CODEWITHSUNDEEP
c++macosg++clangrcpp
Bob
Bob

Reputation: 319

Rcpp not working on R 3.6.3 macOS Catalina 10.15.7

Rcpp used to work on R, but no longer, and I do not know why.

library(Rcpp)
evalCpp("1+1")

A long list of errors is returned, beginning with

Error in sourceCpp(code = code, env = env, rebuild = rebuild, cacheDir = cacheDir,  : 
  Error 1 occurred building shared library.

continuing with

/usr/local/clang7/include/c++/v1/cmath:313:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/usr/local/clang7/include/c++/v1/cmath:314:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/usr/local/clang7/include/c++/v1/cmath:315:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'?
using ::isfinite;
      ~~^
/usr/local/include/math.h:749:12: note: 'finite' declared here
extern int finite(double)
           ^

and ending with

20 errors generated.
make: *** [file35f5fb135d1.o] Error 1

I have installed command line tools and Xcode multiple times. I have also tried the "Coatless Professor" solution at https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos-before-r-4.0.0/, (as well as other multiple solutions), but to no avail.

I am reluctant to upgrade to R 4.0 because a key piece of software will stop working in the newer R environment.

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] RcppArmadillo_0.10.1.0.0 Rcpp_1.0.5              

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3

I would be most grateful for any advice!

Upvotes: 0

Views: 622

Answers (1)

Bob
Bob

Reputation: 319

I found the answer to this question in a post by Christian Herz, here: https://discourse.slicer.org/t/macos-catalina-10-15-5-compilation-error/12807/8

Header files on my Mac were disordered, with symlinked duplicates of the correct header files in /Library/Developer/CommandLineTools incorrectly placed in /usr/local/include. This error occurred as a result of my trying (unsuccessfully) to compile a C program on Catalina using the solution suggested by @Roy here: https://stackoverflow.com/questions/58278260/cant-compile-a-c-program-on-a-mac-after-upgrading-to-catalina-10-15. The solution did not help to compile my C program and lead to the difficulties with Rcpp.

To cure this ailment, I followed the strategy of @Christoffer Hammarström described in https://unix.stackexchange.com/questions/39333/how-can-i-remove-all-symbolic-links-with-a-special-target/39341#39341 and removed all symlinked headerfiles in /usr/local/include that pointed to /Library/Developer/CommandLineTools.

The exact command was: find /usr/local/include -lname '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/*' -delete and now Rcpp correctly compiles.

Upvotes: 1

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