keepSeqlevels and friends have been converted to ordinary functions (rather
than generics with methods); Martin fixed that for ggbio, but it looks like
ggbio is currently totally broken in devel, and the new version is not
propagating.

Michael


On Wed, Jul 10, 2013 at 5:41 PM, Pablo marin-garcia <
harpactocrates@gmail.com> wrote:

> Hello,
>
> I am using R3.0  bioconductor 2.13, ggbio 1.9.2 and GenomicRanges 1.13..26
>
> and when loading ggbio I have the following warning/error:
>
>         || Loading required package: ggbio
>         || No methods found in "GenomicRanges" for requests: keepSeqlevels,
> renameSeqlevels
>         || Need specific help about ggbio? try mailing
>         ||  the maintainer or visit http://tengfei.github.com/ggbio/
>         ||
>         || Attaching package: ^Xggbio^Y
>
>
> I have been following the GenomicRanges thread about keepseqlevel
> deprecation and in
>
> http://permalink.gmane.org/gmane.science.biology.informatics.conductor.devel/4378
> Valerie
> Obenchain  said that from GR 1.13.16 it has been restored but as a
> seqleveles() wrappers not generics with methods.
>
> Q: So, seems to me that ggbio still is trying to access  the old
> keepseqleveles. Is this error preventing ggbio to work properly in some
> circumstances?
>
> Related with that. I am an experienced programmer but my knowledge of
> bioconductor and S4 objects in R is still limited.  I have some copy paste
> code that was using keepseqlevels, I can redo many of the code following
> the ?seqlevels examples, but I tried > ?keepseqlevels and >keepseqlevels
>  but nothing was returned.
>
> Q:  How can I see if keepseqlevels is still in GenomicRanges and how it is
> implemented and how to use it (instead of using my own wrappers to
> seqlevels;-))?
>
> Thanks
>
> Pablo
>
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>
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