[R-SIG-Mac] plier source compilation error related to dylib

[S Kong]

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 12:59 PM, Simon Urbanek wrote:

> 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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