[R-SIG-Mac] Installing current version of lme4 and Matrix on a mac

[Steven McKinney]

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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