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[Rcpp-devel] setup RcppArmadillo for osx maverick 10.9.2

3 messages · Modibo Sidibe, Ahmadou Dicko, Dirk Eddelbuettel

Original
Modibo Sidibe
# 
Hi All, 

I am slowly switching to Rcpp (what a wonderful tool!).. The classic Rcpp works fine.. but when I try to run a code with RccpArmadillo, I get the following error.. 

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I"/Users/ms486/Library/R/3.1/library/Rcpp/include" -I"/Users/ms486/Library/R/3.1/library/RcppArmadillo/include"    -fPIC  -Wall -mtune=core2 -g -O2  -c test2.cpp -o test2.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o sourceCpp_40346.so test2.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation 
Error in sourceCpp("test2.cpp") : 
  Error 1 occurred building shared library.
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_40346.so] Error 1

Here is the outcome of the Rsession

R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Rcpp_0.11.1

loaded via a namespace (and not attached):
[1] parallel_3.1.0          RcppArmadillo_0.4.200.0 tools_3.1.0  

Thanks for your help!
Ahmadou Dicko
# 
Indeed Rcpp is really awesome.

I have some questions :
 - Can we have access to your example (test2.cpp) ?
 - Which version of clang do you use ?

And finally what is the output of the following code :

library(Rcpp)
library(RcppArmadillo)

cppFunction(code =
            'arma::mat armatrans(arma::mat A) {
             return arma::trans(A);
         }', depends = "RcppArmadillo")

armatrans(matrix(1:6, ncol = 3))
##      [,1] [,2]
## [1,]    1    2
## [2,]    3    4
## [3,]    5    6


Now if this code doesn't work you also check if you have a working fortran
compiler (e.g http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2),
you will have more info at
http://cran.r-project.org/doc/manuals/R-admin.html#Mavericks
You can finally try to search the
R-sig-mac<https://stat.ethz.ch/mailman/listinfo/r-sig-mac>archives
too, you will probably find some intersting threads.

Hope it helps
On Sun, Apr 27, 2014 at 3:47 AM, Modibo Sidibe <sidibe.modibo at gmail.com>wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
Ahmadou,

Thanks so much for the follow-up!  As I don't use OS X, I am mostly a
bystander on these usage questions.

        
On 27 April 2014 at 06:47, Ahmadou Dicko wrote:

        
| 
|     I am slowly switching to Rcpp (what a wonderful tool!).. The classic Rcpp
|     works fine.. but when I try to run a code with RccpArmadillo, I get the
|     following error..
| 
| 
| Indeed Rcpp is really awesome.
| 
| I have some questions :
| ?- Can we have access to your example (test2.cpp) ?
| ?- Which version of clang do you use ?
| 
| And finally what is the output of the following code :
| 
| library(Rcpp)
| library(RcppArmadillo)
| 
| cppFunction(code =
| ??????????? 'arma::mat armatrans(arma::mat A) {
| ???????????? return arma::trans(A);
| ???????? }', depends = "RcppArmadillo")
| 
| armatrans(matrix(1:6, ncol = 3))
| ##????? [,1] [,2]
| ## [1,]??? 1??? 2
| ## [2,]??? 3??? 4
| ## [3,]??? 5??? 6
| 
| 
| Now if this code doesn't work you also check if you have a working fortran
| compiler (e.g http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2),
| you will have more info at? http://cran.r-project.org/doc/manuals/R-admin.html#
| Mavericks

All excellent points and straigth to the core of the issue.  There is no
fundamental problem but one needs to get one's ducks into a neat row.  [1] 

| You can finally try to search the R-sig-mac archives too, you will probably
| find some intersting threads.

And even then it seems confusing. I had an (unrelated, different package,
simply using Rcpp too) report on RQuantLib not loading and pointed to Brian
Ripley's recent post 

   http://article.gmane.org/gmane.comp.lang.r.mac/8675

which also indicated that some 3rd party libraries need a rebuild for
Mavericks before binary packages can work:

  Some of the Mavericks binary packages are missing for good reason.  The 
  C++ binary interface for the Xcode 5.x compilers in Mavericks is 
  completely different, so external software has to be compiled with those 
  compilers.  This affects CRAN packages

  RQuantlib RProtoBuf RVowalWabbit rgdal rjags rzmq

I maintain the first three, if someone wants to help ... maybe contact me
off-list? [ And the third ships its own library code, so Brian Ripley would
appear to be wrong here. ]
 
| Hope it helps

Sure did. Thanks again.

Dirk
 
[1] Which to me as a non-user of OS X still seems harder than on other OS's
but whenever I say that I get yelled at by the most vocal OS X fanboys so I
try not to mention it too often :)
 
| ?
| 
|

        
| On Sun, Apr 27, 2014 at 3:47 AM, Modibo Sidibe <sidibe.modibo at gmail.com> wrote:

        
| 
|     Hi All,
| 
|     I am slowly switching to Rcpp (what a wonderful tool!).. The classic Rcpp
|     works fine.. but when I try to run a code with RccpArmadillo, I get the
|     following error..
| 
|     clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG ?-I/
|     usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include ?-I"/
|     Users/ms486/Library/R/3.1/library/Rcpp/include" -I"/Users/ms486/Library/R/
|     3.1/library/RcppArmadillo/include" ? ?-fPIC ?-Wall -mtune=core2 -g -O2 ?-c
|     test2.cpp -o test2.o clang++ -dynamiclib -Wl,-headerpad_max_install_names
|     -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/
|     local/lib -o sourceCpp_40346.so test2.o -L/Library/Frameworks/R.framework/
|     Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib
|     -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran
|     -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R
|     -Wl,-framework -Wl,CoreFoundation
|     Error in sourceCpp("test2.cpp") :
|     ? Error 1 occurred building shared library.
|     ld: warning: directory not found for option '-L/usr/local/lib/gcc/
|     x86_64-apple-darwin13.0.0/4.8.2'
|     ld: library not found for -lquadmath
|     clang: error: linker command failed with exit code 1 (use -v to see
|     invocation)
|     make: *** [sourceCpp_40346.so] Error 1
| 
|     Here is the outcome of the Rsession
| 
|     R version 3.1.0 (2014-04-10)
|     Platform: x86_64-apple-darwin13.1.0 (64-bit)
| 
|     locale:
|     [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
| 
|     attached base packages:
|     [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
| 
|     other attached packages:
|     [1] Rcpp_0.11.1
| 
|     loaded via a namespace (and not attached):
|     [1] parallel_3.1.0 ? ? ? ? ?RcppArmadillo_0.4.200.0 tools_3.1.0
| 
|     Thanks for your help!
|     _______________________________________________
|     Rcpp-devel mailing list
|     Rcpp-devel at lists.r-forge.r-project.org
|     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
| 
| 
| 
| 
| --
| Ahmadou H. DICKO
| statistician economist (Ing?nieur Statisticien ?conomiste)
| PhD candidate in Climate change economics
| Faculty of economics and managment - Cheikh Anta Diop University
| West African Science Service Center on Climate Change and Adaptated Land Use
| (WASCAL)
| Center for Development Research (ZEF) - University of Bonn
| email : ahmadou.dicko at ucad.edu.sn
| twitter : @dickoah
| github : github/dickoa
| tel : +221 33 827 55 16
| portable: +221 77 123 81 69
| 
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