[R] installing package 'kinship'

Katalin Csillery csillery at selway.umt.edu
Mon Oct 18 16:18:55 CEST 2004



Dear All,

I have problem installing the 'kinship' package. I used the
'install.packages' from R command line and had no problem installing other
packages before.
Here is what I get:

* Installing *source* package 'kinship' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c agfit6b.c -o agfit6b.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c bdsmatrix_index1.c -o
bdsmatrix_index1.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c bdsmatrix_index2.c -o
bdsmatrix_index2.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c bdsmatrix_index3.c -o
bdsmatrix_index3.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c bdsmatrix_prod.c -o
bdsmatrix_prod.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c bdsmatrix_prod2.c -o
bdsmatrix_prod2.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c bdsmatrix_prod3.c -o
bdsmatrix_prod3.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c chinv4.c -o chinv4.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c chinv5.c -o chinv5.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c cholesky4.c -o cholesky4.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c cholesky5.c -o cholesky5.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c chsolve4.c -o chsolve4.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c chsolve5.c -o chsolve5.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c coxfit6a.c -o coxfit6a.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c coxfit6b.c -o coxfit6b.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c coxfit6c.c -o coxfit6c.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c gchol.c -o gchol.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include   -fno-common  -g -O2 -c gchol_bds.c -o gchol_bds.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
kinship.so agfit6b.o bdsmatrix_index1.o bdsmatrix_index2.o
bdsmatrix_index3.o bdsmatrix_prod.o bdsmatrix_prod2.o bdsmatrix_prod3.o
chinv4.o chinv5.o cholesky4.o cholesky5.o
chsolve4.o chsolve5.o coxfit6a.o coxfit6b.o coxfit6c.o gchol.o gchol_bds.o
-lcc_dynamic -framework R
ld: multiple definitions of symbol _coxfit6
agfit6b.o definition of _coxfit6 in section (__DATA,__common)
coxfit6a.o definition of _coxfit6 in section (__DATA,__common)
coxfit6b.o definition of _coxfit6 in section (__DATA,__common)
coxfit6c.o definition of _coxfit6 in section (__DATA,__common)
make: *** [kinship.so] Error 1
ERROR: compilation failed for package 'kinship'
** Removing
'/Library/Frameworks/R.framework/Versions/1.9.1/Resources/library/kinship'

Thanks for your help in advance, 
Kati




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