Running ‘testthat.R’ [23s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyseurat)
  Loading required package: ttservice
  Loading required package: SeuratObject
  Loading required package: sp
  
  Attaching package: 'SeuratObject'
  
  The following object is masked from 'package:base':
  
      intersect
  
  ========================================
  tidyseurat version 0.7.4
  If you use TIDYSEURAT in published research, please cite:
  
  Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.
  
  This message can be suppressed by:
    suppressPackageStartupMessages(library(tidyseurat))
    
  To restore the Seurat default display use options("restore_Seurat_show" = TRUE) 
  ========================================
  
  
  Attaching package: 'tidyseurat'
  
  The following object is masked from 'package:ttservice':
  
      plot_ly
  
  > 
  > test_check("tidyseurat")
  
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    |======================================================================| 100%
  [ FAIL 5 | WARN 12 | SKIP 0 | PASS 69 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dplyr.R:8:3'): arrange ─────────────────────────────────────────
  Error in `validObject(object = x)`: invalid class "Seurat" object: 1: all cells in reductions must be in the same order as the Seurat object
  invalid class "Seurat" object: 2: all cells in reductions must be in the same order as the Seurat object
  invalid class "Seurat" object: 3: all cells in graphs must be in the same order as the Seurat object (offending: RNA_snn)
  invalid class "Seurat" object: 4: 'active.idents' must be named with cell names
  Backtrace:
      ▆
   1. ├─Seurat::RunPCA(...) at test-dplyr.R:8:3
   2. ├─Seurat::FindVariableFeatures(...)
   3. ├─Seurat::ScaleData(arrange(pbmc_small, nFeature_RNA))
   4. └─Seurat:::ScaleData.Seurat(arrange(pbmc_small, nFeature_RNA))
   5.   ├─methods (local) `[[<-`(`*tmp*`, assay, value = `<Assay[,80]>`)
   6.   └─SeuratObject (local) `[[<-`(`*tmp*`, assay, value = `<Assay[,80]>`)
   7.     └─methods::validObject(object = x)
  ── Failure ('test-dplyr.R:147:3'): slice_min ───────────────────────────────────
  ... %>% pull(.cell) not equal to colnames(slice_min(pbmc_small, nFeature_RNA, n = 5)).
  2/5 mismatches
  x[3]: "AGTCTTACTTCGGA"
  y[3]: "GACGCTCTCTCTCG"
  
  x[4]: "GACGCTCTCTCTCG"
  y[4]: "AGTCTTACTTCGGA"
  ── Failure ('test-dplyr.R:158:3'): slice_max ───────────────────────────────────
  ... %>% pull(.cell) not equal to colnames(slice_max(pbmc_small, nFeature_RNA, n = 5)).
  4/5 mismatches
  x[1]: "GACATTCTCCACCT"
  y[1]: "TTGAGGACTACGCA"
  
  x[2]: "ACGTGATGCCATGA"
  y[2]: "TTTAGCTGTACTCT"
  
  x[3]: "TTGAGGACTACGCA"
  y[3]: "GACATTCTCCACCT"
  
  x[4]: "TTTAGCTGTACTCT"
  y[4]: "ACGTGATGCCATGA"
  ── Error ('test-methods.R:42:3'): aggregate_cells() returns expected values ────
  Error in `methods::slot(object = object, name = layer)`: no slot of name "ACAP1" for this object of class "Assay"
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-methods.R:42:3
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─...[]
   5. └─SeuratObject:::`[.Assay`(...)
   6.   ├─SeuratObject::LayerData(object = x, layer = i, ...)
   7.   └─SeuratObject:::LayerData.Assay(object = x, layer = i, ...)
   8.     ├─SeuratObject::IsMatrixEmpty(...)
   9.     └─methods::slot(object = object, name = layer)
  ── Error ('test-tidyr.R:8:3'): nest_unnest ─────────────────────────────────────
  Error in `ScaleData(object = object[[assay]], features = features, vars.to.regress = vars.to.regress, 
      latent.data = latent.data, split.by = split.by, model.use = model.use, 
      use.umi = use.umi, do.scale = do.scale, do.center = do.center, 
      scale.max = scale.max, block.size = block.size, min.cells.to.block = min.cells.to.block, 
      verbose = verbose, ...)`: No layer matching pattern 'data' found. Please run NormalizeData and retry
  Backtrace:
      ▆
   1. ├─Seurat::RunPCA(...) at test-tidyr.R:8:3
   2. ├─Seurat::FindVariableFeatures(...)
   3. ├─Seurat::ScaleData(unnest(nest(tt, data = -groups), data))
   4. └─Seurat:::ScaleData.Seurat(unnest(nest(tt, data = -groups), data))
   5.   ├─Seurat::ScaleData(...)
   6.   └─Seurat:::ScaleData.StdAssay(...)
   7.     └─rlang::abort(paste0("No layer matching pattern '", olayer, "' found. Please run NormalizeData and retry"))
  
  [ FAIL 5 | WARN 12 | SKIP 0 | PASS 69 ]
  Error: Test failures
  Execution halted