[BioC] load failed for 'Rlibstree'

[Hervé Pagès]

Paul Shannon wrote:
> 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?

biocLite() accepts the same extra args than install.packages():

   biocLite(..., type="source")

See ?install.packages for more information.

Now of course this requires that you have Xcode installed on your
machine. The primary source of information for installing source
packages on Mac OS X is Section 5.3 of the "R for Mac OS X FAQ":

   http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html

Cheers,
H.

> 
> (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
> 

-- 
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