[R-SIG-Mac] packages failed to load - Now fixed

[Simon Urbanek]

On May 24, 2011, at 7:32 PM, Ian Reeve wrote:

> 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
> 

Usually, it is not needed. Just your setup seemed very unusual so it asked for radical measures ;) (libraries are separate for each major version so what you encountered does not happen in the default R setup).


> 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?
> 

Normally you just install new R and then use Package Manager to install packages to match your previous version. If you blow away old R, you will have no track of packages you installed before.

Cheers,
Simon


> 
> 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
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>> 
>> -- 
>> 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
> 
> 
> 
> 
> 
>