Running ‘testthat.R’ [26s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Work-around for bug (https://github.com/hadley/testthat/issues/144)
  > Sys.setenv("R_TESTS" = "")
  > 
  > # library 
  > library(testthat)
  > library(HTSSIP)
  > 
  > # test check
  > test_check('HTSSIP')
  Sparsity threshold: 0.25 
  Density window: 1.71-1.75 
  Sparsity threshold: 0.25 
  Density window: 1.71-1.75 
  Sparsity threshold: 0 
  Density window: 1.7-1.75 
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (17)
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-DESeq2_l2fc.R:2:3): DESeq2_l2fc runs with default params ────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
      █
   1. └─HTSSIP::DESeq2_l2fc(...) test-DESeq2_l2fc.R:2:2
   2.   └─phyloseq::phyloseq_to_deseq2(physeq, design)
   3.     └─DESeq2::DESeqDataSetFromMatrix(countData, colData, design, ...)
   4.       └─DESeq2::DESeqDataSet(se, design = design, ignoreRank)
   5.         └─methods::as(se, "RangedSummarizedExperiment")
   6.           └─SummarizedExperiment:::asMethod(object)
   7.             └─IRanges::PartitioningByEnd(integer(length(from)), names = names(from))
   8.               └─IRanges:::.numeric2end(x, NG)
   9.                 └─S4Vectors:::isNotSorted(x)
  ── Error (test-DESeq2_l2fc.R:15:3): DESeq2_l2fc runs with sparsity_apply=heavy ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
      █
   1. └─HTSSIP::DESeq2_l2fc(...) test-DESeq2_l2fc.R:15:2
   2.   └─phyloseq::phyloseq_to_deseq2(physeq, design)
   3.     └─DESeq2::DESeqDataSetFromMatrix(countData, colData, design, ...)
   4.       └─DESeq2::DESeqDataSet(se, design = design, ignoreRank)
   5.         └─methods::as(se, "RangedSummarizedExperiment")
   6.           └─SummarizedExperiment:::asMethod(object)
   7.             └─IRanges::PartitioningByEnd(integer(length(from)), names = names(from))
   8.               └─IRanges:::.numeric2end(x, NG)
   9.                 └─S4Vectors:::isNotSorted(x)
  ── Error (test-HRSIP.R:3:3): HRSIP runs with default ───────────────────────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─HTSSIP::HRSIP(...) test-HRSIP.R:3:2
    2.   └─plyr::mdply(...)
    3.     └─plyr::adply(...)
    4.       └─plyr::ldply(...)
    5.         └─plyr::llply(...)
    6.           ├─plyr:::loop_apply(n, do.ply)
    7.           └─(function (i) ...
    8.             └─plyr:::.fun(piece, ...)
    9.               ├─base::do.call(flat, c(args, list(...)))
   10.               └─(function (physeq, density_min, density_max, design, l2fc_threshold = 0.25, ...
   11.                 └─phyloseq::phyloseq_to_deseq2(physeq, design)
   12.                   └─DESeq2::DESeqDataSetFromMatrix(countData, colData, design, ...)
   13.                     └─DESeq2::DESeqDataSet(se, design = design, ignoreRank)
   14.                       └─methods::as(se, "RangedSummarizedExperiment")
   15.                         └─SummarizedExperiment:::asMethod(object)
   16.                           └─IRanges::PartitioningByEnd(integer(length(from)), names = names(from))
   17.                             └─IRanges:::.numeric2end(x, NG)
   18.                               └─S4Vectors:::isNotSorted(x)
  
  [ FAIL 3 | WARN 10 | SKIP 18 | PASS 102 ]
  Error: Test failures
  Execution halted