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

[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:

> 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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