[R] installing package 'kinship'

[Prof Brian Ripley]

On Tue, 19 Oct 2004, Katalin  Csillery wrote:

> 
> Thanks for getting back to me.
> My version is OS 10.3.5, I use X11 and ess.
> Could you please advise me exactly how do I need to change my coxfit6.h
> file? 

Ask someone who knows for sure about the peculiar features of MacOS X.

> How should I install the modified package? I don't know how to use
> 'install.packages' when the package I want to istall has actually been
> downloaded to me computer.

The help page says:

See Also:

     'INSTALL', 'REMOVE', 'library', '.packages', 'read.dcf'

so please do ?INSTALL (or read the `Installation and Administration 
Manual').


> 
> Thanks in advance,
> Kati
> 
> On Mon, 18 Oct 2004, Prof Brian Ripley wrote:
> 
> > Date: Mon, 18 Oct 2004 15:54:16 +0100 (BST)
> > From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
> > To: Katalin  Csillery <csillery at selway.umt.edu>
> > Cc: R-help <R-help at stat.math.ethz.ch>
> > Subject: Re: [R] installing package 'kinship'
> > 
> > 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
> > > 
> > > ______________________________________________
> > > R-help at stat.math.ethz.ch mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
> > > 
> > > 
> > 
> > -- 
> > 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
> > 
> > 
> 
> 
> 

-- 
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