[Bioc-sig-seq] error with MEDIPS.CpGenrich -> resize + segfault in MEDIPS.plotCalibrationPlot

[Steve Lianoglou]

Hi Nora,

On Fri, Oct 22, 2010 at 9:17 AM, Nora Rieber
<n.rieber at dkfz-heidelberg.de> wrote:
> Dear all,
>
> I am working with the MEDIPS package and get the following error when
> calling the function MEDIPS.CpGenrich:
>
>> cpgEnrichment_barr<-MEDIPS.CpGenrich(data=barr,extend=fraglen)
>
>
> Preprocessing...
> Error in .local(x, width, fix, use.names, ...) :
>   unused argument(s) (start = FALSE)
> Calls: MEDIPS.CpGenrich -> resize -> resize -> .local
>
> I checked the resize function which indeed does not require a "start"
> argument, the function call in MEDIPS.CpGenrich however looks like this:
>
> ranges(pos2) <- resize(ranges(pos2), extend + 1, start = FALSE)
>
> This sounds like a version problem.
> This is my sessionInfo:
>
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu

You're correct in thinking that it's a version problem and I'm pretty
sure that upgrading to the latest version of R (2.12) will solve your
problem.

It looks as if the MEDIP package was just released in bioconductor 2.7
(which is only meant to run on R 2.12), so I guess you installed MEDIP
by some "other" (not supported) means?

Keep in mind that using biocLite to install your packages is probably
the best way to ensure that you don't run into versioning problems, so
go ahead and:

(i) download/install the latest R;
(ii) biocLite() your way into the base bioconductor install; and
(iii) biocLite("MEDIP")

You should be good to go after that.

Hope that helps,
-steve

-- 
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