Package Installation Problem with R 2.7 patched

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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.

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
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

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