'Re: [R-SIG-Mac] Problem installing packages from source'

[prev in list] [next in list] [prev in thread] [next in thread] 

List:       r-sig-mac
Subject:    Re: [R-SIG-Mac] Problem installing packages from source
From:       "Nick Isaac" <njbisaac () googlemail ! com>
Date:       2008-02-20 15:52:08
Message-ID: a072ed700802200752r331836e7i6bf0f44e66fb0bce () mail ! gmail ! com
[Download RAW message or body]

Thanks Simon,
This worked a treat. I had the latest version of R (2.6.2) but an old
version of Xcode Tools (2.2).

Cheers, Nick

On 20/02/2008, Simon Urbanek <simon.urbanek@r-project.org> wrote:
>
> 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@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> >
>
>

	[[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
[prev in list] [next in list] [prev in thread] [next in thread] 