[Rcpp-devel] Seamless Rcpp gives errors with RcppArmadillo

[John Swan]

Hi,

I just purchased Dirk's book on Seamless Rcpp and I'm finding it very useful.

However, I'm having a strange error running RcppArmadillo inline, where the book examples seem to manage it effortlessly.
I've been stuck on this for hours. Any help is most appreciated. 

I am using R 3.0 on Mac OS X Mountain Lion 10.8.4, sessionInfo output:
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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

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

other attached packages:
[1] inline_0.3.12           RcppArmadillo_0.3.900.0 Rcpp_0.10.3             BDgraph_2.6             huge_1.2.4              MASS_7.3-26             igraph_0.6.5-2         
[8] Matrix_1.0-12           lattice_0.20-15        

loaded via a namespace (and not attached):
[1] grid_3.0.1  tools_3.0.1


I have the following in a source file (somefile.R):
library(Rcpp)
library(inline)
library(RcppArmadillo)

rowSumsRcppArmadilloFunction <- '
arma::rowvec rowSumsRcppArmadillo(NumericMatrix x){
    arma::mat X = arma::mat(x.begin(), x.nrow(), x.ncol(), false); 
    return arma::sum(X, 1); 
}'

rowSumsRcppArmadillo <- cxxfunction(signature(),
			plugin="Rcpp",
			incl=rowSumsRcppArmadilloFunction,
			body='
return Rcpp::wrap(rowSumsRcppArmadillo());
')


If I try to execute this in R console with the source command, I get:

> source("/Users/me/Desktop/R/somefile.R")
file29967eb06d23.cpp:20: error: ‘arma’ has not been declared
file29967eb06d23.cpp:20: error: expected constructor, destructor, or type conversion before ‘rowSumsRcppArmadillo’
file29967eb06d23.cpp: In function ‘SEXPREC* file29967eb06d23()’:
file29967eb06d23.cpp:35: error: ‘rowSumsRcppArmadillo’ was not declared in this scope
make: *** [file29967eb06d23.o] Error 1

ERROR(s) during compilation: source code errors or compiler configuration errors!

Program source:
  1: 
  2: // includes from the plugin
  3: 
  4: #include <Rcpp.h>
  5: 
  6: 
  7: #ifndef BEGIN_RCPP
  8: #define BEGIN_RCPP
  9: #endif
 10: 
 11: #ifndef END_RCPP
 12: #define END_RCPP
 13: #endif
 14: 
 15: using namespace Rcpp;
 16: 
 17: 
 18: // user includes
 19: 
 20: arma::rowvec rowSumsRcppArmadillo(NumericMatrix x){
 21:     arma::mat X = arma::mat(x.begin(), x.nrow(), x.ncol(), false); 
 22:     return arma::sum(X, 1); 
 23: }
 24: 
 25: // declarations
 26: extern "C" {
 27: SEXP file29967eb06d23( ) ;
 28: }
 29: 
 30: // definition
 31: 
 32: SEXP file29967eb06d23(  ){
 33: BEGIN_RCPP
 34: 
 35: return Rcpp::wrap(rowSumsRcppArmadillo());
 36: 
 37: END_RCPP
 38: }
 39: 
 40: 
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! file29967eb06d23.cpp:20: error: ‘arma’ has not been declared
file29967eb06d23.cpp:20: error: expected constructor, destructor, or type conversion before ‘rowSumsRcppArmadillo’
file29967eb06d23.cpp: In function ‘SEXPREC* file29967eb06d23()’:
file29967eb06d23.cpp:35: error: ‘rowSumsRcppArmadillo’ was not declared in this scope
make: *** [file29967eb06d23.o] Error 1
In addition: Warning message:
running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file29967eb06d23.cpp 2> file29967eb06d23.cpp.err.txt' had status 1 

I added these:
 20: #include <RcppArmadillo.h>
 21: // [[Rcpp::depends(RcppArmadillo)]]
 22: 
 23: // [[Rcpp::export]]
 24: 
 25: arma::rowvec rowSumsRcppArmadillo(NumericMatrix x){
 26:     arma::mat X = arma::mat(x.begin(), x.nrow(), x.ncol(), false); 
 27:     return arma::sum(X, 1); 
 28: }

But then I just get this error:
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! file77e03dcff275.cpp:20:27: error: RcppArmadillo.h: No such file or directory
file77e03dcff275.cpp:25: error: ‘arma’ has not been declared
file77e03dcff275.cpp:25: error: expected constructor, destructor, or type conversion before ‘rowSumsRcppArmadillo’
file77e03dcff275.cpp: In function ‘SEXPREC* file77e03dcff275()’:
file77e03dcff275.cpp:40: error: ‘rowSumsRcppArmadillo’ was not declared in this scope
make: *** [file77e03dcff275.o] Error 1
In addition: Warning message:
running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file77e03dcff275.cpp 2> file77e03dcff275.cpp.err.txt' had status 1 



So, I thought I'd try compilng it as a package, but when I try to call the package in R, I get errors like:
Error in sourceCpp("./R/somefile.R") : 
  Error 1 occurred building shared library.

WARNING: The tools required to build C++ code for R were not found.

Please install Command Line Tools for XCode (or equivalent).

ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
ld: library not found for -lgfortran
collect2: ld returned 1 exit status
make: *** [sourceCpp_13326.so] Error 1


The XCode command line tools *are* installed - I'm an iOS developer so I always make sure that they are there:

John-MBPR:BDGraphSource johnswan$ which llvm-g++
/usr/bin/llvm-g++
John-MBPR:BDGraphSource johnswan$ llvm-g++ --version 
i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


Can anyone help?

Thanks
John
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