Installing current version of lme4 and Matrix on a mac

Hrm.  Well, I just tried that, but got the following output

Warning in install.packages("lme4", repos = "http://R-Forge.R-project.org
") :
  argument 'lib' is missing: using '/Users/jearbear/R/powerpc-apple-
darwin8.10.1-library/2.7'
Warning: unable to access index for repository http://R-Forge.R-project.org/bin/macosx/universal/contrib/2.7
Warning message:
package ?lme4? is not available


This might be a versioning issue (I installed 2.7 the other day -
maybe I should go back!) but,  what is up with the argument lib being
missing?  Odd...

I also had an odd error when installing Matrix from source

* Installing *source* package 'Matrix' ...
** libs
** arch - ppc
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/
Resources/include -I/Library/Frameworks/R.framework/Resources/include/
ppc  -I/usr/local/include   -I./UFconfig -fPIC  -g -O2 -c CHMfactor.c -
o CHMfactor.o
cc1: error: invalid option ?macosx-version-min=10.4?
make: *** [CHMfactor.o] Error 1
ERROR: compilation failed for package 'Matrix'
** Removing '/Users/jearbear/R/powerpc-apple-darwin8.10.1-library/2.7/
Matrix'

The downloaded packages are in
	/private/tmp/RtmpLqlbKP/downloaded_packages
Warning message:
In install.packages("Matrix", repos = "http://R-Forge.R-project.org",  :
  installation of package 'Matrix' had non-zero exit status

What's up with the cc1 error?

Suggestions?

On Apr 24, 2008, at 5:57 PM, Steven McKinney wrote:

Hi Jarrett,

I was able to install the R-forge lme4 and Matrix
packages by invoking R from a Terminal window
(I used $ sudo R
so the process would have enough privileges
to modify directories in the library)


 Dapple:~/Rtest stevenmckinney$ sudo R
 Password:

 R version 2.6.2 (2008-02-08)
 Copyright (C) 2008 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0


I installed lme4 alright with the suggested command
from http://r-forge.r-project.org/R/?group_id=60

install.packages("lme4",repos="http://R-Forge.R-project.org")

 trying URL 'http://R-Forge.R-project.org/bin/macosx/universal/contrib/2.6/lme4_0.999375-13.tgz'
 Content type 'application/x-gzip' length 353734 bytes (345 Kb)
 opened URL
 ==================================================
 downloaded 345 Kb


 The downloaded packages are in
         /tmp/Rtmpakk1fU/downloaded_packages

So lme4 installed alright.

Matrix choked for some reason.

install.packages("Matrix",repos="http://R-Forge.R-project.org")

 trying URL 'http://R-Forge.R-project.org/bin/macosx/universal/contrib/2.6/Matrix_0.999375-10.tgz'
 Content type 'application/x-gzip' length 1783421 bytes (1.7 Mb)
 opened URL
 ==================================================
 downloaded 1.7 Mb

 Error: cannot remove prior installation of package 'Matrix'

This is what I was trying to avoid by running the process via 'sudo',
not sure what went wrong.

Installing from source worked:

install.packages("Matrix",repos="http://R-Forge.R-project.org",
type = "source")

 trying URL 'http://R-Forge.R-project.org/src/contrib/Matrix_0.999375-10.tar.gz'
 Content type 'application/x-gzip' length 1502286 bytes (1.4 Mb)
 opened URL
 ==================================================
 downloaded 1.4 Mb

 * Installing *source* package 'Matrix' ...
 ** libs
 ** arch - ppc
 gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-
version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/
R.framework/Resources/include
 -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/
local/include   -I./UFconfig -fPIC  -g -O2 -c CHMfactor.c -o
CHMfactor.o
 powerpc-apple-darwin8-gcc-4.2.1: unrecognized option '-no-cpp-
precomp'
 .
 .
 .
 xtabs                             text    html    latex   example
 ** building package indices ...
 Loading required package: Matrix
 Loading required package: stats
 Loading required package: methods
 Loading required package: lattice

 Attaching package: 'Matrix'


         The following object(s) are masked from package:stats :

          xtabs

 * DONE (Matrix)

 The downloaded packages are in
         /private/tmp/Rtmpakk1fU/downloaded_packages
 Updating HTML index of packages in '.Library'

require("lme4")

 Loading required package: lme4
 Loading required package: Matrix
 Loading required package: lattice

 Attaching package: 'Matrix'


         The following object(s) are masked from package:stats :

          xtabs

So this is one way to do it.

Hope it works for you.


Best regards

Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney +at+ bccrc +dot+ ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada




-----Original Message-----
From: r-sig-mac-bounces at stat.math.ethz.ch on behalf of Jarrett Byrnes
Sent: Thu 4/24/2008 4:16 PM
To: r-sig-mac at stat.math.ethz.ch
Subject: [R-SIG-Mac] Installing current version of lme4 and Matrix
on a mac

Hey, all!  I'm trying to use the current version of lme4 over at http://R-Forge.R-project.org
 but have been unable to do so thus far.  I get errors stating that
it requires a i686 architecture or otherwise, and installing Matrix is
a mess.  I have a G4 mac.

Has anyone here been able to install it on a non-intel mac?  If so,
could you post instructions as to how?  Thanks!

-Jarrett




----------------------------------------
Jarrett Byrnes
Population Biology Graduate Group, UC Davis
Bodega Marine Lab
707-875-1969
http://www-eve.ucdavis.edu/stachowicz/byrnes.shtml


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