[BioC] cummeRbund masks featureNames and samples from Biobase

[Martin Morgan]

On 01/17/2013 08:43 PM, Francois Lefebvre [guest] wrote:
>
> Hi, I observed that featureNames()<- from cummeRbund masks its homonym from Biobase and can create errors .
>
> Code and error:
> ---------------------------------------
> library(Biobase)
> library(cummeRbund)
> example('ExpressionSet')
>
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function ‘featureNames’ for signature ‘"ExpressionSet"’
> ---------------------------------------
>
> Of course, this can be avoided by calling Biobase::featureNames(), or not loading both packages at the same time or in a different order.
>
> I am not entirely familiar with the details of S4 classes, but couldn't cummeRbund methods be defined in a way to at least not interfere with the actual "base" package of project? Perhaps there is a bug in the signature definition?

Yes, the cummeRbund maintainer (cc'd) should add Biobase to the Imports: field 
of their DESCRIPTION file, add importFrom(Biobase, featureNames) to the 
NAMESPACE file, and remove the setGeneric("featureNames" <...>) from 
R/AllGenerics.R. The documentation also needs to be updated, removing 
\alias{featureNames} from man/featureNames.Rd. Perhaps there are other generics 
that are being re-used.

I would recommend doing this in the 'devel' branch, rather than back-porting to 
the release branch.

Maybe the author did this to avoid a dependency on Biobase, but it seems like 
avoiding the dependency creates problems; hence my advice is to make these 
changes (or to change the accessor name).

Hope that helps,

Martin

> Or has this something to do with my installation.
>
> Thanks for your time.
>
> François Lefebvre
>
>
>   -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] cummeRbund_2.0.0     Gviz_1.2.1           rtracklayer_1.18.2
>   [4] GenomicRanges_1.10.6 IRanges_1.16.4       fastcluster_1.1.7
>   [7] reshape2_1.2.2       ggplot2_0.9.3        RSQLite_0.11.2
> [10] DBI_0.2-5            Biobase_2.18.0       BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.20.3   biomaRt_2.14.0         Biostrings_2.26.2
>   [4] biovizBase_1.6.2       bitops_1.0-4.2         BSgenome_1.26.1
>   [7] cluster_1.14.3         colorspace_1.2-0       dichromat_1.2-4
> [10] digest_0.6.0           GenomicFeatures_1.10.1 gtable_0.1.2
> [13] Hmisc_3.10-1           labeling_0.1           lattice_0.20-13
> [16] MASS_7.3-23            munsell_0.4            parallel_2.15.2
> [19] plyr_1.8               proto_0.3-10           RColorBrewer_1.0-5
> [22] RCurl_1.95-3           Rsamtools_1.10.2       scales_0.2.3
> [25] stats4_2.15.2          stringr_0.6.2          tools_2.15.2
> [28] XML_3.95-0.1           zlibbioc_1.4.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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