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Last seen 10.2 years ago
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.
