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Installing current version of lme4 and Matrix on a mac

5 messages · Steven McKinney, Jarrett Byrnes, Brian Ripley +1 more

Original
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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Jarrett Byrnes
# 
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:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
      #
    

  


  

      
On Thu, 24 Apr 2008, Jarrett Byrnes wrote:

        

            

      
      
      
    

        
Completely normal.   To read the help page for you (fortune(14) applies)

      'install.packages' can be used to install new packages/bundles. It
      takes a vector of names and a destination library, downloads the
      packages from the repositories and installs them.  (If the library
      is omitted it defaults to the first directory in '.libPaths()',
      with a warning if there is more than one.)

I think you need to install from the sources, as it seems R-forge does not 
have a suitable binary.

            

      
      
      
    

        
Update your Xcode (and I know that from past postings on this list).

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
On Apr 24, 2008, at 9:54 PM, Jarrett Byrnes wrote:

        

            

      
      
      
    

        
Please update your Xcode. Xcode 2.4 or higher and gcc 4.0 is required  
if you are using R from CRAN. You can use any other compiler, but then  
you have to compile R from sources as you're using tools different  
from what we use on CRAN.

I'd recommend asking R-forge to fix their Mac OS X binary building  
process - their binaries don't seem to work properly.

Cheers,
Simon