[R-SIG-Mac] error compiling package - ld: library not found for -lSystemStubs
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 ? 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 R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] 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 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 R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] error compiling package - ld: library not found for -lSystemStubs
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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
