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

----- Original Message -----
From: "Tiphaine Martin" <tiphaine.martin at kcl.ac.uk>
To: "Herv? Pag?s" <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: Herv? Pag?s <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

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--
Herv? Pag?s

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

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