On Apr 24, 2008, at 9:54 PM, 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... > > 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’
Please update your Xcode. Xcode 2.4 or higher and gcc 4.0 is required if you are using R from CRAN. You can use any other compiler, but then you have to compile R from sources as you're using tools different from what we use on CRAN. I'd recommend asking R-forge to fix their Mac OS X binary building process - their binaries don't seem to work properly. Cheers, Simon > > 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: [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]] >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac