Compilation ERROR, function(s)/method(s) not created!
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:/trials/217-cross-study/renv/library/R-4.0/x86_64-w64-mingw32/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::P1'; file1dcc21d43106.o:file1dcc21d43106.cpp:(.data$_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:/trials/217-cross-study/renv/library/R-4.0/x86_64-w64-mingw32/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QC[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QC]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long doub
In addition: Warning messages:
1: package ‘rstan’ was built under R version 4.0.3
2: package ‘StanHeaders’ was built under R version 4.0.3
3: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
'C:/rtools40/usr/mingw_/bin/g++' not found
I am not sure if this is a similar issue as https://github.com/stan-dev/rstan/issues/855, but I am getting an error when trying to run the getting started example
console
```r Loading required package: StanHeaders Loading required package: ggplot2 rstan (Version 2.21.2, GitRev: 2e1f913d3ca3) For execution on a local, multicore CPU with excess RAM we recommend calling options(mc.cores = parallel::detectCores()). To avoid recompilation of unchanged Stan programs, we recommend calling rstan_options(auto_write = TRUE) Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file stn_md> stancode <- 'data {real y_mean;} parameters {real y;} model {y ~ normal(y_mean,1);}' stn_md> mod <- stan_model(model_code = stancode, verbose = TRUE) TRANSLATING MODEL '73fc79f8b1915e8208c736914c86d1a1' FROM Stan CODE TO C++ CODE NOW. successful in parsing the Stan model '73fc79f8b1915e8208c736914c86d1a1'. COMPILING THE C++ CODE FOR MODEL '73fc79f8b1915e8208c736914c86d1a1' NOW. OS: x86_64, mingw32; rstan: 2.21.2; Rcpp: 1.0.5; inline: 0.3.17 >> setting environment variables: LOCAL_LIBS = "C:/trials/217-cross-study/renv/library/R-4.0/x86_64-w64-mingw32/rstan/lib/x64/libStanServices.a" -L"C:/Users/jonathan.sidi/AppData/Local/renv/cache/v5/R-4.0/x86_64-w64-mingw32/StanHeaders/2.21.0-7/0459d4dd7a8c239be18469a30c23dd4b/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/jonathan.sidi/AppData/Local/renv/cache/v5/R-4.0/x86_64-w64-mingw32/RcppParallel/5.0.2/551d50addb18c7b99637aa377a25afc8/RcppParallel/lib/x64" -ltbb PKG_CPPFLAGS = -I"C:/Users/jonathan.sidi/AppData/Local/renv/cache/v5/R-4.0/x86_64-w64-mingw32/Rcpp/1.0.5/125dc7a0ed375eb68c0ce533b48d291f/Rcpp/include/" -I"C:/trials/217-cross-study/renv/library/R-4.0/x86_64-w64-mingw32/RcppEigen/include/" -I"C:/trials/217-cross-study/renv/library/R-4.0/x86_64-w64-mingw32/RcppEigen/include/unsupported" -I"C:/trials/217-cross-study/renv/library/R-4.0/x86_64-w64-mingw32/BH/include" -I"C:/Users/jonathan.sidi/AppData/Local/renv/cache/v5/R-4.0/x86_64-w64-mingw32/StanHeaders/2.21.0-7/0459d4dd7a8c239be18469a30c23dd4b/StanHeaders/include/src/" -I"C:/Users/jonathan.sidi/AppData/Local/renv/cache/v5/R-4.0/x86_64-w64-mingw32/StanHeaders/2.21.0-7/0459d4dd7a8c239be18469a30c23dd4b/StanHeaders/include/" -I"C:/Users/jonathan.sidi/AppData/Local/renv/cache/v5/R-4.0/x86_64-w64-mingw32/RcppParallel/5.0.2/551d50addb18c7b99637aa377a25afc8/RcppParallel/include/" -I"C:/trials/217-cross-study/renv/library/R-4.0/x86_64-w64-mingw32/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include "C:/Users/jonathan.sidi/AppData/Local/renv/cache/v5/R-4.0/x86_64-w64-mingw32/StanHeaders/2.21.0-7/0459d4dd7a8c239be18469a30c23dd4b/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp" -std=c++1y >> Program source : 1 : 2 : // includes from the plugin 3 : // [[Rcpp::plugins(cpp14)]] 4 : 5 : 6 : // user includes 7 : #includesession info
```r > devtools::session_info("rstan") - Session info ---------------------------------------------------------------------- setting value version R version 4.0.2 (2020-06-22) os Windows 10 x64 system x86_64, mingw32 ui RStudio language (EN) collate English_United States.1252 ctype English_United States.1252 tz America/New_York date 2021-01-19 - Packages -------------------------------------------------------------------------- ! package * version date lib source P assertthat 0.2.1 2019-03-21 [?] CRAN (R 4.0.2) P backports 1.1.10 2020-09-15 [?] CRAN (R 4.0.3) BH 1.72.0-3 2020-01-08 [1] CRAN (R 4.0.0) P callr 3.5.1 2020-10-13 [?] CRAN (R 4.0.3) checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.2) P cli 2.1.0 2020-10-12 [?] CRAN (R 4.0.3) P colorspace 1.4-1 2019-03-18 [?] CRAN (R 4.0.2) P crayon 1.3.4 2017-09-16 [?] CRAN (R 4.0.2) P curl 4.3 2019-12-02 [?] CRAN (R 4.0.2) P desc 1.2.0 2018-05-01 [?] CRAN (R 4.0.2) P digest 0.6.27 2020-10-24 [?] CRAN (R 4.0.3) P ellipsis 0.3.1 2020-05-15 [?] CRAN (R 4.0.2) P evaluate 0.14 2019-05-28 [?] CRAN (R 4.0.2) P fansi 0.4.1 2020-01-08 [?] CRAN (R 4.0.2) P farver 2.0.3 2020-01-16 [?] CRAN (R 4.0.2) P ggplot2 * 3.3.2 2020-06-19 [?] CRAN (R 4.0.2) P glue 1.4.2 2020-08-27 [?] CRAN (R 4.0.2) P gridExtra 2.3 2017-09-09 [?] CRAN (R 4.0.2) P gtable 0.3.0 2019-03-25 [?] CRAN (R 4.0.2) P inline 0.3.17 2020-12-01 [?] CRAN (R 4.0.3) isoband 0.2.2 2020-06-20 [1] CRAN (R 4.0.2) jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.2) labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0) lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.2) P lifecycle 0.2.0 2020-03-06 [?] CRAN (R 4.0.2) P loo 2.4.1 2020-12-09 [?] CRAN (R 4.0.3) P magrittr 1.5 2014-11-22 [?] CRAN (R 4.0.2) P MASS 7.3-51.6 2020-04-26 [?] CRAN (R 4.0.2) Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.0.2) P matrixStats 0.56.0 2020-03-13 [?] CRAN (R 4.0.2) mgcv 1.8-33 2020-08-27 [1] CRAN (R 4.0.3) P munsell 0.5.0 2018-06-12 [?] CRAN (R 4.0.2) nlme 3.1-148 2020-05-24 [2] CRAN (R 4.0.2) P pillar 1.4.6 2020-07-10 [?] CRAN (R 4.0.2) P pkgbuild 1.1.0 2020-07-13 [?] CRAN (R 4.0.2) P pkgconfig 2.0.3 2019-09-22 [?] CRAN (R 4.0.2) P pkgload 1.1.0 2020-05-29 [?] CRAN (R 4.0.2) praise 1.0.0 2015-08-11 [1] CRAN (R 4.0.2) P prettyunits 1.1.1 2020-01-24 [?] CRAN (R 4.0.2) P processx 3.4.5 2020-11-30 [?] CRAN (R 4.0.3) P ps 1.3.4 2020-08-11 [?] CRAN (R 4.0.2) R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.3) P RColorBrewer 1.1-2 2014-12-07 [?] CRAN (R 4.0.0) P Rcpp 1.0.5 2020-07-06 [?] CRAN (R 4.0.2) RcppEigen 0.3.3.7.0 2019-11-16 [1] CRAN (R 4.0.2) PD RcppParallel 5.0.2 2020-06-24 [?] CRAN (R 4.0.2) P rlang 0.4.10 2020-12-30 [?] CRAN (R 4.0.3) P rprojroot 1.3-2 2018-01-03 [?] CRAN (R 4.0.2) rstan * 2.21.2 2020-07-27 [1] CRAN (R 4.0.3) P rstudioapi 0.11 2020-02-07 [?] CRAN (R 4.0.2) P scales 1.1.1 2020-05-11 [?] CRAN (R 4.0.2) P StanHeaders * 2.21.0-7 2020-12-17 [?] CRAN (R 4.0.3) P testthat 2.3.2 2020-03-02 [?] CRAN (R 4.0.2) P tibble 3.0.3 2020-07-10 [?] CRAN (R 4.0.2) utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.2) P V8 3.4.0 2020-11-04 [?] CRAN (R 4.0.3) vctrs 0.3.6 2020-12-17 [1] CRAN (R 4.0.3) viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.2) P withr 2.3.0 2020-09-22 [?] CRAN (R 4.0.3) [1] C:/trials/217-cross-study/renv/library/R-4.0/x86_64-w64-mingw32 [2] C:/Users/jonathan.sidi/AppData/Local/Temp/RtmpOy9mMd/renv-system-library P -- Loaded and on-disk path mismatch. D -- DLL MD5 mismatch, broken installation. ```