Running ‘testthat.R’ [87s/191s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(digitalDLSorteR)
  
  Attaching package: 'digitalDLSorteR'
  
  The following object is masked from 'package:base':
  
      saveRDS
  
  Warning message:
  replacing previous import 'S4Arrays::read_block' by 'DelayedArray::read_block' when loading 'SummarizedExperiment' 
  > 
  > test_check("digitalDLSorteR")
     user  system elapsed 
    0.486   0.002   1.345 
     user  system elapsed 
    0.513   0.002   1.347 
     user  system elapsed 
    0.596   0.008   1.433 
     user  system elapsed 
    0.398   0.000   0.993 
     user  system elapsed 
    0.468   0.001   1.301 
     user  system elapsed 
    0.368   0.001   0.947 
  [1] "is here"
  [ FAIL 3 | WARN 1 | SKIP 7 | PASS 109 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • .checkPythonDependencies(alert = "none") is not TRUE (7)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_loadData.R:467:5'): Check behaviour with HDF5 files ────────────
  Error in `.read_block_OLD(x, viewport, as.sparse = as.sparse)`: could not find function ".read_block_OLD"
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test_loadData.R:467:4
    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. └─digitalDLSorteR::loadSCProfiles(...)
    7.   └─digitalDLSorteR:::.loadSingleCellData(...)
    8.     └─digitalDLSorteR:::.createSCEObject(...)
    9.       └─digitalDLSorteR:::.useH5backend(...)
   10.         └─HDF5Array::writeHDF5Array(...)
   11.           └─DelayedArray::BLOCK_write_to_sink(sink, x, verbose = verbose)
   12.             └─DelayedArray::sinkApply(...)
   13.               └─DelayedArray::gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose)
   14.                 └─DelayedArray (local) FUN(viewport, init, ...)
   15.                   └─DelayedArray (local) FUN(init, viewport, ...)
   16.                     └─DelayedArray:::verbose_read_block(...)
   17.                       └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse)
  ── Error ('test_simBulk.R:464:5'): Using HDF5 files as back-end simBulkProfiles: the following tests will write file in temp directory/files. Only available if DelayedArray and HDF5Array packages are installed ──
  Error in `.read_block_OLD(x, viewport, as.sparse = as.sparse)`: could not find function ".read_block_OLD"
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test_simBulk.R:464:4
    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. └─digitalDLSorteR::simBulkProfiles(...)
    7.   └─base::lapply(...)
    8.     └─digitalDLSorteR (local) FUN(X[[i]], ...)
    9.       └─digitalDLSorteR:::.generateBulkProfiles(...)
   10.         └─digitalDLSorteR:::.createSEObject(...)
   11.           └─digitalDLSorteR:::.useH5backend(...)
   12.             └─HDF5Array::writeHDF5Array(...)
   13.               └─DelayedArray::BLOCK_write_to_sink(sink, x, verbose = verbose)
   14.                 └─DelayedArray::sinkApply(...)
   15.                   └─DelayedArray::gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose)
   16.                     └─DelayedArray (local) FUN(viewport, init, ...)
   17.                       └─DelayedArray (local) FUN(init, viewport, ...)
   18.                         └─DelayedArray:::verbose_read_block(...)
   19.                           └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse)
  ── Error ('test_simSingleCell.R:344:5'): Using HDF5 files as back-end simSCProfiles: the following tests will write file in temp directory/files. Only available if DelayedArray and HDF5Array packages are installed ──
  Error in `.read_block_OLD(x, viewport, as.sparse = as.sparse)`: could not find function ".read_block_OLD"
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test_simSingleCell.R:344:4
    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. └─digitalDLSorteR::simSCProfiles(...)
    7.   └─digitalDLSorteR:::.createSCEObject(...)
    8.     └─digitalDLSorteR:::.useH5backend(...)
    9.       └─HDF5Array::writeHDF5Array(...)
   10.         └─DelayedArray::BLOCK_write_to_sink(sink, x, verbose = verbose)
   11.           └─DelayedArray::sinkApply(...)
   12.             └─DelayedArray::gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose)
   13.               └─DelayedArray (local) FUN(viewport, init, ...)
   14.                 └─DelayedArray (local) FUN(init, viewport, ...)
   15.                   └─DelayedArray:::verbose_read_block(...)
   16.                     └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse)
  
  [ FAIL 3 | WARN 1 | SKIP 7 | PASS 109 ]
  Error: Test failures
  Execution halted