[Rcpp-devel] Seamless Rcpp gives errors with RcppArmadillo
Anirban Mukherjee
anirban.mukherjee at gmail.com
Wed Jun 26 13:04:40 CEST 2013
library(inline); library(RcppArmadillo)
rowSumsRA <- cxxfunction(signature(x = "numeric"), plugin="RcppArmadillo",
body='return Rcpp::wrap(arma::sum(as<arma::mat>(x),0));')
colSumsRA <- cxxfunction(signature(x = "numeric"), plugin="RcppArmadillo",
body='return Rcpp::wrap(arma::sum(as<arma::mat>(x),1));')
Anirban
> Date: Wed, 26 Jun 2013 11:11:04 +0200
> From: John Swan <johnswan at spamcop.net>
> To: rcpp-devel at lists.r-forge.r-project.org
> Subject: [Rcpp-devel] Seamless Rcpp gives errors with RcppArmadillo
> Message-ID: <99384497-D7C4-4BC6-859E-C3FA1AB5FF7D at spamcop.net>
> Content-Type: text/plain; charset="windows-1252"
>
> 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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