Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(LoopRig)
  > 
  > test_check("LoopRig")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-ConsensusLoops.R:35:3): class output ────────────────────────────
  Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─testthat::expect_is(ConsensusLoops(loops, keep_all = TRUE), "LoopRanges") test-ConsensusLoops.R:35:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─LoopRig::ConsensusLoops(loops, keep_all = TRUE)
    5.   └─base::Reduce(S4Vectors::pc, loop_ranges)
    6.     └─S4Vectors:::f(init, x[[i]])
    7.       ├─stats::setNames(SPLIT.FUN(ans_unlisted, f), names(args[[1L]]))
    8.       ├─S4Vectors:::SPLIT.FUN(ans_unlisted, f)
    9.       └─S4Vectors:::SPLIT.FUN(ans_unlisted, f)
   10.         └─S4Vectors:::.local(x, f, drop, ...)
   11.           └─IRanges:::default_splitAsList(x, f, drop = drop)
   12.             └─IRanges:::.splitAsList_by_factor(x, f, drop)
   13.               └─S4Vectors:::isNotSorted(f)
  ── Error (test-ExportBED.R:31:1): (code run outside of `test_that()`) ──────────
  Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─LoopRig::ConsensusLoops(loops) test-ExportBED.R:31:0
    2.   ├─BiocGenerics::lapply(...)
    3.   └─base::lapply(...)
    4.     └─LoopRig:::FUN(X[[i]], ...)
    5.       ├─BiocGenerics::lapply(...)
    6.       └─base::lapply(loop_ranges, function(y) hit_counter_1(x, y))
    7.         └─LoopRig:::FUN(X[[i]], ...)
    8.           └─LoopRig:::hit_counter_1(x, y)
    9.             ├─IRanges::findOverlaps(looprange1[[1]], looprange2[[1]], minoverlap = threshold)
   10.             └─GenomicRanges::findOverlaps(...)
   11.               └─GenomicRanges:::.local(...)
   12.                 └─GenomicRanges:::findOverlaps_GNCList(...)
   13.                   └─GenomicRanges:::.extract_groups_from_GenomicRanges(query)
   14.                     ├─S4Vectors::splitAsList(seq_along(x) - 1L, seqnames(x))
   15.                     └─S4Vectors::splitAsList(seq_along(x) - 1L, seqnames(x))
   16.                       └─S4Vectors:::.local(x, f, drop, ...)
   17.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                           └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   19.                             └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test-LinkedElements.R:18:1): (code run outside of `test_that()`) ─────
  Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─LoopRig::ConsensusLoops(loops) test-LinkedElements.R:18:0
    2.   ├─BiocGenerics::lapply(...)
    3.   └─base::lapply(...)
    4.     └─LoopRig:::FUN(X[[i]], ...)
    5.       ├─BiocGenerics::lapply(...)
    6.       └─base::lapply(loop_ranges, function(y) hit_counter_1(x, y))
    7.         └─LoopRig:::FUN(X[[i]], ...)
    8.           └─LoopRig:::hit_counter_1(x, y)
    9.             ├─IRanges::findOverlaps(looprange1[[1]], looprange2[[1]], minoverlap = threshold)
   10.             └─GenomicRanges::findOverlaps(...)
   11.               └─GenomicRanges:::.local(...)
   12.                 └─GenomicRanges:::findOverlaps_GNCList(...)
   13.                   └─GenomicRanges:::.extract_groups_from_GenomicRanges(query)
   14.                     ├─S4Vectors::splitAsList(seq_along(x) - 1L, seqnames(x))
   15.                     └─S4Vectors::splitAsList(seq_along(x) - 1L, seqnames(x))
   16.                       └─S4Vectors:::.local(x, f, drop, ...)
   17.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                           └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   19.                             └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test-ScaffoldElements.R:18:1): (code run outside of `test_that()`) ───
  Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─LoopRig::ConsensusLoops(loops) test-ScaffoldElements.R:18:0
    2.   ├─BiocGenerics::lapply(...)
    3.   └─base::lapply(...)
    4.     └─LoopRig:::FUN(X[[i]], ...)
    5.       ├─BiocGenerics::lapply(...)
    6.       └─base::lapply(loop_ranges, function(y) hit_counter_1(x, y))
    7.         └─LoopRig:::FUN(X[[i]], ...)
    8.           └─LoopRig:::hit_counter_1(x, y)
    9.             ├─IRanges::findOverlaps(looprange1[[1]], looprange2[[1]], minoverlap = threshold)
   10.             └─GenomicRanges::findOverlaps(...)
   11.               └─GenomicRanges:::.local(...)
   12.                 └─GenomicRanges:::findOverlaps_GNCList(...)
   13.                   └─GenomicRanges:::.extract_groups_from_GenomicRanges(query)
   14.                     ├─S4Vectors::splitAsList(seq_along(x) - 1L, seqnames(x))
   15.                     └─S4Vectors::splitAsList(seq_along(x) - 1L, seqnames(x))
   16.                       └─S4Vectors:::.local(x, f, drop, ...)
   17.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                           └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   19.                             └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test-StackedElements.R:18:1): (code run outside of `test_that()`) ────
  Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─LoopRig::ConsensusLoops(loops) test-StackedElements.R:18:0
    2.   ├─BiocGenerics::lapply(...)
    3.   └─base::lapply(...)
    4.     └─LoopRig:::FUN(X[[i]], ...)
    5.       ├─BiocGenerics::lapply(...)
    6.       └─base::lapply(loop_ranges, function(y) hit_counter_1(x, y))
    7.         └─LoopRig:::FUN(X[[i]], ...)
    8.           └─LoopRig:::hit_counter_1(x, y)
    9.             ├─IRanges::findOverlaps(looprange1[[1]], looprange2[[1]], minoverlap = threshold)
   10.             └─GenomicRanges::findOverlaps(...)
   11.               └─GenomicRanges:::.local(...)
   12.                 └─GenomicRanges:::findOverlaps_GNCList(...)
   13.                   └─GenomicRanges:::.extract_groups_from_GenomicRanges(query)
   14.                     ├─S4Vectors::splitAsList(seq_along(x) - 1L, seqnames(x))
   15.                     └─S4Vectors::splitAsList(seq_along(x) - 1L, seqnames(x))
   16.                       └─S4Vectors:::.local(x, f, drop, ...)
   17.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                           └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   19.                             └─S4Vectors:::isNotSorted(f_vals)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 26 ]
  Error: Test failures
  Execution halted