Le 27 mars 2012 à 16:49, Simon Urbanek a écrit : > > 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, this probably comes from a previous install of a mysql server implementation. Is there a way to know how these flags get added to the R CMD gcc command line ? I deleted all the R and mysql instances I found on my Mac and re-installed R from CRAN, but the problem remains. Jean _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
