From p.dalgaard at biostat.ku.dk  Tue Oct 31 12:05:21 2006
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 31 Oct 2006 12:05:21 +0100
Subject: [Rd] lme4 install,
	was Re: [R] Which executable is associated with R CMD INSTALL?
In-Reply-To: <20061031091759.GB3676@ihug.co.nz>
References: <20061030193251.GA3676@ihug.co.nz> <4546725A.7000905@stats.uwo.ca>
	<20061031091759.GB3676@ihug.co.nz>
Message-ID: <x24ptkyccu.fsf_-_@viggo.kubism.ku.dk>


[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

Warning in install.packages("lme4", depend = TRUE) :
         argument 'lib' is missing: using foo
trying URL 'http://cran.dk.r-project.org/src/contrib/lme4_0.9975-8.tar.gz'
Content type 'application/x-tar' length 235617 bytes
opened URL
==================================================
downloaded 230Kb

* Installing *source* package 'lme4' ...
** libs

gcc -I/usr/local/src/pd/r-release-branch/BUILD/include
  -I/usr/local/src/pd/r-release-branch/BUILD/include
  -I/usr/local/include -fpic -g -O2 -std=gnu99 -c Wishart.c -o Wishart.o

In file included from Wishart.h:4,
                 from Wishart.c:1:
lme4_utils.h:9:20: Matrix.h: No such file or directory
In file included from Wishart.h:4,
                 from Wishart.c:1:
lme4_utils.h:25: error: syntax error before "c"
lme4_utils.h:25: warning: type defaults to `int' in declaration of `c'
lme4_utils.h:25: warning: data definition has no type or storage class
lme4_utils.h:163: error: syntax error before "cholmod_factor"
lme4_utils.h:177: error: syntax error before "cholmod_factor"
make: *** [Wishart.o] Error 1
ERROR: compilation failed for package 'lme4'

And Matrix.h is sitting happily in foo/Matrix/include/ but obviously
not getting included. Should there have been a copy inside lme4?

What is not obvious to me is how this can work anywhere...

I also tried unpacking the lme4 directory from its tarball, dropping
all files from the Matrix installed include dir into lme4/src and then

$MY_R CMD INSTALL -l foo lme4

but no go

gcc -shared -L/usr/local/lib64 -o lme4.so Matrix_stubs.o Wishart.o
glmer.o init.o lme4_utils.o lmer.o local_stubs.o pedigree.o
-L/usr/local/src/pd/r-release-branch/BUILD/lib -lRlapack
-L/usr/local/src/pd/r-release-branch/BUILD/lib -lRblas -lg2c -lm
-lgcc_s

local_stubs.o(.text+0x0): In function `M_numeric_as_chm_dense':
/home/bs/pd/tmp/lme4/src/Matrix_stubs.c:420: multiple definition of `M_numeric_as_chm_dense'
Matrix_stubs.o(.text+0x0):/home/bs/pd/tmp/lme4/src/Matrix_stubs.c:420: first defined here

local_stubs.o(.text+0x70): In function `M_dpoMatrix_chol':
/home/bs/pd/tmp/lme4/src/Matrix_stubs.c:412: multiple definition of `M_dpoMatrix_chol'
Matrix_stubs.o(.text+0x70):/home/bs/pd/tmp/lme4/src/Matrix_stubs.c:412: first defined here
..etc..

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




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