Then in R (version 4.4.3 with Rstudio version 2024.12.1 Build 563) I do: install.packages("rstan", repos = c('https://stan-dev.r-universe.dev', getOption("repos")))
getting the message:
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/mbrabec/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)
trying URL 'https://stan-dev.r-universe.dev/bin/windows/contrib/4.4/rstan_2.36.0.9000.zip'
Content type 'application/zip' length 2758458 bytes (2.6 MB)
downloaded 2.6 MB
package ‘rstan’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mbrabec\AppData\Local\Temp\RtmpquQLfj\downloaded_packages
I also tried to go through further anyway, but then I got errors when trying compile for the first time.
So that I remove Rtools43, re-install R, install Rtools44 directly from CRAN, i.e. from the Rtool44 installer from Rtools44 for Windows
and do again: install.packages("rstan", repos = c('https://stan-dev.r-universe.dev', getOption("repos")))
and now the installation goes through without problems.
Nevertheless, when I do: example(stan_model, package = "rstan", run.dontrun = TRUE)
I get a lot of messages ending with:
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) :
C:/Users/mbrabec/AppData/Local/R/win-library/4.4/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:0: required from 'double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = model242202a3865db__namespace::model242202a3865db_; BaseRNG = boost::random::mixmax_engine<17, 36, 0>]'C:/Users/mbrabec/AppData/Local/R/win-library/4.4/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from hereC:/Users/mbrabec/AppData/Local/R/win-library/4.4/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes] 654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m); | ^~~~~~~~~make: *** [C:/PROGRA~1/R/R-44~1.3/etc/x64/Makeconf:296: file242207152
It seems to me that the problem is that on the " RStan Getting Started" page, there is no stable version for download. The one I tried is in the section " Latest Development Version: 2.35.x (unreleased)“, while in the section " Latest Released Version: 2.26.3 (September 2023)”, there is currently no link for Stan download (only links to R and RStudio).
pkgbuild::check_build_tools(debug=TRUE)
Found in Rtools 4.4 installation folder
Your system is ready to build packages!
Then I tried to install from a source and realized that there was a problem with access rights. I solved the problem with the help of:
namely, I followed the first suggestion listed there:
C:\Program Files\R - and this is the folder that contains “R” and not RStudio folder!
Right click for properties.
Security.
In “Group or user names” select your name
click “Edit”
select “Full control”
Apply and click >OK<
When I did that, I was able to install Rcpp from source with no problems:
install.packages(“Rcpp”, type = “source”)
Installing package into ‘C:/Users/mbrabec/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)
trying URL ‘https://cran.rstudio.com/src/contrib/Rcpp_1.0.14.tar.gz’
Content type ‘application/x-gzip’ length 3013288 bytes (2.9 MB)
downloaded 2.9 MB
installing source package ‘Rcpp’ …
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘G__~1.EXE (GCC) 13.3.0’
g++ -std=gnu++17 -I"C:/PROGRA~1/R/R-44~1.3/include" -DNDEBUG -I../inst/include/ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c api.cpp -o api.o
g++ -std=gnu++17 -I"C:/PROGRA~1/R/R-44~1.3/include" -DNDEBUG -I../inst/include/ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c attributes.cpp -o attributes.o
g++ -std=gnu++17 -I"C:/PROGRA~1/R/R-44~1.3/include" -DNDEBUG -I../inst/include/ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c barrier.cpp -o barrier.o
g++ -std=gnu++17 -I"C:/PROGRA~1/R/R-44~1.3/include" -DNDEBUG -I../inst/include/ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c date.cpp -o date.o
g++ -std=gnu++17 -I"C:/PROGRA~1/R/R-44~1.3/include" -DNDEBUG -I../inst/include/ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c module.cpp -o module.o
g++ -std=gnu++17 -I"C:/PROGRA~1/R/R-44~1.3/include" -DNDEBUG -I../inst/include/ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_init.cpp -o rcpp_init.o
g++ -std=gnu++17 -shared -s -static-libgcc -o Rcpp.dll tmp.def api.o attributes.o barrier.o date.o module.o rcpp_init.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~1/R/R-44~1.3/bin/x64 -lR
installing to C:/Users/mbrabec/AppData/Local/R/win-library/4.4/00LOCK-Rcpp/00new/Rcpp/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
DONE (Rcpp)
The downloaded source packages are in
‘C:\Users\mbrabec\AppData\Local\Temp\RtmpqOM526\downloaded_packages’
library(Rcpp)
Nevertheless, when I try to install rstan, it still does not work:
Installation seems to be OK:
install.packages(“rstan”, repos = c(‘https://stan-dev.r-universe.dev’, getOption(“repos”)))
Installing package into ‘C:/Users/mbrabec/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)
also installing the dependencies ‘RcppParallel’, ‘RcppEigen’
package ‘RcppParallel’ successfully unpacked and MD5 sums checked
package ‘RcppEigen’ successfully unpacked and MD5 sums checked
package ‘rstan’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mbrabec\AppData\Local\Temp\RtmpGo5sc2\downloaded_packages> install.packages(“rstan”, repos = c(‘https://stan-dev.r-universe.dev’, getOption(“repos”)))
Installing package into ‘C:/Users/mbrabec/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)
also installing the dependencies ‘RcppParallel’, ‘RcppEigen’
package ‘RcppParallel’ successfully unpacked and MD5 sums checked
package ‘RcppEigen’ successfully unpacked and MD5 sums checked
package ‘rstan’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mbrabec\AppData\Local\Temp\RtmpGo5sc2\downloaded_packages
But when I try the example,
I am getting a lot of messages (full transcript is in the attached file) ending by:
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) :
C:/Users/mbrabec/AppData/Local/R/win-library/4.4/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:0: required from 'double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = model25c789a54a17__namespace::model25c789a54a17_; BaseRNG = boost::random::mixmax_engine<17, 36, 0>]'C:/Users/mbrabec/AppData/Local/R/win-library/4.4/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from hereC:/Users/mbrabec/AppData/Local/R/win-library/4.4/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 654 | return internal::first_aligned<int(unpacket_traits::alignment),Derived>(m); | ^~~~~~~~~make: *** [C:/PROGRA~1/R/R-44~1.3/etc/x64/Makeconf:296: file25c785f5337
One thing that seems to be really curious is that previosuly (I think in the middel of the last year), I installed rstan smoothly with absolutely no problems on the same machine (then it was, I think with R 4.3.3 and whatever rstan version then available for download).