Found the following files/directories:
  'Bestmatches.csv' 'ID.csv' 'listsp.csv' 'mylabels.csv'
Found the following files/directories:
  ‘Bestmatches.csv’ ‘ID.csv’ ‘listsp.csv’ ‘mylabels.csv’
Running examples in ‘adhoc-Ex.R’ failed
The error most likely occurred in:

> ### Name: adhoc-package
> ### Title: Calculation of ad hoc distance thresholds for DNA barcoding
> ###   identification.
> ### Aliases: adhoc-package adhoc
> 
> ### ** Examples
> 
> data(tephdata);
> out1<-checkDNAbcd(tephdata);
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences were not assigned to the same haplotype because of ambiguities
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences of different lengths were assigned to the same haplotype
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences of different lengths were assigned to the same haplotype
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences of different lengths were assigned to the same haplotype
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences were not assigned to the same haplotype because of ambiguities
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences of different lengths were assigned to the same haplotype
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  no segregating site detected with these options
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences were not assigned to the same haplotype because of ambiguities
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  no segregating site detected with these options
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences of different lengths were assigned to the same haplotype
> out2<-adhocTHR(out1);
Error in Reg == "linear" && myreg$coefficients < 0 : 
  'length = 4' in coercion to 'logical(1)'
Calls: adhocTHR
Execution halted
Found the following files/directories:
  ‘Bestmatches.csv’ ‘ID.csv’ ‘listsp.csv’ ‘mylabels.csv’
Running examples in ‘adhoc-Ex.R’ failed
The error most likely occurred in:

> ### Name: adhoc-package
> ### Title: Calculation of ad hoc distance thresholds for DNA barcoding
> ###   identification.
> ### Aliases: adhoc-package adhoc
> 
> ### ** Examples
> 
> data(tephdata);
> out1<-checkDNAbcd(tephdata);
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences were not assigned to the same haplotype because of ambiguities
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences of different lengths were assigned to the same haplotype
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences of different lengths were assigned to the same haplotype
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences of different lengths were assigned to the same haplotype
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences were not assigned to the same haplotype because of ambiguities
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences of different lengths were assigned to the same haplotype
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  no segregating site detected with these options
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences were not assigned to the same haplotype because of ambiguities
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  no segregating site detected with these options
Warning in haplotype.DNAbin(seq[grep(listsp$species[[i]], labels(seq)),  :
  some sequences of different lengths were assigned to the same haplotype
> out2<-adhocTHR(out1);
Error in Reg == "linear" && myreg$coefficients < 0 : 
  'length = 4' in coercion to 'logical(1)'
Calls: adhocTHR
Execution halted
Found the following files/directories:
  ‘Bestmatches.csv’ ‘ID.csv’ ‘listsp.csv’ ‘mylabels.csv’
Found the following files/directories:
  ‘Bestmatches.csv’ ‘ID.csv’ ‘listsp.csv’ ‘mylabels.csv’
Found the following files/directories:
  ‘Bestmatches.csv’ ‘ID.csv’ ‘listsp.csv’ ‘mylabels.csv’