[R-SIG-Mac] packages failed to load

[Prof Brian Ripley]

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