Please help -
I am trying to run a stan model (through HBayesDM) and I keep running into this error message. When the run the function:
hBayesDM::ts_par7(data = "example", niter=2000, nwarmup=1000, nchain=4, ncore=4)
it produces the error:
Error in compileCode(f, code, language = language, verbose = verbose) :
In file included from <built-in>:1:In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1:In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:82:In file included from /usr/local/opt/llvm/bin/../include/c++/v1/new:92:In file included from /usr/local/opt/llvm/bin/../include/c++/v1/cstdlib:85:/usr/local/opt/llvm/bin/../include/c++/v1/stdlib.h:93:15: fatal error: 'stdlib.h' file not found#include_next <stdlib.h> ^~~~~~~~~~1 error generated.make: *** [file41a1630639ae.o] Error 1
Error in sink(type = "output") : invalid connection
Here is my r session info:
R version 4.2.3 (2023-03-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.5
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] rstanarm_2.21.3 Rcpp_1.0.11 rstan_2.32.3 StanHeaders_2.32.2
Any help much appreciated!
1 Like
Does the error message occur specifically with hBayesDM, or does it occur with anything involving rstan? Are you able to run this: example(stan_model, package = "rstan", run.dontrun = TRUE)?
When I searched through Discourse with âMac M2â, I found quite a few threads with error messages similar to yours, e.g. this thread may be useful.
Thanks for this Frank -
When I follow the thread you showed it gives some useful instructions to reinstall rstan from source, however, I encounter this error when compiling Rcppeigen:
ld: warning: -single_module is obsolete
ld: warning: -multiply_defined is obsolete
ld: warning: -single_module is obsolete
ld: warning: -multiply_defined is obsolete
ld: warning: search path '/usr/local/opt/qt@5/lib' not found
ld: warning: search path '/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0' not found
ld: warning: search path '/usr/local/gfortran/lib' not found
ld: library 'gfortran' not found
clang-14: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppEigen.so] Error 1
ERROR: compilation failed for package âRcppEigenâ
* removing â/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigenâ
* restoring previous â/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigenâ
Warning in install.packages :
installation of package âRcppEigenâ had non-zero exit status
* installing *source* package ârstanâ ...
** package ârstanâ successfully unpacked and MD5 sums checked
** using staged installation
** libs
Error: package âRcppEigenâ 0.3.3.9.4 was found, but >= 0.3.4.0.0 is required by ârstanâ
* removing â/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstanâ
Warning in install.packages :
installation of package ârstanâ had non-zero exit status
I did try and reinstall âgfortranâ but I get told that it isnât available for my version of RâŚ
Iâve upgraded my R source, but I still get this message after running the line you asked me to try outâŚ
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) :
using C++ compiler: âHomebrew clang version 14.0.6âusing C++17using SDK: ââclang-14: warning: include path for libstdc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]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:/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found#include <cmath> ^~~~~~~1 error generated.make: *** [file6c7b2c424646.o] Error 1
Sorry that this isnât working for you. The error message about RcppEigen suggests you might need to re-install some other packages like Rcpp, which rstan depends on. But I am by no means an expert on this. Perhaps one of the Stan developers like @andrjohns would be able to help?
It looks like youâre using a custom tool chain (Homebrew) instead of Appleâs. How have you configured the tool chain to be used? It looks like thereâs a misconfiguration somewhere
Thanks for this - Ah I see. I hadnât considered this would be conflicting. How would I configure the tool chain to be appropriate and reset the configuration?
How have you set R to use the Homebrew toolchain?
I have now uninstalled it:
brew info --cask rstudio
rstudio: 2022.07.0,548
https://www.rstudio.com/
Not installed
From: https://github.com/caskroom/homebrew-cask/blob/HEAD/Casks/rstudio.rb
==> Name
RStudio
==> Description
Data science software focusing on R and Python
==> Artifacts
RStudio.app (App)
==> Caveats
rstudio depends on R. The R Project provides official binaries:
brew install --cask r
Alternatively, the Homebrew-compiled version of R omits the GUI app:
brew install r
==> Analytics
install: 1,266 (30 days), 3,599 (90 days), 14,486 (365 days)
I still unfortunately get the issue when trying to install anything with Clang, e.g. cmdstanr
Error in compileCode(f, code, language = language, verbose = verbose) :
using C++ compiler: âHomebrew clang version 14.0.6âusing C++17using SDK: ââclang-14: warning: include path for libstdc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]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:/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found#include <cmath> ^~~~~~~1 error generated.make: *** [file24385fb80314.o] Error 1
Error in sink(type = "output") : invalid connection
Thatâs RStudio, how have you installed R and set the Homebrew compilers to be used? Did you change environment variables, profile settings, etc?
Thanks for this @andrjohns. I am not sure exactly - I donât recall changing my compiler or profile to specify the use of homebrew. How would I reset this/change it back to xcode?
r: 4.2.1
https://www.r-project.org/
/usr/local/Caskroom/r/4.2.1 (89.7MB)
From: https://github.com/caskroom/homebrew-cask/blob/HEAD/Casks/r.rb
==> Name
R
==> Description
Environment for statistical computing and graphics
==> Artifacts
R-4.2.1.pkg (Pkg)
==> Caveats
Cask r installs files under /usr/local. The presence of such
files can cause warnings when running `brew doctor`, which is considered
to be a bug in Homebrew Cask.
Ah, I think I see where some issues may be coming from. Your Homebrew installation is installing casks/packages to /usr/local, but Homebrew on Apple Silicon uses /opt/homebrew instead. This indicates that you might be using the intel/x86_64 version of Homebrew instead of the Apple Silicon version.
To double-check this, can you run brew config and post the output?
Thanks for this -
Here is the output:
HOMEBREW_VERSION: 3.5.4
ORIGIN: https://github.com/Homebrew/brew
HEAD: 88a5fac96752f17280e64f60926f58dff45990e0
Last commit: 1 year, 8 months ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: b9229090a43eab220baac2fb5b89649a12b9751e
Core tap last commit: 1 year, 8 months ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_MAKE_JOBS: 12
Homebrew Ruby: 2.6.8 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.6.8_1/bin/ruby
CPU: dodeca-core 64-bit westmere
Clang: 15.0.0 build 1500
Git: 2.39.3 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 8.1.2 => /usr/bin/curl
macOS: 13.5-x86_64
CLT: 14.3.1.0.1.1683849156
Xcode: 15.2
Rosetta 2: true
Yep the Rosetta 2: true confirms it, you have the Intel version of homebrew installed - so itâs installing and running Intel packages instead of Apple Silicon (which are then run through Rosetta). It might not be the direct cause of the compilation issues youâre seeing here, but R is attempting to use these packages.
If you didnât have a reason to prefer the Rosetta-run Homebrew, it would make debugging dramatically easier if you could migrate your installation to the Apple Silicon homebrew. Thereâs a community guide on the process which several people have said works for them: Migrate from Intel (Rosetta2) to ARM brew on M1 ¡ Homebrew ¡ Discussion #417 ¡ GitHub
Thanks for this - I have now completed these steps and it seems to have worked:
HOMEBREW_VERSION: 4.2.12
ORIGIN: https://github.com/Homebrew/brew
HEAD: 780fbbc65e90fbe09629aba180a1839e9e7dbaf2
Last commit: 3 days ago
Core tap: N/A
Core cask tap: N/A
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_MAKE_JOBS: 12
Homebrew Ruby: 3.1.4 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.1.4/bin/ruby
CPU: dodeca-core 64-bit arm_blizzard_avalanche
Clang: 15.0.0 build 1500
Git: 2.39.3 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 8.1.2 => /usr/bin/curl
macOS: 13.5-arm64
CLT: 14.3.1.0.1.1683849156
Xcode: 15.2
Rosetta 2: false
I try to then install rstan once more and I get this still:
trying URL 'https://cran.rstudio.com/src/contrib/rstan_2.32.6.tar.gz'
Content type 'application/x-gzip' length 1555968 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
* installing *source* package ârstanâ ...
** package ârstanâ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: âclang version 14.0.6â
using C++17
using SDK: ââ
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0 -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/BH/include' -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/opt/R/arm64/include -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c Module.cpp -o Module.o
clang-14: warning: include path for libstdc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from Module.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [Module.o] Error 1
ERROR: compilation failed for package ârstanâ
* removing â/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstanâ
* restoring previous â/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstanâ
Warning in install.packages :
installation of package ârstanâ had non-zero exit status
The next step is to cleanup any leftover Homebrew packages in the /usr/local directory, since the old clang compiler still appears to be there (which is causing this compilation error).
What output do you get from:
ls /usr/local/bin
ls /usr/local/include
I get this:
ls /usr/local/bin
2to3 lprsetup.sh python3
2to3-3.10 makeinfo python3-32
2to3-3.7 npm python3-config
2to3-3.9 npx python3-intel64
R pdf2dsc python3.10
Rscript pdf2ps python3.10-config
dvipdf pdftexi2dvi python3.10-intel64
easy_install-3.7 pf2afm python3.7
eps2eps pfbtopfa python3.7-32
font2c pip3.10 python3.7-config
gfortran pip3.7 python3.7m
gs pod2texi python3.7m-config
gs-X11 pphs python3.9
gs-noX11 printafm python3.9-config
gsbj ps2ascii python3.9-intel64
gsdj ps2epsi pyvenv
gsdj500 ps2pdf pyvenv-3.7
gslj ps2pdf12 rclone
gslp ps2pdf13 sqlite3_analyzer
gsnd ps2pdf14 tclsh8.6
idle3 ps2pdfwr texi2any
idle3.10 ps2ps texi2dvi
idle3.7 ps2ps2 texi2pdf
idle3.9 pydoc3 texindex
info pydoc3.10 unix-lpr.sh
infokey pydoc3.7 wftopfa
install-info pydoc3.9 wish8.6
ls /usr/local/include
JAGS mysqlStubs.h tclThread.h
fakemysql.h odbcStubs.h tclTomMath.h
fakepq.h omp-tools.h tclTomMathDecls.h
fakesql.h omp.h tdbc.h
itcl.h ompt.h tdbcDecls.h
itcl2TclOO.h pqStubs.h tdbcInt.h
itclDecls.h tcl.h tk.h
itclInt.h tclDecls.h tkDecls.h
itclIntDecls.h tclOO.h tkPlatDecls.h
itclMigrate2TclCore.h tclOODecls.h
itclTclIntStubsFcn.h tclPlatDecls.h