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

[Stefanie Tauber]

On Mo, 18.03.2013, 17:39, Dan Tenenbaum wrote:
> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

Hi,

Thanks for your help, I changed my description and namespace file
accordingly.

DESCRIPTION File:
Depends: R (>= 2.15.3), BiocGenerics, RJSONIO, ggplot2, gridSVG (>= 1.0-0)
Imports: gridExtra, GenomicRanges, GenomicFeatures, biomaRt, knitr,
fractaldim, xtable, IRanges

Namespace File:
import(RJSONIO)
import(ggplot2)
import(gridSVG)
import(gridExtra)
import(GenomicRanges)
import(GenomicFeatures)
import(biomaRt)
import(knitr)
import(fractaldim)
import(xtable)
import(IRanges)


Still, I get the same warning:
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


I mean, everything is working fine. I just would prefer a clean
installation procedure...

Best,
Stefanie