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Question: Cannot replace subset of DNAStringSet object
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gravatar for jiri.hon
8 months ago by
jiri.hon0
Czech Republic
jiri.hon0 wrote:

Why it is now impossible to replace a subset of DNAStringSet object by a different DNAStringSet object? This certainly worked before. Please, see the example below:

> library(Biostrings)
> dna_set <- DNAStringSet(c("CGT", "ACC"))
> dna_set[1] <- DNAStringSet("GGG")
Error in c(x, value) : 
  could not find symbol "recursive" in environment of the generic function
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=cs_CZ.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=cs_CZ.UTF-8        LC_COLLATE=cs_CZ.UTF-8    
 [5] LC_MONETARY=cs_CZ.UTF-8    LC_MESSAGES=cs_CZ.UTF-8   
 [7] LC_PAPER=cs_CZ.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] Biostrings_2.42.1   XVector_0.14.0      IRanges_2.8.1      
[4] S4Vectors_0.12.1    BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.20.0
ADD COMMENTlink modified 8 months ago by Martin Morgan ♦♦ 20k • written 8 months ago by jiri.hon0
1
gravatar for Martin Morgan
8 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

See here A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC) for a similar problem -- reinstall your Bioconductor packages.

ADD COMMENTlink written 8 months ago by Martin Morgan ♦♦ 20k
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