Re: [Rd] lme4 install, was Re: [R] Which executable is associated with R CMD INSTALL?

From: Douglas Bates <bates_at_stat.wisc.edu>
Date: Mon 06 Nov 2006 - 15:56:37 GMT

On 06 Nov 2006 15:41:11 +0100, Peter Dalgaard <p.dalgaard@biostat.ku.dk> wrote:
> "Douglas Bates" <bates@stat.wisc.edu> writes:
>
> > On 31 Oct 2006 12:05:21 +0100, Peter Dalgaard <p.dalgaard@biostat.ku.dk> wrote:
> > >
> > > [move to r-devel, put maintainer in loop]
> > >
> > > Patrick Connolly <p_connolly@ihug.co.nz> writes:
> > >
> > > > On Mon, 30-Oct-2006 at 04:44PM -0500, Duncan Murdoch wrote:
> > > >
> > > >
> > > > |> Try "R CMD printenv R_HOME" and you'll find which R home directory it is
> > > > |> using. You can see a lot more with "R CMD printenv" or various options
> > > > |> to "R CMD config".
> > > >
> > > > Thanks for that information. It knocks my theory on the head. Pity
> > > > that, because I might have been able to do something about it if that
> > > > was the problem. Now I'm at a loss to work out why lme4 installation
> > > > cannot find Matrix, and more strangely, why nothing else gave a
> > > > similar problem. I think I've tried every version of lme4 and Matrix
> > > > that has emerged since R-2.4.0 has been released.
> > > >
> > > > The fact that no other Red hat user has a problem indicates the
> > > > problem is this end; but I'm short of ideas about where to look.
> > > > Looks like it's back to versions 6 months old -- like proprietary
> > > > software users have to put up with. :-(
> > >
> > > Hmmm, I can provoke this on SUSE too (I was going to ask you to try
> > > this!):
> > >
> > > mkdir foo
> > > MY_R=~/misc/r-release-branch/BUILD/bin/R
> > > R_LIBS=foo $MY_R --vanilla << EOF
> > > options(repos=c(CRAN="http://cran.dk.r-project.org"))
> > > install.packages("lme4", depend=TRUE)
> > > EOF
> > >
> > > This installs Matrix alright, then dies with
> ........
> > > And Matrix.h is sitting happily in foo/Matrix/include/ but obviously
> > > not getting included. Should there have been a copy inside lme4?
> >
> > Not according to my understanding of how the "LinkingTo:"
> > specification in the DESCRIPTION file is to work.
>
> Kurt pointed out the real reason: Using a relative path for R_LIBS was
> asking for trouble.
>
> So it was my own fault, I just got blinded by seeing symptoms so
> close to those reported by Patrick.

Thanks for the clarification.

However, I think it exposes a problem with R CMD INSTALL. If there is a LinkingTo: directive in the DESCRIPTION file and the package's include directory cannot be found I think that R CMD INSTALL should abort.



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