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