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

[Dan Tenenbaum]

----- Original Message -----
> From: "Tiphaine Martin" <tiphaine.martin at kcl.ac.uk>
> To: "Hervé Pagès" <hpages at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Friday, April 10, 2015 11:35:34 AM
> Subject: Re: [Bioc-devel] Warning message: multiple methods tables found for ‘score’
> 
> 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'
> 

Version 2.1.44 is available. You might try starting a fresh R session.

If that doesn't work, wait a few minutes as it could be a CloudFront propagation delay.

Dan


> 
> 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
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