stan-dev
Compalitation errors when running stan_model on Windows
Summary:
I'm getting error when runnung stan_model on Wondows
Description:
library(rstan)
example(stan_model, package = "rstan", run.dontrun = TRUE)
The error message is the following:
Error in compileCode(f, code, language = language, verbose = verbose) :
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/nmuravskaya/Documents/R/R-4.0.5/library/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::P1'; file2bec5ef94a42.o:file2bec5ef94a42.cpp:(.rdata$_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/nmuravskaya/Documents/R/R-4.0.5/library/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>(long double)::QS'; file2bec5ef94a42.o:fi
In addition: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
'C:/rtools40/usr/mingw_/bin/g++' not found
I did try to compile packages using all cores
Sys.setenv(MAKEFLAGS = paste0("-j",parallel::detectCores()))
install.packages(c("StanHeaders","rstan"),type="source")
And other recommendations from Stan forum also didn't work
RStan Version:
`> devtools::session_info("rstan")
-
Session info --------------------------------------------------------------------------------------------------------------------- setting value
version R version 4.0.5 (2021-03-31) os Windows >= 8 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/Los_Angeles
date 2021-05-20 -
Packages ------------------------------------------------------------------------------------------------------------------------- package * version date lib source
backports 1.2.1 2020-12-09 [1] CRAN (R 4.0.3) BH 1.75.0-0 2021-01-11 [1] CRAN (R 4.0.3) callr 3.7.0 2021-04-20 [1] CRAN (R 4.0.5) checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.2) cli 2.5.0 2021-04-26 [1] CRAN (R 4.0.5) colorspace 2.0-1 2021-05-04 [1] CRAN (R 4.0.5) crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.5) curl 4.3.1 2021-04-30 [1] CRAN (R 4.0.5) desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.5) digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.5) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.0.5) fansi 0.4.2 2021-01-15 [1] CRAN (R 4.0.5) farver 2.1.0 2021-02-28 [1] CRAN (R 4.0.5) ggplot2 * 3.3.3 2020-12-30 [1] CRAN (R 4.0.5) glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.5) gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) inline 0.3.17 2020-12-01 [1] CRAN (R 4.0.5) isoband 0.2.4 2021-03-03 [1] CRAN (R 4.0.5) jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.5) labeling 0.4.2 2020-10-20 [1] CRAN (R 4.0.3) lattice 0.20-44 2021-05-02 [1] CRAN (R 4.0.5) lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.5) loo 2.4.1 2020-12-09 [1] CRAN (R 4.0.5) magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.5) MASS 7.3-54 2021-05-03 [1] CRAN (R 4.0.5) Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.3) matrixStats 0.58.0 2021-01-29 [1] CRAN (R 4.0.5) mgcv 1.8-35 2021-04-18 [1] CRAN (R 4.0.5) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2) nlme 3.1-152 2021-02-04 [1] CRAN (R 4.0.5) pillar 1.6.1 2021-05-16 [1] CRAN (R 4.0.2) pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.5) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) processx 3.5.2 2021-04-30 [1] CRAN (R 4.0.5) ps 1.6.0 2021-02-28 [1] CRAN (R 4.0.5) R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.5) RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0) Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.0.5) RcppEigen 0.3.3.9.1 2020-12-17 [1] CRAN (R 4.0.5) RcppParallel 5.1.4 2021-05-04 [1] CRAN (R 4.0.5) rlang 0.4.11 2021-04-30 [1] CRAN (R 4.0.5) rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.5) rstan * 2.21.2 2020-07-27 [1] CRAN (R 4.0.2) scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2) StanHeaders * 2.21.0-7 2020-12-17 [1] CRAN (R 4.0.5) tibble 3.1.1 2021-04-18 [1] CRAN (R 4.0.5) utf8 1.2.1 2021-03-12 [1] CRAN (R 4.0.5) V8 3.4.2 2021-05-01 [1] CRAN (R 4.0.5) vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.0.5) viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.0.5) withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.5)
[1] C:/Users/nmuravskaya/Documents/R/R-4.0.5/library`
Normally that fixes it. Try restarting R first (making sure that rstan doesn't get loaded), and remove the old packages first before installing the new ones:
Sys.setenv(MAKEFLAGS = paste0("-j",parallel::detectCores()))
remove.packages(c("StanHeaders","rstan"))
install.packages(c("StanHeaders","rstan"),type="source")
