Le 27 mars 2012 à 22:02, "Simon Urbanek" <simon.urba...@r-project.org> a écrit : > > On Mar 27, 2012, at 3:44 PM, THIOULOUSE JEAN wrote: > >> >> 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. >> > > It has nothing to do with those -- it is your user setting. It could be in > your environment (try set | grep PKG) or any startup files (.Rprofile, > .Renviron or any of the site-configuration files of .R/Makevars and friends > ..). > > Cheers, > Simon
Yes indeed, it was in my .cshrc file. Thanks a lot, and sorry for the trouble ! Jean _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac