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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diagCharNA
> ### Title: Identification of diagnostic molecular characters in nucleotide
> ###   alignments for the delineation of taxa
> ### Aliases: diagCharNA
> 
> ### ** Examples
> 
> #using a dataset from spider
> #install.packages("spider")
> library(spider)
> data("anoteropsis")
> anoTax <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"),
+ 	function(x) paste(x[1], x[2], sep="_"))
> diagCharNA(anoteropsis, anoTax, taxOfInt="all")
$Artoria_flavimanus
      position type    states compared taxa
 [1,] "4"      "type1" "a"    ""           
 [2,] "10"     "type1" "t"    ""           
 [3,] "79"     "type1" "c"    ""           
 [4,] "106"    "type1" "g"    ""           
 [5,] "133"    "type1" "a"    ""           
 [6,] "169"    "type1" "t"    ""           
 [7,] "218"    "type1" "t"    ""           
 [8,] "220"    "type1" "t"    ""           
 [9,] "241"    "type1" "a"    ""           
[10,] "289"    "type1" "t"    ""           
[11,] "307"    "type1" "a"    ""           

$Artoria_separata
     position type    states compared taxa
[1,] "7"      "type1" "a"    ""           
[2,] "31"     "type1" "a"    ""           
[3,] "40"     "type1" "t"    ""           
[4,] "61"     "type1" "g"    ""           
[5,] "79"     "type1" "a"    ""           
[6,] "232"    "type1" "a"    ""           
[7,] "280"    "type1" "t"    ""           
[8,] "364"    "type1" "t"    ""           

$Anoteropsis_adumbrata
     position type    states compared taxa
[1,] "211"    "type3" "g"    ""           
[2,] "319"    "type1" "g"    ""           

$Anoteropsis_aerescens
     position type states compared taxa

$Anoteropsis_alpina
     position type    states compared taxa
[1,] "112"    "type1" "c"    ""           
[2,] "169"    "type1" "g"    ""           
[3,] "343"    "type1" "c"    ""           

$Anoteropsis_arenivaga
     position type    states compared taxa
[1,] "4"      "type1" "c"    ""           
[2,] "52"     "type1" "a"    ""           

$Anoteropsis_blesti
     position type    states compared taxa
[1,] "193"    "type1" "c"    ""           
[2,] "370"    "type1" "g"    ""           

$Anoteropsis_canescens
     position type    states compared taxa
[1,] "214"    "type1" "g"    ""           

$Anoteropsis_cantuaria
     position type    states compared taxa
[1,] "223"    "type1" "t"    ""           
[2,] "403"    "type1" "c"    ""           

$Anoteropsis_flavescens
     position type states compared taxa

$Anoteropsis_forsteri
     position type states compared taxa

$Anoteropsis_hallae
     position type states compared taxa

$Anoteropsis_hilaris
     position type    states compared taxa
[1,] "1"      "type3" "g"    ""           
[2,] "83"     "type1" "t"    ""           
[3,] "217"    "type3" "g"    ""           
[4,] "295"    "type3" "g"    ""           
[5,] "400"    "type3" "-"    ""           
[6,] "403"    "type3" "-"    ""           

$Anoteropsis_insularis
     position type    states compared taxa
[1,] "73"     "type1" "c"    ""           

$Anoteropsis_lacustris
     position type    states compared taxa
[1,] "70"     "type1" "a"    ""           
[2,] "157"    "type1" "g"    ""           
[3,] "286"    "type1" "c"    ""           

$Anoteropsis_litoralis
     position type    states compared taxa
[1,] "64"     "type1" "g"    ""           
[2,] "281"    "type1" "c"    ""           
[3,] "325"    "type1" "g"    ""           

$Anoteropsis_montana
     position type    states compared taxa
[1,] "166"    "type1" "a"    ""           
[2,] "301"    "type1" "a"    ""           

$Anoteropsis_okatainae
     position type    states compared taxa
[1,] "70"     "type1" "c"    ""           
[2,] "247"    "type1" "g"    ""           
[3,] "340"    "type1" "c"    ""           

$Anoteropsis_ralphi
     position type    states compared taxa
[1,] "142"    "type1" "g"    ""           
[2,] "178"    "type1" "c"    ""           
[3,] "190"    "type1" "c"    ""           

$Anoteropsis_senica
     position type    states compared taxa
[1,] "58"     "type3" "g"    ""           

$Anoteropsis_urquharti
     position type    states compared taxa
[1,] "10"     "type1" "g"    ""           

$Anoteropsis_westlandica
     position type    states compared taxa
[1,] "34"     "type1" "c"    ""           

> diagCharNA(anoteropsis, anoTax, taxOfInt="all", types=c("type1","type2"))
$Artoria_flavimanus
      position type    states compared taxa
 [1,] "4"      "type1" "a"    ""           
 [2,] "10"     "type1" "t"    ""           
 [3,] "79"     "type1" "c"    ""           
 [4,] "106"    "type1" "g"    ""           
 [5,] "133"    "type1" "a"    ""           
 [6,] "169"    "type1" "t"    ""           
 [7,] "218"    "type1" "t"    ""           
 [8,] "220"    "type1" "t"    ""           
 [9,] "241"    "type1" "a"    ""           
[10,] "289"    "type1" "t"    ""           
[11,] "307"    "type1" "a"    ""           

$Artoria_separata
     position type    states compared taxa
[1,] "7"      "type1" "a"    ""           
[2,] "31"     "type1" "a"    ""           
[3,] "40"     "type1" "t"    ""           
[4,] "61"     "type1" "g"    ""           
[5,] "79"     "type1" "a"    ""           
[6,] "232"    "type1" "a"    ""           
[7,] "280"    "type1" "t"    ""           
[8,] "364"    "type1" "t"    ""           

$Anoteropsis_adumbrata
     position type    states compared taxa
[1,] "319"    "type1" "g"    ""           

$Anoteropsis_aerescens
     position type states compared taxa

$Anoteropsis_alpina
     position type    states compared taxa
[1,] "112"    "type1" "c"    ""           
[2,] "169"    "type1" "g"    ""           
[3,] "343"    "type1" "c"    ""           

$Anoteropsis_arenivaga
     position type    states compared taxa
[1,] "4"      "type1" "c"    ""           
[2,] "52"     "type1" "a"    ""           

$Anoteropsis_blesti
     position type    states compared taxa
[1,] "193"    "type1" "c"    ""           
[2,] "370"    "type1" "g"    ""           

$Anoteropsis_canescens
     position type    states compared taxa
[1,] "214"    "type1" "g"    ""           

$Anoteropsis_cantuaria
     position type    states compared taxa
[1,] "223"    "type1" "t"    ""           
[2,] "403"    "type1" "c"    ""           

$Anoteropsis_flavescens
     position type states compared taxa

$Anoteropsis_forsteri
     position type states compared taxa

$Anoteropsis_hallae
     position type states compared taxa

$Anoteropsis_hilaris
     position type    states compared taxa
[1,] "83"     "type1" "t"    ""           

$Anoteropsis_insularis
     position type    states compared taxa
[1,] "73"     "type1" "c"    ""           

$Anoteropsis_lacustris
     position type    states compared taxa
[1,] "70"     "type1" "a"    ""           
[2,] "157"    "type1" "g"    ""           
[3,] "286"    "type1" "c"    ""           

$Anoteropsis_litoralis
     position type    states compared taxa
[1,] "64"     "type1" "g"    ""           
[2,] "281"    "type1" "c"    ""           
[3,] "325"    "type1" "g"    ""           

$Anoteropsis_montana
     position type    states compared taxa
[1,] "166"    "type1" "a"    ""           
[2,] "301"    "type1" "a"    ""           

$Anoteropsis_okatainae
     position type    states compared taxa
[1,] "70"     "type1" "c"    ""           
[2,] "247"    "type1" "g"    ""           
[3,] "340"    "type1" "c"    ""           

$Anoteropsis_ralphi
     position type    states compared taxa
[1,] "142"    "type1" "g"    ""           
[2,] "178"    "type1" "c"    ""           
[3,] "190"    "type1" "c"    ""           

$Anoteropsis_senica
     position type states compared taxa

$Anoteropsis_urquharti
     position type    states compared taxa
[1,] "10"     "type1" "g"    ""           

$Anoteropsis_westlandica
     position type    states compared taxa
[1,] "34"     "type1" "c"    ""           

> #
> #with loading of a fasta file
> #install.packages("adegenet")
> library(adegenet)
Error in library(adegenet) : there is no package called ‘adegenet’
Execution halted