rstan for R 4.2.0 and Rtools 4.2

[ploutal7]

Summary:

Can't install package rstan using R 4.2.0 and Rtools 4.2 on Windows,

Description:

Tried several different installations, including from source and also several binaries from different repositories. The installation from source has nonzero exit status, and the binary installations cause the R gui to shut down, without warning, when I run the command library(rstan).

Here's my system info: sysname release version machine "Windows" "10 x64" "build 19044" "x86-64"

I'm pretty sure this isn't a bug; I'm guessing developers haven't updated rstan for the newest R Windows releases. I'm wondering when they'll get to this--please let me know whenever you find time. Thanks.

[jgman86]

Installing the latest dev version (2.26.11) solved a similiar issue for me!

# run the next line if you already have rstan installed
remove.packages(c("StanHeaders", "rstan"))

install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))

Cheers

[ploutal7]

Unfortunately, using the development version didn't change the behavior. R still shuts down, without warning, when I try to load "rstan" via library(rstan). I ran the remove.packages command shown above first, just to make sure an old installation wasn't messing things up.

Paul Louisell

On Thu, May 5, 2022 at 10:52 AM Jan Göttmann @.***> wrote:

Installing the latest dev Version solved a similiar Issue for me!

run the next line if you already have rstan installed

remove.packages(c("StanHeaders", "rstan"))

install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))

Cheers

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[myaseen208]

rstan and brms cause R 4.2.0 and RStudio session abort. Even re-installation of rstan and brmscause the error.

sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0    pacman_0.5.1 

[jgman86]

I can't replicate this Issue, mine is running fine under following Session Properties:

R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.utf8  
LC_CTYPE=German_Germany.utf8    
LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C                   
LC_TIME=German_Germany.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] brms_2.17.0     Rcpp_1.0.8.3    truncnorm_1.0-8 devtools_2.4.3  usethis_2.1.5

Are you on the Windows Insider Program by Chance?

[ploutal7]

Here's an R session, with session info at the top. R closes, without warning, after invoking the example function at bottom. When I try to load rstan via library(rstan), instead of using the example function, R again closes without warning. See more comments below this first R session.

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C

[5] LC_TIME=English_United States.utf8

attached base packages: [1] stats graphics grDevices datasets utils methods base

loaded via a namespace (and not attached): [1] compiler_4.2.0 tools_4.2.0

remove.packages(c("StanHeaders", "rstan")) Removing packages from ‘C:/R_Libraries’ (as ‘lib’ is unspecified) install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")), dependencies=T) Installing package into ‘C:/R_Libraries’ (as ‘lib’ is unspecified) also installing the dependency ‘StanHeaders’

trying URL ' https://mc-stan.org/r-packages/bin/windows/contrib/4.2/StanHeaders_2.26.11.zip ' Content type 'application/zip' length 3198986 bytes (3.1 MB) downloaded 3.1 MB

trying URL ' https://mc-stan.org/r-packages/bin/windows/contrib/4.2/rstan_2.26.11.zip' Content type 'application/zip' length 2341210 bytes (2.2 MB) downloaded 2.2 MB

package ‘StanHeaders’ successfully unpacked and MD5 sums checked package ‘rstan’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Open Source\Stat Software\TMP\RtmpO8LWHs\downloaded_packages

example(stan_model, package = "rstan", run.dontrun = TRUE) # R gui closes without warning.

Compiling rstan from source yields this (I've removed the intermediate lines--the only error I could find was at the bottom as rstan was being tested for loading, but I didn't check through each line of output):

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C

[5] LC_TIME=English_United States.utf8

attached base packages: [1] stats graphics grDevices datasets utils methods base

loaded via a namespace (and not attached): [1] compiler_4.2.0 tools_4.2.0

remove.packages(c("StanHeaders", "rstan")) Removing packages from ‘C:/R_Libraries’ (as ‘lib’ is unspecified)

install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")), dependencies=T, type="source")

... intermediate lines ...

** testing if installed package can be loaded from temporary location ERROR: loading failed

• removing 'C:/R_Libraries/rstan'

The downloaded source packages are in ‘C:\Open Source\Stat Software\TMP\Rtmpmc8bZv\downloaded_packages’ Warning message: In install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", : installation of package ‘rstan’ had non-zero exit status

On Mon, May 9, 2022 at 10:29 AM Jan Göttmann @.***> wrote:

[image: grafik] https://user-images.githubusercontent.com/81758548/167431759-5a9027aa-d88d-4629-8544-ce6ad08d8444.png

I can't replicate this Issue, mine is running fine under following Session Properties:

R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C LC_TIME=German_Germany.utf8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] brms_2.17.0 Rcpp_1.0.8.3 truncnorm_1.0-8 devtools_2.4.3 usethis_2.1.5

— Reply to this email directly, view it on GitHub https://github.com/stan-dev/rstan/issues/1007#issuecomment-1121179384, or unsubscribe https://github.com/notifications/unsubscribe-auth/AY7BAO7L7KR7QLYWDH5M2GTVJEONRANCNFSM5U223DZA . You are receiving this because you authored the thread.Message ID: @.***>

[ploutal7]

Additional info, although I don't know how helpful it will be. I opened the Windows event viewer to see what info showed, and an instance of the Rgui crash shows below:

Faulting application name: Rgui.exe, version: 4.20.16693.0, time stamp: 0x62629b8f Faulting module name: ntdll.dll, version: 10.0.19041.1682, time stamp: 0x7b5414ec Exception code: 0xc0000005 Fault offset: 0x00000000000a6c3b Faulting process id: 0x3154 Faulting application start time: 0x01d864145cd8de85 Faulting application path: C:\Program Files\R\R-4.2.0\bin\x64\Rgui.exe Faulting module path: C:\WINDOWS\SYSTEM32\ntdll.dll

It looks like it has something to do with a dll in the SYSTEM32 folder.

On Mon, May 9, 2022 at 10:40 PM Paul @.***> wrote:

Here's an R session, with session info at the top. R closes, without warning, after invoking the example function at bottom. When I try to load rstan via library(rstan), instead of using the example function, R again closes without warning. See more comments below this first R session.

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C

[5] LC_TIME=English_United States.utf8

attached base packages: [1] stats graphics grDevices datasets utils methods base

loaded via a namespace (and not attached): [1] compiler_4.2.0 tools_4.2.0

remove.packages(c("StanHeaders", "rstan")) Removing packages from ‘C:/R_Libraries’ (as ‘lib’ is unspecified) install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")), dependencies=T) Installing package into ‘C:/R_Libraries’ (as ‘lib’ is unspecified) also installing the dependency ‘StanHeaders’

trying URL ' https://mc-stan.org/r-packages/bin/windows/contrib/4.2/StanHeaders_2.26.11.zip ' Content type 'application/zip' length 3198986 bytes (3.1 MB) downloaded 3.1 MB

trying URL ' https://mc-stan.org/r-packages/bin/windows/contrib/4.2/rstan_2.26.11.zip' Content type 'application/zip' length 2341210 bytes (2.2 MB) downloaded 2.2 MB

package ‘StanHeaders’ successfully unpacked and MD5 sums checked package ‘rstan’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Open Source\Stat Software\TMP\RtmpO8LWHs\downloaded_packages

example(stan_model, package = "rstan", run.dontrun = TRUE) # R gui closes without warning.

Compiling rstan from source yields this (I've removed the intermediate lines--the only error I could find was at the bottom as rstan was being tested for loading, but I didn't check through each line of output):

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C

[5] LC_TIME=English_United States.utf8

attached base packages: [1] stats graphics grDevices datasets utils methods base

loaded via a namespace (and not attached): [1] compiler_4.2.0 tools_4.2.0

remove.packages(c("StanHeaders", "rstan")) Removing packages from ‘C:/R_Libraries’ (as ‘lib’ is unspecified)

install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")), dependencies=T, type="source")

... intermediate lines ...

** testing if installed package can be loaded from temporary location ERROR: loading failed

• removing 'C:/R_Libraries/rstan'

The downloaded source packages are in ‘C:\Open Source\Stat Software\TMP\Rtmpmc8bZv\downloaded_packages’ Warning message: In install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", : installation of package ‘rstan’ had non-zero exit status

On Mon, May 9, 2022 at 10:29 AM Jan Göttmann @.***> wrote:

[image: grafik] https://user-images.githubusercontent.com/81758548/167431759-5a9027aa-d88d-4629-8544-ce6ad08d8444.png

I can't replicate this Issue, mine is running fine under following Session Properties:

R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C LC_TIME=German_Germany.utf8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] brms_2.17.0 Rcpp_1.0.8.3 truncnorm_1.0-8 devtools_2.4.3 usethis_2.1.5

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[ChenghuFeng]

maybe you can try lower R version like 4.0.2 or 4.0.5， and lower Rtool40， i found R 4.0.2 and Rtool40 can match perfectly

[ploutal7]

Yes, I had *rstan *working with R version 4.1.3 and RTools4.0.1--I can always reinstall these if necessary. I know it must be somewhat hard on STAN developers because the Windows version of R updates so frequently, but I'm wondering when *rstan *will work with RTools4.2.

On Tue, May 17, 2022 at 9:03 PM ChenghuFeng @.***> wrote:

maybe you can try lower R version like 4.0.2 or 4.0.5， and lower Rtool40， i found R 4.0.2 and Rtool40 can match perfectly

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[bschneidr]

I had this same issue, whether I used RStudio or just plain R. Attempting to load rstan with library(rstan) caused my R session to immediately crash after I updated R to 4.2.0.

I don't understand why, but the issue was resolved for me by resinstalling rstan and some of its dependencies.

install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel",
                             "inline", "loo", "pkgbuild", "rstan"))

[myaseen208]

Thanks @bschneidr for your comment. Reinstalling rstan along with its some dependencies as you given also works for me. Thanks

install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"))

[ploutal7]

So I tried what Ben Schneider suggested; specifically, I did this:

remove.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"))

And then I restarted R 4.2.0 and did this:

install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"), dependencies=T) example(stan_model, package = "rstan", run.dontrun = TRUE)

The good news is R didn't crash. The bad news is I got a lot of screen output with this final error:

Compilation ERROR, function(s)/method(s) not created! Error in compileCode(f, code, language = language, verbose = verbose) : C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file1b9c1bde7373.o:file1b9c1bde7373.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file1b9c1bde7373.o:file1b9c1bde7373.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file1b9c1bde7373.o:file1b9c1bde7373.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x3a): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file1b9c1bde7373.o:file1b9c1bde7373.cpp:(.text$_ZN3tbb10interface

Loading *rstan *via library(rstan) no longer causes a crash, but when I try to run the Eight Schools example, I get this:

fit <- stan(file = 'schools.stan', data = schools_dat) hash mismatch so recompiling; make sure Stan code ends with a blank line make cmd is make -f "C:/PROGRA~1/R/R-42~1.0/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-42~1.0/share/make/winshlib.mk" -f "C:\Users\louta\Documents/.R/Makevars.win" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file1b9c545430b5.dll" WIN=64 TCLBIN= OBJECTS="file1b9c545430b5.o"

make would use if test "zfile1b9c545430b5.o" != "z"; then
if test -e "file1b9c545430b5-win.def"; then
echo g++ -shared -s -static-libgcc -o file1b9c545430b5.dll file1b9c545430b5-win.def file1b9c545430b5.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA~1/R/R-42~1.0/bin/x64" -lR ;
g++ -shared -s -static-libgcc -o file1b9c545430b5.dll file1b9c545430b5-win.def file1b9c545430b5.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA~1/R/R-42~1.0/bin/x64" -lR ;
else
echo EXPORTS > tmp.def;
nm file1b9c545430b5.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def;
echo g++ -shared -s -static-libgcc -o file1b9c545430b5.dll tmp.def file1b9c545430b5.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA~1/R/R-42~1.0/bin/x64" -lR ;
g++ -shared -s -static-libgcc -o file1b9c545430b5.dll tmp.def file1b9c545430b5.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA~1/R/R-42~1.0/bin/x64" -lR ;
rm -f tmp.def;
fi
fi Error in compileCode(f, code, language = language, verbose = verbose) : C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file1b9c545430b5.o:file1b9c545430b5.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file1b9c545430b5.o:file1b9c545430b5.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file1b9c545430b5.o:file1b9c545430b5.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x3a): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file1b9c545430b5.o:file1b9c545430b5.cpp:(.text$_ZN3tbb10interface Error in sink(type = "output") : invalid connection

On Wed, May 18, 2022 at 9:57 AM myaseen208 @.***> wrote:

Thanks @bschneidr https://github.com/bschneidr for your comment. Reinstalling rstan along with its some dependencies as you given also works for me. Thanks

install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"))

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[LeoSokolovic]

Hi,

I'm using Windows 11 in Windows Insider Program and had the same issue. I managed to solve it by:

1. Removing the following packages:

remove.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel",
                             "inline", "loo", "pkgbuild", "rstan"))

2. Restarting R 4.2.0
3. Following https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Windows for R4.0. I basically just copy-pasted the code. However, I changed writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron") to writeLines('PATH="${RTOOLS42_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
4. Then,

install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen",
"RcppParallel", "inline", "loo", "pkgbuild", "rstan"), dependencies=T)

5. I also ran install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))

I guess the steps 4 and 5 are somewhat redundant. But configuring the C toolchain for rtools 4.2 and configuring the makevars file probably did the trick.

[ploutal7]

This didn't work for me; I'd already configured the toolchain for Rtools 4.2, and modifying the PATH variable didn't change it--it only causes "C:\rtools42\usr\bin;" to repeat in the PATH.

But I finally found something that WORKED for me:

remove.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"))

Quit and restart R.

install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"), repos = c(" https://mc-stan.org/r-packages/", getOption("repos")))

Note I'm attempting to install ALL the packages from

https://mc-stan.org/r-packages/ FIRST, not only "StanHeaders" and "rstan". This will also work with the slightly broader option "dependencies = TRUE" inserted, instead of the default "dependencies = NA".

And that was all it took--everything worked.

On Sat, May 21, 2022 at 3:47 AM LeoS @.***> wrote:

Hi,

I'm using Windows 11 in Windows Insider Program and had the same issue. I managed to solve it by:

Removing the following packages: remove.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan")) 2.

Restarting R 4.2.0 3.

Following https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Windows for R4.0. I basically just copy-pasted the code. However, I changed 'writeLines('PATH="${RTOOLS40_HOME}\usr\bin;${PATH}"', con = "/.Renviron")' to 'writeLines('PATH="${RTOOLS42_HOME}\usr\bin;${PATH}"', con = " /.Renviron")' 4.

Then, install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"), dependencies=T) 5.

I also ran install.packages("rstan", repos = c(" https://mc-stan.org/r-packages/", getOption("repos")))

I guess the steps 4 and 5 are somewhat redundant. But configuring the C toolchain for rtools 4.2 and configuring the makevars file probably did the trick.

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[ploutal7]

Thanks to everyone for their help; it was a combination of Jan Göttmann's and Ben Schneider's advice that solved my problem. For anyone wondering, here's my default repository:

options("repos") $repos [1] "http://lib.stat.cmu.edu/R/CRAN/"

So at least one of the packages (*besides **StanHeaders *and rstan) in the list *BH, StanHeaders, Rcpp, RcppEigen, RcppParallel, inline, loo, pkgbuild, rstan *must have a different version at https://mc-stan.org/r-packages/ than at http://lib.stat.cmu.edu/R/CRAN/. That difference, along with possible differences between *StanHeaders *and rstan going between the repositories, was what caused my error.

On Sat, May 21, 2022 at 8:06 AM Paul @.***> wrote:

This didn't work for me; I'd already configured the toolchain for Rtools 4.2, and modifying the PATH variable didn't change it--it only causes "C:\rtools42\usr\bin;" to repeat in the PATH.

But I finally found something that WORKED for me:

remove.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"))

Quit and restart R.

install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"), repos = c(" https://mc-stan.org/r-packages/", getOption("repos")))

Note I'm attempting to install ALL the packages from

https://mc-stan.org/r-packages/ FIRST, not only "StanHeaders" and "rstan". This will also work with the slightly broader option "dependencies = TRUE" inserted, instead of the default "dependencies = NA".

And that was all it took--everything worked.

On Sat, May 21, 2022 at 3:47 AM LeoS @.***> wrote:

Hi,

I'm using Windows 11 in Windows Insider Program and had the same issue. I managed to solve it by:

Removing the following packages: remove.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan")) 2.

Restarting R 4.2.0 3.

Following https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Windows for R4.0. I basically just copy-pasted the code. However, I changed 'writeLines('PATH="${RTOOLS40_HOME}\usr\bin;${PATH}"', con = "/.Renviron")' to 'writeLines('PATH="${RTOOLS42_HOME}\usr\bin;${PATH}"', con = " /.Renviron")' 4.

Then, install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"), dependencies=T) 5.

I also ran install.packages("rstan", repos = c(" https://mc-stan.org/r-packages/", getOption("repos")))

I guess the steps 4 and 5 are somewhat redundant. But configuring the C toolchain for rtools 4.2 and configuring the makevars file probably did the trick.

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[rempsyc]

rstan and brms cause R 4.2.0 and RStudio session abort. Even re-installation of rstan and brmscause the error.

Same here. The solution,

install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel",
                             "inline", "loo", "pkgbuild", "rstan"))

also fixed it for me.

[knowbrightly]

This page saved my day. I've been struggling so long with this issue.

install.packages(c("BH",`` "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"))

This worked out for me. Lots of appreciation!

[whzhuscu]

rstan and brms cause R 4.2.0 and RStudio session abort. Even re-installation of rstan and brmscause the error.

sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0    pacman_0.5.1 

hello, I wonder if you had deal with the problem? Thank you!

[ploutal7]

I don't use Rstudio so I'm not a good contact for this. Also, you're using R 4.2.0, and the most recent version is R 4.2.3. I was able to run the examples from package rstan without problem using R 4.2.3, but it's the *same *procedure I followed to get around R crashing in R 4.2.0:

1. First, open R and run this command: remove.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"))
2. Then quit and restart R, and run this command: install.packages(c("BH", "StanHeaders", "Rcpp", "RcppEigen", "RcppParallel", "inline", "loo", "pkgbuild", "rstan"), repos = c(" https://mc-stan.org/r-packages/", getOption("repos"))) # Note I'm attempting to install ALL the packages from https://mc-stan.org/r-packages/ FIRST, not only "StanHeaders" and "rstan". This will also work with the slightly broader option "dependencies = TRUE" inserted, instead of the default "dependencies = NA".
   1. You don't need to include anything that appears after the "#" in the command above--that's just a comment explaining how the command works, and it mentions another option that also works with the "dependencies" parameter.

Good luck, Paul

On Wed, May 10, 2023 at 9:50 AM whzhuscu @.***> wrote:

rstan and brms cause R 4.2.0 and RStudio session abort. Even re-installation of rstan and brmscause the error.

[image: enter image description here] https://i.stack.imgur.com/HFf3U.png

[image: enter image description here] https://i.stack.imgur.com/6OZ1M.png

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 [2] LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.utf8

attached base packages: [1] stats graphics grDevices utils datasets methods [7] base

loaded via a namespace (and not attached): [1] compiler_4.2.0 tools_4.2.0 pacman_0.5.1

hello, I wonder if you had deal with the problem? Thank you!

— Reply to this email directly, view it on GitHub https://github.com/stan-dev/rstan/issues/1007#issuecomment-1542253413, or unsubscribe https://github.com/notifications/unsubscribe-auth/AY7BAO6YSYKEB35CVON4IADXFOMKHANCNFSM5U223DZA . You are receiving this because you authored the thread.Message ID: @.***>

[knowbrightly]

RStudio did not abort after installing the dependencies mentioned above, but when I ran the rstan functions to fit the model, it returned an error.

I finally resolved the issue by downgrading from R 4.2.1 to 4.1.3 and Rtools42 to Rtools40. It appears that R 4.2 and Rtools42 are not yet compatible with the stan package.

Interestingly, it works fine with R 4.2 and Rtools42 on my laptop, but not in my desktop. It seems to vary from device to device.

These links might be helpful:

RStan error in R 4.2.2 (not in R 4.1.3) Stan & R 4.2 on Windows

[jgman86]

i would recommend using cmdstan and cmdstanr - much more stable and I have zero issues with it

[kjayhan]

I have the same problem. I first had this problem with my Windows. And I solved it. It was ok on my mac, but now it doesn't work on Mac at all. When I run "example(stan_model, package = "rstan", run.dontrun = TRUE)", Rstudio crashes with "fatal error". Tried everything on the Stan forums but nothing worked.

R version 4.3.0 (2023-04-21) Platform: aarch64-apple-darwin20 (64-bit)

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Seoul tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] tensorA_0.36.2 utf8_1.2.3 generics_0.1.3
[4] stringi_1.7.12 digest_0.6.31 magrittr_2.0.3
[7] grid_4.3.0 pkgload_1.3.2 fastmap_1.1.1
[10] processx_3.8.1 pkgbuild_1.4.0 sessioninfo_1.2.2
[13] backports_1.4.1 urlchecker_1.0.1 ps_1.7.5
[16] promises_1.2.0.1 fansi_1.0.4 purrr_1.0.1
[19] scales_1.2.1 abind_1.4-5 cli_3.6.1
[22] shiny_1.7.4 rlang_1.1.1 crayon_1.5.2
[25] cmdstanr_0.5.3 ellipsis_0.3.2 munsell_0.5.0
[28] remotes_2.4.2 cachem_1.0.8 devtools_2.4.5
[31] tools_4.3.0 memoise_2.0.1 checkmate_2.2.0
[34] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2
[37] httpuv_1.6.11 vctrs_0.6.2 posterior_1.4.1
[40] R6_2.5.1 mime_0.12 lifecycle_1.0.3
[43] stringr_1.5.0 fs_1.6.2 htmlwidgets_1.6.2
[46] usethis_2.1.6 miniUI_0.1.1.1 pkgconfig_2.0.3
[49] callr_3.7.3 pillar_1.9.0 later_1.3.1
[52] gtable_0.3.3 glue_1.6.2 profvis_0.3.8
[55] Rcpp_1.0.10 xfun_0.39 tidyselect_1.2.0
[58] tibble_3.2.1 knitr_1.43 rstudioapi_0.14
[61] farver_2.1.1 xtable_1.8-4 htmltools_0.5.5
[64] compiler_4.3.0 prettyunits_1.1.1 distributional_0.3.2

[kjayhan]

I have the same problem. I first had this problem with my Windows. And I solved it. It was ok on my mac, but now it doesn't work on Mac at all. When I run "example(stan_model, package = "rstan", run.dontrun = TRUE)", Rstudio crashes with "fatal error". Tried everything on the Stan forums but nothing worked.

R version 4.3.0 (2023-04-21) Platform: aarch64-apple-darwin20 (64-bit)

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Seoul tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] tensorA_0.36.2 utf8_1.2.3 generics_0.1.3 [4] stringi_1.7.12 digest_0.6.31 magrittr_2.0.3 [7] grid_4.3.0 pkgload_1.3.2 fastmap_1.1.1 [10] processx_3.8.1 pkgbuild_1.4.0 sessioninfo_1.2.2 [13] backports_1.4.1 urlchecker_1.0.1 ps_1.7.5 [16] promises_1.2.0.1 fansi_1.0.4 purrr_1.0.1 [19] scales_1.2.1 abind_1.4-5 cli_3.6.1 [22] shiny_1.7.4 rlang_1.1.1 crayon_1.5.2 [25] cmdstanr_0.5.3 ellipsis_0.3.2 munsell_0.5.0 [28] remotes_2.4.2 cachem_1.0.8 devtools_2.4.5 [31] tools_4.3.0 memoise_2.0.1 checkmate_2.2.0 [34] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 [37] httpuv_1.6.11 vctrs_0.6.2 posterior_1.4.1 [40] R6_2.5.1 mime_0.12 lifecycle_1.0.3 [43] stringr_1.5.0 fs_1.6.2 htmlwidgets_1.6.2 [46] usethis_2.1.6 miniUI_0.1.1.1 pkgconfig_2.0.3 [49] callr_3.7.3 pillar_1.9.0 later_1.3.1 [52] gtable_0.3.3 glue_1.6.2 profvis_0.3.8 [55] Rcpp_1.0.10 xfun_0.39 tidyselect_1.2.0 [58] tibble_3.2.1 knitr_1.43 rstudioapi_0.14 [61] farver_2.1.1 xtable_1.8-4 htmltools_0.5.5 [64] compiler_4.3.0 prettyunits_1.1.1 distributional_0.3.2

I got it to work on my Windows after deleting renv folder in one of my project folders which is on Onedrive (shared across Windows and Mac). I think that was the main problem.

[ploutal7]

This has evolved to a different issue than the one I opened, which was on Windows 10 for rstan in R 4.2.0 and Rtools 4.2 (not Rstudio). The fix I published above on May 1, 2022 with the help / suggestions of several people continues to work on my Windows 10 machine with R 4.3.0 and Rtools 4.3.

Users with other issues (not every crash has the same cause), e.g., on a Mac OS / Rstudio should open a new thread.

[ploutal7]

Everyone, This has evolved to a different issue than the one I opened, which was on Windows 10 for rstan in R 4.2.0 and Rtools 4.2 (not Rstudio). The fix I put on GitHub (May 1, 2022) with the help / suggestions of several people continues to work on my Windows 10 machine with R 4.3.0 and Rtools 4.3. Hence, I've closed the thread, something I should have done as soon as I found the fix.

People who are having problems with a Mac OS / Rstudio should open a *new *thread on GitHub. Not every crash has the same cause, and asking for help under the thread I started won't get the attention of developers for separate issues.

Paul

On Tue, Jun 6, 2023 at 1:47 AM Kadir Jun Ayhan @.***> wrote:

I have the same problem. I first had this problem with my Windows. And I solved it. It was ok on my mac, but now it doesn't work on Mac at all. When I run "example(stan_model, package = "rstan", run.dontrun = TRUE)", Rstudio crashes with "fatal error". Tried everything on the Stan forums but nothing worked.

R version 4.3.0 (2023-04-21) Platform: aarch64-apple-darwin20 (64-bit)

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Seoul tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] tensorA_0.36.2 utf8_1.2.3 generics_0.1.3 [4] stringi_1.7.12 digest_0.6.31 magrittr_2.0.3 [7] grid_4.3.0 pkgload_1.3.2 fastmap_1.1.1 [10] processx_3.8.1 pkgbuild_1.4.0 sessioninfo_1.2.2 [13] backports_1.4.1 urlchecker_1.0.1 ps_1.7.5 [16] promises_1.2.0.1 fansi_1.0.4 purrr_1.0.1 [19] scales_1.2.1 abind_1.4-5 cli_3.6.1 [22] shiny_1.7.4 rlang_1.1.1 crayon_1.5.2 [25] cmdstanr_0.5.3 ellipsis_0.3.2 munsell_0.5.0 [28] remotes_2.4.2 cachem_1.0.8 devtools_2.4.5 [31] tools_4.3.0 memoise_2.0.1 checkmate_2.2.0 [34] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 [37] httpuv_1.6.11 vctrs_0.6.2 posterior_1.4.1 [40] R6_2.5.1 mime_0.12 lifecycle_1.0.3 [43] stringr_1.5.0 fs_1.6.2 htmlwidgets_1.6.2 [46] usethis_2.1.6 miniUI_0.1.1.1 pkgconfig_2.0.3 [49] callr_3.7.3 pillar_1.9.0 later_1.3.1 [52] gtable_0.3.3 glue_1.6.2 profvis_0.3.8 [55] Rcpp_1.0.10 xfun_0.39 tidyselect_1.2.0 [58] tibble_3.2.1 knitr_1.43 rstudioapi_0.14 [61] farver_2.1.1 xtable_1.8-4 htmltools_0.5.5 [64] compiler_4.3.0 prettyunits_1.1.1 distributional_0.3.2

I got it to work on my Windows after deleting renv file in one of my project folders which is on Onedrive (shared across Windows and Mac). I think that was the main problem.

— Reply to this email directly, view it on GitHub https://github.com/stan-dev/rstan/issues/1007#issuecomment-1577952891, or unsubscribe https://github.com/notifications/unsubscribe-auth/AY7BAO2O3FQVT2GR4X3CECTXJ276DANCNFSM5U223DZA . You are receiving this because you authored the thread.Message ID: @.***>