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

[Martin, Tiphaine]

I will commit my fix to coMET and cross fingers that the error doesn't appear in the build system

Tiphaine
________________________________________
From: Hervé Pagès <hpages at fredhutch.org>
Sent: 10 April 2015 20:30
To: Michael Lawrence; Martin, Tiphaine
Cc: bioc-devel
Subject: Re: [Bioc-devel] Warning message: multiple methods tables found for ‘score’

On 04/10/2015 11:45 AM, Michael Lawrence wrote:
> 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...

That's a good point.

In any case, this should not prevent you from committing your fix to
coMET. The issue is specific to the state of your current installation
and it won't show up on the build system (where all dependencies are
re-installed every day at the beginning of the builds).

Also, for you, the issue will automatically go away when all package
versions get bumped the day of the release.

Cheers,
H.

>
> On Fri, Apr 10, 2015 at 11:35 AM, Martin, Tiphaine
> <tiphaine.martin at kcl.ac.uk <mailto: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 <mailto: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 <mailto:tiphaine.martin at kcl.ac.uk>
>      > Fax: +44 (0) 207 188 6761 <tel:%2B44%20%280%29%20207%20188%206761>
>      >
>      >       [[alternative HTML version deleted]]
>      >
>      >
>      >
>      > _______________________________________________
>      > Bioc-devel at r-project.org <mailto: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 <mailto:hpages at fredhutch.org>
>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>     _______________________________________________
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>
>

--
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