[Bioc-devel] as.list of a GRanges

[Bernat Gel]

Hi,

I'm having an error in the devel version of my package karyoploteR due 
to an error when converting a GRanges into a list of GRanges with "as.list".

This used to be possible and it was working a few weeks ago.

Am I suposed to use a different approach or is there a problem somewhere?

Thanks!

Bernat

Here's an example

rr <- GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(start=c(1, 
2), end=c(11, 12)))
as.list(rr)

And the error message

Error in (function (classes, fdef, mtable)  :
   unable to find an inherited method for function 'getListElement' for 
signature '"GRanges"'


and the sessionInfo

 > sessionInfo()
R Under development (unstable) (2018-02-14 r74250)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/libRblas.so
LAPACK: 
/software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/libRlapack.so

locale:
  [1] LC_CTYPE=en_US.UTF-8      LC_NUMERIC=C LC_TIME=C                 
LC_COLLATE=en_US.utf8
  [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8 
LC_PAPER=es_ES.UTF-8      LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C LC_MEASUREMENT=en_US.utf8 
LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils datasets  
methods   base

other attached packages:
[1] GenomicRanges_1.31.20 GenomeInfoDb_1.15.5 IRanges_2.13.26       
S4Vectors_0.17.32     BiocGenerics_0.25.3

loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0        compiler_3.5.0 XVector_0.19.8         
tools_3.5.0            GenomeInfoDbData_1.1.0
[6] RCurl_1.95-4.10        bitops_1.0-6



-- 

*Bernat Gel Moreno*
Bioinformatician

Hereditary Cancer Program
Program of Predictive and Personalized Medicine of Cancer (PMPPC)
Germans Trias i Pujol Research Institute (IGTP)

Campus Can Ruti
Carretera de Can Ruti, Camí de les Escoles s/n
08916 Badalona, Barcelona, Spain

Tel: (+34) 93 554 3068
Fax: (+34) 93 497 8654
08916 Badalona, Barcelona, Spain
bgel at igtp.cat <mailto:bgel at igtp.cat>
www.germanstrias.org <http://www.germanstrias.org/>

<http://www.germanstrias.org/>