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
b...@igtp.cat <mailto:b...@igtp.cat>
www.germanstrias.org <http://www.germanstrias.org/>
<http://www.germanstrias.org/>
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