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

> ### Name: [.taxa_classification
> ### Title: Taxonomy class
> ### Aliases: [.taxa_classification [[.taxa_classification taxonomy
> ###   names.taxa_taxonomy names<-.taxa_taxonomy [.taxa_taxonomy
> ###   [[.taxa_taxonomy
> ### Keywords: internal
> 
> ### ** Examples
> 
> 
> x <- taxonomy(c('Carnivora', 'Felidae', 'Panthera', 'Panthera leo',
+                 'Panthera tigris', 'Ursidae', 'Ursus', 'Ursus arctos'),
+               supertaxa = c(NA, 1, 2, 3, 3, 1, 6, 7))
> 
> x <- taxonomy(taxon(name = c('Carnivora', 'Felidae', 'Panthera', 'Panthera leo',
+                              'Panthera tigris', 'Ursidae', 'Ursus', 'Ursus arctos'),
+                     rank = c('order', 'family', 'genus', 'species',
+                              'species', 'family', 'genus', 'species'),
+                     id = taxon_id(c('33554', '9681', '9688', '9689',
+                                     '9694', '9632', '9639', '9644'),
+                                   db = 'ncbi'),
+                     auth = c('Bowdich, 1821', 'Fischer de Waldheim, 1817', 'Oken, 1816', 'L., 1758',
+                              'L., 1758', 'Fischer de Waldheim, 1817', 'L., 1758', 'L., 1758')),
+               supertaxa = c(NA, 1, 2, 3, 3, 1, 6, 7))
> names(x) <- letters[1:8]
> 
> # Subset taxonomy vector
> x[2] # By default, all subtaxa are included
<taxonomy[4]>
1[b]: 9681|Felidae Fischer de Waldheim 1817|family
\-2[c]: 9688|Panthera Oken 1816|genus
  +-3[d]: 9689|Panthera leo L. 1758|species
  \-4[e]: 9694|Panthera tigris L. 1758|species
Rank levels: order < family < genus < species
> x['b'] # Names can also be used
<taxonomy[4]>
1[b]: 9681|Felidae Fischer de Waldheim 1817|family
\-2[c]: 9688|Panthera Oken 1816|genus
  +-3[d]: 9689|Panthera leo L. 1758|species
  \-4[e]: 9694|Panthera tigris L. 1758|species
Rank levels: order < family < genus < species
> x[2:3, subtaxa = FALSE] # Disable subtaxa
<taxonomy[2]>
1[b]: 9681|Felidae Fischer de Waldheim 1817|family
\-2[c]: 9688|Panthera Oken 1816|genus
Rank levels: order < family < genus < species
> x[3, supertaxa = TRUE] # include supertaxa
<taxonomy[5]>
1[a]: 33554|Carnivora Bowdich 1821|order
\-2[b]: 9681|Felidae Fischer de Waldheim 1817|family
  \-3[c]: 9688|Panthera Oken 1816|genus
    +-4[d]: 9689|Panthera leo L. 1758|species
    \-5[e]: 9694|Panthera tigris L. 1758|species
Rank levels: order < family < genus < species
> x[is_leaf(x)] # Subset by logical vector
<taxonomy[3]>
1[d]: 9689|Panthera leo L. 1758|species
2[e]: 9694|Panthera tigris L. 1758|species
3[h]: 9644|Ursus arctos L. 1758|species
Rank levels: order < family < genus < species
> 
> # Get parts of the taxonomy vector
> tax_name(x)
                a                 b                 c                 d 
      "Carnivora"         "Felidae"        "Panthera"    "Panthera leo" 
                e                 f                 g                 h 
"Panthera tigris"         "Ursidae"           "Ursus"    "Ursus arctos" 
> tax_rank(x)
<taxon_rank[8]>
      a       b       c       d       e       f       g       h 
  order  family   genus species species  family   genus species 
Rank levels: order < family < genus < species
> tax_id(x)
<taxon_id[8]>
           a            b            c            d            e            f 
33554 (ncbi)  9681 (ncbi)  9688 (ncbi)  9689 (ncbi)  9694 (ncbi)  9632 (ncbi) 
           g            h 
 9639 (ncbi)  9644 (ncbi) 
> tax_db(x)
<taxon_db[8]>
   a    b    c    d    e    f    g    h 
ncbi ncbi ncbi ncbi ncbi ncbi ncbi ncbi 
> tax_auth(x)
<taxon_authority[8]>
                       a                        b                        c 
            Bowdich 1821 Fischer de Waldheim 1817                Oken 1816 
                       d                        e                        f 
                 L. 1758                  L. 1758 Fischer de Waldheim 1817 
                       g                        h 
                 L. 1758                  L. 1758 
> tax_author(x)
                    a                     b                     c 
            "Bowdich" "Fischer de Waldheim"                "Oken" 
                    d                     e                     f 
                 "L."                  "L." "Fischer de Waldheim" 
                    g                     h 
                 "L."                  "L." 
> tax_date(x)
     a      b      c      d      e      f      g      h 
"1821" "1817" "1816" "1758" "1758" "1817" "1758" "1758" 
> tax_cite(x)
 a  b  c  d  e  f  g  h 
NA NA NA NA NA NA NA NA 
> 
> # Set parts of the taxonomy vector
> tax_name(x) <- tolower(tax_name(x))
> tax_rank(x)[1] <- NA
> tax_id(x) <- '9999'
> tax_db(x) <- 'itis'
> tax_auth(x) <- NA
> tax_author(x)[2:3] <- c('Joe', 'Billy')
> tax_date(x) <- c('1999', '2013', '1796', '1899',
+                  '1997', '2003', '1996', '1859')
> tax_cite(x)['c'] <- 'Linnaeus, C. (1771). Mantissa plantarum altera generum.'
> 
> # Convert to table
> tibble::as_tibble(x)
# A tibble: 8 x 8
  supertaxon tax_name        tax_rank tax_id tax_db tax_author tax_date tax_cite
       <int> <chr>           <chr>    <chr>  <chr>  <chr>      <chr>    <chr>   
1         NA carnivora       <NA>     9999   itis   <NA>       1999     <NA>    
2          1 felidae         family   9999   itis   Joe        2013     <NA>    
3          2 panthera        genus    9999   itis   Billy      1796     Linnaeu~
4          3 panthera leo    species  9999   itis   <NA>       1899     <NA>    
5          3 panthera tigris species  9999   itis   <NA>       1997     <NA>    
6          1 ursidae         family   9999   itis   <NA>       2003     <NA>    
7          6 ursus           genus    9999   itis   <NA>       1996     <NA>    
8          7 ursus arctos    species  9999   itis   <NA>       1859     <NA>    
> as_data_frame(x)
  supertaxon        tax_name tax_rank tax_id tax_db tax_author tax_date
1         NA       carnivora     <NA>   9999   itis       <NA>     1999
2          1         felidae   family   9999   itis        Joe     2013
3          2        panthera    genus   9999   itis      Billy     1796
4          3    panthera leo  species   9999   itis       <NA>     1899
5          3 panthera tigris  species   9999   itis       <NA>     1997
6          1         ursidae   family   9999   itis       <NA>     2003
7          6           ursus    genus   9999   itis       <NA>     1996
8          7    ursus arctos  species   9999   itis       <NA>     1859
                                                 tax_cite
1                                                    <NA>
2                                                    <NA>
3 Linnaeus, C. (1771). Mantissa plantarum altera generum.
4                                                    <NA>
5                                                    <NA>
6                                                    <NA>
7                                                    <NA>
8                                                    <NA>
> 
> # Get taxonomy attributes
> subtaxa(x)
$a
b c d e f g h 
2 3 4 5 6 7 8 

$b
c d e 
3 4 5 

$c
d e 
4 5 

$d
named integer(0)

$e
named integer(0)

$f
g h 
7 8 

$g
h 
8 

$h
named integer(0)

> subtaxa(x, value = tax_name(x))
$a
                b                 c                 d                 e 
        "felidae"        "panthera"    "panthera leo" "panthera tigris" 
                f                 g                 h 
        "ursidae"           "ursus"    "ursus arctos" 

$b
                c                 d                 e 
       "panthera"    "panthera leo" "panthera tigris" 

$c
                d                 e 
   "panthera leo" "panthera tigris" 

$d
named character(0)

$e
named character(0)

$f
             g              h 
       "ursus" "ursus arctos" 

$g
             h 
"ursus arctos" 

$h
named character(0)

> subtaxa(x, value = as_taxon(x))
$a
<taxon[7]>
                                   b                                    c 
        9999|felidae Joe 2013|family       9999|panthera Billy 1796|genus 
                                   d                                    e 
   9999|panthera leo NA 1899|species 9999|panthera tigris NA 1997|species 
                                   f                                    g 
         9999|ursidae NA 2003|family             9999|ursus NA 1996|genus 
                                   h 
   9999|ursus arctos NA 1859|species 
Rank levels: order < family < genus < species

$b
<taxon[3]>
                                   c                                    d 
      9999|panthera Billy 1796|genus    9999|panthera leo NA 1899|species 
                                   e 
9999|panthera tigris NA 1997|species 
Rank levels: order < family < genus < species

$c
<taxon[2]>
                                   d                                    e 
   9999|panthera leo NA 1899|species 9999|panthera tigris NA 1997|species 
Rank levels: order < family < genus < species

$d
<taxon[0]>
Rank levels: order < family < genus < species

$e
<taxon[0]>
Rank levels: order < family < genus < species

$f
<taxon[2]>
                                g                                 h 
         9999|ursus NA 1996|genus 9999|ursus arctos NA 1859|species 
Rank levels: order < family < genus < species

$g
<taxon[1]>
                                h 
9999|ursus arctos NA 1859|species 
Rank levels: order < family < genus < species

$h
<taxon[0]>
Rank levels: order < family < genus < species

> n_subtaxa(x)
a b c d e f g h 
7 3 2 0 0 2 1 0 
> supertaxa(x)
$a
named integer(0)

$b
a 
1 

$c
b a 
2 1 

$d
c b a 
3 2 1 

$e
c b a 
3 2 1 

$f
a 
1 

$g
f a 
6 1 

$h
g f a 
7 6 1 

> n_supertaxa(x)
a b c d e f g h 
0 1 2 3 3 1 2 3 
> leaves(x)
$a
d e h 
4 5 8 

$b
d e 
4 5 

$c
d e 
4 5 

$d
named integer(0)

$e
named integer(0)

$f
h 
8 

$g
h 
8 

$h
named integer(0)

> n_leaves(x)
a b c d e f g h 
3 2 2 0 0 1 1 0 
> is_leaf(x)
    a     b     c     d     e     f     g     h 
FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE 
> stems(x)
$a
named integer(0)

> is_stem(x)
    a     b     c     d     e     f     g     h 
FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 
> roots(x)
a 
1 
> is_root(x)
    a     b     c     d     e     f     g     h 
 TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 
> internodes(x)
b f g 
2 6 7 
> is_internode(x)
    a     b     c     d     e     f     g     h 
FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE 
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  6.04 0.11 6.16 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')