[R] installing package 'kinship'

[Prof Brian Ripley]

Please read the posting guide, and do tell us what OS this is.

I can guess it is MacOS X, an OS on which quite a number of packages do
not compile.  You need to change coxfit6.h to have the object extern in
all but one of the files it is included in.  That is a peculiarity of
MacOS X.


On Mon, 18 Oct 2004, Katalin  Csillery wrote:

> 
> 
> 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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> 
> 

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595