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

Martin, Tiphaine tiphaine.martin at kcl.ac.uk
Fri Apr 10 20:35:34 CEST 2015

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?

Bioconductor version 3.1 (BiocInstaller 1.17.7), ?biocLite for help
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'


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.


> 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

More information about the Bioc-devel mailing list