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

Martin, Tiphaine tiphaine.martin at kcl.ac.uk
Fri Apr 10 21:47:24 CEST 2015

Ok, thanks. I have just updated all package and run Martin's command line "BiocInstaller::biocValid() ". Everything was updated,

 I run a new session of R and load only Gviz package, Gviz finish with the same error messages and,  for example, impossible to create the plot GC content .

How to find the packages with the function "score", because when I do ??"score", I found only in BiocGenerics package the function "score". So I don't know how to correct that.

If you have any advice, i'm all ears




to <- 65980988

from <- 65921878

gcContent1 <- UcscTrack(genome = "mm9", chromosome = "chrX",
 track = "GC Percent", table = "gc5Base", from = from ,
 to = to, trackType = "DataTrack", start = "start",
 end = "end", data = "score", type = "hist", window = -1,
 windowSize = 1500, fill.histogram = "black",
 col.histogram = "black", ylim = c(30, 70), name = "GC Percent")

plotTracks(gcContent1,from= start, to=end)


R Under development (unstable) (2014-12-17 r67184)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_GB.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils
 [8] datasets  methods   base

other attached packages:
[1] Gviz_1.11.15          GenomicRanges_1.19.52 GenomeInfoDb_1.3.18
[4] IRanges_2.1.44        S4Vectors_0.5.23      BiocGenerics_0.13.11

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3           AnnotationDbi_1.29.23
 [3] Biobase_2.27.3            BiocParallel_1.1.27
 [5] biomaRt_2.23.5            Biostrings_2.35.12
 [7] biovizBase_1.15.4         bitops_1.0-6
 [9] BSgenome_1.35.20          cluster_2.0.1
[11] colorspace_1.2-6          DBI_0.3.1
[13] dichromat_2.0-0           digest_0.6.8
[15] foreign_0.8-63            Formula_1.2-1
[17] futile.logger_1.4         futile.options_1.0.0
[19] GenomicAlignments_1.3.34  GenomicFeatures_1.19.37
[21] ggplot2_1.0.1             gtable_0.1.2
[23] Hmisc_3.15-0              lambda.r_1.1.7
[25] lattice_0.20-31           latticeExtra_0.6-26
[27] MASS_7.3-40               matrixStats_0.14.0
[29] munsell_0.4.2             nnet_7.3-9
[31] plyr_1.8.1                proto_0.3-10
[33] RColorBrewer_1.1-2        Rcpp_0.11.5
[35] RCurl_1.95-4.5            reshape2_1.4.1
[37] rpart_4.1-9               Rsamtools_1.19.52
[39] RSQLite_1.0.0             rtracklayer_1.27.12
[41] scales_0.2.4              splines_3.2.0
[43] stringr_0.6.2             survival_2.38-1
[45] tools_3.2.0               VariantAnnotation_1.13.48
[47] XML_3.98-1.1              XVector_0.7.4
[49] zlibbioc_1.13.3

From: Michael Lawrence <lawrence.michael at gene.com>
Sent: 10 April 2015 19:45
To: Martin, Tiphaine
Cc: Hervé Pagès; bioc-devel
Subject: Re: [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<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?

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<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.


> 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>
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
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E-mail: hpages at fredhutch.org<mailto:hpages at fredhutch.org>
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