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

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.