Running examples in ‘shipunov-Ex.R’ failed
The error most likely occurred in:

> ### Name: keys
> ### Title: Diagnostic keys
> ### Aliases: keys
> ### Keywords: datasets
> 
> ### ** Examples
> 
> attach(keys)
> 
> head(bracket1)
  V1               V2       V3
1  1  It is an animal        2
2  1    It is a plant        3
3  2            Spiny Hedgehog
4  2   Not very spiny    Swift
5  2 Not at all spiny    Horse
6  3       Very woody   Spruce
> head(bracket2)
  V1                                                              V2
1  1                                               Leaves pinnatifid
2  1                                                   Leaves entire
3  2 Plants perennial, leaves dissected to numerous lanceolate lobes
4  2                         Annual plants, leaves with narrow lobes
5  3      The compact inflorescence is surrounded by leaflike bracts
6  3             The sparse inflorescence without specialised bracts
              V3
1              2
2              3
3  Polemonium L.
4       Gilia L.
5 Collomia Nutt.
6        Plox L.
> head(branched)
  V1                                                                       V2
1  1                                                          Leaves cauline.
2  2                                              Perennials, sometimes woody
3  2                                                                 Annuals.
4  3                               Spikes glandular-hairy; all bracts similar
5  3 Spikes eglandular; proximal bracts strongly differing from distal bracts
6  1                                                            Leaves basal.
                     V3
1                      
2 Plantago sempervirens
3                      
4         Plantago afra
5     Plantago arenaria
6                      
> head(serial)
  V1 V2
1  1  6
2  2  5
3  3  4
4  4  3
5  5  2
6  6  1
                                                                                                                                                                          V3
1                                                                     Leaves opposite. Stems with long internodes. Inflorescences nearly capitate. Capsula with 2 big seeds.
2                                                                                                                                                                   Annuals.
3          Bracts of lower flowers with long, narrowed appendages. Bracts of upper flowers nearly spathulate, with keel, which extend to the tip. Greyish, branching plants.
4 Bracts of lower flowers with straight appendages. Bracts of upper flowers egg-shaped, with keel, which not extend to the tip. Greenish plants, usually with rare branches.
5                                                        Perennials with lignose stems; bracts of lower flowers are very broad, covered the most part of inflorescence base.
6                                                     Leaves alternate, in the rosette. Inflorescences long or short cylindrical. Capsula with 12 or bigger number of seeds.
                     V4
1                  <NA>
2                  <NA>
3     Plantago arenaria
4         Plantago afra
5 Plantago sempervirens
6                  <NA>
> 
> ## convert keys with Biokey()
> sii <- Biokey(serial, from="serial", to="indented")
> sbb <- Biokey(serial, from="serial", to="bracket")
> bbr <- Biokey(branched, from="branched", to="bracket")
> 
> ## convert keys and visualize them as trees
> library(ape) # load 'ape' library to plot Newick trees
> plot(read.tree(text=Biokey(bracket1, from="bracket", to="newick")))
> plot(read.tree(text=Biokey(bracket2, from="bracket", to="newick")))
> plot(read.tree(text=Biokey(branched, from="branched", to="newick")))
> plot(read.tree(text=Biokey(serial, from="serial", to="newick")))
> 
> detach(keys)
> 
> ## to make a new bracket key (without backreferences)
> ## supply three columns: id, description and 'goto'+terminal
> bracket3 <- read.table(as.is=TRUE, text="
+ 1 Small Ant
+ 1 Big 2
+ 2 Blue Sky
+ 2 Green Grass
+ ")
> bracket3
  V1    V2    V3
1  1 Small   Ant
2  1   Big     2
3  2  Blue   Sky
4  2 Green Grass
> Biokey(bracket3, from="bracket", to="newick")
[1] "(Ant,(Sky,Grass));"
> cophenetic(ape::read.tree(text=Biokey(bracket3, from="bracket", to="newick")))

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: dist.nodes(x)
 2: cophenetic.phylo(ape::read.tree(text = Biokey(bracket3, from = "bracket",     to = "newick")))
 3: cophenetic(ape::read.tree(text = Biokey(bracket3, from = "bracket",     to = "newick")))
An irrecoverable exception occurred. R is aborting now ...