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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BIGDAWG
> ### Title: BIGDAWG wrapper function
> ### Aliases: BIGDAWG
> 
> ### ** Examples
> 
> ### The following examples use the synthetic data set bundled with BIGDAWG
> 
> # Haplotype analysis with no missing genotypes for two loci
> # Significant haplotypic association with phenotype 
> BIGDAWG(Data="HLA_data", Run.Tests="H", Missing=0, Loci.Set=list(c("DRB1","DQB1")))

>>>>>>>>>>>>>>>>>>>>>>>>> BIGDAWG Analysis <<<<<<<<<<<<<<<<<<<<<<<<<

>>>> CASE - CONTROL SUMMARY STATISTICS
  Sample Summary
    Sample Size (n): 2000 
    ...Number of Controls/Cases: 1002/998 
    Allele Count (2n): 4000 
    Total loci in file: 6 
    Unique loci: A, DRB1, DQB1, DRB3, DRB4, DRB5 
    Unique alleles per locus: 22, 20, 20, 8, 6, 4 
    ...Unique in Controls/Cases: 22/22, 17/18, 17/19, 7/8, 6/4, 3/4 
    Missing alleles per locus: 0, 30, 0, 30, 30, 30 
    ...Missing in Controls/Cases: 0/0, 22/8, 0/0, 22/8, 22/8, 22/8 

  Observed Allele Resolution
    Max Resolution Controls: 4-Field 
    Max Resolution Cases: 4-Field 
    Defined Resolution: Not Defined 

>>>> DATA PROCESSING AND CHECKS.
Removing any missing data. This will affect Hardy-Weinberg Equilibrium test.

>>>>>>>>>>>>>>>>>>>>>>>>> Begin Locus Sets <<<<<<<<<<<<<<<<<<<<<<<<<

Your analysis has 1 set(s). 

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running Set 1 
>>>> STARTING HAPLOTYPE ANALYSIS... 
Estimating Haplotypes ... DRB1~DQB1 
> HAPLOTYPE ANALYSIS COMPLETED: DRB1~DQB1 
 X.square df    p.value sig
 287.3406 60 < 2.22e-16   *


>>>>>>>>>>>>>>>>>>>>>>>>>> End Analysis <<<<<<<<<<<<<<<<<<<<<<<<<<
> 
> # Hardy-Weinberg and Locus analysis ignoring missing data
> # Significant locus associations with phenotype at all but DQB1
> BIGDAWG(Data="HLA_data", Run.Tests=c("HWE","L"), Missing="ignore")

>>>>>>>>>>>>>>>>>>>>>>>>> BIGDAWG Analysis <<<<<<<<<<<<<<<<<<<<<<<<<

>>>> CASE - CONTROL SUMMARY STATISTICS
  Sample Summary
    Sample Size (n): 2000 
    ...Number of Controls/Cases: 1002/998 
    Allele Count (2n): 4000 
    Total loci in file: 6 
    Unique loci: A, DRB1, DQB1, DRB3, DRB4, DRB5 
    Unique alleles per locus: 22, 20, 20, 8, 6, 4 
    ...Unique in Controls/Cases: 22/22, 17/18, 17/19, 7/8, 6/4, 3/4 
    Missing alleles per locus: 0, 30, 0, 30, 30, 30 
    ...Missing in Controls/Cases: 0/0, 22/8, 0/0, 22/8, 22/8, 22/8 

  Observed Allele Resolution
    Max Resolution Controls: 4-Field 
    Max Resolution Cases: 4-Field 
    Defined Resolution: Not Defined 

>>>> DATA PROCESSING AND CHECKS.
Ignoring any missing data.
Consider setting a missing threshold or running without the haplotype ('H') analysis.

>>>> STARTING HARDY-WEINBERG ANALYSIS...
HWE performed at maximum available resolution.

> HARDY-WEINBERG ANALYSIS COMPLETED

Controls (Group 0):
 Locus X.square df    p.value sig
     A    0.558 54          1  NS
  DRB1    0.526 37          1  NS
  DQB1 184.7565 64 1.1813e-13   *
  DRB3   0.5334 10    0.99999  NS
  DRB4   0.1415  3    0.98642  NS
  DRB5    0.133  2    0.93568  NS

Cases (Group 1):
 Locus X.square df p.value sig
     A   0.6176 52       1  NS
  DRB1   0.2035 29       1  NS
  DQB1   1.3687 65       1  NS
  DRB3   0.1473  8       1  NS
  DRB4   0.0287  2 0.98577  NS
  DRB5   0.0183  1  0.8924  NS


>>>>>>>>>>>>>>>>>>>>>>>>> Begin Locus Sets <<<<<<<<<<<<<<<<<<<<<<<<<

Your analysis has 1 set(s). 

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running Set 1 
Error in setwd(OutSetDir) : cannot change working directory
Calls: BIGDAWG -> setwd
Error in setwd(MainDir) : cannot change working directory
Calls: BIGDAWG -> setwd
Execution halted