Dear list,
I'm fairly new to Rcpp but have been using it without any problems for
a few weeks.
Yesterday I made the unfortunate error to upgrade from OS X 10.8 to OS
X 10.9 (Mavericks), which
seriously broke something. Using a new user account/admin account
didn't change anything
(apparently this has worked for someone once on this list).
I know that Problems with Mavericks have been discussed on this list
before, but my CC and CXX in ~/.R/Makevars are set to clang and clang++
and I don't really know what else to do.
I'm using the pre-built R binary CRAN provides. Nothing fancy.
XCode 5.0.1 is installed along with the Command Line Tools (OS X
Mavericks) and gfortran-4.2.3 from CRAN.)
I ran the the unit tests for RcppArmadillo, they almost all fail:
http://pastebin.com/C60xcvzh
One simple example (this is from the docs, Rcpp-modules p6):
In a clean R session with --vanilla:
require(Rcpp)
Loading required package: Rcpp
require(inline)
Loading required package: inline
Attaching package: ‘inline’
The following object is masked from ‘package:Rcpp’:
registerPlugin
inc <- '
using namespace Rcpp;
double norm( double x, double y ) {
return sqrt( x*x + y*y );
}
RCPP_MODULE(mod) {
function( "norm", &norm );
}
'
fx <- cxxfunction(signature(), plugin="Rcpp", include=inc,
verbose=TRUE)
Compilation argument:
/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB
file10451508f324.cpp 2> file10451508f324.cpp.err.txt
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include
-I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
-fPIC "-mtune=native -g -O2 -Wall -pedantic -Wconversion" -c
file10451508f324.cpp -o file10451508f324.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -L/usr/local/lib -o file10451508f324.so
file10451508f324.o
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
-L/Library/Frameworks/R.framework/Resources/lib -lRlapack
-L/Library/Frameworks/R.framework/Resources/lib -lRblas -lgfortran
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
Error in dyn.load(libLFile) :
unable to load shared object
'/var/folders/9x/w2b7c7k50g3749c7gqjrdz980000gn/T//Rtmp671JcT/file10451508f324.so':
dlopen(/var/folders/9x/w2b7c7k50g3749c7gqjrdz980000gn/T//Rtmp671JcT/file10451508f324.so,
6): Symbol not found:
__Z8demangleRKNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEE
Referenced from:
/var/folders/9x/w2b7c7k50g3749c7gqjrdz980000gn/T//Rtmp671JcT/file10451508f324.so
Expected in: flat namespace
in
/var/folders/9x/w2b7c7k50g3749c7gqjrdz980000gn/T//Rtmp671JcT/file10451508f324.so
$ c++filt
__Z8demangleRKNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEE
demangle(std::__1::basic_string<char, std::__1::char_traits<char>,
std::__1::allocator<char> > const&)
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] inline_0.3.13 Rcpp_0.10.6
loaded via a namespace (and not attached):
[1] tools_3.0.2
I also ran the unit tests for RcppArmadillo. Here are the results:
http://pastebin.com/cp29bBDJ
.libPaths()
[1] "/Library/Frameworks/R.framework/Versions/3.0/Resources/library"
require(devtools)
Loading required package: devtools
has_devel()
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD SHLIB
foo.c
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -fPIC "-mtune=native -g -O2 -Wall -pedantic
-Wconversion" -c foo.c -o foo.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -L/usr/local/lib -o foo.so foo.o
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
-L/Library/Frameworks/R.framework/Resources/lib -lRlapack
-L/Library/Frameworks/R.framework/Resources/lib -lRblas -lgfortran
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
[1] TRUE
Simple things work, though:
require("Rcpp")
Loading required package: Rcpp
evalCpp("1+1")
[1] 2
Please let me know if I forgot to include relevant information.
I would greatly appreciate any pointers in the right direction. Thank
you for your help.
Michael Cone
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