Package Installation Problem with R 2.7 patched
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]]
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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
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