Stan model will not compile in R or Rstudio - c++

Question

I am having a strange problem that I have not encountered before while using R, Rstudio, or stan. I am not able to get any model to compile in stan. I am pretty confident it is not the models. trivial models in brms do not compile either. Whereas rstanarm models have no problem, being pre-compiled, as I understand. Likewise, similar models compile without problems on another computer. So, something is wrong with my configurations, but that stuff is above my understanding. I have tried the old delete everything and re-install trick to no avail. I am worried that I deleted something without realizing it while cleaning up files.
I am on a PC with windows 10 pro. I have R 4.0.4. Rstudio 1.4.1103.
Everytime I try to compile a stan model I get the following output:
make cmd is
make -f "C:/PROGRA~1/R/R-40~1.4/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-40~1.4/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file735032f41a17.dll" WIN=64 TCLBIN=64 OBJECTS="file735032f41a17.o"
make would use
if test "zfile735032f41a17.o" != "z"; then \
if test -e "file735032f41a17-win.def"; then \
echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file735032f41a17.dll file735032f41a17-win.def file735032f41a17.o "C:/Users/loren/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/loren/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/loren/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.4/bin/x64" -lR ; \
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file735032f41a17.dll file735032f41a17-win.def file735032f41a17.o "C:/Users/loren/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/loren/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/loren/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.4/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
"C:/rtools40/mingw64/bin/"nm file735032f41a17.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def; \
echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file735032f41a17.dll tmp.def file735032f41a17.o "C:/Users/loren/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/loren/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/loren/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.4/bin/x64" -lR ; \
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file735032f41a17.dll tmp.def file735032f41a17.o "C:/Users/loren/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/loren/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/loren/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.4/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
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/loren/Documents/R/win-library/4.0/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'; file735032f41a17.o:file735032f41a17.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): first defined hereC:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/loren/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QS[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QS]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::QS'; file735032f41a17.o:file735032f41a
Error in sink(type = "output") : invalid connection
This is the first time I have asked a question in the forums. So, if I have not given you all the information you need, don't hesitate to ask for it. Thanks much for your help.
Seems this is common:
> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rstan_2.21.2 StanHeaders_2.21.0-7 bayesplot_1.8.0 sjPlot_2.8.7 survminer_0.4.8
[6] ggpubr_0.4.0 survival_3.2-7 rstanarm_2.21.1 brms_2.14.4 Rcpp_1.0.6
[11] finalfit_1.0.2 lubridate_1.7.9.2 reshape2_1.4.4 googlesheets4_0.2.0 forcats_0.5.1
[16] stringr_1.4.0 dplyr_1.0.4 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2
[21] tibble_3.0.6 ggplot2_3.3.3 tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.2.1 plyr_1.8.6 igraph_1.2.6 splines_4.0.4
[6] crosstalk_1.1.1 TH.data_1.0-10 rstantools_2.1.1 inline_0.3.17 digest_0.6.27
[11] htmltools_0.5.1.1 rsconnect_0.8.16 magrittr_2.0.1 openxlsx_4.2.3 modelr_0.1.8
[16] RcppParallel_5.0.2 matrixStats_0.58.0 xts_0.12.1 sandwich_3.0-0 askpass_1.1
[21] prettyunits_1.1.1 colorspace_2.0-0 rvest_0.3.6 xfun_0.20 haven_2.3.1
[26] callr_3.5.1 crayon_1.4.1 jsonlite_1.7.2 lme4_1.1-26 zoo_1.8-8
[31] glue_1.4.2 gargle_0.5.0 gtable_0.3.0 emmeans_1.5.4 sjstats_0.18.1
[36] sjmisc_2.8.6 V8_3.4.0 car_3.0-10 pkgbuild_1.2.0 abind_1.4-5
[41] scales_1.1.1 mvtnorm_1.1-1 DBI_1.1.1 ggeffects_1.0.1 rstatix_0.7.0
[46] miniUI_0.1.1.1 performance_0.7.0 xtable_1.8-4 foreign_0.8-81 km.ci_0.5-2
[51] stats4_4.0.4 DT_0.17 htmlwidgets_1.5.3 httr_1.4.2 threejs_0.3.3
[56] ellipsis_0.3.1 mice_3.13.0 pkgconfig_2.0.3 loo_2.4.1 dbplyr_2.1.0
[61] effectsize_0.4.3 tidyselect_1.1.0 rlang_0.4.10 later_1.1.0.1 munsell_0.5.0
[66] cellranger_1.1.0 tools_4.0.4 cli_2.3.0 generics_0.1.0 sjlabelled_1.1.7
[71] broom_0.7.4 ggridges_0.5.3 fastmap_1.1.0 knitr_1.31 processx_3.4.5
[76] fs_1.5.0 zip_2.1.1 survMisc_0.5.5 nlme_3.1-152 mime_0.9
[81] projpred_2.0.2 xml2_1.3.2 compiler_4.0.4 shinythemes_1.2.0 rstudioapi_0.13
[86] gamm4_0.2-6 curl_4.3 ggsignif_0.6.0 reprex_1.0.0 statmod_1.4.35
[91] stringi_1.5.3 parameters_0.11.0 ps_1.5.0 Brobdingnag_1.2-6 lattice_0.20-41
[96] Matrix_1.3-2 nloptr_1.2.2.2 markdown_1.1 KMsurv_0.1-5 shinyjs_2.0.0
[101] vctrs_0.3.6 pillar_1.4.7 lifecycle_1.0.0 bridgesampling_1.0-0 estimability_1.3
[106] insight_0.13.0 data.table_1.13.6 httpuv_1.5.5 R6_2.5.0 promises_1.1.1
[111] gridExtra_2.3 rio_0.5.16 codetools_0.2-18 boot_1.3-26 colourpicker_1.1.0
[116] MASS_7.3-53 gtools_3.8.2 assertthat_0.2.1 openssl_1.4.3 withr_2.4.1
[121] shinystan_2.5.0 multcomp_1.4-16 bayestestR_0.8.2 mgcv_1.8-33 parallel_4.0.4
[126] hms_1.0.0 grid_4.0.4 coda_0.19-4 minqa_1.2.4 carData_3.0-4
[131] googledrive_1.0.1 shiny_1.6.0 base64enc_0.1-3 dygraphs_1.1.1.6
The following very simple stan model elicits the above error
model <- "
data{
int<lower=0> N;
vector[N] Y;
vector[N] X;
}
parameters{
real beta;
real mu;
real<lower=0> sigma;
}
model{
Y ~ normal(mu + beta*X, sigma);
mu ~ normal(0, 1);
beta ~ normal(0, 1);
sigma ~ gamma(0.1, 0.1);
}"
stan_model(model_code = model)

Answer 1

I was able to stumble onto a solution. I re-installed rstan. I have no idea what the problem was or why this fixed it. If others would like to weigh in, that would be much appreciated. Thanks to those who put any thought into my query.