Hello everyone,
I?m getting a weird error anytime I try to use a NumericMatrix in a function compiled using the sourceCpp function. In case it matters, I?m running Mac OS X 10.9.1.
I compiled a simple NumericVector function with no problem:
library(Rcpp)
src <- '
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
NumericVector fun1()
{
NumericVector a(3, 10.0);
return(a);
}
'
sourceCpp(code = src)
fun1()
When I try a similar function with a NumericMatrix, I get an error. I tried to compile:
src2 <- '
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
NumericMatrix fun2()
{
NumericMatrix a(3, 2);
return a;
}
'
sourceCpp(code = src2)
And get the following error:
Error in dyn.load("/var/folders/x7/cm9jq3nn6mxdn31r9sw3sbv80000gn/T//RtmpaRBweq/sourcecpp_15e0218ec23e/sourceCpp_38196.so") :
unable to load shared object '/var/folders/x7/cm9jq3nn6mxdn31r9sw3sbv80000gn/T//RtmpaRBweq/sourcecpp_15e0218ec23e/sourceCpp_38196.so':
dlopen(/var/folders/x7/cm9jq3nn6mxdn31r9sw3sbv80000gn/T//RtmpaRBweq/sourcecpp_15e0218ec23e/sourceCpp_38196.so, 6): Symbol not found: __ZNK4Rcpp7RObject4attrERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
Referenced from: /var/folders/x7/cm9jq3nn6mxdn31r9sw3sbv80000gn/T//RtmpaRBweq/sourcecpp_15e0218ec23e/sourceCpp_38196.so
Expected in: flat namespace
in /var/folders/x7/cm9jq3nn6mxdn31r9sw3sbv80000gn/T//RtmpaRBweq/sourcecpp_15e0218ec23e/sourceCpp_38196.so
Thinking perhaps I messed up, I tried to compile a stripped down Gibbs sampler example from Dirk to no avail (http://gallery.rcpp.org/articles/gibbs-sampler/).
src3 <- '
// load Rcpp
#include <Rcpp.h>
using namespace Rcpp; // shorthand
// [[Rcpp::export]]
NumericMatrix RcppGibbs(int n, int thn) {
int i,j;
NumericMatrix mat(n, 2);
return mat; // Return to R
}
'
sourceCpp(code = src3)
What is going on? If I am missing something very simple, please forgive me. I?ve been beating my head against the wall for over an hour now looking at examples, trying to create the simplest tests possible, to no avail.
Thanks,
Joshua
--
Joshua French, Ph.D.
Assistant Professor
Department of Mathematical and Statistical Sciences
University of Colorado Denver
Joshua.French at ucdenver.edu<mailto:Joshua.French at ucdenver.edu>
http://math.ucdenver.edu/~jfrench/
Ph: 303-315-1709 Fax: 303-315-1701
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[Rcpp-devel] Error with NumericMatrix using SourceCpp
2 messages · French, Joshua, Jaime Ashander
I can't reproduce your error, but had some similar issues before updating gcc and reinstalling Rcpp. Providing output of
sessionInfo()
from R, and details on compiler versions might help others point you to a more specific solution. - jaime For reference, I have gcc i686-apple-darwin10-llvm-gcc-4.2 via mac ports and my sessionInfo() gives: R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) # ... attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] RcppArmadillo_0.3.930.1 Rcpp_0.10.6 On Thu, Jan 2, 2014 at 2:20 PM, French, Joshua
<JOSHUA.FRENCH at ucdenver.edu>wrote:
Hello everyone,
I?m getting a weird error anytime I try to use a NumericMatrix in a
function compiled using the sourceCpp function. In case it matters, I?m
running Mac OS X 10.9.1.
I compiled a simple NumericVector function with no problem:
library(Rcpp)
src <- '
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
NumericVector fun1()
{
NumericVector a(3, 10.0);
return(a);
}
'
sourceCpp(code = src)
fun1()
When I try a similar function with a NumericMatrix, I get an error. I
tried to compile:
src2 <- '
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
NumericMatrix fun2()
{
NumericMatrix a(3, 2);
return a;
}
'
sourceCpp(code = src2)
And get the following error:
Error in
dyn.load("/var/folders/x7/cm9jq3nn6mxdn31r9sw3sbv80000gn/T//RtmpaRBweq/sourcecpp_15e0218ec23e/sourceCpp_38196.so")
:
unable to load shared object
'/var/folders/x7/cm9jq3nn6mxdn31r9sw3sbv80000gn/T//RtmpaRBweq/sourcecpp_15e0218ec23e/sourceCpp_38196.so':
dlopen(/var/folders/x7/cm9jq3nn6mxdn31r9sw3sbv80000gn/T//RtmpaRBweq/sourcecpp_15e0218ec23e/sourceCpp_38196.so,
6): Symbol not found:
__ZNK4Rcpp7RObject4attrERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
Referenced from:
/var/folders/x7/cm9jq3nn6mxdn31r9sw3sbv80000gn/T//RtmpaRBweq/sourcecpp_15e0218ec23e/sourceCpp_38196.so
Expected in: flat namespace
in
/var/folders/x7/cm9jq3nn6mxdn31r9sw3sbv80000gn/T//RtmpaRBweq/sourcecpp_15e0218ec23e/sourceCpp_38196.so
Thinking perhaps I messed up, I tried to compile a stripped down Gibbs
sampler example from Dirk to no avail (
http://gallery.rcpp.org/articles/gibbs-sampler/).
src3 <- '
// load Rcpp
#include <Rcpp.h>
using namespace Rcpp; // shorthand
// [[Rcpp::export]]
NumericMatrix RcppGibbs(int n, int thn) {
int i,j;
NumericMatrix mat(n, 2);
return mat; // Return to R
}
'
sourceCpp(code = src3)
What is going on? If I am missing something very simple, please forgive
me. I?ve been beating my head against the wall for over an hour now
looking at examples, trying to create the simplest tests possible, to no
avail.
Thanks,
Joshua
--
Joshua French, Ph.D.
Assistant Professor
Department of Mathematical and Statistical Sciences
University of Colorado Denver
Joshua.French at ucdenver.edu
http://math.ucdenver.edu/~jfrench/
Ph: 303-315-1709 Fax: 303-315-1701
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