error compiling package - ld: library not found for -lSystemStubs

On Mar 27, 2012, at 10:40 AM, THIOULOUSE JEAN wrote:

Hi,

Sorry to bother you about what is probably a bad configuration of my system. I have the following error when checking a package on my Mac (Mac Pro mid-2010 with Mac OS X Lion 10.7.3 (11D50), running R-2.14.2 from CRAN). I have Xcode 4.3.2 and the GNU Fortran compiler from http://r.research.att.com/. The package is prepRISA and it compiles without problem on R-Forge.

Here is the install.out file of R CMD check prepRISA:

* installing *source* package ?prepRISA? ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/mysql/include -I/usr/local/include    -fPIC  -g -O2 -c repClass.c -o repClass.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o prepRISA.so repClass.o -L/usr/local/mysql/lib -lmysqlclient -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: library not found for -lSystemStubs
collect2: ld returned 1 exit status
make: *** [prepRISA.so] Error 1
ERROR: compilation failed for package ?prepRISA?
* removing ?/Volumes/Macintosh-HD/Users/jthioulo/Desktop/prepRISA.Rcheck/prepRISA?

I tried to search about this SystemStubs library, but could only find that it is deprecated in MacOS X 10.7.

Here is my sessionInfo:

sessionInfo()

R version 2.14.2 (2012-02-29)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  tcltk     methods  
[8] base     

other attached packages:
[1] ade4TkGUI_0.2-5 ade4_1.4-17    

What can I do to get rid of this problem ?

The problem seems local to your R or settings - did you perhaps override any PKG_* with bogus flags? This is what you get with released R:

** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -Wall -pedantic -g -O2 -c repClass.c -o repClass.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o prepRISA.so repClass.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/prepRISA/libs/i386

note that you have superfluous "-L/usr/local/mysql/lib -lmysqlclient -lSystemStubs" in your linking step which is *not* part of R ...

Cheers,
Simon