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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assess_missing_data_pca
> ### Title: Vizualise how missing data thresholds affect sample clustering
> ### Aliases: assess_missing_data_pca
> 
> ### ** Examples
> 
> assess_missing_data_pca(vcfR = SNPfiltR::vcfR.example,
+ popmap = SNPfiltR::popmap,
+ thresholds = c(.6,.8))
cutoff is specified, filtered vcfR object will be returned
41% of SNPs fell below a completeness cutoff of 0.6 and were removed from the VCF
Loading required namespace: adegenet
Error in dfs[[i]] <- pca.scores : 
  attempt to select less than one element in OneIndex <real>
Calls: assess_missing_data_pca
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'reproducible-vignette.Rmd' using rmarkdown
Quitting from lines 102-104 (reproducible-vignette.Rmd) 
Error: processing vignette 'reproducible-vignette.Rmd' failed with diagnostics:
attempt to select less than one element in OneIndex <real>
--- failed re-building 'reproducible-vignette.Rmd'

SUMMARY: processing the following file failed:
  'reproducible-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in ‘SNPfiltR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assess_missing_data_pca
> ### Title: Vizualise how missing data thresholds affect sample clustering
> ### Aliases: assess_missing_data_pca
> 
> ### ** Examples
> 
> assess_missing_data_pca(vcfR = SNPfiltR::vcfR.example,
+ popmap = SNPfiltR::popmap,
+ thresholds = c(.6,.8))
cutoff is specified, filtered vcfR object will be returned
41% of SNPs fell below a completeness cutoff of 0.6 and were removed from the VCF
Loading required namespace: adegenet
Error in dfs[[i]] <- pca.scores : 
  attempt to select less than one element in OneIndex <real>
Calls: assess_missing_data_pca
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘reproducible-vignette.Rmd’ using rmarkdown
Quitting from lines 102-104 (reproducible-vignette.Rmd) 
Error: processing vignette ‘reproducible-vignette.Rmd’ failed with diagnostics:
attempt to select less than one element in OneIndex <real>
--- failed re-building ‘reproducible-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘reproducible-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘SNPfiltR-Ex.R’ failed
The error most likely occurred in:

> ### Name: assess_missing_data_pca
> ### Title: Vizualise how missing data thresholds affect sample clustering
> ### Aliases: assess_missing_data_pca
> 
> ### ** Examples
> 
> assess_missing_data_pca(vcfR = SNPfiltR::vcfR.example,
+ popmap = SNPfiltR::popmap,
+ thresholds = c(.6,.8))
cutoff is specified, filtered vcfR object will be returned
41% of SNPs fell below a completeness cutoff of 0.6 and were removed from the VCF
Loading required namespace: adegenet
Error in dfs[[i]] <- pca.scores : 
  attempt to select less than one element in OneIndex <real>
Calls: assess_missing_data_pca
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘reproducible-vignette.Rmd’ using rmarkdown
Quitting from lines 102-104 (reproducible-vignette.Rmd) 
Error: processing vignette 'reproducible-vignette.Rmd' failed with diagnostics:
attempt to select less than one element in OneIndex <real>
--- failed re-building ‘reproducible-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘reproducible-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘SNPfiltR-Ex.R’ failed
The error most likely occurred in:

> ### Name: assess_missing_data_pca
> ### Title: Vizualise how missing data thresholds affect sample clustering
> ### Aliases: assess_missing_data_pca
> 
> ### ** Examples
> 
> assess_missing_data_pca(vcfR = SNPfiltR::vcfR.example,
+ popmap = SNPfiltR::popmap,
+ thresholds = c(.6,.8))
cutoff is specified, filtered vcfR object will be returned
41% of SNPs fell below a completeness cutoff of 0.6 and were removed from the VCF
Loading required namespace: adegenet
Error in dfs[[i]] <- pca.scores : 
  attempt to select less than one element in OneIndex <real>
Calls: assess_missing_data_pca
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘reproducible-vignette.Rmd’ using rmarkdown
Quitting from lines 102-104 (reproducible-vignette.Rmd) 
Error: processing vignette 'reproducible-vignette.Rmd' failed with diagnostics:
attempt to select less than one element in OneIndex <real>
--- failed re-building ‘reproducible-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘reproducible-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in 'SNPfiltR-Ex.R' failed
The error most likely occurred in:

> ### Name: assess_missing_data_pca
> ### Title: Vizualise how missing data thresholds affect sample clustering
> ### Aliases: assess_missing_data_pca
> 
> ### ** Examples
> 
> assess_missing_data_pca(vcfR = SNPfiltR::vcfR.example,
+ popmap = SNPfiltR::popmap,
+ thresholds = c(.6,.8))
cutoff is specified, filtered vcfR object will be returned
41% of SNPs fell below a completeness cutoff of 0.6 and were removed from the VCF
Loading required namespace: adegenet
Error in dfs[[i]] <- pca.scores : 
  attempt to select less than one element in OneIndex <real>
Calls: assess_missing_data_pca
Execution halted
Error(s) in re-building vignettes:
--- re-building 'reproducible-vignette.Rmd' using rmarkdown
Quitting from lines 102-104 (reproducible-vignette.Rmd) 
Error: processing vignette 'reproducible-vignette.Rmd' failed with diagnostics:
attempt to select less than one element in OneIndex <real>
--- failed re-building 'reproducible-vignette.Rmd'

SUMMARY: processing the following file failed:
  'reproducible-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in 'SNPfiltR-Ex.R' failed
The error most likely occurred in:

> ### Name: assess_missing_data_pca
> ### Title: Vizualise how missing data thresholds affect sample clustering
> ### Aliases: assess_missing_data_pca
> 
> ### ** Examples
> 
> assess_missing_data_pca(vcfR = SNPfiltR::vcfR.example,
+ popmap = SNPfiltR::popmap,
+ thresholds = c(.6,.8))
cutoff is specified, filtered vcfR object will be returned
41% of SNPs fell below a completeness cutoff of 0.6 and were removed from the VCF
Loading required namespace: adegenet
Error in dfs[[i]] <- pca.scores : 
  attempt to select less than one element in OneIndex <real>
Calls: assess_missing_data_pca
Execution halted
Error(s) in re-building vignettes:
--- re-building 'reproducible-vignette.Rmd' using rmarkdown
Quitting from lines 102-104 (reproducible-vignette.Rmd) 
Error: processing vignette 'reproducible-vignette.Rmd' failed with diagnostics:
attempt to select less than one element in OneIndex <real>
--- failed re-building 'reproducible-vignette.Rmd'

SUMMARY: processing the following file failed:
  'reproducible-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in ‘SNPfiltR-Ex.R’ failed
The error most likely occurred in:

> ### Name: assess_missing_data_pca
> ### Title: Vizualise how missing data thresholds affect sample clustering
> ### Aliases: assess_missing_data_pca
> 
> ### ** Examples
> 
> assess_missing_data_pca(vcfR = SNPfiltR::vcfR.example,
+ popmap = SNPfiltR::popmap,
+ thresholds = c(.6,.8))
cutoff is specified, filtered vcfR object will be returned
41% of SNPs fell below a completeness cutoff of 0.6 and were removed from the VCF
Loading required namespace: adegenet
Error in dfs[[i]] <- pca.scores : 
  attempt to select less than one element in integerOneIndex
Calls: assess_missing_data_pca
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘reproducible-vignette.Rmd’ using rmarkdown
Quitting from lines 102-104 (reproducible-vignette.Rmd) 
Error: processing vignette 'reproducible-vignette.Rmd' failed with diagnostics:
attempt to select less than one element in integerOneIndex
--- failed re-building ‘reproducible-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘reproducible-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in 'SNPfiltR-Ex.R' failed
The error most likely occurred in:

> ### Name: assess_missing_data_pca
> ### Title: Vizualise how missing data thresholds affect sample clustering
> ### Aliases: assess_missing_data_pca
> 
> ### ** Examples
> 
> assess_missing_data_pca(vcfR = SNPfiltR::vcfR.example,
+ popmap = SNPfiltR::popmap,
+ thresholds = c(.6,.8))
cutoff is specified, filtered vcfR object will be returned
41% of SNPs fell below a completeness cutoff of 0.6 and were removed from the VCF
Loading required namespace: adegenet
Error in dfs[[i]] <- pca.scores : 
  attempt to select less than one element in integerOneIndex
Calls: assess_missing_data_pca
Execution halted
Error(s) in re-building vignettes:
--- re-building 'reproducible-vignette.Rmd' using rmarkdown
Quitting from lines 102-104 (reproducible-vignette.Rmd) 
Error: processing vignette 'reproducible-vignette.Rmd' failed with diagnostics:
attempt to select less than one element in integerOneIndex
--- failed re-building 'reproducible-vignette.Rmd'

SUMMARY: processing the following file failed:
  'reproducible-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted