You may have leftover files, but it should only be using the new ones. What is the output of
example(stan_model, package = "rstan", run.dontrun = TRUE)
now?
That ran fine (although saving it in Word makes it harder to read). What is the output when you encounter the error but specify verbose = TRUE when calling stan or sampling?
Here is the output:
TRANSLATING MODEL ‘lm_2wayanova’ FROM Stan CODE TO C++ CODE NOW.
successful in parsing the Stan model ‘lm_2wayanova’.
CHECKING DATA AND PREPROCESSING FOR MODEL ‘lm_2wayanova’ NOW.
COMPILING MODEL ‘lm_2wayanova’ NOW.
STARTING SAMPLER FOR MODEL ‘lm_2wayanova’ NOW.
SAMPLING FOR MODEL ‘lm_2wayanova’ NOW (CHAIN 1).
Chain 1: empty_nested() must be true before calling recover_memory()
[1] “Error in sampler$call_sampler(args_list[[i]]) : "
[2] " empty_nested() must be true before calling recover_memory()”
error occurred during calling the sampler; sampling not done
Hi, I wanted to mention an error I get that may be related to the whole Catalina thing - please let me know if you prefer I open a separate thread for this.
When I run a Stan model that is syntactically incorrect, I get
Error in stanc(file = file, model_code = model_code, model_name = model_name, : c++ exception (unknown reason)
I don’t get any error when running a correct Stan model. I thought it might be related because of the c++ exception (unknown reason).
Also, when I click the “check” button for Stan syntax in RStudio, it doesn’t return anything if the model is incorrect.
This is a simple problem to bypass - whenever check syntax doesn’t return anything I’ll just assume I made an error in coding my Stan model. I just wanted to make sure you’re aware of this. Do other people experience this too?
I assume that problem goes away if you compile rstan from source via
install.packages("rstan", type = "source")
?
1 Like
Yes it does! Thanks for the quick reply.
Hello everyone,
I am still not able to have rstan working properly.
I now freshly installed R, Rstudio and installed the macos-rtools [v3.2.2] without having XCode installed on the mac, but I am still having the same issue as before.
Do you have any new suggestion?
Thanks
I also just tried to freshly install everything having XCode already installed…
And I modified Makevars as you suggested, but I’m still getting
[1] “Error in sampler$call_sampler(args_list[[i]]) : " " c++ exception (unknown reason)”
error occurred during calling the sampler; sampling not done
Hi @Save,
- Install Xcode. Make sure to install the command line tools and accept the license.
- Install
macos-rtools. Follow these instructions.
I use this in my.R/Makevars:
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
SHLIB_CXXLDFLAGS+=-Wl,-rpath,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib
SHLIB_CXX11LDFLAGS+=-Wl,-rpath,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib
SHLIB_CXX14LDFLAGS+=-Wl,-rpath,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib
- Recompile
rstanfrom source:
install.packages("rstan", type = "source")
The above worked for me :)
3 Likes
Thanks for the reply @torkar
I now used a mac just restored to factory settings and updated to Catalina.
Installed R 3.6.2
Installed R studio 1.2.5033
Installed Xcode 11.3, licence accepted
Installed macos.-rtools 3.2.2
Modified .R/Makevars using the terminal as you just suggested me…
Installed rstan from source…
But I still get the same error:
[1] “Error in sampler$call_sampler(args_list[[i]]) : " " c++ exception (unknown reason)”
error occurred during calling the sampler; sampling not done
What am I doing differently?
Did you install Xcode command line tools?
1 Like
yes I did. the macos-rtools does it…
I tried anyway to install them from the terminal afterwards and it says it’s installed already…
I have the exact same software that you have and it works for me. Could you post a minimum working example here so I can try it out?
I removed everything again and then reinstalled manually the Command Line Tools, clang7 and gfortran6.1(without using the macos-rtools)… and now models are sampling fine!
Thanks again for all the support you gave me!
2 Likes
Managed to stumble across R’s build settings for CRAN official binaries here:
https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R-build
Relevant file is:
https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R-build/fixpathR
The bug is related to clang4 complier being hard coded inside the fixpathR script.
Instances:
find . -name \*.dylib -or -name \*.so| xargs -n 1 install_name_tool -change /usr/local/clang4/lib/$gcclib $R/lib/$gcclib
and
install_name_tool -change /usr/local/clang4/lib/$gcclib $R/lib/$gcclib $rbin
I’ve flagged it for Simon and should hear back soon ™.
Hi I’m on Catalina and recently I installed the rstan on my rstudio but it doesn’t work with the following error though I also installed the Xcode according to its recommendation to run the package.
Error in sink(type = “output”) :
: Warning message:
In system(cmd, intern = !verbose) :
‘/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file248670b432b1.cpp 2> file248670b432b1.cpp.err.txt’
Error in map2stan(alist(y ~ dnorm(mu, sigma), mu ~ dnorm(0, 14.14), sigma ~ :
Something went wrong, when calling Stan. Check any debug messages for clues, detective.
#####################
the code I run is the following:
require(rstan)
require(rethinking)
y<-rnorm(1e2,mean=0,sd=1)
m8.5b<-map2stan(
alist(
y~dnorm(mu,sigma),
mu~dnorm(0,14.14),
sigma~dcauchy(0,1)
),
data=list(y=y),
start=list(mu=0,sigma=1),
chains=2,iter=4e3,
warmup=1e3
)
Can anyone help me to figure it out?
FYI - I have found this issues can be solved (at least on the systems I have access to - YMMV) WITHOUT modifying the Makevars file or installing mac-rtools by re-installing the dependencies in order (i.e. one at a time, not all at once):
- Rcpp
- StanHeaders
- rstan
As a general rule, editing the Makevars should be a last resort - it can potentially affect every compiled R package on the system. You can end up with some difficult to diagnose bugs in other packages.
1 Like
Not to add to the fun, but having a different but related problem. Upgraded to Catalina, followed all @coatless steps (thanks for those!). Rcpp::sourceCpp(“helloworld.cpp”) example works fine. rstan and rstanarm both work fine (sampling etc). The test program works fine. But, once I run library(rstan), while I can compile and run stan models, I can no longer compile any other c++ files. e.g this fails, with a bunch of messages about " #pragma clang diagnostic pop"
library(rstan)
Rcpp::sourceCpp(code =
'
#include <RcppArmadillo.h>
// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::export]]
void hello_world() {
Rcpp::Rcout << "Hello World!" << std::endl;
}
/*** R
hello_world()
*/
'
)
hello_world()
But, if I restart R, and comment out #library(rstan) everything works fine. Same problem for cpp files that don’t use RcppArmadillo, or for compiling models with Template Model Builder… Not sure if this counts as a stan problem, but since the behavior only starts after loading stan figured I’d start here. The above example does work if I load ggplot2 first, in reference to the issues noted in the results of test program; it’s only loading rstan that seems to cause the issues. Same problem on a colleagues Mac that I didn’t set up, so doesn’t seem likely to be a result of esoteric setup on my end?
1 Like
Those are only warning messages. We need the actual error message, which should be on a line that includes error: (with the colon).