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

[Simon Urbanek]

On Apr 30, 2008, at 5:27 AM, Prof Brian Ripley wrote:
> 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
>


Indeed, and just for completeness, from:
http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#How-to-install-packages

"5.3 Installation of source packages"
[...]
Important: When using binary R installation from CRAN, you must use  
Xcode 2.4.0 or higher (available from see Apple Developer Connection).  
Although R can be built using older tools, the way it is build depends  
on the version of the tools and therefore your must upgrade at least  
to the version of Xcode that the CRAN build uses.

Cheers,
Simon



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