Ian, I agree with Brian. I checked the CRAN binaries of class and deldir and they are correctly linking to 2.13, so I suspect you have old packages in your tree. I don't think this can happen with stock R binary, it seems that at some point you moved packages or there is/was a symlink between some libraries of 2.12 and 2.13. If the latter is true, to avoid future issues I would suggest sudo rm -rf /Library/Frameworks/R.framework and re-installing R.
Cheers, Simon On May 24, 2011, at 9:48 AM, Prof Brian Ripley wrote: > On Tue, 24 May 2011, Carl Witthoft wrote: > >> Just wanted to mention that I saw the same behavior with a package or two, >> and found the same workaround (copying libs to the 2.12 tree). > > Maybe, but this is about the recommended package 'class'. In the CRAN > distribution oF R 2.13.0 > > tystie% otool -L > /Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so > /Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so: > class.so (compatibility version 0.0.0, current version 0.0.0) > > /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib > (compatibility version 2.13.0, current version 2.13.0) > > /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation > (compatibility version 150.0.0, current version 476.19.0) > /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version > 1.0.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > version 111.1.5) > > So class.so is linked to the correct libR.dylib. > > Something odd has happened on Ian Reeve's system, and I suspect that a binary > copy of 'class' built for R 2.12.x has been installed into 2.13.0. > > I suggest at a minimum running > > update.packages(checkBuilt=TRUE) > > and if the problems persist a complete clear out and re-install. > >> >> Carl >> >> <quote> >> Message: 4 >> Date: Tue, 24 May 2011 16:32:41 +1000 >> From: Ian Reeve <[email protected]> >> To: "[email protected]" <[email protected]> >> Subject: [R-SIG-Mac] Packages deldir, class and gpclib fail to load in >> R 2.13.0 >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset="us-ascii" >> >> Hi, >> >> I've been running rgdal, RColorBrewer, maptools, classInt, spdep, gpclib, >> raster, zoo, cluster and lattice in R2.12 on Mac OSX 10.6.7 for the last 6 >> months with no problems. Today I installed R 2.13.0, and downloaded the >> latest versions of the above packages. Most of them load without problems, >> but class (a depend of classInt), and deldir (a depend of spdep) failed to >> load. The error message is of the form: >> >> ------------------------------- >> Loading required package: class >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared object >> '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so': >> >> dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so, >> 6): Library not loaded: >> /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib >> Referenced from: >> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so >> Reason: image not found >> Error: package 'class' could not be loaded >> ------------------------------- >> >> The problem seems to be either the package is looking in the wrong place (a >> subdirectory of 2.12 instead of a subdirectory of 2.13) for the file >> libR.dylib, or the install of R failed to put the files that package class >> needs in the 2.12 directory. In the case of deldir, the errant file is >> libgfortran.2.dylib. >> >> I can get package class to load without error by taking a copy of >> libR.dylib from the subdirectory of 2.13 and putting it in the subdirectory >> of 2.12 where class expects it to be. >> >> I'm concerned this might be a stupid short-term fix, as calls to the >> functions in class might also fail due to other files not being in the >> expected places. >> >> Can anyone suggest any leads to other approaches I could take to get these >> previously trouble-free packages to behave themselves in R 2.13? >> >> Thank you. >> >> Ian Reeve >> >> Institute for Rural Futures >> University of New England >> Armidale, NSW 2351 >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > -- > Brian D. Ripley, [email protected] > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > _______________________________________________ > 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
