Re: [R-SIG-Mac] Installing current version of lme4 and Matrix on a mac
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 texthtmllatex 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
Re: [R-SIG-Mac] Installing current version of lme4 and Matrix on a mac
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 texthtmllatex 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
Re: [R-SIG-Mac] Installing current version of lme4 and Matrix on a mac
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 texthtmllatex 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
