packages failed to load - Now fixed

Thanks Brian and Simon for the suggestions.

update.packages(checkBuilt=TRUE)

fixed the load problem and all the functions I was using in R 2.12 are running identically in R 2.13.0.

For future reference, when I update to a new version of R, is it good practice to:

sudo rm -rf /Library/Frameworks/R.framework

and then download and install the contributed packages one needs?  Otherwise, does the installing process for the base R package look at what is already there in R.framework tree and retain the contributed packages that were installed under the previous version?

On 24/05/2011, at 11:48 PM, 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

-- 
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

Ian Reeve
Institute for Rural Futures
University of New England
Armidale, NSW 2351

02 67735145