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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Biokey
> ### Title: Convert diagnostic keys and classification lists
> ### Aliases: Biokey Numranks
> ### Keywords: classif
> 
> ### ** Examples
> 
> ## Biokey() # makes (harmless) error message but also shows which conversions are available
> Numranks() # shows the conversion table
   num         rank
1  0.5     Varietes
2  0.8   Subspecies
3    1      Species
4  1.2    Subsectio
5  1.5       Sectio
6  1.8     Subgenus
7    2        Genus
8  2.2    Subtribus
9  2.5       Tribus
10 2.8   Subfamilia
11   3      Familia
12 3.2 Superfamilia
13 3.5    Infraordo
14 3.8      Subordo
15   4         Ordo
16 4.2    Superordo
17 4.5 Infraclassis
18 4.8   Subclassis
19   5      Classis
20 5.2 Superclassis
21 5.8    Subphylum
22   6       Phylum
23 6.2  Superphylum
24 6.5  Infraregnum
25 6.8    Subregnum
26   7       Regnum
27 7.2  Superregnum
> 
> ## ===
> 
> Numranks(nums=1:7)
[1] "Species" "Genus"   "Familia" "Ordo"    "Classis" "Phylum"  "Regnum" 
> Numranks(ranks="kingdom") # "kingdom", "order", "family" and "tribe" translate into Latin
[1] 7
> 
> ## ===
> 
> ## three branched keys
> i1 <- c("1 A ", "2 B Name1", "2 BB Name2", "1 AA ", "3 C Name3", "3 CC Name4")
> i2 <- c("1 A Name1", "2 B Name2", "2 BB ", "3 C Name3", "3 CC Name4")
> i3 <- c("1 A Name1", "2 B Name2", "2 BB ", "3 C Name3",
+  "3 CC Name4", "2 BBB ", "4 D Name5", "4 DD Name6", "4 DDD Name7")
> k1 <- read.table(textConnection(i1), sep=" ", as.is=TRUE)
> k2 <- read.table(textConnection(i2), sep=" ", as.is=TRUE)
> k3 <- read.table(textConnection(i3), sep=" ", as.is=TRUE)
> 
> ## convert them into phylogeny trees and plot
> t1 <- Biokey(k1, from="branched", to="newick")
> t2 <- Biokey(k2, from="branched", to="newick")
> t3 <- Biokey(k3, from="branched", to="newick")
> library(ape) # load 'ape' to plot Newick trees below
Error in library(ape) : there is no package called ‘ape’
Execution halted