[R-SIG-Mac] Installing current version of lme4 and Matrix on a mac
Prof Brian Ripley
ripley at stats.ox.ac.uk
Fri Apr 25 06:30:35 CEST 2008
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: 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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>
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--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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