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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: jaguar_process
> ### Title: Obtain significant gene-SNP pairs based on a predetermined
> ###   threshold value
> ### Aliases: jaguar_process
> ### Keywords: score test GWAS eQTL
> 
> ### ** Examples
> 
> ## Example
> # 
> # Load the example data
> data(jaguar_example);
> 
> # Genome-wide analysis
> Gene_Mat = as.matrix(jaguar_example$GENE_EXP[1:10,])
> Geno_Mat = as.matrix(jaguar_example$GENO_MAT)
> jag.out = jaguar_gwa(Gene_Mat,Geno_Mat);

Running Genome-Wide eQTL analysis on  10  genes and  1036  SNPs 

boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> dim(jag.out);
[1]   10 1036
> 
> # Process results based on a predetermined threshold
> result = jaguar_process(jag.out,0.05);

Processing JAGUAR results

 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
JAGUAR
 --- call from context --- 
jaguar_process(jag.out, 0.05)
 --- call from argument --- 
if (class(jaguar.out) != "matrix") stop("Wrong data type passed!")
 --- R stacktrace ---
where 1: jaguar_process(jag.out, 0.05)

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (jaguar.out, threshold, plot = FALSE) 
{
    cat("\nProcessing JAGUAR results\n\n")
    if (class(jaguar.out) != "matrix") 
        stop("Wrong data type passed!")
    if (plot) {
        U.vec = as.vector(jaguar.out)
        if (length(U.vec) > 50000) {
            U.vec.temp = U.vec[sample(1:length(U.vec), 50000, 
                replace = F)]
        }
        else {
            U.vec.temp = U.vec[sample(1:length(U.vec), length(U.vec), 
                replace = F)]
        }
        theoretical.quantiles = (1:length(U.vec.temp))/(1 + length(U.vec.temp))
        data.quantiles = sort(U.vec.temp)
        plot(-log10(theoretical.quantiles), -log10(data.quantiles), 
            main = "QQ-plot of the score test pvals", xlab = "Theoritical Quantiles", 
            ylab = "Data Quantiles")
        abline(0, 1, col = "red")
    }
    w = which(jaguar.out < threshold, arr.ind = T)
    val = jaguar.out[jaguar.out < threshold]
    genes = rownames(jaguar.out)[w[, 1]]
    snps = colnames(jaguar.out)[w[, 2]]
    eQTL = data.frame(Gene = genes, SNP = snps, pvalue = val)
    return(eQTL)
}
<bytecode: 0x556e1db8ffd8>
<environment: namespace:JAGUAR>
 --- function search by body ---
Function jaguar_process in namespace JAGUAR has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1