When I tried to call “stan()” to get the fitted result from the school example using the Rstan package. I am using Macbook M1 MacOS Sonoma Version 14.4.1 (23E224); Rstan 2.32.6. I thought it could be something related to my C compiler stuff, but I have no idea what I should do.
> fit <- stan(
+ file = here("homework", "HW10", "10-1.stan"),
+ data = data_ls
+ )
Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘clang version 14.0.6’
using SDK: ‘’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o foo.so foo.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: library 'System' not found
clang-14: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [/Library/Frameworks/R.framework/Resources/share/make/shlib.mk:10: foo.so] Error 1
make cmd is
make -f '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk' -f '/Users/yizhi_liang/.R/Makevars' CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB='file6c1d593e96fd.so' OBJECTS='file6c1d593e96fd.o'
make would use
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -O3 -mtune=native -arch arm64 -ftemplate-depth-256 -c file6c1d593e96fd.cpp -o file6c1d593e96fd.o
if test "zfile6c1d593e96fd.o" != "z"; then \
echo clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file6c1d593e96fd.so file6c1d593e96fd.o '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/lib//libStanServices.a' -L'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/lib/' -lStanHeaders -L'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/lib/' -ltbb -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation; \
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file6c1d593e96fd.so file6c1d593e96fd.o '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/lib//libStanServices.a' -L'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/lib/' -lStanHeaders -L'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/lib/' -ltbb -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation; \
fi
Error in compileCode(f, code, language = language, verbose = verbose) :
using C++ compiler: ‘clang version 14.0.6’using C++17using SDK: ‘’In file included from <built-in>:1:In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:In file included from /Users/yizhi_liang/miniconda3/bin/../include/c++/v1/cmath:308:/Users/yizhi_liang/miniconda3/bin/../include/c++/v1/math.h:300:15: fatal error: 'math.h' file not found#include_next <math.h> ^~~~~~~~1 error generated.make: *** [/Library/Frameworks/R.framework/Resources/etc/Makeconf:198: file6c1d593e96fd.o] Error 1
Error in sink(type = "output") : invalid connection
- Output of
writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
CXX17FLAGS += -O3 -mtune=native -arch arm64 -ftemplate-depth-256
- Output of
devtools::session_info("rstan")
devtools::session_info("rstan")
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.3 (2024-02-29)
os macOS Sonoma 14.4.1
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2024-04-12
rstudio 2023.12.1+402 Ocean Storm (desktop)
pandoc 3.1.11.1 @ /opt/homebrew/bin/pandoc
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.0)
BH 1.84.0-0 2024-01-10 [1] CRAN (R 4.3.1)
callr 3.7.6 2024-03-25 [1] CRAN (R 4.3.1)
checkmate 2.3.1 2023-12-04 [1] CRAN (R 4.3.1)
cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
desc 1.4.3 2023-12-10 [1] CRAN (R 4.3.1)
distributional 0.4.0 2024-02-07 [1] CRAN (R 4.3.1)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1)
farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
ggplot2 * 3.5.0 2024-02-23 [1] CRAN (R 4.3.1)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.3.0)
gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0)
inline 0.3.19 2021-05-31 [1] CRAN (R 4.3.0)
isoband 0.2.7 2022-12-20 [1] CRAN (R 4.3.0)
jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.1)
labeling 0.4.3 2023-08-29 [1] CRAN (R 4.3.0)
lattice 0.22-6 2024-03-20 [1] CRAN (R 4.3.1)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1)
loo 2.7.0 2024-02-24 [1] CRAN (R 4.3.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
MASS 7.3-60.0.1 2024-01-13 [1] CRAN (R 4.3.3)
Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.3)
matrixStats 1.2.0 2023-12-11 [1] CRAN (R 4.3.1)
mgcv 1.9-1 2023-12-21 [1] CRAN (R 4.3.3)
munsell 0.5.1 2024-04-01 [1] CRAN (R 4.3.1)
nlme 3.1-164 2023-11-27 [1] CRAN (R 4.3.3)
numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
posterior 1.5.0 2023-10-31 [1] CRAN (R 4.3.1)
processx 3.8.4 2024-03-16 [1] CRAN (R 4.3.1)
ps 1.7.6 2024-01-18 [1] CRAN (R 4.3.1)
QuickJSR 1.1.3 2024-01-31 [1] CRAN (R 4.3.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.0)
Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1)
RcppEigen 0.3.4.0.0 2024-02-28 [1] CRAN (R 4.3.1)
RcppParallel 5.1.7 2023-02-27 [1] CRAN (R 4.3.0)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1)
rstan * 2.32.6 2024-03-05 [1] CRAN (R 4.3.1)
scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.1)
StanHeaders * 2.32.6 2024-03-01 [1] CRAN (R 4.3.1)
tensorA 0.36.2.1 2023-12-13 [1] CRAN (R 4.3.1)
tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1)
[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
Thank you so much for anyone who could help!