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

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Mon 06 Nov 2006 - 14:41:11 GMT

"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.

-- 
   O__  ---- Peter Dalgaard             Ă˜ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)                  FAX: (+45) 35327907

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