Dear all,

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]]

