Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("adjclust")
  > 
  > test_check("adjclust")
  Warning: stack imbalance in '{', 73 then 76
  object has no names - using numeric order for row/column names
  [ FAIL 21 | WARN 0 | SKIP 4 | PASS 33 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • No NA value: nothing to test here! (3): 'test_snpClust_NA-in-LD.R:21:3',
    'test_snpClust_NA-in-LD.R:56:3', 'test_snpClust_NA-in-LD.R:77:3'
  • empty test (1): 'test_adjClust.R:89:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_adjClust.R:9:3'): adjClust methods returns expected 'calls' ────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim, "similarity") at test_adjClust.R:9:3
   2. └─adjclust:::adjClust.matrix(sim, "similarity")
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_adjClust.R:47:3'): adjClust methods properly catches unexpected  'calls' ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(mat, strictCheck = FALSE) at test_adjClust.R:47:3
   2. └─adjclust:::adjClust.matrix(mat, strictCheck = FALSE)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_adjclust_equivalentTo_hclust.R:14:3'): 'hclust' and 'adjClust' give identical results on toy data when the
            best merges are always adjacent merges ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim * 2/9) at test_adjclust_equivalentTo_hclust.R:14:3
   2. └─adjclust:::adjClust.matrix(sim * 2/9)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_adjclust_equivalentTo_rioja.R:16:3'): rioja and adjClust with full band give identical results on toy data ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim, "similarity", p - 1) at test_adjclust_equivalentTo_rioja.R:16:3
   2. └─adjclust:::adjClust.matrix(sim, "similarity", p - 1)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_ascendingCompatibility.R:33:3'): snpClust gives results identical to those of adjclust 0.3.0 ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test_ascendingCompatibility.R:33:3
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─adjclust::snpClust(ld.ceph, h = 100)
    7. └─adjclust:::snpClust.dsCMatrix(ld.ceph, h = 100)
    8.   └─adjclust:::run.snpClust(x, h = h, stats = stats)
    9.     ├─adjclust::adjClust(x, type = "similarity", h = h)
   10.     └─adjclust:::adjClust.dsCMatrix(x, type = "similarity", h = h)
   11.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   12.         ├─MatrixGenerics::colCumsums(rCumL)
   13.         └─MatrixGenerics::colCumsums(rCumL)
   14.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   15.             └─matrixStats::colCumsums(...)
   16.               └─matrixStats:::deprecatedUseNamesNA()
   17.                 └─base::.Defunct(...)
  ── Error ('test_chac.R:5:3'): Methods of class 'chac' ──────────────────────────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim) at test_chac.R:5:3
   2. └─adjclust:::adjClust.matrix(sim)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_correct.R:7:3'): 'diagnose' and 'correct' must return a warning or a message when no reversals are found. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim) at test_correct.R:7:3
   2. └─adjclust:::adjClust.matrix(sim)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_corrected_plot.R:8:3'): 'adjClust' returns a dendrogram with increasing heights for 
            'mode=corrected' ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim) at test_corrected_plot.R:8:3
   2. └─adjclust:::adjClust.matrix(sim)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_cuttree.R:8:3'): 'cuttree_chac' must ignore 'h' when reversals are present. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim) at test_cuttree.R:8:3
   2. └─adjclust:::adjClust.matrix(sim)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_dense_sparse_comparison.R:35:3'): test that adjClust gives identical results for sparse and dense matrices when h < p-1 ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(mat, h = 2) at test_dense_sparse_comparison.R:35:3
   2. └─adjclust:::adjClust.matrix(mat, h = 2)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_dense_sparse_comparison.R:73:3'): test that adjClust gives identical results for sparse and dense matrices when h is p-1 ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(mat) at test_dense_sparse_comparison.R:73:3
   2. └─adjclust:::adjClust.matrix(mat)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_final_height.R:8:3'): 'adjClust' returns an object for which the sum of heights is the 
            dataset (pseudo) inertia ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim) at test_final_height.R:8:3
   2. └─adjclust:::adjClust.matrix(sim)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_hicClust.R:8:3'): 'hicClust' gives identical results regardless of data input format ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. ├─adjclust::hicClust(hic_imr90_40_XX) at test_hicClust.R:8:3
    2. └─adjclust:::hicClust.HTCexp(hic_imr90_40_XX)
    3.   ├─adjclust::hicClust(x, h = h, log = log)
    4.   └─adjclust:::hicClust.dsCMatrix(x, h = h, log = log)
    5.     └─adjclust:::run.hicclust(x, h = h)
    6.       ├─adjclust::adjClust(x, type = "similarity", h = h)
    7.       └─adjclust:::adjClust.dsCMatrix(x, type = "similarity", h = h)
    8.         └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    9.           ├─MatrixGenerics::colCumsums(rCumL)
   10.           └─MatrixGenerics::colCumsums(rCumL)
   11.             └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   12.               └─matrixStats::colCumsums(...)
   13.                 └─matrixStats:::deprecatedUseNamesNA()
   14.                   └─base::.Defunct(...)
  ── Error ('test_modify.R:8:1'): (code run outside of `test_that()`) ────────────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim) at test_modify.R:8:1
   2. └─adjclust:::adjClust.matrix(sim)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_plotSim.R:12:3'): 'plotSim' works for 'matrix' ─────────────────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim, "similarity") at test_plotSim.R:12:3
   2. └─adjclust:::adjClust.matrix(sim, "similarity")
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_plotSim.R:57:20'): 'plotSim' works for 'dgCMatrix' ─────────────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test_plotSim.R:57:3
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─adjclust::adjClust(1 - 2 * sim, "similarity") at test_plotSim.R:57:20
    7. └─adjclust:::adjClust.dgeMatrix(1 - 2 * sim, "similarity")
    8.   ├─adjclust::adjClust(mat, type = type, h = h, strictCheck = strictCheck)
    9.   └─adjclust:::adjClust.dsyMatrix(mat, type = type, h = h, strictCheck = strictCheck)
   10.     └─adjclust:::run.adjclust(as.matrix(mat), type = type, h = h, strictCheck = strictCheck)
   11.       ├─MatrixGenerics::colCumsums(rCumL)
   12.       └─MatrixGenerics::colCumsums(rCumL)
   13.         └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   14.           └─matrixStats::colCumsums(...)
   15.             └─matrixStats:::deprecatedUseNamesNA()
   16.               └─base::.Defunct(...)
  ── Error ('test_plotSim.R:73:20'): 'plotSim' works for 'dsCMatrix' ─────────────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test_plotSim.R:73:3
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─adjclust::adjClust(sim, "similarity") at test_plotSim.R:73:20
    7. └─adjclust:::adjClust.dsCMatrix(sim, "similarity")
    8.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    9.     ├─MatrixGenerics::colCumsums(rCumL)
   10.     └─MatrixGenerics::colCumsums(rCumL)
   11.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   12.         └─matrixStats::colCumsums(...)
   13.           └─matrixStats:::deprecatedUseNamesNA()
   14.             └─base::.Defunct(...)
  ── Error ('test_plotSim.R:97:3'): 'plotSim' works for 'dist' ───────────────────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim * 2/9) at test_plotSim.R:97:3
   2. └─adjclust:::adjClust.matrix(sim * 2/9)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_similarity_equivalentTo_dissimilarity.R:6:1'): (code run outside of `test_that()`) ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
      ▆
   1. ├─adjclust::adjClust(sim) at test_similarity_equivalentTo_dissimilarity.R:6:1
   2. └─adjclust:::adjClust.matrix(sim)
   3.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   4.     ├─MatrixGenerics::colCumsums(rCumL)
   5.     └─MatrixGenerics::colCumsums(rCumL)
   6.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   7.         └─matrixStats::colCumsums(...)
   8.           └─matrixStats:::deprecatedUseNamesNA()
   9.             └─base::.Defunct(...)
  ── Error ('test_snpClust.R:39:3'): 'snpClust' gives identical results regardless of data input format ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test_snpClust.R:39:3
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─adjclust::snpClust(ld.ceph, h = 100)
    7. └─adjclust:::snpClust.dgCMatrix(ld.ceph, h = 100)
    8.   └─adjclust:::run.snpClust(x, h = h, stats = stats)
    9.     ├─adjclust::adjClust(x, type = "similarity", h = h)
   10.     └─adjclust:::adjClust.dgCMatrix(x, type = "similarity", h = h)
   11.       ├─adjclust::adjClust(mat, type = type, h = h, strictCheck = strictCheck)
   12.       └─adjclust:::adjClust.dsCMatrix(mat, type = type, h = h, strictCheck = strictCheck)
   13.         └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
   14.           ├─MatrixGenerics::colCumsums(rCumL)
   15.           └─MatrixGenerics::colCumsums(rCumL)
   16.             └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   17.               └─matrixStats::colCumsums(...)
   18.                 └─matrixStats:::deprecatedUseNamesNA()
   19.                   └─base::.Defunct(...)
  ── Error ('test_warning_with_decreasing_height_plots.R:10:3'): 'adjClust' returns a note when decreasing heights are produced and
            warnings when such results are plotted with 'mode=standard' and
            'mode=average-disp' ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. ├─testthat::expect_message(fit <- adjClust(sim), "merges with non increasing heights") at test_warning_with_decreasing_height_plots.R:10:3
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─adjclust::adjClust(sim)
    7. └─adjclust:::adjClust.matrix(sim)
    8.   └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    9.     ├─MatrixGenerics::colCumsums(rCumL)
   10.     └─MatrixGenerics::colCumsums(rCumL)
   11.       └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   12.         └─matrixStats::colCumsums(...)
   13.           └─matrixStats:::deprecatedUseNamesNA()
   14.             └─base::.Defunct(...)
  
  [ FAIL 21 | WARN 0 | SKIP 4 | PASS 33 ]
  Error: Test failures
  Execution halted