Entering edit mode
I get the following error whenever I try to do anything with an XStringSet or derivative, any idea what's wrong?
library(Biostrings)
filepath1 <- system.file("extdata", "someORF.fa", package="Biostrings")
x1 <- readDNAStringSet(filepath1)
x1
#>A DNAStringSet instance of length 7
#> width seq names
#>Error in x@pool[[x@ranges@group[i]]] : invalid subscript
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)
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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Biostrings_2.38.1 XVector_0.10.0 IRanges_2.4.2
[4] S4Vectors_0.8.3 BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0 tools_3.2.0

See IRanges/ShortRead causing crash?; the problem is with IRanges_2.4.2, with an updated version on the way.