeX 2.9\miktex\bin\x64”
readLines("~/.Renviron")
[1] “PATH=”{RTOOLS40_HOME}\\usr\\bin;{PATH}""
readLines("~/.Rprofile")
[1] “Sys.setenv(BINPREF = “C:/rtools40/usr/mingw_$(WIN)/bin/”)”
readLines("~/.R/Makevars.win")
[1] “”
[2] " CXX14FLAGS += -mtune=native -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2"

andrjohns · March 4, 2021, 12:41pm

Hi Laura,

The issue is caused by your setting of BINPREF in your .Rprofile file. See the RStan Getting Started Instructions for information on how to fix this.

Laura_Verbeek · March 4, 2021, 5:03pm

Hi there,

Thank you for your quick reply! I had already deleted my Rprofile file before, but there was a new one now. I again deleted it, as was in the instructions. The problem is still there though. Do you have any idea how I can fix it?

andrjohns · March 5, 2021, 12:12am

What do you get from:

Sys.getenv("BINPREF")
readLines("~/.Rprofile")

Laura_Verbeek · March 5, 2021, 6:50am

The first one gives:

Sys.getenv(“BINPREF”)
[1] “”

And the second one:

readLines("~/.Rprofile")
Error in file(con, “r”) : cannot open the connection
In addition: Warning message:
In file(con, “r”) :
cannot open file ‘C:/Users/laura/OneDrive/Documenten/.Rprofile’: No such file or directory

andrjohns · March 5, 2021, 7:03am

If you restart your R session and run the example model:

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

What error do you get? If you’re still getting an error now that the .Rprofile file has been deleted then there is a different issue to be fixed