Running ‘testthat.R’ [79s/101s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rliger)
  Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.
  
  We recommand you backup your old analysis before overwriting any existing result.
  
  `readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
  
  Package "RcppPlanc" is required for performing integrative factorizations but is not detected. It is currently not on CRAN, so please install it with `devtools::install_github('welch-lab/RcppPlanc')`
  > 
  > test_check("rliger")
  Working ctrl H5 file path:  /tmp/Rtmpj1ft1h/ctrltest.h5 
  Working stim H5 file path:  /tmp/Rtmpj1ft1h/stimtest.h5 
  
  
  
  
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating gene variances
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating feature variances of standardized and clipped values
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Working ctrl H5 file path:  /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rliger.Rcheck/tests/testthat/ctrltest.h5 
  Working stim H5 file path:  /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rliger.Rcheck/tests/testthat/stimtest.h5 
  
  
  Working ctrl H5 file path:  /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rliger.Rcheck/tests/testthat/ctrltest.h5 
  Working stim H5 file path:  /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rliger.Rcheck/tests/testthat/stimtest.h5 
  
  
  
  
  Working ctrl H5 file path:  /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rliger.Rcheck/tests/testthat/ctrltest.h5 
  Working stim H5 file path:  /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rliger.Rcheck/tests/testthat/stimtest.h5 
  
  
  
  
  
  
  Working ctrl H5 file path:  /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rliger.Rcheck/tests/testthat/ctrltest.h5 
  Working stim H5 file path:  /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rliger.Rcheck/tests/testthat/stimtest.h5 
  
  
  
  
  
  
  
  
  
  
  [ FAIL 1 | WARN 0 | SKIP 16 | PASS 1034 ]
  
  ══ Skipped tests (16) ══════════════════════════════════════════════════════════
  • has_RcppPlanc is not TRUE (16): 'test_downstream.R:66:5',
    'test_downstream.R:116:5', 'test_downstream.R:140:5',
    'test_downstream.R:186:5', 'test_downstream.R:259:5',
    'test_factorization.R:55:5', 'test_factorization.R:91:5',
    'test_factorization.R:112:5', 'test_factorization.R:145:5',
    'test_factorization.R:188:5', 'test_factorization.R:229:5',
    'test_object.R:125:5', 'test_object.R:227:5', 'test_object.R:331:5',
    'test_subset.R:55:5', 'test_subset.R:70:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_downstream.R:246:13'): gsea ────────────────────────────────────
  Error in `runGSEA(pbmcPlot, genesets = "Immune System")`: Package org.Hs.eg.db is needed for this function to work. Please install
  it by command: `BiocManager::install('org.Hs.eg.db')`
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test_downstream.R:245:9
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─testthat::expect_is(...) at test_downstream.R:246:13
    7. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    8. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    9. └─rliger::runGSEA(pbmcPlot, genesets = "Immune System")
   10.   └─cli::cli_abort("Package {.pkg org.Hs.eg.db} is needed for this function to work.\n            Please install it by command:\n            {.code BiocManager::install('org.Hs.eg.db')}")
   11.     └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 16 | PASS 1034 ]
  Error: Test failures
  Execution halted