[BioC] load failed for 'Rlibstree'

[Paul Shannon]

  biocLite (c ("microRNA", "Rlibstree"), type='source')

worked like a charm!  Thanks you all!

 - Paul

On Apr 8, 2010, at 1:37 PM, Tony Chiang wrote:

> Hi Paul,
> 
> 2010/4/8 Paul Shannon <pshannon at systemsbiology.org>
> 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?
> 
> 
> try biocLite(c(microRNA, Rlibstree), type="source")
> 
> make sure you install the proper compilers from the Install DVD (in XCode tools)
>  
> (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
> > Phone:  (206) 667-5791
> > Fax:    (206) 667-1319
> 
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