[R-SIG-Mac] packages failed to load

[Simon Urbanek]

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 <ireeve at une.edu.au>
>> To: "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
>> Subject: [R-SIG-Mac] Packages deldir,	class and gpclib fail to load in
>> 	R 2.13.0
>> Message-ID: <23292B0B-0329-454C-9A17-5BB1CCB45337 at une.edu.au>
>> 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
>> 
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>> 
> 
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> 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
> 
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