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

[Martin Morgan]

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...


BiocInstaller::biocValid() can help flag these situations. Martin

>
> 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: 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
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


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