Nick, something seems to be broken in your system and/or R quite badly. What Xcode tools and which R are you using? (Specifically, did you compile the R yourself or is it from CRAN?). Note that you will need at least Xcode 2.4 (latest version of Tiger is Xcode 2.5) - if you have an earlier version, update first.
If in doubt, clean up things and re-install: 1) remove R sudo rm -rf /Library/Frameworks/R.framework 2) remove gfortran sudo /usr/local/bin/gfortran-uninstall 2a) if you don't need /usr/local, delete it sudo rm -rf /usr/local 3) install Xcode 2.5 4) install R (the full version!) Cheers, Simon On Feb 20, 2008, at 9:06 AM, Nick Isaac wrote: > I am trying to install the development version of lme4, without > success (see > below). > > > I get the same error when installing the package direct from the > desktop. > > I suspect the problem may be with gfortran. I downloaded version > 4.2.1(from > http://r.research.att.com/tools/) and installed it using the > installer. > However, typing "gfortran --version" in Terminal returns an error ("- > bash: > gfortran: command not found"). I have gcc version 4.0.1. > > > Any suggestions for the solution? > > > Best wishes, Nick Isaac > > > > > > > >> install.packages("lme4", repos = "http://r-forge.r-project.org";, > type="source") > > > trying URL 'http://r-forge.r-project.org/src/contrib/lme4_0.999375-4.tar.gz' > Content type 'application/x-gzip' length 626663 bytes (611 Kb) > opened URL > ================================================== > downloaded 611 Kb > > WARNING: ignoring environment value of R_HOME > * Installing *source* package 'lme4' ... > ** libs > ** arch - i386 > gcc -arch i386 -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/i386 -msse3 > -I"/Library/Frameworks/R.framework/Versions/2.6/Resources/library/ > Matrix/include" > -fPIC -g -O2 -march=nocona -c init.c -o init.o > gcc -arch i386 -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/i386 -msse3 > -I"/Library/Frameworks/R.framework/Versions/2.6/Resources/library/ > Matrix/include" > -fPIC -g -O2 -march=nocona -c lmer.c -o lmer.o > gcc -arch i386 -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/i386 -msse3 > -I"/Library/Frameworks/R.framework/Versions/2.6/Resources/library/ > Matrix/include" > -fPIC -g -O2 -march=nocona -c local_stubs.c -o local_stubs.o > gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk > -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib > -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 - > undefined > dynamic_lookup -single_module -multiply_defined suppress -L/usr/ > local/lib -o > lme4.so init.o lmer.o local_stubs.o > -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRlapack > -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas > -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.1 -lgfortran -lgcc_s.10.4 > -F/Library/Frameworks/R.framework/.. -framework R > ** 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"/Library/Frameworks/R.framework/Versions/2.6/Resources/library/ > Matrix/include" > -fPIC -g -O2 -c init.c -o init.o > /usr/bin/libtool: for architecture ppc object: > /Library/Frameworks/R.framework/Resources/lib/i386/libRlapack.dylib > malformed object (unknown load command 12) > /usr/bin/libtool: for architecture: (null) file: -lRlapack is not an > object > file (not allowed in a library) > /usr/bin/libtool: for architecture i386 object: > /Library/Frameworks/R.framework/Resources/lib/i386/libRlapack.dylib > malformed object (unknown load command 12) > /usr/bin/libtool: for architecture i386 object: > /Library/Frameworks/R.framework/Resources/lib/i386/libRblas.dylib > malformed > object (unknown load command 12) > /usr/bin/libtool: for architecture: (null) file: -lRblas is not an > object > file (not allowed in a library) > /usr/bin/libtool: for architecture ppc object: > /Library/Frameworks/R.framework/Resources/lib/i386/libRblas.dylib > malformed > object (unknown load command 11) > /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) > object: > /usr/local/lib/libgfortran.dylib malformed object (unknown load > command 4) > /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) > object: > /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown load > command 4) > /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) > object: > /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown load > command 4) > make: *** [lme4.so] Error 1 > chmod: > /Library/Frameworks/R.framework/Versions/2.6/Resources/library/lme4/ > libs/i386/*: > No such file or directory > 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"/Library/Frameworks/R.framework/Versions/2.6/Resources/library/ > Matrix/include" > -fPIC -g -O2 -c lmer.c -o lmer.o > 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"/Library/Frameworks/R.framework/Versions/2.6/Resources/library/ > Matrix/include" > -fPIC -g -O2 -c local_stubs.c -o local_stubs.o > > The downloaded packages are in > /private/tmp/RtmpMu8Z9H/downloaded_packages > Updating HTML index of packages in '.Library' > Warning message: > In install.packages("lme4", repos = "http://r-forge.r-project.org";, : > installation of package 'lme4' had non-zero exit status > gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk > -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib > -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 - > undefined > dynamic_lookup -single_module -multiply_defined suppress -L/usr/ > local/lib -o > lme4.so init.o lmer.o local_stubs.o > -L/Library/Frameworks/R.framework/Resources/lib/ppc -lRlapack > -L/Library/Frameworks/R.framework/Resources/lib/ppc -lRblas > -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.2.1 -lgfortran -lgcc_s. > 10.4 > -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R > ** Removing > '/Library/Frameworks/R.framework/Versions/2.6/Resources/library/lme4' > ** Restoring previous > '/Library/Frameworks/R.framework/Versions/2.6/Resources/library/lme4' > /usr/bin/libtool: for architecture ppc object: > /Library/Frameworks/R.framework/Resources/lib/ppc/libRlapack.dylib > malformed > object (unknown load command 12) > /usr/bin/libtool: for architecture: (null) file: -lRlapack is not an > object > file (not allowed in a library) > /usr/bin/libtool: for architecture i386 object: > /Library/Frameworks/R.framework/Resources/lib/ppc/libRlapack.dylib > malformed > object (unknown load command 12) > /usr/bin/libtool: for architecture i386 object: > /Library/Frameworks/R.framework/Resources/lib/ppc/libRblas.dylib > malformed > object (unknown load command 12) > /usr/bin/libtool: for architecture: (null) file: -lRblas is not an > object > file (not allowed in a library) > /usr/bin/libtool: for architecture ppc object: > /Library/Frameworks/R.framework/Resources/lib/ppc/libRblas.dylib > malformed > object (unknown load command 11) > /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) > object: > /usr/local/lib/libgfortran.dylib malformed object (unknown load > command 4) > /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) > object: > /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown load > command 4) > /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) > object: > /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown load > command 4) > make: *** [lme4.so] Error 1 > chmod: > /Library/Frameworks/R.framework/Versions/2.6/Resources/library/lme4/ > libs/ppc/*: > No such file or directory > ERROR: compilation failed for package 'lme4' > > > > > > > > >> sessionInfo() > R version 2.6.2 (2008-02-08) > i386-apple-darwin8.10.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.6.2 > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
