[R-SIG-Mac] Problem installing packages from source

Simon Urbanek simon.urbanek at r-project.org
Wed Feb 20 15:28:49 CET 2008 

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
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>

More information about the R-SIG-Mac mailing list