Running ‘testthat.R’ [22s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RGCCA)
  > 
  > test_check("RGCCA")
  [ FAIL 10 | WARN 0 | SKIP 41 | PASS 824 ]
  
  ══ Skipped tests (41) ══════════════════════════════════════════════════════════
  • On CRAN (6): 'test_print_call.R:11:3', 'test_print_call.R:24:3',
    'test_print_comp.R:10:3', 'test_print_comp.R:19:3', 'test_print_comp.R:28:3',
    'test_print_comp.R:37:3'
  • as.logical(Sys.getenv("TEST_SNAPSHOTS")) is not TRUE (34):
    'test_plot.rgcca.r:27:3', 'test_plot.rgcca.r:36:3', 'test_plot.rgcca.r:47:3',
    'test_plot.rgcca.r:55:3', 'test_plot.rgcca.r:65:3', 'test_plot.rgcca.r:72:3',
    'test_plot.rgcca.r:79:3', 'test_plot.rgcca.r:86:3', 'test_plot.rgcca.r:93:3',
    'test_plot.rgcca.r:100:3', 'test_plot.rgcca.r:109:3',
    'test_plot.rgcca_bootstrap.R:30:3', 'test_plot.rgcca_bootstrap.R:37:3',
    'test_plot.rgcca_stability.R:16:3', 'test_print.rgcca.R:10:3',
    'test_print.rgcca.R:19:3', 'test_print.rgcca_bootstrap.R:13:3',
    'test_print.rgcca_cv.R:17:3', 'test_print.rgcca_cv.R:30:3',
    'test_print.rgcca_stability.R:13:3', 'test_summary.rgcca.r:11:3',
    'test_summary.rgcca.r:20:3', 'test_summary.rgcca.r:30:3',
    'test_summary.rgcca.r:39:3', 'test_summary.rgcca.r:49:3',
    'test_summary.rgcca_bootstrap.r:12:3', 'test_summary.rgcca_bootstrap.r:21:3',
    'test_summary.rgcca_cv.R:17:3', 'test_summary.rgcca_cv.R:30:3',
    'test_summary.rgcca_cv.R:43:3', 'test_summary.rgcca_cv.R:56:3',
    'test_summary.rgcca_permutation.R:12:3',
    'test_summary.rgcca_permutation.R:24:3',
    'test_summary.rgcca_stability.R:13:3'
  • gliomaData cannot be loaded (1): 'test_rgcca_predict.r:54:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_plot.rgcca_cv.R:15:1'): (code run outside of `test_that()`) ────
  <1/simpleError/error/condition>
  Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test_plot.rgcca_cv.R:15:0
   2. │ └─base::withCallingHandlers(...)
   3. └─RGCCA::rgcca_cv(...)
   4.   └─RGCCA:::set_parameter_grid(...)
   5.     └─RGCCA (local) check_param_type(par_value, blocks)
   6.       └─RGCCA:::stop_rgcca(...)
  ── Error ('test_plot.rgcca_permutation.r:10:1'): (code run outside of `test_that()`) ──
  <1/simpleError/error/condition>
  Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
  Backtrace:
      ▆
   1. └─RGCCA::rgcca_permutation(...) at test_plot.rgcca_permutation.r:10:0
   2.   └─RGCCA:::set_parameter_grid(...)
   3.     └─RGCCA (local) check_param_type(par_value, blocks)
   4.       └─RGCCA:::stop_rgcca(...)
  ── Error ('test_print.rgcca_permutation.R:11:1'): (code run outside of `test_that()`) ──
  <1/simpleError/error/condition>
  Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
  Backtrace:
      ▆
   1. └─RGCCA::rgcca_permutation(...) at test_print.rgcca_permutation.R:11:0
   2.   └─RGCCA:::set_parameter_grid(...)
   3.     └─RGCCA (local) check_param_type(par_value, blocks)
   4.       └─RGCCA:::stop_rgcca(...)
  ── Error ('test_rgcca_cv.r:52:3'): rgcca_cv generates a warning if tau is null and block has more
            columns than rows ──
  <1/simpleError/error/condition>
  Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 4).
  Backtrace:
      ▆
   1. ├─testthat::expect_warning(...) at test_rgcca_cv.r:52:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─RGCCA::rgcca_cv(bad_blocks, response = 4, prediction_model = "lm")
   7.   └─RGCCA:::set_parameter_grid(...)
   8.     └─RGCCA (local) check_param_type(par_value, blocks)
   9.       └─RGCCA:::stop_rgcca(...)
  ── Error ('test_rgcca_cv.r:61:3'): rgcca_cv changes par_type to sparsity if a sparse method is given
            with par_type = 'tau' ──
  <1/simpleError/error/condition>
  Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
  Backtrace:
      ▆
   1. └─RGCCA::rgcca_cv(...) at test_rgcca_cv.r:61:2
   2.   └─RGCCA:::set_parameter_grid(...)
   3.     └─RGCCA (local) check_param_type(par_value, blocks)
   4.       └─RGCCA:::stop_rgcca(...)
  ── Error ('test_rgcca_cv.r:74:3'): rgcca_cv computes k * n_run scores per parameter value ──
  <1/simpleError/error/condition>
  Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
  Backtrace:
      ▆
   1. └─RGCCA::rgcca_cv(...) at test_rgcca_cv.r:74:2
   2.   └─RGCCA:::set_parameter_grid(...)
   3.     └─RGCCA (local) check_param_type(par_value, blocks)
   4.       └─RGCCA:::stop_rgcca(...)
  ── Error ('test_rgcca_permutation.R:18:3'): rgcca_permutation changes par_type to sparsity if a sparse method is
            given with par_type = 'tau' ──
  <1/simpleError/error/condition>
  Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
  Backtrace:
      ▆
   1. └─RGCCA::rgcca_permutation(...) at test_rgcca_permutation.R:18:2
   2.   └─RGCCA:::set_parameter_grid(...)
   3.     └─RGCCA (local) check_param_type(par_value, blocks)
   4.       └─RGCCA:::stop_rgcca(...)
  ── Error ('test_rgcca_permutation.R:32:3'): rgcca_permutation computes n_perms permuted scores and one non
            permuted score per parameter value ──
  <1/simpleError/error/condition>
  Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
  Backtrace:
      ▆
   1. └─RGCCA::rgcca_permutation(...) at test_rgcca_permutation.R:32:2
   2.   └─RGCCA:::set_parameter_grid(...)
   3.     └─RGCCA (local) check_param_type(par_value, blocks)
   4.       └─RGCCA:::stop_rgcca(...)
  ── Error ('test_rgcca_permutation.R:59:3'): rgcca imports the parameters from a permutation object ──
  <1/simpleError/error/condition>
  Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
  Backtrace:
      ▆
   1. └─RGCCA::rgcca_permutation(...) at test_rgcca_permutation.R:59:2
   2.   └─RGCCA:::set_parameter_grid(...)
   3.     └─RGCCA (local) check_param_type(par_value, blocks)
   4.       └─RGCCA:::stop_rgcca(...)
  ── Error ('test_set_parameter_grid.R:44:3'): set_parameter_grid returns a valid grid of parameters when par_value
            is NULL ──
  <1/simpleError/error/condition>
  Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
  Backtrace:
      ▆
   1. └─RGCCA:::set_parameter_grid(...) at test_set_parameter_grid.R:44:2
   2.   └─RGCCA (local) check_param_type(par_value, blocks)
   3.     └─RGCCA:::stop_rgcca(...)
  
  [ FAIL 10 | WARN 0 | SKIP 41 | PASS 824 ]
  Error: Test failures
  Execution halted