Running ‘testthat.R’ [68s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Seurat)
  > 
  > test_check("Seurat")
  ── 1. Error: (unknown) (@test_load_10X.R#34)  ──────────────────────────────────
  HDF5-API H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  Backtrace:
   1. Seurat::Load10X_Spatial(data.dir = "../testdata/visium")
   2. Seurat::Read10X_h5(...)
   4. hdf5r:::`[.H5D`(...)
   5. x$read(...)
   6. self$read_low_level(...)
  
  ── 2. Failure: SCTransform wrapper works as expected (@test_preprocessing.R#295)
  as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "scale.data"))[1]) not equal to 13.3303864.
  1/1 mismatches
  [1] 11.4 - 13.3 == -1.93
  
  ── 3. Failure: SCTransform wrapper works as expected (@test_preprocessing.R#299)
  as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "counts"))[1]) not equal to 123.
  1/1 mismatches
  [1] 129 - 123 == 6
  
  ── 4. Failure: SCTransform ncells param works (@test_preprocessing.R#312)  ─────
  as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "scale.data"))[1]) not equal to 11.834969847.
  1/1 mismatches
  [1] 9.41 - 11.8 == -2.42
  
  ── 5. Failure: SCTransform ncells param works (@test_preprocessing.R#316)  ─────
  as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "counts"))[1]) not equal to 121.
  1/1 mismatches
  [1] 119 - 121 == -2
  
  ── 6. Failure: SCTransform ncells param works (@test_preprocessing.R#317)  ─────
  as.numeric(rowSums(GetAssayData(object = object[["SCT"]], slot = "counts"))[5]) not equal to 25.
  1/1 mismatches
  [1] 26 - 25 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 450 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 6 ]
  1. Error: (unknown) (@test_load_10X.R#34) 
  2. Failure: SCTransform wrapper works as expected (@test_preprocessing.R#295) 
  3. Failure: SCTransform wrapper works as expected (@test_preprocessing.R#299) 
  4. Failure: SCTransform ncells param works (@test_preprocessing.R#312) 
  5. Failure: SCTransform ncells param works (@test_preprocessing.R#316) 
  6. Failure: SCTransform ncells param works (@test_preprocessing.R#317) 
  
  Error: testthat unit tests failed
  Execution halted