# Compile issue with Rstan on Macbook Pro M1

**URL:** <https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195>\
**Category:** RStan\
**Tags:** installation, compiler, rstan\
**Created:** [October 30, 2023, 9:24am UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195 "2023-10-30T09:24:27Z")\
**Posts on this page:** 17\
**Page:** 1

<div class="post-metadata">

**Author:** ![Tikavdm](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/tikavdm/32/9466_2.png) [@Tikavdm](https://discourse.mc-stan.org/u/Tikavdm)\
**Post date:** [October 30, 2023, 9:24am UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/1 "2023-10-30T09:24:27Z")

</div>

Good day

I have struggling to get my Rstan working again on my M1 Mac, perhaps some updates messed with it.

I have followed the instructions on the [Getting Started Page](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started) from scratch, but when running the example I get the following error.

```stan
Error in compileCode(f, code, language = language, verbose = verbose) : 
                                          ^/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ __config:835:49: note: expanded from macro '_LIBCPP_DEPRECATED'# define _LIBCPP_DEPRECATED__ attribute__((deprecated)) ^97 warnings and 1 error generated.make: *** [file158a97e3a7a53.o] Error 1
Error in sink(type = "output") : invalid connection

```

Session Info:

```plaintext
sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 14.0

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base     

other attached packages:
[1] rstan_2.32.3 StanHeaders_2.32.2 ggplot2_3.4.2     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.11 compiler_4.2.0 pillar_1.8.1 QuickJSR_1.0.7 prettyunits_1.1.1 
 [6] tools_4.2.0 pkgbuild_1.3.1 jsonlite_1.8.0 lifecycle_1.0.3 tibble_3.1.8      
[11] gtable_0.3.1 pkgconfig_2.0.3 rlang_1.1.1 cli_3.6.1 rstudioapi_0.14   
[16] curl_4.3.2 parallel_4.2.0 loo_2.5.1 gridExtra_2.3 withr_2.5.0       
[21] dplyr_1.0.10 generics_0.1.3 vctrs_0.6.2 tidyselect_1.1.2 stats4_4.2.0      
[26] grid_4.2.0 inline_0.3.19 glue_1.6.2 R6_2.5.1 processx_3.7.0    
[31] fansi_1.0.3 purrr_0.3.4 callr_3.7.2 magrittr_2.0.3 codetools_0.2-18  
[36] matrixStats_0.62.0 scales_1.2.1 ps_1.7.1 colorspace_2.0-3 V8_4.2.1          
[41] utf8_1.2.2 RcppParallel_5.1.5 munsell_0.5.0 crayon_1.5.1      

```

Anything obvious I can try, since I"'m really having a hard time with compilers on the Mac.

Thanks

---

<div class="post-metadata">

**Author:** ![Ara\_Winter](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/ara_winter/32/4284_2.png) [@Ara\_Winter](https://discourse.mc-stan.org/u/Ara_Winter)\
**Post date:** [October 30, 2023, 11:09pm UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/2 "2023-10-30T23:09:59Z")

</div>

Can you provide which version of the OS and Xcode?

---

<div class="post-metadata">

**Author:** ![Tikavdm](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/tikavdm/32/9466_2.png) [@Tikavdm](https://discourse.mc-stan.org/u/Tikavdm)\
**Post date:** [October 31, 2023, 9:14am UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/3 "2023-10-31T09:14:54Z")

</div>

Sure, sorry I should have done that from the start:

```plaintext
macOS Sonoma Version 14.0 (23A344)
xcode-select version 2399

```

I’m not sure I needed the full installation of Xcode? I didn’t gather from the quickstart of Rstan that that is a requirement, but I think you are on to something. How do I know which compiler Rstan is going to use.

---

<div class="post-metadata">

**Author:** ![Tikavdm](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/tikavdm/32/9466_2.png) [@Tikavdm](https://discourse.mc-stan.org/u/Tikavdm)\
**Post date:** [October 31, 2023, 10:40am UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/4 "2023-10-31T10:40:52Z")

</div>

I installed XCode `Version 15.0.1`, but I got the same error.

---

<div class="post-metadata">

**Author:** ![Ara\_Winter](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/ara_winter/32/4284_2.png) [@Ara\_Winter](https://discourse.mc-stan.org/u/Ara_Winter)\
**Post date:** [October 31, 2023, 1:20pm UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/5 "2023-10-31T13:20:08Z")

</div>

I know back a version I had to remove all the rstan stuff and reinstall it for it to work. I am a version back on the M1 OS and Xcode at the moment. Once my models finishing running I’ll upgrade and see what’s going on.

This thread might help [Error in sink(type = "output") : invalid connection on Mac OS](https://discourse.mc-stan.org/t/error-in-sink-type-output-invalid-connection-on-mac-os/26117)

---

<div class="post-metadata">

**Author:** ![Tikavdm](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/tikavdm/32/9466_2.png) [@Tikavdm](https://discourse.mc-stan.org/u/Tikavdm)\
**Post date:** [November 2, 2023, 9:21am UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/6 "2023-11-02T09:21:01Z")

</div>

Thanks @Ara_Winter, I will look into this, but unfortunately, so far it looks like most of the libraries like gfortran are for Mac OS 13 and not 14, so there might be a version issue. For security reasons, I will probably not be allowed to downgrade. I will repeat the steps in the linked thread again and see if I have any luck.

---

<div class="post-metadata">

**Author:** ![Ara\_Winter](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/ara_winter/32/4284_2.png) [@Ara\_Winter](https://discourse.mc-stan.org/u/Ara_Winter)\
**Post date:** [November 4, 2023, 2:21pm UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/7 "2023-11-04T14:21:09Z")

</div>

Just upgraded. So before I upgraded, I removed rstan, brms, and other packages that use rstan. Not sure that’s necessary. Quit out of R and ran the upgrade.

Clean reinstall of rstan and brms through the package manager in RStudio (really need to bail out of RStudio).

So now I am running on OS14 and Xcode version 2403 on the M1 chips. Both brms models and stan models compile and run.

---

<div class="post-metadata">

**Author:** ![Tikavdm](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/tikavdm/32/9466_2.png) [@Tikavdm](https://discourse.mc-stan.org/u/Tikavdm)\
**Post date:** [November 9, 2023, 12:04pm UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/8 "2023-11-09T12:04:37Z")

</div>

Unfortunately, these steps didn’t work for me. The only difference is that I didn’t remove all the packages before upgrading, because I have already the latest OS. I guess I will repeat those steps sometime soon. In the meantime I got `cmdstan` working, which is strange, because if there was a compiler issue, I would assume that `cmdstan` would also not work.

---

<div class="post-metadata">

**Author:** ![Ara\_Winter](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/ara_winter/32/4284_2.png) [@Ara\_Winter](https://discourse.mc-stan.org/u/Ara_Winter)\
**Post date:** [November 9, 2023, 2:16pm UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/9 "2023-11-09T14:16:26Z")

</div>

Oh weird. Yeah last time I had errors due to the mac os and xcode neither rstan, brms, or cmdstan worked. Let dig around and see if I can recreate your error message on my machine.

---

<div class="post-metadata">

**Author:** ![Ara\_Winter](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/ara_winter/32/4284_2.png) [@Ara\_Winter](https://discourse.mc-stan.org/u/Ara_Winter)\
**Post date:** [November 9, 2023, 2:20pm UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/10 "2023-11-09T14:20:07Z")

</div>

Is your include directory still intact after the update. I know on some upgrades in the past mac os will wipe that out.

---

<div class="post-metadata">

**Author:** ![Justin\_Savoie](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/justin_savoie/32/12366_2.png) [@Justin\_Savoie](https://discourse.mc-stan.org/u/Justin_Savoie)\
**Post date:** [November 14, 2023, 2:37am UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/11 "2023-11-14T02:37:03Z")

</div>

Thanks for all the help. I also have an unsolved issue. Also originally here: [Can't compile code using RStan](https://discourse.mc-stan.org/t/cant-compile-code-using-rstan/33121)

Here’s the full error now. I reinstalled everything including CommandLineTools. I really don’t know what the problem is.

```no-highlight
> brm(mpg~1,mtcars)
Compiling Stan program...
make cmd is
  make -f '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk' -f '/Users/justinsavoie/.R/Makevars' CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB='file18ab72d229a7.so' OBJECTS='file18ab72d229a7.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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -O3 -fPIC -c file18ab72d229a7.cpp -o file18ab72d229a7.o
if test "zfile18ab72d229a7.o" != "z"; then \
	  echo clang++ -arch arm64 -std=gnu++17 -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 file18ab72d229a7.so file18ab72d229a7.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 -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file18ab72d229a7.so file18ab72d229a7.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) : 
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstring:66:5: error: <cstring> tried including <string.h> but didn't find libc++'s <string.h> header. This usually means that your header search paths are not configured properly. The header search paths should contain the C++ Standard Library headers before any C Standard Library, and you are probably using compiler flags that make that not be the case.# error <cstring> tried including <string.h> but didn't find libc++'s <string.h> header. \ ^fatal error: too many errors emitted, stopping now [-ferror-limit=]20 errors generated.make: *** [file18ab72d229a7.o] Error 1
Error in sink(type = "output") : invalid connection

```

I have Sonoma 14.0 (23A344).  
I have xcode-select version 2399.

Additionally:

g++ --version  
Apple clang version 15.0.0 (clang-1500.0.40.1)  
Target: arm64-apple-darwin23.0.0  
Thread model: posix  
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

I found this here: [⚙ D131441 [libc++] Diagnose when header search paths are set up incorrectly](https://reviews.llvm.org/D131441) which says "For example, people will manually add -isystem /usr/include, which ends up messing up the layering of header search paths required by libc++ (because the C Standard Library now appears _before_ libc++ in  
the search paths). " but I still don’t know how to fix it.

At the end of the day it’s probably this: “The header search paths should contain the C++ Standard Library headers before any C Standard Library, and you are probably using compiler flags that make that not be the case.” but again; not sure.

---

<div class="post-metadata">

**Author:** ![Ara\_Winter](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/ara_winter/32/4284_2.png) [@Ara\_Winter](https://discourse.mc-stan.org/u/Ara_Winter)\
**Post date:** [November 14, 2023, 2:09pm UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/12 "2023-11-14T14:09:15Z")

</div>

There are some folks here [terminal - Unable to find include file on newly updated macOS(C/C++) - Ask Different](https://apple.stackexchange.com/questions/458062/unable-to-find-include-file-on-newly-updated-macosc-c) wrangling with a similar issue.

Let me see what versions I have of g++, apple clang.

---

<div class="post-metadata">

**Author:** ![Tikavdm](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/tikavdm/32/9466_2.png) [@Tikavdm](https://discourse.mc-stan.org/u/Tikavdm)\
**Post date:** [November 16, 2023, 7:33am UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/13 "2023-11-16T07:33:47Z")

</div>

Hi @Ara_Winter it appears that it is still intact. Unfortunately that Stan typically has these compiler issues, especially after updates, which makes it so hard to get going. Still a mystery that my `cmdstan` works.

---

<div class="post-metadata">

**Author:** ![Tikavdm](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/tikavdm/32/9466_2.png) [@Tikavdm](https://discourse.mc-stan.org/u/Tikavdm)\
**Post date:** [November 16, 2023, 8:48am UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/14 "2023-11-16T08:48:46Z")

</div>

Okay I got it working, but not sure what fixed it. I can tell you what I did. I simply updated all my R packages in Rstudio, by clicking on the “update” button in the library tab. I suspect that some libraries related to Stan headers or other C++ libraries (like `RcppParallel`) maybe helped to resolve the issue.

Here are some Stan-related libraries:

 ![Screenshot 2023-11-16 at 10.43.42](https://canada1.discourse-cdn.com/flex030/uploads/mc_stan/original/3X/b/5/b563a763f99939382fff8300c3ec4c5e0b6b6ae8.png)

Here is my latest SessionInfo:

```no-highlight
R version 4.2.0 (2022-04-22)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 14.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base     

other attached packages:
[1] rstan_2.32.3 StanHeaders_2.32.2 ggplot2_3.4.4     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.11 pillar_1.9.0 compiler_4.2.0 QuickJSR_1.0.7 prettyunits_1.2.0 tools_4.2.0       
 [7] pkgbuild_1.4.2 jsonlite_1.8.7 lifecycle_1.0.4 tibble_3.2.1 gtable_0.3.4 pkgconfig_2.0.3   
[13] rlang_1.1.1 cli_3.6.1 rstudioapi_0.15.0 curl_5.1.0 parallel_4.2.0 loo_2.6.0         
[19] gridExtra_2.3 withr_2.5.2 dplyr_1.1.3 generics_0.1.3 vctrs_0.6.4 stats4_4.2.0      
[25] grid_4.2.0 tidyselect_1.2.0 glue_1.6.2 inline_0.3.19 R6_2.5.1 processx_3.8.2    
[31] fansi_1.0.5 callr_3.7.3 magrittr_2.0.3 codetools_0.2-19 matrixStats_0.62.0 scales_1.2.1      
[37] ps_1.7.5 colorspace_2.1-0 V8_4.4.0 utf8_1.2.4 RcppParallel_5.1.7 munsell_0.5.0     
[43] crayon_1.5.2

```

---

<div class="post-metadata">

**Author:** ![Ara\_Winter](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/ara_winter/32/4284_2.png) [@Ara\_Winter](https://discourse.mc-stan.org/u/Ara_Winter)\
**Post date:** [November 16, 2023, 1:55pm UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/15 "2023-11-16T13:55:45Z")

</div>

Glad it’s working. Maybe we should get something together about what do when the mac os updates breaks things.

---

<div class="post-metadata">

**Author:** ![Justin\_Savoie](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/justin_savoie/32/12366_2.png) [@Justin\_Savoie](https://discourse.mc-stan.org/u/Justin_Savoie)\
**Post date:** [November 17, 2023, 2:19pm UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/16 "2023-11-17T14:19:02Z")

</div>

Also fixed the problem.

What I did:I removed Command Line Tools. I updated Sonoma to 14.1.1. I deleted completely Homebrew (this was radical and I’m not sure it was needed, but I didn’t really need Homebrew). I installed the latest regular (non-beta) Xcode. I had tried before with CLT only; that didn’t work. CLT 15.1 beta didn’t work for me. Actually all CLT didn’t work for me.

So, update sonoma to latest, update Xcode to latest.

This: [Gcc 13.1.0 macOS Sonoma not compiling Ada or any languages on Intel or M1 Macs - Stack Overflow](https://stackoverflow.com/questions/77244801/gcc-13-1-0-macos-sonoma-not-compiling-ada-or-any-languages-on-intel-or-m1-macs)

explains that there’s a problem with Sonoma and Xcode. I suspect this was the issue.

---

<div class="post-metadata">

**Author:** ![Tikavdm](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/tikavdm/32/9466_2.png) [@Tikavdm](https://discourse.mc-stan.org/u/Tikavdm)\
**Post date:** [November 22, 2023, 1:58pm UTC](https://discourse.mc-stan.org/t/compile-issue-with-rstan-on-macbook-pro-m1/33195/17 "2023-11-22T13:58:38Z")

</div>

I wish I could be more specific as to what worked. All I can say is that I uninstalled all things related to Rstan, then followed the steps in the [Getting Started Page](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started) multiple times, downloaded Xcode and made sure that all R-libraries were up to date. It sounds a bit like “have tried restarting your computer” since these are just all the basic steps.