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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MutectVCFFilesToCatalogAndPlotToPdf
> ### Title: Create SBS, DBS and Indel catalogs from Mutect VCF files and
> ###   plot them to PDF
> ### Aliases: MutectVCFFilesToCatalogAndPlotToPdf
> 
> ### ** Examples
> 
> file <- c(system.file("extdata",
+                       "Mutect.GRCh37.vcf",
+                       package = "ICAMS"))
> if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
+   catalogs <- 
+     MutectVCFFilesToCatalogAndPlotToPdf(file, ref.genome = "hg19", 
+                                         trans.ranges = trans.ranges.GRCh37,
+                                         region = "genome",
+                                         output.file = 
+                                         file.path(tempdir(), "Mutect.pdf"))}
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
ICAMS
 --- call from context --- 
`[.SBS96Catalog`(catalog, , i, drop = FALSE)
 --- call from argument --- 
if (class(y) %in% c("integer", "numeric")) {
    return(y)
} else {
    class(y) <- class(x)
    for (at in c("ref.genome", "catalog.type", "abundance", "region")) {
        attr(y, at) <- attr(x, at, exact = TRUE)
    }
    return(y)
}
 --- R stacktrace ---
where 1: `[.SBS96Catalog`(catalog, , i, drop = FALSE)
where 2: catalog[, i, drop = FALSE]
where 3: PlotCatalogToPdf.SBS96Catalog(catalogs$catSBS96, file = sub(".pdf", 
    ".SBS96Catalog.pdf", output.file, ignore.case = TRUE))
where 4: PlotCatalogToPdf(catalogs$catSBS96, file = sub(".pdf", ".SBS96Catalog.pdf", 
    output.file, ignore.case = TRUE))
where 5: MutectVCFFilesToCatalogAndPlotToPdf(file, ref.genome = "hg19", 
    trans.ranges = trans.ranges.GRCh37, region = "genome", output.file = file.path(tempdir(), 
        "Mutect.pdf"))

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (x, i, j, drop = if (missing(i)) TRUE else length(cols) == 
    1) 
{
    y <- NextMethod("[")
    if (class(y) %in% c("integer", "numeric")) {
        return(y)
    }
    else {
        class(y) <- class(x)
        for (at in c("ref.genome", "catalog.type", "abundance", 
            "region")) {
            attr(y, at) <- attr(x, at, exact = TRUE)
        }
        return(y)
    }
}
<bytecode: 0x565426beeee8>
<environment: namespace:ICAMS>
 --- function search by body ---
Function [.SBS96Catalog in namespace ICAMS has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1