[Bioc-devel] Warning in .simpleDuplicateClass(def, prev)

[Dan Tenenbaum]

On Mon, Mar 18, 2013 at 5:39 AM, Stefanie Tauber
<stefanie.tauber at univie.ac.at> wrote:
> Hi,
>
> I am currently working on new BioC package.
> R CMD build, check and INSTALL are successfully passed.
> I just always get the following warning (when installing the package):
>
> Warning in .simpleDuplicateClass(def, prev) :
>   the specification for S3 class “AsIs” in package ‘RJSONIO’ seems
> equivalent to one from package ‘BiocGenerics’ and is not turning on
> duplicate class definitions for this class
>
> Here are the relevant slots from my Description file:
>
> Depends: R (>= 2.15.3), BiocGenerics, ggplot2, gridSVG (>= 1.0-0)
> Imports: BiocGenerics, gridSVG, gridExtra, GenomicRanges, GenomicFeatures,
> biomaRt, knitr, fractaldim, xtable, IRanges
>
> And my Namespace File:
>
> import(BiocGenerics)
> import(ggplot2)
> import(gridSVG)
> import(gridExtra)
> import(GenomicRanges)
> import(GenomicFeatures)
> import(biomaRt)
> import(knitr)
> import(fractaldim)
> import(xtable)
> import(IRanges)
>
>
> This is my SessionInfo when loading my package:
>> sessionInfo()
> R Under development (unstable) (2013-02-27 r62087)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      parallel  stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] fractalQC_0.99     gridSVG_1.0-0      XML_3.95-0.2       RJSONIO_1.0-1
> [5] ggplot2_0.9.3.1    BiocGenerics_0.5.6
>
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.21.16   Biobase_2.19.3          biomaRt_2.15.1
>  [4] Biostrings_2.27.11      bitops_1.0-5            BSgenome_1.27.1
>  [7] colorspace_1.2-1        DBI_0.2-5               dichromat_2.0-0
> [10] digest_0.6.3            evaluate_0.4.3          formatR_0.7
> [13] fractaldim_0.8-1        GenomicFeatures_1.11.16 GenomicRanges_1.11.38
> [16] gridExtra_0.9.1         gtable_0.1.2            IRanges_1.17.37
> [19] knitr_1.1               labeling_0.1            MASS_7.3-24
> [22] munsell_0.4             plyr_1.8                proto_0.3-10
> [25] RColorBrewer_1.0-5      RCurl_1.95-4.1          reshape2_1.2.2
> [28] Rsamtools_1.11.25       RSQLite_0.11.2          rtracklayer_1.19.11
> [31] scales_0.2.3            stats4_3.0.0            stringr_0.6.2
> [34] tools_3.0.0             xtable_1.7-1            zlibbioc_1.5.0
>
>
> What can I do so that the warning gets resolved?

You could put RJSONIO and BiocGenerics in Depends even though you
don't depend directly on RJSONIO (and you can remove BiocGenerics from
Imports and NAMESPACE).

This is caused by the fact that RJSONIO and BiocGenerics use
setOldClass on the same 'old' S3 classes; The behavior is probably a
bug in R.

Dan


>
> Best,
> Stefanie
>
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