Error with DNAStringSet
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@cskennerton-9235
Last seen 8.4 years ago
United States

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 

 

 

biostrings iranges • 908 views
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See IRanges/ShortRead causing crash?; the problem is with IRanges_2.4.2, with an updated version on the way.

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