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

[Stefanie Tauber]

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?

Best,
Stefanie