[Rcpp-devel] Rcpp and RcppArmadillo errors on OSX Mavericks

[Romain Francois]

Le 04/11/2013 15:43, Michael Cone a écrit :
> 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.

This is not an unfortunate error. The transition is not as smooth as it 
ought to be. Partly due to Apple, partly due to R.

> 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.

Did you compile Rcpp from source ? If not then you are using Rcpp from 
cran that was built with another compiler (gcc 4.2 or an llvm emulation 
of it).

Judging from what I see below, it is likely to be the extent of the 
problem.

Romain

> 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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-- 
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30