plier source compilation error related to dylib

Dear Simon

This is what I get from the screen. Is there a way to specify the  
library directory

[Quad:~/Desktop/pliersrc] skong% ls
affy_ptr.h      affyheapsort.h  affyplier.cpp   affyplier.h      
error.h         iaffyplier.h    plier_impl.cpp  plieralg.cpp     
plieralg.h      rwrapper.cpp
[Quad:~/Desktop/pliersrc] skong% R64 CMD SHLIB affyplier.cpp  
plieralg.cpp plier_impl.cpp rwrapper.cpp
g++ -no-cpp-precomp -I/usr/local/lib64/R/include  -I/usr/local/ 
include   -fno-common  -arch ppc64 -m64 -mcpu=G5 -mtune=G5 -mpowerpc- 
gpopt -force_cpusubtype_ALL -c affyplier.cpp -o affyplier.o
g++ -no-cpp-precomp -I/usr/local/lib64/R/include  -I/usr/local/ 
include   -fno-common  -arch ppc64 -m64 -mcpu=G5 -mtune=G5 -mpowerpc- 
gpopt -force_cpusubtype_ALL -c plieralg.cpp -o plieralg.o
plieralg.cpp:30:20: error: malloc.h: No such file or directory
make: *** [plieralg.o] Error 1
[Quad:~/Desktop/pliersrc] skong%

Then I modified the plieralg.cpp

from
#include <malloc.h>

to
#include <stdlib.h>

After changing one line,

[Quad:~/Desktop/pliersrc] skong% R64 CMD SHLIB affyplier.cpp  
plieralg.cpp plier_impl.cpp rwrapper.cpp
g++ -no-cpp-precomp -I/usr/local/lib64/R/include  -I/usr/local/ 
include   -fno-common  -arch ppc64 -m64 -mcpu=G5 -mtune=G5 -mpowerpc- 
gpopt -force_cpusubtype_ALL -c plieralg.cpp -o plieralg.o
g++ -no-cpp-precomp -I/usr/local/lib64/R/include  -I/usr/local/ 
include   -fno-common  -arch ppc64 -m64 -mcpu=G5 -mtune=G5 -mpowerpc- 
gpopt -force_cpusubtype_ALL -c plier_impl.cpp -o plier_impl.o
g++ -no-cpp-precomp -I/usr/local/lib64/R/include  -I/usr/local/ 
include   -fno-common  -arch ppc64 -m64 -mcpu=G5 -mtune=G5 -mpowerpc- 
gpopt -force_cpusubtype_ALL -c rwrapper.cpp -o rwrapper.o
g++ -bundle -flat_namespace -undefined suppress -m64 -L/usr/local/lib  
-L/usr/local/lib64/R/lib -o affyplier.so affyplier.o plieralg.o  
plier_impl.o rwrapper.o   -L/usr/local/lib64/R/lib -lR
ld64 warning: indirect library libgfortran.0.dylib could not be  
loaded: file not found: libgfortran.0.dylib
ld64 warning: indirect library libgcc_s.1.0.dylib could not be  
loaded: file not found: libgcc_s.1.0.dylib
ld64 warning: indirect library libreadline.5.dylib could not be  
loaded: file not found: libreadline.5.dylib
[Quad:~/Desktop/pliersrc] skong%


Also I attached the codes I used.

Thank you very much for the helps!!!
-S


?

On Apr 20, 2006, at 12:47 PM, S Kong wrote:

Hello, I was trying to install BioConductor plier package under  
R64 of Simon's.  ( Quad G5 + 10.4.6 + Xcode 2.2.1 + powerpc-apple- 
darwin8-gcc-4.0.1) The plier package is an expression index  
calculation algorithm for  Affymetrix microarray In the end, I  
gave up with the BioConductor plier package and started with  
Affymetrix plier source code to build .so. But errors were that  
dylib could not be found for libgfortran.0.dylib,  ibgcc_s. 
1.0.dylib, and libreadline.5.dylib. Those dylib are located at / 
usr/local/lib64/R/lib/
Could anyone help me with this?
Thanks!!!

% R64 CMD SHLIB affyplier.cpp plieralg.cpp plier_impl.cpp  
rwrapper.cpp
g++ -bundle -flat_namespace -undefined suppress -m64 -L/usr/local/lib
-L/usr/local/lib64/R/lib -o affyplier.so affyplier.o plieralg.o
plier_impl.o rwrapper.o   -L/usr/local/lib64/R/lib -lR
ld64 warning: in affyplier.o, file does not contain requested
architecture

^^^- this is the actual error - it seems that something went wrong  
during the compilation, but you omitted that part, so we can't see  
what that was. Please send me the full output of the build process.

Cheers,
Simon

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