building R package

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Guillaume,

although your package may be ok, your system is not. You have  
apparently broken libraries in /usr/local/lib that override your  
system libraries and thus cause your package to fail to build (from  
the output it's at least libstdc++). This is likely from some broken  
local compiler installations. I strongly recommend removing all 3rd  
party compilers, especially from /usr/local, and install only the GNU  
Fortran that R supplies (if needed).

Cheers,
Simon

Hi all !

I just installed Mac OS X 10.5.1 on my Intel MacBook Pro. Since I  
have my
personal packages that I build and modify every so often I also  
installed
Xcode 3. My packages contain either some C code, some Fortran code  
or both.

However, I can not build a binary of my package, which I know to be
error-free since they were running without any bugs when I was  
running Tiger
(Mac OS 10.4.11).

The message that is sent to me when I launch the command "R CMD build
--binary AEM" (AEM being the name of my package) in the terminal is:

macintosh:AEM Package ti-guiblanc$ R CMD build --binary AEM
* checking for file 'AEM/DESCRIPTION' ... OK
* preparing 'AEM':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
/var/folders/+5/+5Ch2A6BEb4+iULWkg5XEU+++TI/-Tmp-/Rinst965351719
* Installing *source* package 'AEM' ...
** libs
** arch - i386
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    - 
fPIC
-g -O2 -march=nocona -c buildbinary.c -o buildbinary.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -dynamiclib
-Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 - 
undefined
dynamic_lookup -single_module -multiply_defined suppress -L/usr/ 
local/lib -o
AEM.so buildbinary.o   -F/Library/Frameworks/R.framework/.. - 
framework R
ld: warning, duplicate dylib
/Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libgcc_s.1.dylib
** arch - ppc
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc
-I/usr/local/include    -fPIC  -g -O2 -c buildbinary.c -o  
buildbinary.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -dynamiclib
-Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 - 
undefined
dynamic_lookup -single_module -multiply_defined suppress -L/usr/ 
local/lib -o
AEM.so buildbinary.o   -F/Library/Frameworks/R.framework/.. - 
framework R
ld: warning, duplicate dylib
/Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libgcc_s.1.dylib
ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libstdc++. 
6.dylib, file
is not of required architecture
collect2: ld returned 1 exit status
make: *** [AEM.so] Error 1
chmod:
/var/folders/+5/+5Ch2A6BEb4+iULWkg5XEU+++TI/-Tmp-/Rinst965351719/AEM/ 
libs/ppc/*:
No such file or directory
ERROR: compilation failed for package 'AEM'
** Removing
'/var/folders/+5/+5Ch2A6BEb4+iULWkg5XEU+++TI/-Tmp-/Rinst965351719/AEM'
ERROR
* installation failed

My knowledge of the UNIX code and the terminal is limited, so please  
be
gentle !

Thanks in advance for any help.

Have a nice day !

Guillaume Blanchet
PhD. candidate
University of Alberta

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