Mac compileCode() error

Interfaces
1

Hello all,

I’m having problems similar to the ones windows folks were having compiling stan models after upgrading to R 4.0.2. Unfortunately none of their solutions worked for me.

Software
macOS Catalina 10.15.5
R 4.0.2 (2020-06-22)
RStudio 1.2.5033
rstan 2.21.1 (2020-07-08)
StanHeaders 2.21.0-5 (2020-06-09)

~/.R/Makevars contents:

 CXX=clang++ -arch x86_64 -ftemplate-depth-256 -stdlib=libstdc++

 CXXFLAGS="-mtune=native  -O3 -Wall -pedantic -Wconversion" 
 #set_by_rstan
 R_XTRA_CPPFLAGS =  -I$(R_INCLUDE_DIR)   #set_by_rstan
 CC=clang
 CXX=clang++ -arch x86_64 -ftemplate-depth-256

 CC=clang
 CXX=clang++ -arch x86_64 -ftemplate-depth-256

 CC=clang
 CXX=clang++ -arch x86_64 -ftemplate-depth-256

 CC=clang
 CXX=clang++ -arch x86_64 -ftemplate-depth-256

 CC=clang
 CXX=clang++ -arch x86_64 -ftemplate-depth-256

When I ran the code below

example(stan_model, run.dontrun = TRUE)

I get the following error

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:82:
In file included from /Library/Developer/CommandLineTools/usr/bin/…/include/c++/v1/new:90:
In file included from /Library/Developer/CommandLineTools/usr/bin/…/include/c++/v1/exception:81:
In file included from /Library/Developer/CommandLineTools/usr/bin/…/include/c++/v1/cstdlib:85:
In file included from /Library/Developer/CommandLineTools/usr/bin/…/include/c++/v1/stdlib.h:93:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdlib.h:66:
In file included from /Library/Developer
In addition: Warning messages:
1: In system2(CXX, args = ARGS) : error in running command
2: In file.remove(c(unprocessed, processed)) :
cannot remove file ‘/var/folders/bj/v8pg71qd5wdfm8nl9kf5qjqm0000gn/T//RtmpRRpWKB/file30c5a38b13b.stan’, reason ‘No such file or directory’

There have been quite a few of these errors reported over the past month or so and I was hoping to be able to solve it based on the previous answers, but I couldn’t get any of them to work. Thanks in advance for the help!

Elise

2

This should be fixed on CRAN, although you might have to install rstan from source until binaries are rebuilt. But I don’t know why the -arch x86_64 -ftemplate-depth-256 stuff has to be part of the compiler invocation. If that stuff really is needed, it should be part of CXX1*FLAGS.

3

When I try installing rstan from source I get the following errors at many points in the attempted installation process to the point where it says there are too many errors and it is aborting the installation ( fatal error: too many errors emitted, stopping now [-ferror-limit=])

Error type 1:

/usr/local/include/stdint.h:2:10: error: #include nested too deeply
#include <stddef.h>

Error type 2:

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/resource.h:197:2: error: unknown type name ‘uint64_t’
uint64_t ri_user_time;
^

Also I have no idea about the things the makevars file. I can try removing them if you think that would help though.

Thanks again.
Elise

4

My guess is that this is caused by having something in your ~/.Rprofile or ~/.Renviron files that changes the PATH environmental variable. If you comment that out, it should work with the clang++ in Xcode.

5

Both my ~/.Rprofile and ~/.Renviron files are empty. Is there any way I could look at my path from inside R to see if anything is wrong with it?

Thanks.
Elise

6

@echellwig I’m also using Catalina and R 4.0.2 and this simple Makevars works for me:

CXX14FLAGS=-O3 -march=native -mtune=native 
CXX14FLAGS += -arch x86_64 -ftemplate-depth-256

I think it’s probably worth trying emptying out Makevars and starting fresh with just that. (I’m not sure if -arch x86_64 is actually necessary but it shouldn’t hurt.)

I think to check the contents of the PATH environment variable from R you can do Sys.getenv("PATH")

7

Updated the Makevars file and it didn’t make the error go away, but it didn’t appear to break anything additional so that’s good. Also my path is

/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/opt/X11/bin:/opt/ImageMagick/bin:/usr/local/git/bin:/opt/local/bin

I’m not sure how it got that way or if it is even a problem.

Elise

8

Sorry that’s still not working. @bgoodri any ideas here?

9

Not really. It is picking up the wrong clang++ and the wrong library headers somehow.

10

@echellwig Sorry we don’t have any good ideas here. Since both @bgoodri and I are out of ideas maybe it’s worth trying our other R interface CmdStanR instead of RStan and seeing that works?

Here’s a tutorial for getting started:

11

I didn’t even know there was more than one interface! I will definitely try that. Thanks again for all your help!

Elise

12

It’s brand new. Hopefully it works for you! Definitely let us know.