[BioC] no method for coercing S4 class to a vector

[Andrzej Oleś]

Dear Ninni,

you probably need to import the 'as.data.frame' method for GRanges
objects in your NAMESPACE file:

importMethodsFrom(GenomicRanges, as.data.frame)


Cheers,
Andrzej

On Fri, Sep 12, 2014 at 10:27 AM, Ninni Nahm [guest]
<guest at bioconductor.org> wrote:
>
> Dear all,
>
> I have a similar problem to this poster here:
>
> http://grokbase.com/t/r/bioc-devel/141cegqvpf/no-method-for-coercing-this-s4-class-to-a-vector
>
> The error message is:
>
> Error in as.vector(x) : no method for coercing this S4 class to a vector
>
>
> In my case, however, I'm using the as.data.frame function on a GRanges object. When I source my function it works fine, but when I make it into a package and then run the function I get the S4 class error.
>
> The function seems to be from BiocGenerics:
>
>> as.data.frame
> standardGeneric for "as.data.frame" defined from package "BiocGenerics"
>
> function (x, row.names = NULL, optional = FALSE, ...)
> standardGeneric("as.data.frame")
> <environment: 0x3801ad8>
> Methods may be defined for arguments: x
> Use  showMethods("as.data.frame")  for currently available ones.
>
>
> So, I have included this
> importFrom("BiocGenerics", as.data.frame)
> in NAMESPACE
>
> and this
> Depends: BiocGenerics
> in DESCRIPTION.
>
> It still does not work. I must be missing something.
>
> Any help is highly appreciated!
>
> Thanks
> Ninni
>
>
>  -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-pc-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=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] rtracklayer_1.24.0   GenomicRanges_1.16.2 GenomeInfoDb_1.0.2
> [4] IRanges_1.22.10      BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
>  [1] BatchJobs_1.2           BBmisc_1.6              BiocParallel_0.6.0
>  [4] Biostrings_2.32.0       bitops_1.0-6            brew_1.0-6
>  [7] BSgenome_1.32.0         codetools_0.2-9         DBI_0.2-7
> [10] digest_0.6.4            fail_1.2                foreach_1.4.2
> [13] GenomicAlignments_1.0.0 iterators_1.0.7         plyr_1.8.1
> [16] Rcpp_0.11.1             RCurl_1.95-4.1          Rsamtools_1.16.0
> [19] RSQLite_0.11.4          sendmailR_1.1-2         stats4_3.1.1
> [22] stringr_0.6.2           tools_3.1.1             XML_3.98-1.1
> [25] XVector_0.4.0           zlibbioc_1.10.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor