Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("SISIR")
  Loading required package: foreach
  Loading required package: doParallel
  Loading required package: iterators
  Loading required package: parallel
  > 
  > test_check("SISIR")
  [ FAIL 15 | WARN 0 | SKIP 0 | PASS 10 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_sfcb.R:11:3'): `sfcb` works for one `at` and no selection. ─────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(...) at test_sfcb.R:11:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcb.R:35:3'): `sfcb` works for `range_at` and no selection. ───
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(...) at test_sfcb.R:35:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcb.R:53:3'): `sfcb` works for one `at` with selection. ───────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(...) at test_sfcb.R:53:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcb.R:74:3'): `sfcb` works for one `at` with selection. ───────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(...) at test_sfcb.R:74:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbextract.R:11:3'): extract works as expected without selection. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(...) at test_sfcbextract.R:11:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbextract.R:39:3'): extract works as expected with selection. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(...) at test_sfcbextract.R:39:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbextract.R:57:3'): extract returns errors as expected. ──────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(...) at test_sfcbextract.R:57:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbplots.R:9:3'): graphics for 'importance' work as expected. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(rainfall, truffles, group.method = "adjclust", summary.method = "pls") at test_sfcbplots.R:9:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbplots.R:50:3'): graphics for 'selection' work as expected. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(rainfall, truffles, group.method = "adjclust", summary.method = "pls") at test_sfcbplots.R:50:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbplots.R:123:3'): graphics for 'dendrogram' work as expected. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(rainfall, truffles, group.method = "adjclust", summary.method = "pls") at test_sfcbplots.R:123:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbquality.R:13:3'): quality computation works as expected without selection. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(rainfall, truffles, group.method = "adjclust", summary.method = "pls") at test_sfcbquality.R:13:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbquality.R:35:3'): quality computation works as expected with selection. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(...) at test_sfcbquality.R:35:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbquality.R:62:3'): quality graphics works as expected. ──────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(rainfall, truffles, group.method = "adjclust", summary.method = "pls") at test_sfcbquality.R:62:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbquality.R:111:3'): quality computation returns errors as expected. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(rainfall, truffles, group.method = "adjclust", summary.method = "pls") at test_sfcbquality.R:111:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  ── Error ('test_sfcbquality.R:128:3'): quality graphics return errors as expected. ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─SISIR::sfcb(rainfall, truffles, group.method = "adjclust", summary.method = "pls") at test_sfcbquality.R:128:3
    2.   ├─base::system.time(...)
    3.   └─SISIR (local) group_function(X)
    4.     ├─adjclust::adjClust(corr_inputs, type = "similarity")
    5.     └─adjclust:::adjClust.matrix(corr_inputs, type = "similarity")
    6.       └─adjclust:::run.adjclust(mat, type = type, h = h, strictCheck = strictCheck)
    7.         ├─MatrixGenerics::colCumsums(rCumL)
    8.         └─MatrixGenerics::colCumsums(rCumL)
    9.           └─MatrixGenerics (local) .local(x, rows, cols, ..., useNames = useNames)
   10.             └─matrixStats::colCumsums(...)
   11.               └─matrixStats:::deprecatedUseNamesNA()
   12.                 └─base::.Defunct(...)
  
  [ FAIL 15 | WARN 0 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted