[BioC] load failed for 'Rlibstree'

[Paul Shannon]

Herve & Seth,

Thanks for your replies.  Yes, it must be the snow leopard binary problem. 

I've tried biocLite (c ('microRNA', 'Rlibstree'))  a few times, always with the same problem.

I should know this, but don't:  what's the best way to install from source?  An option or argument provided to install.packages?

(I have been spoiled by the binary packages you provide...)

 - Paul


On Apr 8, 2010, at 12:44 PM, Hervé Pagès wrote:

> Hi Paul,
> 
> Seth Falcon wrote:
>> Hi Paul,
>> On 4/8/10 10:21 AM, Paul Shannon wrote:
>>> While working my way through the rtracklayer pdf, I get stuck when
>>> 
>>>   library (microRNA)
>>> 
>>> tries to load Rlibstree, with this error message:
>>> 
>>>   Loading required package: Rlibstree
>>>   Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>     unable to load shared library '/Library/Frameworks/R.framework/Resources/library/Rlibstree/libs/x86_64/Rlibstree.so': 
>>>     dlopen(/Library/Frameworks/R.framework/Resources/library/Rlibstree/libs/x86_64/Rlibstree.so, 6): Symbol not found: _lst_alg_longest_repeated_substring
>>>    Referenced from: /Library/Frameworks/R.framework/Resources/library/Rlibstree/libs/x86_64/Rlibstree.so 
>>>    Expected in: dynamic lookup
>>> 
>>>   Error: package 'Rlibstree' could not be loaded
>>> 
>>> The package is installed (version 0.3-2) on my OS X 10.6.3 MacBook.
> 
> Mmmh, isn't 10.6 the OS version for Snow Leopard? What output
> is getOption("pkgType") giving you?
> I suspect it is "mac.binary.leopard", which means that you are
> installing the binaries we are producing for OS X 10.5 (Leopard).
> Those binaries are currently built on pelham (Mac OS X Leopard
> (10.5.8)):
>  http://bioconductor.org/checkResults/2.5/bioc-LATEST/pelham-index.html
> and some of them are apparently not compatible with Snow Leopard.
> 
> The good news is that we have plans to start building binaries for
> Snow Leopard in the near future (we recently purchased new hardware
> for this).
> 
>>> 
>>> Any suggestions?  SessionInfo follows.
>> Have you tried reinstalling?  I just did
>> biocLite(c("microRNA", "Rlibstree"))
>> And both packages load fine on my Mac where I'm building packages from source.
> 
> Yep. Installing from source will solve the problem in the mean time.
> 
> Cheers,
> H.
> 
>> + seth
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages at fhcrc.org
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