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

[Ninni Nahm [guest]]

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.