Running examples in 'SimRAD-Ex.R' failed
The error most likely occurred in:

> ### Name: SimRAD-package
> ### Title: Simulations to predict the number of loci expected in RAD and
> ###   GBS approaches.
> ### Aliases: SimRAD-package SimRAD
> ### Keywords: package double digestion restriction enzyme library
> ###   construction adaptator ligation fragment selection restriction
> ###   exclusion RESTseq RAD GBS ddRAD ezRAD
> 
> ### ** Examples
> 
> ### Example 1: a single digestion (RAD)
> simseq <-  sim.DNAseq(size=100000, GCfreq=0.51)
> #Restriction Enzyme 1
> #SbfI
> cs_5p1 <- "CCTGCA"
> cs_3p1 <- "GG"
> simseq.dig <- insilico.digest(simseq, cs_5p1, cs_3p1, verbose=TRUE)
Number of restriction sites: 0
> 
> ### Example 2: a single digestion (GBS)
> simseq <-  sim.DNAseq(size=100000, GCfreq=0.51)
> #Restriction Enzyme 1
> # ApeKI : G|CWGC  which is equivalent of either G|CAGC or  G|CTGC
> cs_5p1 <- "G"
> cs_3p1 <- "CAGC"
> cs_5p2 <- "G"
> cs_3p2 <- "CTGC"
> simseq.dig <- insilico.digest(simseq, cs_5p1, cs_3p1, cs_5p1, cs_3p1, verbose=TRUE)
Number of restriction sites for the first enzyme: 81
Number of restriction sites for the second enzyme: 81
Warning in NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  subscript is an array, passing it thru as.vector() first
Warning in NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  subscript is an array, passing it thru as.vector() first
Number of type AB and BA fragments:160
Warning in NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  subscript is an array, passing it thru as.vector() first
Number of type AA fragments:80
Warning in NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  subscript is an array, passing it thru as.vector() first
Number of type BB fragments:80
> 
> ### Example3: a double digestion (ddRAD)
> # simulating some sequence:
> simseq <-  sim.DNAseq(size=1000000, GCfreq=0.433)
> 
> #Restriction Enzyme 1
> #TaqI
> cs_5p1 <- "T"
> cs_3p1 <- "CGA"
> #Restriction Enzyme 2
> #MseI #
> cs_5p2 <- "T"
> cs_3p2 <- "TAA"
> 
> simseq.dig <- insilico.digest(simseq, cs_5p1, cs_3p1, cs_5p2, cs_3p2, verbose=TRUE)
Number of restriction sites for the first enzyme: 3782
Number of restriction sites for the second enzyme: 6416
Warning in NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  subscript is an array, passing it thru as.vector() first
Warning in NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  subscript is an array, passing it thru as.vector() first
Number of type AB and BA fragments:10197
Warning in NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  subscript is an array, passing it thru as.vector() first
Number of type AA fragments:3781
Warning in NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  subscript is an array, passing it thru as.vector() first
Number of type BB fragments:6416
> simseq.sel <- adapt.select(simseq.dig, type="AB+BA", cs_5p1, cs_3p1, cs_5p2, cs_3p2)
Warning in NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  subscript is an array, passing it thru as.vector() first
Warning in NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  subscript is an array, passing it thru as.vector() first
Error in c(dig2, dig2bis) : 
  could not find symbol "recursive" in environment of the generic function
Calls: adapt.select -> c
Execution halted