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

> ### Name: HiC2Tree
> ### Title: Hi-C to trees
> ### Aliases: HiC2Tree
> 
> ### ** Examples
> 
> replicates <- 1:3
> cond <- c("90", "110")
> all_begins <- interaction(expand.grid(replicates, cond), sep = "-")
> all_begins <- as.character(all_begins)
> 
> # single chromosome
> nb_chr <- 1
> chromosomes <- 1:nb_chr
> all_mat_chr <- lapply(chromosomes, function(chr) {
+   all_mat <- lapply(all_begins, function(ab) {
+     mat_file <- paste0("Rep", ab, "-chr", chr, "_200000.bed")
+   })
+   all_mat <- unlist(all_mat)
+ })
> index <- system.file("extdata", "index.200000.longest18chr.abs.bed",
+                      package = "treediff")
> format <- rep("HiC-Pro", length(replicates) * length(cond) * nb_chr)
> binsize <- 200000
> files <- system.file("extdata", unlist(all_mat_chr), package = "treediff")
> replicates <- c(3, 3)
> HiC2Tree(files, format, binsize, index, chromosomes, replicates)

Parsing 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/Rep1-90-chr1_200000.bed' and 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/index.200000.longest18chr.abs.bed'.

Parsing 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/Rep2-90-chr1_200000.bed' and 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/index.200000.longest18chr.abs.bed'.

Parsing 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/Rep3-90-chr1_200000.bed' and 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/index.200000.longest18chr.abs.bed'.

Parsing 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/Rep1-110-chr1_200000.bed' and 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/index.200000.longest18chr.abs.bed'.

Parsing 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/Rep2-110-chr1_200000.bed' and 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/index.200000.longest18chr.abs.bed'.

Parsing 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/Rep3-110-chr1_200000.bed' and 'D:/RCompile/CRANpkg/lib/4.2/treediff/extdata/index.200000.longest18chr.abs.bed'.
Note: modifying similarity to ensure positive heights...
        added 0.622605020611983 to diagonal (merges will not be affected)
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Execution halted