sen
January 13, 2021, 1:29pm
1
I tried to reinstall R, Rstudio, Rtools, but it still didn’t work. Thank you for your help
Error in compileCode(f, code, language = language, verbose = verbose) :boost::math::detail::bessel_j0<long double>(long double)::P1'; file3dfc2ff67f5.o:file3dfc2ff67f5.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): first defined hereC:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/zhangsen/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QS[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QS]+0x0): multiple definition of boost::math::detail::bessel_j0(long double)::QS’; file3dfc2ff67f5.o:file3dfc2ff67f
Hi Sen, sorry about these troubles! There was a recent update to the BH package that has broken rstan a little.
Can you restart R, and then reinstall the packages from source:
install.packages(c("StanHeaders","rstan"),type="source")
1 Like
sen
January 14, 2021, 1:41pm
3
Thank you for your attention, your code works.
1 Like
hi there, i’ve tried all the tricks proposed in the forum, still got this error.
Can you post the full error message that you get?
hi, thx for the prompt reply.
stn_md> mod ← stan_model(model_code = stancode, verbose = TRUE)
TRANSLATING MODEL ‘73fc79f8b1915e8208c736914c86d1a1’ FROM Stan CODE TO C++ CODE NOW.
setting environment variables:
after ther program source, i get the famous {Compilation ERROR, function(s)/method(s) not created!
also, may be of interest:
devtools::session_info(“rstan”)
Session info --------------------------------------------------
Packages ------------------------------------------------------
[1] C:/R/library
D – DLL MD5 mismatch, broken installation.
I need a bit more of the error message, sorry. Can you copy as much of the output as possible above the : Compilation ERROR, function(s)/method(s) not created! section?
If it’s easier, you can also copy it into a text file and upload that here instead
here it is:stan_err_msg.txt (31.7 KB)
ok now i c that it fails at the Rccp level and the RccpParallel library has a brocken installation.
Hmm that’s odd, it doesn’t actually have an error message in there. Let’s check that your c++ toolchain is working. Can you post the output from the following:
system("touch foo.cpp")
system("R CMD SHLIB foo.cpp")
Ok, that indicates some issues with your toolchain. To get a better idea of the issue, can you post the outputs from:
readLines("~/.Renviron")
readLines("~/.Rprofile")
readLines("~/.R/Makevars.win")
Sys.getenv("PATH")
It looks like your configuration is a little off. Can you go through the steps in the RStan Getting Started Guide to get everything setup?
can you please be precise? to which config is off?
is this config then ok? because i still get the error
system(“touch foo.cpp”)
system(“R CMD SHLIB foo.cpp”){RTOOLS40_HOME}\\usr\\bin; {PATH}"”
Yep, that looks better. Can you now restart R and try the rstan install from source again:
remove.packages(c("StanHeaders","rstan"))
install.packages(c("StanHeaders","rstan"),type="source")
smtg is odd here:
install.packages(c(“StanHeaders”,“rstan”),type=“source”)https://cran.rstudio.com/src/contrib/StanHeaders_2.21.0-7.tar.gz ’
trying URL ‘https://cran.rstudio.com/src/contrib/rstan_2.21.2.tar.gz ’
Warning in install.packages :
The downloaded source packages are in
Restarting R session…
library(rstan)
Are there any errors other than:
Warning in install.packages :
installation of package ‘StanHeaders’ had non-zero exit status
Warning in install.packages :
installation of package ‘rstan’ had non-zero exit status
Or is that all that is displayed?