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 [[alternative HTML version deleted]]
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