[R-SIG-Mac] kinship

[Andrew Beckerman]

Dear all -

OS 10.4.2, R 2.2.0 + Tcltk and Fortran

I am trying to install the package "kinship", only available through  
source.  The package seems to do well until the very end, where a  
multiple definitions error crops up (see below).   A previous post  
and response from B. Ripley suggested the following:

"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."

Any advice on how to accomplish this?  Is it in the works with  
regards to packaging a binary?

Cheers
andrew

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tar: Read 3584 bytes from -
* Installing *source* package 'kinship' ...
** libs
gcc-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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-3.3 -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

The downloaded packages are in
     /private/tmp/RtmpUlQDSt/downloaded_packages
gcc-3.3 -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 -F/Library/Frameworks/R.framework/.. - 
framework R
** Removing '/Library/Frameworks/R.framework/Versions/2.2/Resources/ 
library/kinship'
ld: multiple definitions of symbol _c6
agfit6b.o definition of _c6 in section (__DATA,__common)
coxfit6a.o definition of _c6 in section (__DATA,__common)
coxfit6b.o definition of _c6 in section (__DATA,__common)
coxfit6c.o definition of _c6 in section (__DATA,__common)
ld: can't locate file for: -lcc_dynamic
make: *** [kinship.so] Error 1
ERROR: compilation failed for package 'kinship'

------------------------------------------------------------------------ 
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Dr. Andrew Beckerman
Department of Animal and Plant Sciences, University of Sheffield,
Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
ph +44 (0)114 222 0026; fx +44 (0)114 222 0002
http://www.shef.ac.uk/beckslab
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