[Bioc-devel] Warning message: multiple methods tables found for ‘score’

[Michael Lawrence]

The score generic was removed from IRanges in version 2.1.41. So your
IRanges is up to date. My guess is that something is cached and you need to
reinstall one or more of the other Bioc infrastructure packages...

On Fri, Apr 10, 2015 at 11:35 AM, Martin, Tiphaine <
tiphaine.martin at kcl.ac.uk> wrote:

> Hi Herve,
>
> When I tried to update IRanges, I have only the version 2.1.43 and not
> 2.1.44.
> How to force BiocLite to have the lastest version of IRanges. did I miss
> something?
>
> source("http://bioconductor.org/biocLite.R")
> Bioconductor version 3.1 (BiocInstaller 1.17.7), ?biocLite for help
> biocLite("IRanges")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 3.1 (BiocInstaller 1.17.7), R version 3.2.0.
> Installing package(s) ‘IRanges’
> trying URL '
> http://bioconductor.org/packages/3.1/bioc/src/contrib/IRanges_2.1.43.tar.gz
> '
>
>
> Tiphaine
>
> ________________________________________
> From: Hervé Pagès <hpages at fredhutch.org>
> Sent: 10 April 2015 19:20
> To: Martin, Tiphaine; bioc-devel
> Subject: Re: [Bioc-devel] Warning message: multiple methods tables found
> for ‘score’
>
> Hi Martin,
>
> On 04/10/2015 11:12 AM, Martin, Tiphaine wrote:
> > Dear Everybody,
> >
> >
> > I updated my package because I have an error message. Before submitting
> my package on svn, I run
> >
> > R CMD check coMET
> >
> > I receive a new error message:
> >
> >
> > Warning message:
> > multiple methods tables found for �score�
> >
> >
> > If I am looking at the reference manual of IRanges, I see that there is
> the function "score" and before updating, when I run ?score, the function
> "score" belonged to the package IRanges
> >
> > But now when I run ?score,  the function "score" belongs to the
> package:BiocGenerics.
> >
> >
> > I am wondering if there is an conflict between two packages. How can I
> manage it?
>
> AFAIK there is no conflict. Your IRanges version is probably lagging
> behind. Remember to keep your installation up-to-date by running
> biocLite() (with no arguments) on a regular basis.
>
> >
> > How can I know which packages have the function "score"?
>
> Only the BiocGenerics package now defines the score() generic. There is
> no score() generic in the latest IRanges (2.1.44).
>
> Thanks for taking care of coMET.
>
> H.
>
> >
> >
> > Thanks,
> >
> > Tiphaine
> >
> >
> > ----------------------------
> > Tiphaine Martin
> > PhD Research Student | King's College
> > The Department of Twin Research & Genetic Epidemiology | Genetics &
> Molecular Medicine Division
> > St Thomas' Hospital
> > 4th Floor, Block D, South Wing
> > SE1 7EH, London
> > United Kingdom
> >
> > email : tiphaine.martin at kcl.ac.uk
> > Fax: +44 (0) 207 188 6761
> >
> >       [[alternative HTML version deleted]]
> >
> >
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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