Running 'testthat.R' [43s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clustermole)
  > 
  > test_check("clustermole")
  [ FAIL 5 | WARN 7 | SKIP 0 | PASS 29 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-enrichment.R:30:3'): clustermole_enrichment() human input default method ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─clustermole::clustermole_enrichment(expr_mat = log_cpm_mat, species = "hs") at test-enrichment.R:30:3
    2.   └─clustermole:::get_scores(...)
    3.     ├─GSVA::gsva(...)
    4.     └─GSVA::gsva(...)
    5.       └─GSVA (local) .local(expr, gset.idx.list, ...)
    6.         └─GSVA:::.filterFeatures(expr, method)
    7.           ├─DelayedMatrixStats::rowSds(expr)
    8.           └─DelayedMatrixStats::rowSds(expr)
    9.             └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
   10.               └─matrixStats::rowSds(...)
   11.                 └─matrixStats::rowVars(...)
   12.                   └─matrixStats:::deprecatedUseNamesNA()
   13.                     └─base::.Defunct(...)
  ── Error ('test-enrichment.R:38:3'): clustermole_enrichment() human input gsva method ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─clustermole::clustermole_enrichment(...) at test-enrichment.R:38:3
    2.   └─clustermole:::get_scores(...)
    3.     ├─GSVA::gsva(...)
    4.     └─GSVA::gsva(...)
    5.       └─GSVA (local) .local(expr, gset.idx.list, ...)
    6.         └─GSVA:::.filterFeatures(expr, method)
    7.           ├─DelayedMatrixStats::rowSds(expr)
    8.           └─DelayedMatrixStats::rowSds(expr)
    9.             └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
   10.               └─matrixStats::rowSds(...)
   11.                 └─matrixStats::rowVars(...)
   12.                   └─matrixStats:::deprecatedUseNamesNA()
   13.                     └─base::.Defunct(...)
  ── Error ('test-enrichment.R:46:3'): clustermole_enrichment() human input ssgsea method ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─clustermole::clustermole_enrichment(...) at test-enrichment.R:46:3
    2.   └─clustermole:::get_scores(...)
    3.     ├─GSVA::gsva(...)
    4.     └─GSVA::gsva(...)
    5.       └─GSVA (local) .local(expr, gset.idx.list, ...)
    6.         └─GSVA:::.filterFeatures(expr, method)
    7.           ├─DelayedMatrixStats::rowSds(expr)
    8.           └─DelayedMatrixStats::rowSds(expr)
    9.             └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
   10.               └─matrixStats::rowSds(...)
   11.                 └─matrixStats::rowVars(...)
   12.                   └─matrixStats:::deprecatedUseNamesNA()
   13.                     └─base::.Defunct(...)
  ── Error ('test-enrichment.R:62:3'): clustermole_enrichment() human input all combined method ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─clustermole::clustermole_enrichment(...) at test-enrichment.R:62:3
    2.   └─clustermole:::get_scores(...)
    3.     ├─GSVA::gsva(...)
    4.     └─GSVA::gsva(...)
    5.       └─GSVA (local) .local(expr, gset.idx.list, ...)
    6.         └─GSVA:::.filterFeatures(expr, method)
    7.           ├─DelayedMatrixStats::rowSds(expr)
    8.           └─DelayedMatrixStats::rowSds(expr)
    9.             └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
   10.               └─matrixStats::rowSds(...)
   11.                 └─matrixStats::rowVars(...)
   12.                   └─matrixStats:::deprecatedUseNamesNA()
   13.                     └─base::.Defunct(...)
  ── Error ('test-enrichment.R:76:3'): clustermole_enrichment() mouse input ──────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─clustermole::clustermole_enrichment(expr_mat = log_cpm_mat, species = "mm") at test-enrichment.R:76:3
    2.   └─clustermole:::get_scores(...)
    3.     ├─GSVA::gsva(...)
    4.     └─GSVA::gsva(...)
    5.       └─GSVA (local) .local(expr, gset.idx.list, ...)
    6.         └─GSVA:::.filterFeatures(expr, method)
    7.           ├─DelayedMatrixStats::rowSds(expr)
    8.           └─DelayedMatrixStats::rowSds(expr)
    9.             └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
   10.               └─matrixStats::rowSds(...)
   11.                 └─matrixStats::rowVars(...)
   12.                   └─matrixStats:::deprecatedUseNamesNA()
   13.                     └─base::.Defunct(...)
  
  [ FAIL 5 | WARN 7 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted