[R-SIG-Mac] Installing current version of lme4 and Matrix on a mac
Jarrett Byrnes
jebyrnes at ucdavis.edu
Fri Apr 25 03:54:59 CEST 2008
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
>
>
> [[alternative HTML version deleted]]
>
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