Running 'testthat.R' [37s/43s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clustermole)
  > 
  > test_check("clustermole")
  == Failed tests ================================================================
  -- Error (test-enrichment.R:30:3): clustermole_enrichment() human input default method --
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. \-clustermole::clustermole_enrichment(expr_mat = log_cpm_mat, species = "hs") test-enrichment.R:30:2
    2.   \-clustermole:::get_scores(...)
    3.     +-GSVA::gsva(...)
    4.     \-GSVA::gsva(...)
    5.       \-GSVA:::.local(expr, gset.idx.list, ...)
    6.         \-GSVA:::.mapGeneSetsToFeatures(gset.idx.list, rownames(expr))
    7.           +-base::as.list(mt[!is.na(mt)])
    8.           +-mt[!is.na(mt)]
    9.           \-mt[!is.na(mt)]
   10.             \-S4Vectors:::subset_List_by_List(x, i)
   11.               +-methods::as(fast_path_FUN(x, i), class(x))
   12.               | \-methods:::.class1(object)
   13.               \-S4Vectors:::fast_path_FUN(x, i)
   14.                 \-IRanges::PartitioningByEnd(group, NG = length(x), names = names(x))
   15.                   \-IRanges:::.numeric2end(x, NG)
   16.                     \-S4Vectors:::isNotSorted(x)
  -- Error (test-enrichment.R:38:3): clustermole_enrichment() human input gsva method --
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. \-clustermole::clustermole_enrichment(...) test-enrichment.R:38:2
    2.   \-clustermole:::get_scores(...)
    3.     +-GSVA::gsva(...)
    4.     \-GSVA::gsva(...)
    5.       \-GSVA:::.local(expr, gset.idx.list, ...)
    6.         \-GSVA:::.mapGeneSetsToFeatures(gset.idx.list, rownames(expr))
    7.           +-base::as.list(mt[!is.na(mt)])
    8.           +-mt[!is.na(mt)]
    9.           \-mt[!is.na(mt)]
   10.             \-S4Vectors:::subset_List_by_List(x, i)
   11.               +-methods::as(fast_path_FUN(x, i), class(x))
   12.               | \-methods:::.class1(object)
   13.               \-S4Vectors:::fast_path_FUN(x, i)
   14.                 \-IRanges::PartitioningByEnd(group, NG = length(x), names = names(x))
   15.                   \-IRanges:::.numeric2end(x, NG)
   16.                     \-S4Vectors:::isNotSorted(x)
  -- Error (test-enrichment.R:46:3): clustermole_enrichment() human input ssgsea method --
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. \-clustermole::clustermole_enrichment(...) test-enrichment.R:46:2
    2.   \-clustermole:::get_scores(...)
    3.     +-GSVA::gsva(...)
    4.     \-GSVA::gsva(...)
    5.       \-GSVA:::.local(expr, gset.idx.list, ...)
    6.         \-GSVA:::.mapGeneSetsToFeatures(gset.idx.list, rownames(expr))
    7.           +-base::as.list(mt[!is.na(mt)])
    8.           +-mt[!is.na(mt)]
    9.           \-mt[!is.na(mt)]
   10.             \-S4Vectors:::subset_List_by_List(x, i)
   11.               +-methods::as(fast_path_FUN(x, i), class(x))
   12.               | \-methods:::.class1(object)
   13.               \-S4Vectors:::fast_path_FUN(x, i)
   14.                 \-IRanges::PartitioningByEnd(group, NG = length(x), names = names(x))
   15.                   \-IRanges:::.numeric2end(x, NG)
   16.                     \-S4Vectors:::isNotSorted(x)
  -- Error (test-enrichment.R:62:3): clustermole_enrichment() human input all combined method --
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. \-clustermole::clustermole_enrichment(...) test-enrichment.R:62:2
    2.   \-clustermole:::get_scores(...)
    3.     +-GSVA::gsva(...)
    4.     \-GSVA::gsva(...)
    5.       \-GSVA:::.local(expr, gset.idx.list, ...)
    6.         \-GSVA:::.mapGeneSetsToFeatures(gset.idx.list, rownames(expr))
    7.           +-base::as.list(mt[!is.na(mt)])
    8.           +-mt[!is.na(mt)]
    9.           \-mt[!is.na(mt)]
   10.             \-S4Vectors:::subset_List_by_List(x, i)
   11.               +-methods::as(fast_path_FUN(x, i), class(x))
   12.               | \-methods:::.class1(object)
   13.               \-S4Vectors:::fast_path_FUN(x, i)
   14.                 \-IRanges::PartitioningByEnd(group, NG = length(x), names = names(x))
   15.                   \-IRanges:::.numeric2end(x, NG)
   16.                     \-S4Vectors:::isNotSorted(x)
  -- Error (test-enrichment.R:76:3): clustermole_enrichment() mouse input --------
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. \-clustermole::clustermole_enrichment(expr_mat = log_cpm_mat, species = "mm") test-enrichment.R:76:2
    2.   \-clustermole:::get_scores(...)
    3.     +-GSVA::gsva(...)
    4.     \-GSVA::gsva(...)
    5.       \-GSVA:::.local(expr, gset.idx.list, ...)
    6.         \-GSVA:::.mapGeneSetsToFeatures(gset.idx.list, rownames(expr))
    7.           +-base::as.list(mt[!is.na(mt)])
    8.           +-mt[!is.na(mt)]
    9.           \-mt[!is.na(mt)]
   10.             \-S4Vectors:::subset_List_by_List(x, i)
   11.               +-methods::as(fast_path_FUN(x, i), class(x))
   12.               | \-methods:::.class1(object)
   13.               \-S4Vectors:::fast_path_FUN(x, i)
   14.                 \-IRanges::PartitioningByEnd(group, NG = length(x), names = names(x))
   15.                   \-IRanges:::.numeric2end(x, NG)
   16.                     \-S4Vectors:::isNotSorted(x)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted