I had to reinstall the system and after installing brand new R 3.6.2 I am having issues while using STAN/brms on Windows 10.
After following the instructions: https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started
The model fails:
‘compileCode(f, code, language = language, verbose = verbose)’:
Compilation ERROR, function(s)/method(s) not created! In file included from C:/R/R-3.6.2/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:0,
C:/R/R-3.6.2/library/BH/include/boost/numeric/odeint.hpp:31:76: fatal error: boost/numeric/odeint/stepper/runge_kutta_cash_karp54_classic.hpp: No such file or directory
system(“g++ -v”) results in 127
I’m having the same issue on Windows 10. I wonder if it is related to this change in R 3.6.2:
- The default standard for C++ in package installation is C++11 (as it has been on other platforms where available since R 3.6.0: the default toolchain on Windows was defaulting to C++98).
DEPRECATED AND DEFUNCT
- Support for specifying C++98 in package installation is deprecated.
- Support in
R CMD config for F77, FCPIFCPLAGS, CPP, CXXCPP and CXX98 and similar is deprecated. (CPP is found from the system
make and may well not be set.) Use $CC -E and $CXX -E instead of CPP and CXXCPP.
My C++ toolchain configuration is:
Perhaps some of this needs to change?
This is a BH bug. Do
install.packages("BH", type = "win.binary")
This fixed it! Hopefully the next BH release will address the issue.
Thank you, @bgoodri ! It worked on my home PC, gotta try it out @ work. :)
@bgoodri Still getting an error after installing BH, any pointers?
install.packages(“BH”, type = “win.binary”)
Installing package into ‘C:/Users/Cucumber15/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL ‘https://cran.rstudio.com/bin/windows/contrib/3.6/BH_1.72.0-1.zip’
Content type ‘application/zip’ length 18170647 bytes (17.3 MB)
downloaded 17.3 MB
package ‘BH’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
fit <- stan(file = ‘8schools.stan’, data = schools_dat)
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from C:/Users/Cucumber15/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:0,
C:/Users/Cucumber15/Documents/R/win-library/3.6/BH/include/boost/numeric/odeint.hpp:31:76: fatal error: boost/numeric/odeint/stepper/runge_kutta_cash_karp54_clas
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command ‘C:/PROGRA~1/R/R-36~1.2/bin/x64/R CMD SHLIB file3d787ed77a85.cpp 2> file3d787ed77a85.cpp.err.txt’ had status 1
Error in sink(type = “output”) : invalid connection
I ran into the same issue mid model tuning now. Seems ‘BH’ pushed an update today and that must have broken it?
I removed it and installed an old version and that fixed it for me:
install_version(“BH”, version = “1.69.0-1”, repos = “http://cran.us.r-project.org”)
I would do
This one worked wow, thank you so much!
Another weird thing is now that I can fit the 8 schools example is that I got a divergent transition warning. I just ran the line a few times and it went away however.
MCMC is not deterministic (without a fixed
seed), so sometimes you get a divergent transition or two and sometimes you don’t. All the more reason to run at least four chains.
I see, weird that isn’t in the quick start guide. Although I am a complete novice so… Thanks so much again!
BH 1.72.0-2 is now on CRAN and has the fix
- inst/include/boost/numeric/odeint/stepper/: Correct accidental
renaming in this directory, only rename in …/generation/
Glad this barrier is solved.