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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biogram-package
> ### Title: biogram - analysis of biological sequences using n-grams
> ### Aliases: biogram biogram-package
> 
> ### ** Examples
> 
> # use data set from package
> data(human_cleave)
> # first nine columns represent subsequent nine amino acids from cleavage sites
> # degenerate the sequence to reduce the dimensionality of the problem
> # (use five groups instead of 20 amino acids)
> deg_seqs <- degenerate(human_cleave[, 1L:9], 
+                       list(`a` = c(1, 6, 8, 10, 11, 18), 
+                            `b` = c(2, 13, 14, 16, 17), 
+                            `c` = c(5, 19, 20), 
+                            `d` = c(7, 9, 12, 15), 
+                            'e' = c(3, 4)))
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
biogram
 --- call from context --- 
degenerate(human_cleave[, 1L:9], list(a = c(1, 6, 8, 10, 11, 
    18), b = c(2, 13, 14, 16, 17), c = c(5, 19, 20), d = c(7, 
    9, 12, 15), e = c(3, 4)))
 --- call from argument --- 
if (class(seq) == "matrix") dim(tmp_seq) <- dim(seq)
 --- R stacktrace ---
where 1: degenerate(human_cleave[, 1L:9], list(a = c(1, 6, 8, 10, 11, 
    18), b = c(2, 13, 14, 16, 17), c = c(5, 19, 20), d = c(7, 
    9, 12, 15), e = c(3, 4)))

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (seq, element_groups) 
{
    tmp_seq <- seq
    if (!all(unique(tmp_seq) %in% unlist(element_groups))) {
        warning("'seq' contains elements not present in 'element_groups'. \n            Element(s): ", 
            paste0(setdiff(unique(tmp_seq), unlist(element_groups)), 
                collapse = ", "), " will be replaced by NA.")
        tmp_seq[!(tmp_seq %in% unlist(element_groups))] <- NA
    }
    if (is.null(names(element_groups))) {
        warning("'element_groups' is unnamed. Assumed names of groups are their ordinal numbers.")
        names(element_groups) <- 1L:length(element_groups)
    }
    if (length(unique(names(element_groups))) != length(names(element_groups))) {
        stop("'element_groups' must have unique names.")
    }
    for (i in 1L:length(element_groups)) {
        tmp_seq[tmp_seq %in% element_groups[[i]]] <- names(element_groups)[i]
    }
    if (class(seq) == "matrix") 
        dim(tmp_seq) <- dim(seq)
    tmp_seq
}
<bytecode: 0x5602b23695d0>
<environment: namespace:biogram>
 --- function search by body ---
Function degenerate in namespace biogram has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1