[R-SIG-Mac] Package Installation Problem with R 2.7 patched

[Prof Brian Ripley]

You need to update your tools.  Since you are using a binary version of 
R, you need the same (or later, I guess but cannot predict future 
versions) version of Xcode as that used to build R.  The FAQ at

http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Additional-resources

says Xcode 2.4.1 is required

I know because this comes up on this list quite often, e.g. the thread 
starting at 
https://stat.ethz.ch/pipermail/r-sig-mac/2008-April/004886.html last week.

On Tue, 29 Apr 2008, Tony Chiang wrote:

> Hi all,
>
> I am having some problems with the released version of R. I will admit that
> I am trying to install Bioconductor packages, but I think that the problem
> should be addressed here (I have also grab the source files for R 2.8 from
> SVN and built it from source and everything there works fine). I am also
> trying to install all the packages that I download from Bioconductor as
> source packages. Here is the error from one of the packages that I tried to
> install:
>
> ---------
> * Installing *source* package 'affyio' ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking for main in -lz... yes
> checking zlib.h usability... yes
> checking zlib.h presence... yes
> checking for zlib.h... yes
> checking if zlib version >= 1.1.3... yes
> checking for pthread_create in -lpthread... yes
> checking if we can use pthreads... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> ** arch - i386
> gcc -arch i386 -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/i386 -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
> -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -msse3   -g -O2   -fPIC
> -g -O2 -march=nocona -c fread_functions.c -o fread_functions.o
> cc1: error: invalid option 'macosx-version-min=10.4'
> make: *** [fread_functions.o] Error 1
> chmod:
> /Library/Frameworks/R.framework/Versions/2.7/Resources/library/affyio/libs/i386/*:
> No such file or directory
> ERROR: compilation failed for package 'affyio'
> ** Removing
> '/Library/Frameworks/R.framework/Versions/2.7/Resources/library/affyio'
> ---------
>
> and for the package Biobase:
>
> ---------
> * Installing *source* package 'Biobase' ...
> ** libs
> ** arch - i386
> gcc -arch i386 -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/i386  -msse3    -fPIC
> -g -O2 -march=nocona -c Rinit.c -o Rinit.o
> cc1: error: invalid option 'macosx-version-min=10.4'
> make: *** [Rinit.o] Error 1
> chmod:
> /Library/Frameworks/R.framework/Versions/2.7/Resources/library/Biobase/libs/i386/*:
> No such file or directory
> ** 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    -fPIC  -g -O2 -c Rinit.c -o Rinit.o
> cc1: error: invalid option 'macosx-version-min=10.4'
> make: *** [Rinit.o] Error 1
> chmod:
> /Library/Frameworks/R.framework/Versions/2.7/Resources/library/Biobase/libs/ppc/*:
> No such file or directory
> ERROR: compilation failed for package 'Biobase'
> ** Removing
> '/Library/Frameworks/R.framework/Versions/2.7/Resources/library/Biobase'
> ----------
>
>
> The error is cryptic. If 10.4 is an invalid option, why does it work for R
> devel? Anyhow, any help would be appreciated.
>
> Cheers,
> --Tony
>
>> sessionInfo()
> R version 2.7.0 Patched (2008-04-28 r45540)
> i386-apple-darwin8.10.1
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.0
>
> 	[[alternative HTML version deleted]]
>
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>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595