Suddenly I am no longer able to compile a Stan model that I have compiled successfully many times recently. I can sample() from the already previously compiled SDO versions, but stan_model() generates an error if I force it to recompile (e.g., by making a tiny innocuous change to the model).
The problem is not with my model. I also am now unable to compile the dinky little normal model that shows up as the default Stan model that appears in a new stan file under RStudio. Basically the same error message as below (somewhat less wordy but ends the same way).
I suspect this is due to my performing a blanket upgrade to all my R packages yesterday. Perhaps I dug myself a hole. But I need some help climbing out of it :-). I’m pretty much dead in the water now.
Any suggestions would be greatly appreciated so I can get back to work. Thank you!!
Below is the attempt to compile followed by the rather long and (for me) uninterpretable diagnostic message:
*> StabDSO ← stan_model( ‘UC3 Model for Fit exGAUS Stan Y prestudy no plate3-impact of prior.stan’ ) **
hash mismatch so recompiling; make sure Stan code ends with a blank line
make cmd is
make -f “C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf” -f “C:/PROGRA~1/R/R-40~1.2/share/make/winshlib.mk” CXX=’(CXX14) (CXX14STD)’ CXXFLAGS=’(CXX14FLAGS)' CXXPICFLAGS='(CXX14PICFLAGS)’ SHLIB_LDFLAGS=’(SHLIB_CXX14LDFLAGS)' SHLIB_LD='(SHLIB_CXX14LD)’ SHLIB=“file470135e76c0.dll” WIN=64 TCLBIN=64 OBJECTS=“file470135e76c0.o”
make would use
if test “zfile470135e76c0.o” != “z”; then
if test -e “file470135e76c0-win.def”; then
echo “C:/rtools40/mingw64/bin/“g++ -shared -s -static-libgcc -o file470135e76c0.dll file470135e76c0-win.def file470135e76c0.o “C:/Users/Dave/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a” -L"C:/Users/Dave/Documents/R/win-library/4.0/StanHeaders/libs/x64” -lStanHeaders -L"C:/Users/Dave/Documents/R/win-library/4.0/RcppParallel/lib/x64” -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ;
“C:/rtools40/mingw64/bin/“g++ -shared -s -static-libgcc -o file470135e76c0.dll file470135e76c0-win.def file470135e76c0.o “C:/Users/Dave/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a” -L"C:/Users/Dave/Documents/R/win-library/4.0/StanHeaders/libs/x64” -lStanHeaders -L"C:/Users/Dave/Documents/R/win-library/4.0/RcppParallel/lib/x64” -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ;
else
echo EXPORTS > tmp.def;
"C:/rtools40/mingw64/bin/"nm file470135e76c0.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 file470135e76c0.dll tmp.def file470135e76c0.o “C:/Users/Dave/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a” -L"C:/Users/Dave/Documents/R/win-library/4.0/StanHeaders/libs/x64” -lStanHeaders -L"C:/Users/Dave/Documents/R/win-library/4.0/RcppParallel/lib/x64” -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ;
“C:/rtools40/mingw64/bin/“g++ -shared -s -static-libgcc -o file470135e76c0.dll tmp.def file470135e76c0.o “C:/Users/Dave/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a” -L"C:/Users/Dave/Documents/R/win-library/4.0/StanHeaders/libs/x64” -lStanHeaders -L"C:/Users/Dave/Documents/R/win-library/4.0/RcppParallel/lib/x64” -ltbb -L"C:/PROGRA~1/R/R-40~1.2/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/Dave/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): multiple definition of boost::math::detail::bessel_j0<long double>(long double)::P1'; file470135e76c0.o:file470135e76c0.cpp:(.rdata$_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/Dave/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’; file470135e76c0.o:file470135e76c0.cpp
In addition: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
'C:/rtools40/usr/mingw/bin/g++’ not found
Error in sink(type = “output”) : invalid connection
Below is what I as able to determine about my system configuration…
> sessionInfo()
RStudio version 1.3.1056
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
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] parallel splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] gridExtra_2.3 rstan_2.21.2 StanHeaders_2.21.0-7 qqplotr_0.0.5 outliers_0.14
[6] EnvStats_2.4.0 gamlss_5.3-4 nlme_3.1-148 gamlss.dist_5.3-2 MASS_7.3-51.6
[11] gamlss.data_6.0-1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[16] readr_2.0.1 tidyr_1.1.3 tibble_3.1.4 ggplot2_3.3.5 tidyverse_1.3.1
[21] readxl_1.3.1
loaded via a namespace (and not attached):
[1] httr_1.4.2 jsonlite_1.7.2 modelr_0.1.8 RcppParallel_5.1.4 assertthat_0.2.1 stats4_4.0.2
[7] cellranger_1.1.0 robustbase_0.93-8 pillar_1.6.2 backports_1.2.1 lattice_0.20-41 glue_1.4.2
[13] rvest_1.0.1 colorspace_2.0-2 Matrix_1.2-18 pkgconfig_2.0.3 broom_0.7.9 haven_2.4.3
[19] scales_1.1.1 processx_3.5.2 tzdb_0.1.2 generics_0.1.0 ellipsis_0.3.2 withr_2.4.2
[25] cli_3.0.1 survival_3.1-12 magrittr_2.0.1 crayon_1.4.1 ps_1.6.0 fs_1.5.0
[31] fansi_0.5.0 xml2_1.3.2 pkgbuild_1.2.0 loo_2.4.1 tools_4.0.2 prettyunits_1.1.1
[37] hms_1.1.0 matrixStats_0.60.1 lifecycle_1.0.0 V8_3.4.2 munsell_0.5.0 reprex_2.0.1
[43] callr_3.7.0 compiler_4.0.2 rlang_0.4.11 grid_4.0.2 rstudioapi_0.13 codetools_0.2-16
[49] gtable_0.3.0 curl_4.3.2 inline_0.3.19 DBI_1.1.1 R6_2.5.1 lubridate_1.7.10
[55] utf8_1.2.2 stringi_1.7.4 Rcpp_1.0.7 vctrs_0.3.8 DEoptimR_1.0-9 dbplyr_2.1.1
[61] tidyselect_1.1.1
> stan_version()
[1] "2.21.0"
NOTE ADDED: My rubber ducky suggested I take a look at RStan Getting Started · stan-dev/rstan Wiki · GitHub . Scary stuff… but I was desperate. I tried a few things that failed miserably, then saw on the following advice…
Then restart R and reinstall rstan and StanHeaders from source:
Compile packages using all cores Sys.setenv(MAKEFLAGS = paste0("-j",parallel::detectCores())) install.packages(c(“StanHeaders”,“rstan”),type=“source”)
So what the heck… brushed my teeth while it screamed on all 4 cores… now the example code and my own code compiles. I have no idea why this did what it did. What on earth is a “StanHeader”? Any thoughts appreciated. Thank you ducky!!