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 > Thank you, > Jean > > > -- > Jean Thioulouse - Labo Biometrie et Biologie Evolutive, UMR CNRS 5558 > Universite Lyon 1, Batiment Mendel, 69622 Villeurbanne Cedex - France > Tel : (33)(0)472432756 Fax : (33)(0)472431388 Cel : (33)(0)675122302 > > http://pbil.univ-lyon1.fr/JTHome/Biblio/ > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
