[R-SIG-Mac] building R package

[Simon Urbanek]

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


On Jan 14, 2008, at 10:42 PM, Guillaume Blanchet wrote:

> 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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>
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