[Bioc-devel] rtracklayer import Error

Dario Strbenac dstr7320 at uni.sydney.edu.au
Mon Jul 15 08:00:25 CEST 2013


The import function depends on a function in Biostrings that is not imported.

> library(rtracklayer)
> import("E:\\Dario\\scaffolds.fasta")
Error in get(paste("read", match.arg(type), "StringSet", sep = "")) : 
  object 'readDNAStringSet' not found

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

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

other attached packages:
[1] rtracklayer_1.20.4   GenomicRanges_1.12.4 IRanges_1.18.2       BiocGenerics_0.6.0  

loaded via a namespace (and not attached):
[1] Biostrings_2.28.0 bitops_1.0-5      BSgenome_1.28.0   RCurl_1.95-4.1   
[5] Rsamtools_1.12.3  stats4_3.0.1      tools_3.0.1       XML_3.98-1.1     
[9] zlibbioc_1.6.0

Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050

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