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

> ### Name: BootstrapQTL
> ### Title: Bootstrap QTL analysis for accurate effect size estimation
> ### Aliases: BootstrapQTL
> 
> ### ** Examples
> 
> # Locations for example data from the MatrixEQTL package
> base.dir = find.package('MatrixEQTL');
> SNP_file_name = paste(base.dir, "/data/SNP.txt", sep="");
> snps_location_file_name = paste(base.dir, "/data/snpsloc.txt", sep="");
> expression_file_name = paste(base.dir, "/data/GE.txt", sep="");
> gene_location_file_name = paste(base.dir, "/data/geneloc.txt", sep="");
> covariates_file_name = paste(base.dir, "/data/Covariates.txt", sep="");
> 
> # Load the SNP data
> snps = SlicedData$new();
> snps$fileDelimiter = "\t";      # the TAB character
> snps$fileOmitCharacters = "NA"; # denote missing values;
> snps$fileSkipRows = 1;          # one row of column labels
> snps$fileSkipColumns = 1;       # one column of row labels
> snps$fileSliceSize = 2000;      # read file in slices of 2,000 rows
> snps$LoadFile(SNP_file_name);
Rows read: 15 done.
> 
> # Load the data detailing the position of each SNP
> snpspos = read.table(snps_location_file_name, header = TRUE, stringsAsFactors = FALSE);
> 
> # Load the gene expression data
> gene = SlicedData$new();
> gene$fileDelimiter = "\t";      # the TAB character
> gene$fileOmitCharacters = "NA"; # denote missing values;
> gene$fileSkipRows = 1;          # one row of column labels
> gene$fileSkipColumns = 1;       # one column of row labels
> gene$fileSliceSize = 2000;      # read file in slices of 2,000 rows
> gene$LoadFile(expression_file_name);
Rows read: 10 done.
> 
> # Load the data detailing the position of each gene
> genepos = read.table(gene_location_file_name, header = TRUE, stringsAsFactors = FALSE);
> 
> # Load the covariates data
> cvrt = SlicedData$new();
> cvrt$fileDelimiter = "\t";      # the TAB character
> cvrt$fileOmitCharacters = "NA"; # denote missing values;
> cvrt$fileSkipRows = 1;          # one row of column labels
> cvrt$fileSkipColumns = 1;       # one column of row labels
> if(length(covariates_file_name)>0) {
+   cvrt$LoadFile(covariates_file_name);
+ }
Rows read: 2 done.
> 
> # Run the BootstrapQTL analysis
> eQTLs <- BootstrapQTL(snps, gene, snpspos, genepos, cvrt, n_bootstraps=10, n_cores=2)
Registering 2 cores for bootstrap procedure.
Mapping QTLs and obtaining nominal effect size estimates...
10 of 10 genes matched
15 of 15 SNPs matched

100.00% done, 100 cis-eQTLs
Error in `[.data.table`(cis_assocs, , `:=`(local_pval, adjust_p(pvalue,  : 
  attempt access index 6/6 in VECTOR_ELT
Calls: BootstrapQTL -> hierarchical_correction -> [ -> [.data.table
Restoring global environment...
Execution halted