Running ‘testthat.R’ [24s/25s]
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
  'SeuratObject' was built with package 'Matrix' 1.6.1.1 but the current
  version is 1.6.2; it is recomended that you reinstall 'SeuratObject' as
  the ABI for 'Matrix' may have changed
  
  Attaching package: 'SeuratObject'
  
  The following objects are 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")
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  [ FAIL 19 | WARN 8 | SKIP 0 | PASS 37 ]
  
  ══ 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)
  ── Error ('test-dplyr.R:41:3'): filter ─────────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:41:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(filter(pbmc_small, groups == "g1"))
    5. ├─dplyr::filter(pbmc_small, groups == "g1")
    6. ├─tidyseurat:::filter.Seurat(pbmc_small, groups == "g1")
    7. │ ├─subset(.data, cells = rownames(new_meta)) %>% ...
    8. │ ├─base::subset(.data, cells = rownames(new_meta))
    9. │ └─SeuratObject:::subset.Seurat(.data, cells = rownames(new_meta))
   10. │   ├─base::suppressWarnings(...)
   11. │   │ └─base::withCallingHandlers(...)
   12. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   13. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   15. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   16. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   17. ├─tidyseurat:::clean_seurat_object(.)
   18. │ └─methods::.hasSlot(.data, "images")
   19. └─methods::.selectSuperClasses(...)
   20.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   21.     └─methods (local) FUN(X[[i]], ...)
   22.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:63:3'): rename ─────────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:63:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(...)
    5. ├─dplyr::select(rename(pbmc_small, s_score = nFeature_RNA), s_score)
    6. ├─dplyr::rename(pbmc_small, s_score = nFeature_RNA)
    7. ├─tidyseurat:::rename.Seurat(pbmc_small, s_score = nFeature_RNA)
    8. │ ├─tibble::as_tibble(.data[1, 1])
    9. │ ├─.data[1, 1]
   10. │ └─SeuratObject:::`[.Seurat`(.data, 1, 1)
   11. │   └─SeuratObject:::subset.Seurat(...)
   12. │     ├─base::suppressWarnings(...)
   13. │     │ └─base::withCallingHandlers(...)
   14. │     ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   15. │     ├─x[[g]][cells.g, cells.g, drop = FALSE]
   16. │     └─x[[g]][cells.g, cells.g, drop = FALSE]
   17. │       └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   18. │         └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   19. └─methods::.selectSuperClasses(...)
   20.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   21.     └─methods (local) FUN(X[[i]], ...)
   22.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:74:3'): inner_join ─────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:74:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(...)
    5. ├─dplyr::inner_join(...)
    6. ├─tidyseurat:::inner_join.Seurat(...)
    7. │ └─... %>% ...
    8. ├─purrr::when(...)
    9. │ └─base::eval(dots[[i]][[action]], env, env)
   10. │   └─base::eval(dots[[i]][[action]], env, env)
   11. │     ├─base::subset(x, cells = pull(., c_(x)$name))
   12. │     └─SeuratObject:::subset.Seurat(x, cells = pull(., c_(x)$name))
   13. │       ├─base::suppressWarnings(...)
   14. │       │ └─base::withCallingHandlers(...)
   15. │       ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   16. │       ├─x[[g]][cells.g, cells.g, drop = FALSE]
   17. │       └─x[[g]][cells.g, cells.g, drop = FALSE]
   18. │         └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   19. │           └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   20. └─methods::.selectSuperClasses(...)
   21.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   22.     └─methods (local) FUN(X[[i]], ...)
   23.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:81:3'): right_join ─────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:81:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(...)
    5. ├─dplyr::right_join(...)
    6. ├─tidyseurat:::right_join.Seurat(...)
    7. │ └─... %>% ...
    8. ├─purrr::when(...)
    9. │ └─base::eval(dots[[i]][[action]], env, env)
   10. │   └─base::eval(dots[[i]][[action]], env, env)
   11. │     ├─base::subset(x, cells = (.) %>% pull(c_(x)$name))
   12. │     └─SeuratObject:::subset.Seurat(x, cells = (.) %>% pull(c_(x)$name))
   13. │       ├─base::suppressWarnings(...)
   14. │       │ └─base::withCallingHandlers(...)
   15. │       ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   16. │       ├─x[[g]][cells.g, cells.g, drop = FALSE]
   17. │       └─x[[g]][cells.g, cells.g, drop = FALSE]
   18. │         └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   19. │           └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   20. └─methods::.selectSuperClasses(...)
   21.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   22.     └─methods (local) FUN(X[[i]], ...)
   23.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:95:3'): slice ──────────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(ncol(slice(pbmc_small, 1)), 1) at test-dplyr.R:95:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(slice(pbmc_small, 1))
    5. ├─dplyr::slice(pbmc_small, 1)
    6. ├─tidyseurat:::slice.Seurat(pbmc_small, 1)
    7. │ ├─base::subset(.data, cells = colnames(.data)[idx])
    8. │ └─SeuratObject:::subset.Seurat(.data, cells = colnames(.data)[idx])
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:102:3'): sample_n ──────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(ncol(sample_n(pbmc_small, 50)), 50) at test-dplyr.R:102:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(sample_n(pbmc_small, 50))
    5. ├─dplyr::sample_n(pbmc_small, 50)
    6. ├─tidyseurat:::sample_n.Seurat(pbmc_small, 50)
    7. │ ├─base::subset(tbl, cells = new_meta %>% pull(!!c_(tbl)$symbol))
    8. │ └─SeuratObject:::subset.Seurat(tbl, cells = new_meta %>% pull(!!c_(tbl)$symbol))
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:110:5'): slice_sample ──────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:110:5
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(slice_sample(pbmc_small, n = 50))
    5. ├─dplyr::slice_sample(pbmc_small, n = 50)
    6. ├─tidyseurat:::slice_sample.Seurat(pbmc_small, n = 50)
    7. │ ├─base::subset(.data, cells = new_meta %>% pull(!!c_(.data)$symbol))
    8. │ └─SeuratObject:::subset.Seurat(.data, cells = new_meta %>% pull(!!c_(.data)$symbol))
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:121:3'): slice_head ────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:121:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(slice_head(pbmc_small, n = 50))
    5. ├─dplyr::slice_head(pbmc_small, n = 50)
    6. ├─tidyseurat:::slice_head.Seurat(pbmc_small, n = 50)
    7. │ ├─base::subset(.data, cells = colnames(.data)[idx])
    8. │ └─SeuratObject:::subset.Seurat(.data, cells = colnames(.data)[idx])
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:132:3'): slice_tail ────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:132:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(slice_tail(pbmc_small, n = 50))
    5. ├─dplyr::slice_tail(pbmc_small, n = 50)
    6. ├─tidyseurat:::slice_tail.Seurat(pbmc_small, n = 50)
    7. │ ├─base::subset(.data, cells = colnames(.data)[idx])
    8. │ └─SeuratObject:::subset.Seurat(.data, cells = colnames(.data)[idx])
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:143:3'): slice_min ─────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:143:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(slice_min(pbmc_small, nFeature_RNA, n = 5))
    5. ├─dplyr::slice_min(pbmc_small, nFeature_RNA, n = 5)
    6. ├─tidyseurat:::slice_min.Seurat(pbmc_small, nFeature_RNA, n = 5)
    7. │ ├─base::subset(.data, cells = colnames(.data)[idx])
    8. │ └─SeuratObject:::subset.Seurat(.data, cells = colnames(.data)[idx])
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:154:3'): slice_max ─────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:154:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(slice_max(pbmc_small, nFeature_RNA, n = 5))
    5. ├─dplyr::slice_max(pbmc_small, nFeature_RNA, n = 5)
    6. ├─tidyseurat:::slice_max.Seurat(pbmc_small, nFeature_RNA, n = 5)
    7. │ ├─base::subset(.data, cells = colnames(.data)[idx])
    8. │ └─SeuratObject:::subset.Seurat(.data, cells = colnames(.data)[idx])
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:165:3'): slice_min slice_max tibble input for order_by ──
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:165:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(...)
    5. ├─dplyr::slice_min(...)
    6. ├─tidyseurat:::slice_min.Seurat(...)
    7. │ ├─base::subset(.data, cells = colnames(.data)[idx])
    8. │ └─SeuratObject:::subset.Seurat(.data, cells = colnames(.data)[idx])
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:181:3'): sample_frac ───────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:181:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::ncol(sample_frac(pbmc_small, 0.1))
    5. ├─dplyr::sample_frac(pbmc_small, 0.1)
    6. ├─tidyseurat:::sample_frac.Seurat(pbmc_small, 0.1)
    7. │ ├─base::subset(tbl, cells = new_meta %>% pull(!!c_(tbl)$symbol))
    8. │ └─SeuratObject:::subset.Seurat(tbl, cells = new_meta %>% pull(!!c_(tbl)$symbol))
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-dplyr.R:206:3'): rowwise ───────────────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr.R:206:3
    2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::unname(((pbmc_small[, 1]$nCount_RNA + pbmc_small[, 1]$nFeature_RNA)/2))
    5. ├─pbmc_small[, 1]
    6. ├─SeuratObject:::`[.Seurat`(pbmc_small, , 1)
    7. │ └─SeuratObject:::subset.Seurat(...)
    8. │   ├─base::suppressWarnings(...)
    9. │   │ └─base::withCallingHandlers(...)
   10. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   11. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   12. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   14. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   15. └─methods::.selectSuperClasses(...)
   16.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   17.     └─methods (local) FUN(X[[i]], ...)
   18.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-methods.R:6:3'): join_features_long ────────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-methods.R:6:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─dplyr::pull(...)
    5. ├─dplyr::slice(...)
    6. ├─tidyseurat:::slice.Seurat(...)
    7. │ ├─base::subset(.data, cells = colnames(.data)[idx])
    8. │ └─SeuratObject:::subset.Seurat(.data, cells = colnames(.data)[idx])
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-methods.R:14:3'): join_features_wide ───────────────────────────
  Error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-methods.R:14:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─dplyr::pull(...)
    5. ├─dplyr::slice(...)
    6. ├─tidyseurat:::slice.Seurat(...)
    7. │ ├─base::subset(.data, cells = colnames(.data)[idx])
    8. │ └─SeuratObject:::subset.Seurat(.data, cells = colnames(.data)[idx])
    9. │   ├─base::suppressWarnings(...)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─SeuratObject::as.Graph(x = x[[g]][cells.g, cells.g, drop = FALSE])
   12. │   ├─x[[g]][cells.g, cells.g, drop = FALSE]
   13. │   └─x[[g]][cells.g, cells.g, drop = FALSE]
   14. │     └─Matrix:::.subscript.2ary(x, i, j, drop = drop)
   15. │       └─Matrix:::..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L])
   16. └─methods::.selectSuperClasses(...)
   17.   └─base::vapply(ext, F, NA, USE.NAMES = FALSE)
   18.     └─methods (local) FUN(X[[i]], ...)
   19.       └─methods (local) isVirtualExt(exti)
  ── Error ('test-methods.R:23:3'): aggregate_cells() returns expected values ────
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `mutate(., `:=`(!!as.symbol(col_name_data), map(!!as.symbol(col_name_data), 
      ~my_data__ %>% filter(!!c_(.data)$symbol %in% pull(.x, !!c_(.data)$symbol)) %>% 
          select(colnames(.x)))))`: ℹ In argument: `data = map(...)`.
  Caused by error in `map()`:
  ℹ In index: 1.
  Caused by error in `getClassDef(x@superClass, package = packageSlot(x))@virtual`:
  ! no applicable method for `@` applied to an object of class "NULL"
  ── Error ('test-tidyr.R:4:1'): (code run outside of `test_that()`) ─────────────
  Error in `validObject(.Object)`: invalid class "LogMap" object: superclass "mMatrix" not defined in the environment of the object's class
  Backtrace:
       ▆
    1. ├─dplyr::mutate(...) at test-tidyr.R:4:1
    2. ├─SeuratObject::CreateSeuratObject(...)
    3. └─SeuratObject:::CreateSeuratObject.default(...)
    4.   └─SeuratObject::CreateAssay5Object(...)
    5.     ├─SeuratObject::.CreateStdAssay(...)
    6.     └─SeuratObject:::.CreateStdAssay.list(...)
    7.       ├─methods::new(...)
    8.       │ ├─methods::initialize(value, ...)
    9.       │ └─methods::initialize(value, ...)
   10.       └─SeuratObject::LogMap(y = features.all)
   11.         └─methods::new(...)
   12.           ├─methods::initialize(value, ...)
   13.           └─methods::initialize(value, ...)
   14.             └─methods (local) initMatrix(.Object, ...)
   15.               └─methods::validObject(.Object)
  
  [ FAIL 19 | WARN 8 | SKIP 0 | PASS 37 ]
  Error: Test failures
  Execution halted