- using R Under development (unstable) (2025-12-18 r89199)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 21.1.7 (1)
Debian flang version 21.1.7 (1)
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
- checking for file ‘treediff/DESCRIPTION’ ... OK
- this is package ‘treediff’ version ‘0.2.1’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [1s/1s] OK
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘treediff’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [16s/20s] OK
- checking whether the package can be loaded with stated dependencies ... [15s/19s] OK
- checking whether the package can be unloaded cleanly ... [15s/19s] OK
- checking whether the namespace can be loaded with stated dependencies ... [15s/19s] OK
- checking whether the namespace can be unloaded cleanly ... [15s/19s] OK
- checking loading without being on the library search path ... [16s/21s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [64s/83s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking examples ... [16s/21s] ERROR
Running examples in ‘treediff-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HiC2Tree
> ### Title: Convert 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 '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/treediff/extdata/Rep1-90-chr1_200000.bed' and '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/treediff/extdata/index.200000.longest18chr.abs.bed'.
Error in `[.data.table`(tabChromosomes, index == minIndex, `:=`(minStart, :
attempt access index 7/7 in VECTOR_ELT
Calls: HiC2Tree ... .fillHiCDOCDataSet -> .determineChromosomeSizes -> [ -> [.data.table
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [22s/29s] ERROR
Running ‘testthat.R’ [22s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> library("treediff")
>
> test_check("treediff")
Saving _problems/test-HiC2Tree-26.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HiC2Tree.R:26:1'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(tabChromosomes, index == minIndex, `:=`(minStart, round(start/width)), by = .(seqnames))`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─treediff::HiC2Tree(...) at test-HiC2Tree.R:26:1
2. └─treediff::HiCDOCDataSet(...)
3. └─base::sapply(...)
4. └─base::lapply(X = X, FUN = FUN, ...)
5. └─treediff (local) FUN(X[[i]], ...)
6. └─HiCDOC::HiCDOCDataSetFromHiCPro(...)
7. └─HiCDOC:::.fillHiCDOCDataSet(object)
8. └─HiCDOC:::.determineChromosomeSizes(object)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
Error:
! Test failures.
Execution halted
- checking PDF version of manual ... [4s/6s] OK
- checking HTML version of manual ... [0s/1s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs