Re: [R-SIG-Mac] error compiling package - ld: library not found for -lSystemStubs
Le 27 mars 2012 à 22:02, "Simon Urbanek" 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
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
Re: [R-SIG-Mac] error compiling package - ld: library not found for -lSystemStubs
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
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
