Thanks, Dirk, Romain, for your insights.
The problem was the following line in my .bashrc
export PKG_CPPFLAGS='-I/TL/opt/R-2.13.2/library/Rcpp/include'
which included Rcpp 0.9.0 in the compilation, creating the
undefined symbol (since Rcpp 0.10.1 has a different signature for
r_vector_start).
Wishing you both and the rest of the list a good weekend,
+glenn
On 12/13/2012 05:21 PM, Romain Francois wrote:
Do you have the same version of Rcpp as root and as non root ?
You can use c++filt to demangle the name, e.g. what does this
give you:
$ c++filt _ZN4Rcpp8internal14r_vector_startILi14EdEEPT0_P7SEXPREC
r_vector_start has changed in 0.10.1, i.e. it lost a template
parameter, which is likely to be the case here. I suppose you
have two versions of Rcpp installed;
Romain
Le 13/12/12 17:08, Glenn Lawyer a écrit :
The problem seems to be file privileges. When I run R as
superuser, it
works. When I run as a normal user, I continue getting
Error in dyn.load(libLFile) :
unable to load shared object
'/tmp/RtmpTFHtzm/file1d365e7eaf51.so':
/tmp/RtmpTFHtzm/file1d365e7eaf51.so: undefined symbol:
_ZN4Rcpp8internal14r_vector_startILi14EdEEPT0_P7SEXPREC
Note that the names of the undefined symbol is the same for all
of the
ways and examples I have tested, which include:
cxxfunction (following the vignette)
cppFunction (following Hadley's tutorial)
R CMD INSTALL -l foo mypackage
where "mypackage" is created by Rcpp.package.skeleton("mypackage")
R CMD INSTALL -l foo somepackage.tar.gz
where "somepackage" is a package downloaded from CRAN which
uses Rcpp.
I would very much appreciate a hint/suggestion as to which
folders/directories/paths I may need to check to get the file
permissions correct.
Does the name of the undefined symbol tell you anything? If you
ignore
some characters, it reads
...Rccp.internal..r_vector_start...SEXPR..
+glenn
On 12/12/2012 05:15 PM, Dirk Eddelbuettel wrote:
Works for me:
R> require(Rcpp)
R> require(inline)
Loading required package: inline
R> inc <- '
+ using namespace Rcpp;
+ double norm( double x, double y ) {
+ return sqrt( x*x + y*y );
+ }
+ RCPP_MODULE(mod) {
+ function( "norm", &norm );
+ }
+ '
R> fx <- cxxfunction(signature(), plugin="Rcpp", include=inc)
R>
R> mod <- Module( "mod", getDynLib(fx) )
R>
R> mod$norm( 3, 4 )
[1] 5
R>
R> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C
LC_NAME=C LC_ADDRESS=C
LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets
methods base
other attached packages:
[1] inline_0.3.10 RQuantLib_0.3.9 Rcpp_0.10.1.5
loaded via a namespace (and not attached):
[1] compiler_2.15.2 tools_2.15.2
R>
That is with Rcpp from SVN but that shouldn't matter.
Dirk
--
--------------------------------------------------------------
Pirating science, because open access isn't always open enough
www.scipirate.com @piratesci
Dr. Glenn Lawyer
+352 661 967 244
Max-Planck-Institut für Informatik
Computational Biology and Applied Algorithmics
Campus E1 4
66123 Saarbrücken, Germany
http://bioinf.mpi-inf.mpg.de/~lawyer
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--
--------------------------------------------------------------
Pirating science, because open access isn't always open enough
www.scipirate.com @piratesci
Dr. Glenn Lawyer
+352 661 967 244
Max-Planck-Institut für Informatik
Computational Biology and Applied Algorithmics
Campus E1 4
66123 Saarbrücken, Germany
http://bioinf.mpi-inf.mpg.de/~lawyer
_______________________________________________
Rcpp-devel mailing list
[email protected]
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
