From bates at stat.wisc.edu  Mon Nov  6 16:56:37 2006
From: bates at stat.wisc.edu (Douglas Bates)
Date: Mon, 6 Nov 2006 09:56:37 -0600
Subject: [Rd] lme4 install,
	was Re: [R] Which executable is associated with R CMD INSTALL?
In-Reply-To: <x2wt68y6wo.fsf@viggo.kubism.ku.dk>
References: <20061030193251.GA3676@ihug.co.nz> <4546725A.7000905@stats.uwo.ca>
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	<x24ptkyccu.fsf_-_@viggo.kubism.ku.dk>
	<40e66e0b0611060629q4d431b64w4b866aada55c0a80@mail.gmail.com>
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Message-ID: <40e66e0b0611060756n38bc5e85w2f2bd6fdb52cf5e1@mail.gmail.com>

On 06 Nov 2006 15:41:11 +0100, Peter Dalgaard <p.dalgaard at biostat.ku.dk> wrote:
> "Douglas Bates" <bates at stat.wisc.edu> writes:
>
> > On 31 Oct 2006 12:05:21 +0100, Peter Dalgaard <p.dalgaard at biostat.ku.dk> wrote:
> > >
> > > [move to r-devel, put maintainer in loop]
> > >
> > > Patrick Connolly <p_connolly at 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.



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