Running ‘testthat.R’ [170s/422s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SpatialDDLS)
  
  Attaching package: 'SpatialDDLS'
  
  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("SpatialDDLS")
     user  system elapsed 
    0.498   0.017   1.107 
     user  system elapsed 
    0.554   0.047   1.801 
     user  system elapsed 
    0.534   0.016   1.406 
     user  system elapsed 
    0.428   0.015   1.138 
     user  system elapsed 
    0.488   0.052   1.457 
     user  system elapsed 
    0.436   0.035   1.356 
  [1] "Check Python dependencies"
  [ FAIL 3 | WARN 1 | SKIP 7 | PASS 108 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • .checkPythonDependencies(alert = "none") is not TRUE (7)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_loadData.R:499:5'): 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:499:4
    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. └─SpatialDDLS::createSpatialDDLSobject(...)
    7.   └─SpatialDDLS:::.loadSCData(...)
    8.     └─SpatialDDLS:::.createSCEObject(...)
    9.       └─SpatialDDLS:::.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_simMixedSpots.R:353:5'): Using HDF5 files as back-end simMixedProfiles: 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_simMixedSpots.R:353:4
    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. └─SpatialDDLS::simMixedProfiles(...)
    7.   └─base::lapply(...)
    8.     └─SpatialDDLS (local) FUN(X[[i]], ...)
    9.       └─SpatialDDLS:::.generateBulkProfiles(...)
   10.         └─SpatialDDLS:::.createSEObject(...)
   11.           └─SpatialDDLS:::.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. └─SpatialDDLS::simSCProfiles(...)
    7.   └─SpatialDDLS:::.createSCEObject(...)
    8.     └─SpatialDDLS:::.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 108 ]
  Error: Test failures
  Execution halted