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
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