Can't compile simple stan code on M1 MacOS Ventura

Interfaces RStan
1

I just switched back to MacOS and I’m trying to get Rstan up and running. I’ve followed the instructions, but I think R is having a problem finding the right C (c++? I’m a dilettante) compiler. I can compile C++ code in my terminal, but it doesn’t work in R.

For example, if I run the simple schools example:

library(rstan)
schools_dat <- list(J = 8, 
                    y = c(28,  8, -3,  7, -1,  1, 18, 12),
                    sigma = c(15, 10, 16, 11,  9, 11, 10, 18))
fit <- stan(file = '~/Desktop/schools.stan', data = schools_dat)

I get this output (and R studio prompts me to install the command line tools that I’ve already installed):

Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘clang version 5.0.1 (tags/RELEASE_501/final)’
using SDK: ‘’
clang -arch arm64 -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  -DBOOST_NO_AUTO_PTR  -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  -c foo.c -o foo.o
clang-5.0: warning: optimization flag '-falign-functions=64' is not supported [-Wignored-optimization-argument]
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:88:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
namespace Eigen {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
namespace Eigen {
               ^
               ;
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:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#include <complex>
         ^~~~~~~~~
3 errors generated.
make: *** [foo.o] Error 1
make cmd is
  make -f '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk' CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB='fileea29267c6a80.so' OBJECTS='fileea29267c6a80.o'

make would use
clang++ -arch arm64 -std=gnu++14 -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  -DBOOST_NO_AUTO_PTR  -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  -c fileea29267c6a80.cpp -o fileea29267c6a80.o
if test  "zfileea29267c6a80.o" != "z"; then \
	  echo clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o fileea29267c6a80.so fileea29267c6a80.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++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o fileea29267c6a80.so fileea29267c6a80.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 5.0.1 (tags/RELEASE_501/final)’using C++14using SDK: ‘’clang-5.0: warning: optimization flag '-falign-functions=64' is not supported [-Wignored-optimization-argument]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:/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:82:12: fatal error: 'new' file not found  #include <new>           ^~~~~1 error generated.make: *** [fileea29267c6a80.o] Error 1
Error in sink(type = "output") : invalid connection

I’ve spent the last 3 days working on this and I’ve tried a million different combinations of things in my Makevars, but nothing seems to work. I’ve also reinstalled R, Rstudio, command line tools, and Xcode several times.

Here is the session info:

devtools::session_info("rstan")
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.1 (2023-06-16)
 os       macOS Ventura 13.5
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2023-07-29
 rstudio  2023.06.1+524 Mountain Hydrangea (desktop)
 pandoc   2.16.2 @ /usr/local/bin/pandoc

─ Packages ───────────────────────────────────────────────────────────────────
 package      * version   date (UTC) lib source
 backports      1.4.1     2021-12-13 [1] CRAN (R 4.3.0)
 BH             1.81.0-1  2023-01-22 [1] CRAN (R 4.3.0)
 callr          3.7.3     2022-11-02 [1] CRAN (R 4.3.0)
 checkmate      2.2.0     2023-04-27 [1] CRAN (R 4.3.0)
 cli            3.6.1     2023-03-23 [1] CRAN (R 4.3.0)
 colorspace     2.1-0     2023-01-23 [1] CRAN (R 4.3.0)
 crayon         1.5.2     2022-09-29 [1] CRAN (R 4.3.0)
 desc           1.4.2     2022-09-08 [1] CRAN (R 4.3.0)
 fansi          1.0.4     2023-01-22 [1] CRAN (R 4.3.0)
 farver         2.1.1     2022-07-06 [1] CRAN (R 4.3.0)
 ggplot2      * 3.4.2     2023-04-03 [1] CRAN (R 4.3.0)
 glue           1.6.2     2022-02-24 [1] CRAN (R 4.3.0)
 gridExtra      2.3       2017-09-09 [1] CRAN (R 4.3.0)
 gtable         0.3.3     2023-03-21 [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)
 labeling       0.4.2     2020-10-20 [1] CRAN (R 4.3.0)
 lattice        0.21-8    2023-04-05 [1] CRAN (R 4.3.1)
 lifecycle      1.0.3     2022-10-07 [1] CRAN (R 4.3.0)
 loo            2.6.0     2023-03-31 [1] CRAN (R 4.3.0)
 magrittr       2.0.3     2022-03-30 [1] CRAN (R 4.3.0)
 MASS           7.3-60    2023-05-04 [1] CRAN (R 4.3.1)
 Matrix         1.5-4.1   2023-05-18 [1] CRAN (R 4.3.1)
 matrixStats    1.0.0     2023-06-02 [1] CRAN (R 4.3.0)
 mgcv           1.8-42    2023-03-02 [1] CRAN (R 4.3.1)
 munsell        0.5.0     2018-06-12 [1] CRAN (R 4.3.0)
 nlme           3.1-162   2023-01-31 [1] CRAN (R 4.3.1)
 pillar         1.9.0     2023-03-22 [1] CRAN (R 4.3.0)
 pkgbuild       1.4.2     2023-06-26 [1] CRAN (R 4.3.0)
 pkgconfig      2.0.3     2019-09-22 [1] CRAN (R 4.3.0)
 prettyunits    1.1.1     2020-01-24 [1] CRAN (R 4.3.0)
 processx       3.8.2     2023-06-30 [1] CRAN (R 4.3.0)
 ps             1.7.5     2023-04-18 [1] CRAN (R 4.3.0)
 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           1.0.11    2023-07-06 [1] CRAN (R 4.3.0)
 RcppEigen      0.3.3.9.3 2022-11-05 [1] CRAN (R 4.3.0)
 RcppParallel   5.1.7     2023-02-27 [1] CRAN (R 4.3.0)
 rlang          1.1.1     2023-04-28 [1] CRAN (R 4.3.0)
 rprojroot      2.0.3     2022-04-02 [1] CRAN (R 4.3.0)
 rstan        * 2.21.8    2023-01-17 [1] CRAN (R 4.3.0)
 scales         1.2.1     2022-08-20 [1] CRAN (R 4.3.0)
 StanHeaders  * 2.26.27   2023-06-14 [1] CRAN (R 4.3.0)
 tibble         3.2.1     2023-03-20 [1] CRAN (R 4.3.0)
 utf8           1.2.3     2023-01-31 [1] CRAN (R 4.3.0)
 vctrs          0.6.3     2023-06-14 [1] CRAN (R 4.3.0)
 viridisLite    0.4.2     2023-05-02 [1] CRAN (R 4.3.0)
 withr          2.5.0     2022-03-03 [1] CRAN (R 4.3.0)

 [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
2

Your output shows that your system is using the clang-5 compiler, whereas the current version in the CommandLineTools is clang-14.

In the terminal, what output do you get from the following commands:

clang -v
xcode-select -p
xcode-select -v
ls -l /Library/Developer/CommandLineTools/SDKs
3

Here is the output:

clang -v
clang version 5.0.1 (tags/RELEASE_501/final)
Target: x86_64-apple-darwin22.6.0
Thread model: posix
InstalledDir: /usr/local/bin

xcode-select -p
/Applications/Xcode.app/Contents/Developer

xcode-select -v
xcode-select version 2397.

total 0
lrwxr-xr-x  1 root  wheel   14 Jul 28 18:24 MacOSX.sdk -> MacOSX13.3.sdk
drwxr-xr-x  7 root  wheel  224 Jul 28 18:24 MacOSX12.3.sdk
lrwxr-xr-x  1 root  wheel   14 Jul 28 18:23 MacOSX12.sdk -> MacOSX12.3.sdk
drwxr-xr-x  7 root  wheel  224 Nov 12  2022 MacOSX13.1.sdk
drwxr-xr-x  7 root  wheel  224 Mar  9 19:58 MacOSX13.3.sdk
lrwxr-xr-x  1 root  wheel   14 Jul 28 18:22 MacOSX13.sdk -> MacOSX13.3.sdk
4

It looks like your system might be looking for the commandline tools in the wrong directory. Can you try running:

sudo xcode-select --switch /Library/Developer/CommandLineTools

Then restarting your terminal and running the debug commands again:

clang -v
xcode-select -p
5

Sure thing. Here is the output:

clang version 5.0.1 (tags/RELEASE_501/final)
Target: x86_64-apple-darwin22.6.0
Thread model: posix
InstalledDir: /usr/local/bin

/Library/Developer/CommandLineTools
6

Hmm still not finding the right compiler. The next issue is that I believe binaries in usr/local/bin take precedence over the commandline-tools, so your system is defaulting to this older clang version.

Let’s double-check that the commandline-tools clang version are all the right versions, can you run:

/Library/Developer/CommandLineTools/usr/bin/clang -v 
/usr/bin/clang -v
7

Those look like the 14.0 versions.

/Library/Developer/CommandLineTools/usr/bin/clang -v

Apple clang version 14.0.3 (clang-1403.0.22.14.1)
Target: x86_64-apple-darwin22.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

/usr/bin/clang -v

Apple clang version 14.0.3 (clang-1403.0.22.14.1)
Target: x86_64-apple-darwin22.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
8

Alright, so then it’s just the stray clang-5 in your /usr/local/bin.

Let’s rename the clang and clang++ binaries so that the newer system binaries will be found instead:

sudo mv /usr/local/bin/clang /usr/local/bin/clang-5
sudo mv /usr/local/bin/clang++ /usr/local/bin/clang++-5

Then if you run clang -v it should (hopefully) show the clang-14 version. If so, you can restart R and try the installation/example again

9

So, it’s now showing the right version in the terminal:

clang -v

Apple clang version 14.0.3 (clang-1403.0.22.14.1)
Target: x86_64-apple-darwin22.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

But the example is now throwing different a C-related error (I think):

Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.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 -single_module -multiply_defined suppress -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: in '/usr/local/lib/libunwind.dylib', building for macOS-arm64 but attempting to link with file built for macOS-x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [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' CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB='file1052f7873b2dc.so' OBJECTS='file1052f7873b2dc.o'

make would use
if test  "zfile1052f7873b2dc.o" != "z"; then \
	  echo clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file1052f7873b2dc.so file1052f7873b2dc.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++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file1052f7873b2dc.so file1052f7873b2dc.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) : 
                         ^55 warnings generated.ld: warning: ignoring file /usr/local/lib/libc++.dylib, building for macOS-arm64 but attempting to link with file built for macOS-x86_64ld: in '/usr/local/lib/libunwind.dylib', building for macOS-arm64 but attempting to link with file built for macOS-x86_64clang: error: linker command failed with exit code 1 (use -v to see invocation)make: *** [file1052f7873b2dc.so] Error 1
Error in sink(type = "output") : invalid connection
10

These are more stray files in your /usr/local folders. Are you using homebrew/macports?

Can you post the output from the following R commands:

Sys.getenv("PATH")
Sys.getenv("LDLIBS")
readLines("~/.R/Makevars")
readLines("~/.Renviron")
readLines("~/.Rprofile")
11

OK sorry for the double post, but I tried the example() model and it gave a more informative error at the bottom.

> example(stan_model, package = "rstan", run.dontrun = TRUE)

[ deleted stuff in here]

Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) : 
                         ^55 warnings generated.ld: warning: ignoring file /usr/local/lib/libc++.dylib, building for macOS-arm64 but attempting to link with file built for macOS-x86_64ld: in '/usr/local/lib/libunwind.dylib', building for macOS-arm64 but attempting to link with file built for macOS-x86_64clang: error: linker command failed with exit code 1 (use -v to see invocation)make: *** [file10756488d913f.so] Error 1
>
12 
> Sys.getenv("PATH")
[1] "/opt/homebrew/bin:/opt/homebrew/bin:/opt/local/bin:/opt/local/sbin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/andrew/Applications/quarto/bin:/usr/texbin:/Applications/RStudio.app/Contents/Resources/app/quarto/bin:/Applications/RStudio.app/Contents/Resources/app/bin/postback:/Applications/RStudio.app/Contents/Resources/app/bin/postback"

> Sys.getenv("LDLIBS")
[1] ""

> readLines("~/.R/Makevars")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/Users/andrew/.R/Makevars': No such file or directory

> readLines("~/.Renviron")
[1] "" "" ""

> readLines("~/.Rprofile")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/Users/andrew/.Rprofile': No such file or directory
13

It looks like it is attempting to link against the old (x86) toolchain by default.

What output do you get from:

Sys.getenv("LDFLAGS")
readLines("~/.zshrc")
readLines("~/.bashrc")
14 
> Sys.getenv("LDFLAGS")
[1] ""

> readLines("~/.zshrc")
 [1] ""                                                                                            
 [2] "# >>> conda initialize >>>"                                                                  
 [3] "# !! Contents within this block are managed by 'conda init' !!"                              
 [4] "__conda_setup=\"$('/Users/andrew/opt/anaconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)\""
 [5] "if [ $? -eq 0 ]; then"                                                                       
 [6] "    eval \"$__conda_setup\""                                                                 
 [7] "else"                                                                                        
 [8] "    if [ -f \"/Users/andrew/opt/anaconda3/etc/profile.d/conda.sh\" ]; then"                  
 [9] "        . \"/Users/andrew/opt/anaconda3/etc/profile.d/conda.sh\""                            
[10] "    else"                                                                                    
[11] "        export PATH=\"/Users/andrew/opt/anaconda3/bin:$PATH\""                               
[12] "    fi"                                                                                      
[13] "fi"                                                                                          
[14] "unset __conda_setup"                                                                         
[15] "# <<< conda initialize <<<"                                                                  
[16] "" 

> readLines("~/.bashrc")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/Users/andrew/.bashrc': No such file or directory
15

Hmm nothing obvious there, so I’m not sure where this old toolchain came from in your system or how to remove it.

We can try adding a compiler flag for R to look at the libraries provided by the commandline-tools. Can you add the following to your Makevars file:

LDFLAGS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib

Then trying the example model/installation again?

16

It threw a different error this time:

Error in compileCode(f, code, language = language, verbose = verbose) : 
          typedef double local_scalar_t__;                       ^55 warnings generated.ld: in '/usr/local/lib/libunwind.dylib', building for macOS-arm64 but attempting to link with file built for macOS-x86_64clang: error: linker command failed with exit code 1 (use -v to see invocation)make: *** [file1139371e1717c.so] Error 1

Do you think something weird is going on with the homebrew stuff? Here is the path and other output:

> Sys.getenv("PATH")
[1] "/opt/homebrew/bin:/opt/local/bin:/opt/local/sbin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/andrew/Applications/quarto/bin:/usr/texbin:/Applications/RStudio.app/Contents/Resources/app/quarto/bin:/Applications/RStudio.app/Contents/Resources/app/bin/postback"
> Sys.getenv("LDLIBS")
[1] ""
> readLines("~/.R/Makevars")
[1] "LDFLAGS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
> readLines("~/.Renviron")
[1] "" "" ""
> readLines("~/.Rprofile")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/Users/andrew/.Rprofile': No such file or directory

> Sys.getenv("LDFLAGS")
[1] ""
> readLines("~/.zshrc")
 [1] ""                                                                                            
 [2] "# >>> conda initialize >>>"                                                                  
 [3] "# !! Contents within this block are managed by 'conda init' !!"                              
 [4] "__conda_setup=\"$('/Users/andrew/opt/anaconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)\""
 [5] "if [ $? -eq 0 ]; then"                                                                       
 [6] "    eval \"$__conda_setup\""                                                                 
 [7] "else"                                                                                        
 [8] "    if [ -f \"/Users/andrew/opt/anaconda3/etc/profile.d/conda.sh\" ]; then"                  
 [9] "        . \"/Users/andrew/opt/anaconda3/etc/profile.d/conda.sh\""                            
[10] "    else"                                                                                    
[11] "        export PATH=\"/Users/andrew/opt/anaconda3/bin:$PATH\""                               
[12] "    fi"                                                                                      
[13] "fi"                                                                                          
[14] "unset __conda_setup"                                                                         
[15] "# <<< conda initialize <<<"                                                                  
[16] ""                                                                                            
> readLines("~/.bashrc")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/Users/andrew/.bashrc': No such file or directory```
17

It’s still the same issue unfortunately:

ld: in '/usr/local/lib/libunwind.dylib', building for macOS-arm64 but attempting to link with file built for macOS-x86_64

It looks like libunwind only exists for Intel Macs , which is why there is the error about the different architectures.

Can you try removing it:

brew remove libunwind
18

OK it’s working.

I uninstalled libunwind from /opt and from /usr/local/lib and now everything looks to be working. Thanks so much for helping me with this!

1 Like
19

Oh perfect, glad that was the magic bullet!

1 Like