[R] compiling gap on mac os x

From: Kenny Ye <kye_at_aecom.yu.edu>
Date: Fri 24 Jun 2005 - 04:19:50 EST


Hi, I am having trouble compiling package gap http://www.hgmp.mrc.ac.uk/~jzhao/r-progs.htm on Tiger. I have installed XcodeTools 2.1. The binary version of gap currently available on CRAN has some bug and is fixed in the latest version.

The message I get from R is below. Any help is greatly appreciated.

best regards,

Kenny Ye

tar: Read 1536 bytes from -
* Installing *source* package 'gap' ...
** libs
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c 2k.c -o 2k.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c 2ld.c -o 2ld.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c cline.c -o cline.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c gc.c -o gc.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c gcontrol.c -o gcontrol.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c gif.c -o gif.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c hap.c -o hap.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c hwe.hardy.c -o hwe.hardy.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c kin.morgan.c -o kin.morgan.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c makeped.c -o makeped.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c mia.c -o mia.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c muvar.c -o muvar.o
g77 -fno-common -g -O2 -c pfc.f -o pfc.o g77 -fno-common -g -O2 -c pfc.sim.f -o pfc.sim.o gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c pgc.c -o pgc.o
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c whscore.c -o whscore.o
gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o gap.so 2k.o 2ld.o cline.o gc.o gcontrol.o gif.o hap.o hwe.hardy.o kin.morgan.o makeped.o mia.o muvar.o pfc.o pfc.sim.o pgc.o whscore.o
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -lg2c -lSystem
-framework R
** Removing
'/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library/gap'

    npackage installation failed
ld: warning multiple definitions of symbol _i1mach_ pfc.sim.o definition of _i1mach_ in section (__TEXT,__text) /Library/Frameworks/R.framework/R(i1mach.lo) definition of _i1mach_ ld: 2ld.o has external relocation entries in non-writable section (__TEXT,__text) for symbols:
restFP
saveFP
make: *** [gap.so] Error 1
ERROR: compilation failed for package 'gap' ** Restoring previous
'/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library/gap' ** Removing
'/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library/pathmix' ** Removing
'/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library/pointer'



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