[R-SIG-Mac] JGR on Mac OS X 10.6 (Snow Leopard)

Erich Neuwirth erich.neuwirth at univie.ac.at
Sun Sep 13 10:52:35 CEST 2009


Thanks for the hints.
It turns out that the part I originally missed was
> install.packages("JGR",type="mac.binary")

which I had never used before.
Now, getting more adventurous, I am trying to build the gmp package
in R64.

 > install.packages("gmp",type="mac.binary")
....

 > library(gmp)
Error: package 'gmp' is not installed for 'arch=x86_64'

So I am trying to build the package
I downloaded gmp from gmplig.org and it compiled and passed all the  
tests.
The output alsi indicated that it compiled a 64bit version.
Now for the R build:

Mini:devel neuwirth$ sudo R CMD INSTALL gmp_0.4-10.tar.gz
* Installing to library ‘/Library/Frameworks/R.framework/Resources/ 
library’
* Installing *source* package ‘gmp’ ...
creating cache ./config.cache
checking for __gmpz_ui_sub in -lgmp... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c apply.cc -o apply.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c biginteger.cc -o  
biginteger.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigintegerR.cc -o  
bigintegerR.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigmod.cc -o  
bigmod.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigrational.cc -o  
bigrational.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigrationalR.cc -o  
bigrationalR.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigvec.cc -o  
bigvec.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigvec_q.cc -o  
bigvec_q.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c extract_matrix.cc - 
o extract_matrix.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c factor.cc -o  
factor.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c matrix.cc -o  
matrix.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c matrixq.cc -o  
matrixq.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c solve.cc -o solve.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names - 
undefined dynamic_lookup -single_module -multiply_defined suppress -L/ 
usr/local/lib -o gmp.so apply.o biginteger.o bigintegerR.o bigmod.o  
bigrational.o bigrationalR.o bigvec.o bigvec_q.o extract_matrix.o  
factor.o matrix.o matrixq.o solve.o -L/usr/local/lib/ -lgmp -F/Library/ 
Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: in /usr/local/lib/libgmp.dylib, file is not of required  
architecture
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  >>> Building/Updating help pages for package 'gmp'
      Formats: text html latex example
   Oakley                            text    html    latex   example
   add.biginteger                    text    html    latex   example
   apply                             text    html    latex   example
   biginteger                        text    html    latex   example
   biginteger.rand                   text    html    latex   example
   bigrational                       text    html    latex   example
   comp.biginteger                   text    html    latex   example
   comp.bigq                         text    html    latex   example
   cumsum                            text    html    latex   example
   extract                           text    html    latex   example
   extract.bigq                      text    html    latex   example
   extreme                           text    html    latex   example
   factor                            text    html    latex   example
   fibonacci                         text    html    latex   example
   gcd                               text    html    latex   example
   gcdex                             text    html    latex   example
   isprime                           text    html    latex   example
Note: removing empty section \examples in file 'matrix.Rd'
   matrix                            text    html    latex
   modulus                           text    html    latex   example
   nextprime                         text    html    latex   example
   operators_bigq                    text    html    latex   example
   powm                              text    html    latex   example
   sizeinbase                        text    html    latex   example
   solve                             text    html    latex   example
** building package indices ...
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared library '/Library/Frameworks/R.framework/ 
Resources/library/gmp/libs/i386/gmp.so':
   dlopen(/Library/Frameworks/R.framework/Resources/library/gmp/libs/ 
i386/gmp.so, 6): Symbol not found: ___gmpq_add
   Referenced from: /Library/Frameworks/R.framework/Resources/library/ 
gmp/libs/i386/gmp.so
   Expected in: flat namespace
  in /Library/Frameworks/R.framework/Resources/library/gmp/libs/i386/ 
gmp.so
Warning in eval(expr, envir, enclos) :
   Data for RFC 2409 Oakley groups requires package 'gmp'
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared library '/Library/Frameworks/R.framework/ 
Resources/library/gmp/libs/i386/gmp.so':
   dlopen(/Library/Frameworks/R.framework/Resources/library/gmp/libs/ 
i386/gmp.so, 6): Symbol not found: ___gmpq_add
   Referenced from: /Library/Frameworks/R.framework/Resources/library/ 
gmp/libs/i386/gmp.so
   Expected in: flat namespace
  in /Library/Frameworks/R.framework/Resources/library/gmp/libs/i386/ 
gmp.so
Warning in eval(expr, envir, enclos) :
   Data for RFC 2409 Oakley groups requires package 'gmp'
* DONE (gmp)
Mini:devel neuwirth$



trying to do 'library(gmp)' in R64 then produces
 > library(gmp)
Error: package 'gmp' is not installed for 'arch=x86_64'
again, therefore I tried

Mini:devel neuwirth$ R_ARCH=x86_64 sudo R CMD INSTALL --libs-only  
gmp_0.4-10.tar.gz
and this produced the following output

* Installing to library ‘/Library/Frameworks/R.framework/Resources/ 
library’
* Installing *source* package ‘gmp’ ...
creating cache ./config.cache
checking for __gmpz_ui_sub in -lgmp... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c apply.cc -o apply.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c biginteger.cc -o  
biginteger.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigintegerR.cc -o  
bigintegerR.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigmod.cc -o  
bigmod.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigrational.cc -o  
bigrational.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigrationalR.cc -o  
bigrationalR.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigvec.cc -o  
bigvec.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c bigvec_q.cc -o  
bigvec_q.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c extract_matrix.cc - 
o extract_matrix.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c factor.cc -o  
factor.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c matrix.cc -o  
matrix.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c matrixq.cc -o  
matrixq.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include  
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ 
include/   -I/usr/local/include    -fPIC  -g -O2 -c solve.cc -o solve.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names - 
undefined dynamic_lookup -single_module -multiply_defined suppress -L/ 
usr/local/lib -o gmp.so apply.o biginteger.o bigintegerR.o bigmod.o  
bigrational.o bigrationalR.o bigvec.o bigvec_q.o extract_matrix.o  
factor.o matrix.o matrixq.o solve.o -L/usr/local/lib/ -lgmp -F/Library/ 
Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: in /usr/local/lib/libgmp.dylib, file is not of required  
architecture
* DONE (gmp)
Mini:devel neuwirth$


What am I doing wrong here. My guess is that I am still getting some  
switches wrong.







On Sep 13, 2009, at 1:59 AM, Simon Urbanek wrote:

> To answer all those recent posts on both mailing lists regarding JGR  
> on OS X 10.6 (Snow Leopard):
> 2) install necessary packages as follows:
> install.packages(c("rJava","JavaGD","iplots"))
> install.packages("JGR",type="mac.binary")



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