CODEWITHSUNDEEP
rrcpp
Cauchy
Cauchy

Reputation: 1747

RcppArmadillo: Error when installing package on Mac

I have an R package which I am trying to install on a MAC OS (yosemite), and I am getting a linker problem. This is the error that I am getting

clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o File1.so File2.o File3.o File4.o RcppExports.o Utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mypackage.so] Error 1
ERROR: compilation failed for package ‘mypackage’

My Makevars file contain:

PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

In DESCRIPTION, I have:

Depends:
    R (>= 3.2.0),
    Rcpp,
    RcppArmadillo
LinkingTo: Rcpp, RcppArmadillo

and in R/help.R, I have:

#' @importFrom Rcpp evalCpp
#' @import RcppArmadillo
#' @useDynLib mypackage
NULL

This is not the same issue as this question because I already included the Armadillo dependencies in the header file that is being indluced by the other .cpp files:

#include <iostream>
#include <algorithm>
#include <cmath>
#include <Rmath.h>
#include <RcppArmadillo.h>

// [[Rcpp::depends(RcppArmadillo)]]

Am I missing something? Should the makefile be modified?

Upvotes: 3

Views: 3669

Answers (1)

coatless
coatless

Reputation: 20746

Fixes:

Easy fix

Open the Terminal from /Applications/Utilities/

Type the following into Terminal

curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

More time consuming:

Use homebrew or macports to grab gcc which contains gfortran. Change the ~/.R/Makevars. (See the openmp post for more details on the gfortran install with homebrew.)

See:

  1. http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-os-x/
  2. http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/
  3. http://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/
  4. https://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-FAQ.pdf#page=8

Upvotes: 8

Related Questions