Michael Kubovy
2005-May-18 20:50 UTC
[R] Advice requested: installation failing for foreign_0.8-7, mgcv_1.2-4, rpart_3.1-23, VR_7.2-15
I'm running R Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0 on Machine Model: Power Mac G5 CPU Type: PowerPC 970 (2.2) Number Of CPUs: 2 CPU Speed: 2 GHz L2 Cache (per CPU): 512 KB Memory: 2 GB with software: System Version: Mac OS X 10.3.9 (7W98) Kernel Version: Darwin 7.9.0 Here is what happened when I tried to update the "foreign" package (similar failures for the other packages in the Subject line). * Installing *source* package 'foreign' ... 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 ANSI C... none needed checking whether gcc accepts -Wno-long-long... yes checking how to run the C preprocessor... gcc -E checking for egrep... 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 byteswap.h usability... no checking byteswap.h presence... no checking for byteswap.h... no checking for double... yes checking size of double... 8 checking for int... yes checking size of int... 4 checking for long... yes checking size of long... 4 configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/swap_bytes.h config.status: creating src/var.h ** libs gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c R_systat.c -o R_systat.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c Rdbfread.c -o Rdbfread.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c Rdbfwrite.c -o Rdbfwrite.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c SASxport.c -o SASxport.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c avl.c -o avl.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c dbfopen.c -o dbfopen.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c file-handle.c -o file-handle.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c format.c -o format.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c minitab.c -o minitab.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c pfm-read.c -o pfm-read.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c sfm-read.c -o sfm-read.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c spss.c -o spss.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -Wno-long-long -fno-common -g -O2 -c stataread.c -o stataread.o gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -lcc_dynamic -framework R ld: warning multiple definitions of symbol _xerbla_ /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_ /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of _xerbla_ ld: warning multiple definitions of symbol _BC /Library/Frameworks/R.framework/Versions/2.1.0/Resources/lib/ libreadline.5.0.dylib(terminal.so) definition of _BC /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC ld: warning multiple definitions of symbol _UP /Library/Frameworks/R.framework/Versions/2.1.0/Resources/lib/ libreadline.5.0.dylib(terminal.so) definition of _UP /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP ld: warning multiple definitions of symbol _PC /Library/Frameworks/R.framework/Versions/2.1.0/Resources/lib/ libreadline.5.0.dylib(terminal.so) definition of _PC /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC ** R ** inst ** preparing package for lazy loading Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/Resources/library/grDevices/libs/ grDevices.so': dlcompat: dyld: /Library/Frameworks/R.framework/Resources/bin/exec/R version mismatch for library: /usr/local/lib/libxml2.2.dylib (compatibility version of user: 9.0.0 greater than library's version: 8.0.0) Loading required package: grDevices Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/Resources/library/grDevices/libs/ grDevices.so': dlcompat: dyld: /Library/Frameworks/R.framework/Resources/bin/exec/R version mismatch for library: /usr/local/lib/libxml2.2.dylib (compatibility version of user: 9.0.0 greater than library's version: 8.0.0) In addition: Warning message: package grDevices in options("defaultPackages") was not found Error: package 'grDevices' could not be loaded Execution halted ERROR: lazy loading failed for package 'foreign' ** Removing '/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library/ foreign' ** Restoring previous '/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library/ foreign'