I removed it from the namespace file,
still the same warning,

(btw gridSVG depends on RJSONIO)

best,
Stefanie

Am 19.03.2013 um 15:31 schrieb Dan Tenenbaum <dtenenba@fhcrc.org>:

> On Tue, Mar 19, 2013 at 12:59 AM, Stefanie Tauber
> <stefanie.tauber@univie.ac.at> wrote:
>> 
>> On Mo, 18.03.2013, 17:39, Dan Tenenbaum wrote:
>>> On Mon, Mar 18, 2013 at 5:39 AM, Stefanie Tauber
>>> <stefanie.tauber@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@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...
>> 
> 
> 
> Try removing
> import(RJSONIO)
> from NAMESPACE.
> 
> Dan
> 
>> Best,
>> Stefanie
>> 

DI Stefanie Tauber

Center for Integrative Bioinformatics Vienna (CIBIV)
(CIBIV is a joint institute of Vienna University and Medical University)
Max F. Perutz Laboratories (MFPL)
Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2
Dr. Bohr Gasse 9
A-1030 Wien, Austria
Phone: ++43 +1 / 42772-4030
Fax:     ++43 +1 / 42772-4098
email:   stefanie.tauber@univie.ac.at
www.cibiv.at


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