Interesting. First running
rstan_options(javascript = FALSE)
Then the model
> fit <- stan(model_code=model, data = schools_dat, verbose=T)
causes the same stuck process, but this time I get an Apple spinning colorwheel and cannot Esc out of the process, which I could do before.
And
example(cxxfunction, package = "inline", run.dontrun = TRUE)
works?
No, still the same.
> rstan_options(javascript = FALSE)
>
> example(cxxfunction, package = "inline", run.dontrun = TRUE)
cxxfnc> # default plugin
cxxfnc> fx <- cxxfunction( signature(x = "integer", y = "numeric" ) , '
cxxfnc+ return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
cxxfnc+ ' )
And even after quitting out of the console, activity monitor still shows an R process running in the background.
OK. This is probably an issue with your toolchain, rather than something specific to Stan. @coatless might have previously encountered someone with this hanging under
R 4.0.2
Mac OS X Mojave or High Sierra
No Makevars file
No Renviron file
Fresh install of the latest RStanOdd, not sure why RStan is hanging in this instance.
Few quick questions:
Rcpp::evalCpp("1 + 1", verbose = TRUE)
sessionInfo()
cat(readLines(file.path(Sys.getenv("HOME"), ".R", "Makevars")), sep = "\n")
update.packages(ask = FALSE, checkBuilt = TRUE)
Another consideration, but maybe upgrade from macOS Mojave 10.14.6 to macOS Catalina 10.15?
Thanks much. Iām reporting outputs here from a machine running Mohave, but I get the same behavior on a different machine I just upgraded to Catalina (and did a fresh R and RStan install on).
> Rcpp::evalCpp("1 + 1", verbose = TRUE)
Generated code for function definition:
--------------------------------------------------------
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
SEXP get_value(){ return wrap( 1 + 1 ) ; }
Generated extern "C" functions
--------------------------------------------------------
#include <Rcpp.h>
// get_value
SEXP get_value();
RcppExport SEXP sourceCpp_1_get_value() {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
rcpp_result_gen = Rcpp::wrap(get_value());
return rcpp_result_gen;
END_RCPP
}
Generated R functions
-------------------------------------------------------
`.sourceCpp_1_DLLInfo` <- dyn.load('/private/var/folders/_t/y8rbmtzj4jz0qxpl_bt_wqlw0000gp/T/Rtmpf0xuzk/sourceCpp-x86_64-apple-darwin17.0-1.0.5/sourcecpp_131e1414200d5/sourceCpp_2.so')
get_value <- Rcpp:::sourceCppFunction(function() {}, FALSE, `.sourceCpp_1_DLLInfo`, 'sourceCpp_1_get_value')
rm(`.sourceCpp_1_DLLInfo`)
Building shared library
--------------------------------------------------------
DIR: /private/var/folders/_t/y8rbmtzj4jz0qxpl_bt_wqlw0000gp/T/Rtmpf0xuzk/sourceCpp-x86_64-apple-darwin17.0-1.0.5/sourcecpp_131e1414200d5
/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o 'sourceCpp_2.so' 'file131e138e8e1d3.cpp'
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include" -I"/private/var/folders/_t/y8rbmtzj4jz0qxpl_bt_wqlw0000gp/T/Rtmpf0xuzk/sourceCpp-x86_64-apple-darwin17.0-1.0.5" -I/usr/local/include -fPIC -Wall -g -O2 -c file131e138e8e1d3.cpp -o file131e138e8e1d3.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o sourceCpp_2.so file131e138e8e1d3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 2
>
And,
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2 Rcpp_1.0.5
>
And,
> cat(readLines(file.path(Sys.getenv("HOME"), ".R", "Makevars")), sep = "\n")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
cannot open file '/Users/jdsal/.R/Makevars': No such file or directory
>
Then following
update.packages(ask = FALSE, checkBuilt = TRUE)
I get the same hanging behavior as described above if I run the schools example.
Iām not sure whatās going on exactly.
My suggestion is double check whether Xcode CLI is up-to-date. I think a new update was released recently.
Try to update with Software Update in System Preferences or open up Terminal and type:
softwareupdate --all --install --force
If that doesnāt provide an option to upgrade Xcode CLI, please remove the old version and update to a newer one:
sudo rm -rf /Library/Developer/CommandLineTools
sudo xcode-select --install
I really appreciate the help. I updated to Catalina (10.15.6). I followed this Reinstall compiler tools for MacOS. hellowworld.cpp worked, but the schools example caused the same hanging.
Following https://discourse.mc-stan.org/t/rstan-compilation-hangs/15150 I did from-scratch install of XCode CLI, R, and RStan. Still no fix.
Hi folks. I gave up on this thread back in September, without solving the hanging problem. Ended up reverting to R v3.6x to get work done.
I recently upgraded to R 4.1.0 for a few reasons, and with fresh updates and installs of Rccp, RStan, and CLI. Hopefully revisiting this again someone can help. Hereās the session info:
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.6 plyr_1.8.6 rethinking_2.13 rstan_2.21.2 ggplot2_3.3.3 StanHeaders_2.21.0-7
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 pillar_1.6.1 compiler_4.1.0 prettyunits_1.1.1 tools_4.1.0 pkgbuild_1.2.0 lattice_0.20-44 jsonlite_1.7.2 lifecycle_1.0.0
[10] tibble_3.1.2 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.11 cli_2.5.0 curl_4.3.1 mvtnorm_1.1-1 loo_2.4.1 coda_0.19-4
[19] gridExtra_2.3 withr_2.4.2 generics_0.1.0 vctrs_0.3.8 stats4_4.1.0 grid_4.1.0 tidyselect_1.1.1 glue_1.4.2 inline_0.3.19
[28] R6_2.5.0 processx_3.5.2 fansi_0.5.0 purrr_0.3.4 callr_3.7.0 magrittr_2.0.1 MASS_7.3-54 codetools_0.2-18 matrixStats_0.59.0
[37] scales_1.1.1 ps_1.6.0 ellipsis_0.3.2 shape_1.4.6 colorspace_2.0-1 V8_3.4.2 utf8_1.2.1 RcppParallel_5.1.4 munsell_0.5.0
[46] crayon_1.4.1
>
Can you try the preview of the next version of rstan to see if the problem is still there?
Restart R,making sure that rstan doesnāt get loaded and run:
remove.packages(c("StanHeaders", "rstan"))
install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
This worked! Andrew, you just fixed a 10-month problem, you are amazing.
thanks!!