[Bioc-devel] GenomicFeatures TranscriptDb no applicable method for 'metadata' applied to an object of class "c('TranscriptDb', 'GenomicFeatures')"

[Steve Lianoglou]

Hi Malcolm,

On Wed, Jul 20, 2011 at 9:40 AM, Cook, Malcolm <MEC at stowers.org> wrote:
> Can anyone advise me as to which is wrong: the library, the documentation, or my understanding, in the following:
>
> in ?GenomicFeatures I read:
>
> 'metadata(x)': Returns 'x''s metadata in a data frame.
>
> But I find:
>
>> metadata(txdb)
> Error in UseMethod("metadata") :
>  no applicable method for 'metadata' applied to an object of class "c('TranscriptDb', 'GenomicFeatures')"

Are you still having this problem?

This a strange error -- it looks like 'metadata' might have been
trampled on by something (another package?), as this error indicates
that `metadata` is registered as an S3 type of
function/dispatch/mojo/thing.

What does `showMethods('metadata')` show?

I'm guessing you won't have problems if you fire up a new / clean R
environment, just load GenomicFeatures and then call `metadata` on
your object.

If I'm correct, and another package is "trampling" on `metadata`,
perhaps you can it like so:

R> IRanges::metadata(txdb)

If you're curious you can look for the offending package that
redefines metadata -- it most likely won't be any of the other
bioconductor packages that were listed in your session info, nor plyr
or ggplot2 for that matter (since I use those lots to, and I don't
have this problem).

-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