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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.