On Thu, 24 Apr 2008, Jarrett Byrnes wrote:
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...
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.
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?
Update your Xcode (and I know that from past postings on this list).
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: [EMAIL PROTECTED] on behalf of Jarrett Byrnes
Sent: Thu 4/24/2008 4:16 PM
To: r-sig-mac@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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