[BioC] svn version of rtracklayer error

[Steve Lianoglou]

Hi,

On Mon, Oct 18, 2010 at 9:55 AM, Michael Dondrup <Michael.Dondrup at uni.no> wrote:
>
> On Oct 18, 2010, at 3:32 PM, Martin Morgan wrote:
>
>> On 10/18/2010 03:15 AM, Michael Dondrup wrote:
>>> Hi,
>>>
>>> I am trying to install the the latest rtracklayer version from svn, it's revision 50298.
>>>
>>> But that doesn't install:
>>> ** testing if installed package can be loaded
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>  unable to load shared library '/Library/Frameworks/R.framework/Resources/library/rtracklayer/libs/x86_64/rtracklayer.so':
>>>  dlopen(/Library/Frameworks/R.framework/Resources/library/rtracklayer/libs/x86_64/rtracklayer.so, 6): Symbol not found: _new_CHARACTER_from_CharAEAE
>>
>> I would guess that your version of IRanges (and other dependencies /
>> imports?) is out of date with respect to rtracklayer.
>>
> Yes, I think you are right. Do I have to update to R 2.12.0 in general, or to the svn version of R and Bioconductor even?

If you want to be installing packages from SVN, then I believe the
recommendation is to be using R-devel (so: svn version of R). It looks
like you're on a Mac, so you can get R-devel builds that are built for
you and easily installable from here:

http://r.research.att.com/

Then use biocLite from the correct version of R to get the correct
bioconductor ecosystem (then install your package from SVN if you
can't wait for it's changing to auto-build + propagate to biocLite)

Depending on how comfortable you are with that (or not), you might
just consider installing R-2.12 which just came out, and installing
rtracklayer with biocLite from there since I guess the one rolled for
Bioconductor 2.7 (which goes with R-2.12) is very close to the version
in SVN you what ... but I might be wrong. Also, I reckon it might take
another day or two for bioconductor 2.7 to officially hit the shelves.

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact