* using log directory ‘/srv/hornik/tmp/CRAN/tidyseurat.Rcheck’
* using R Under development (unstable) (2023-11-09 r85497)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (16)
    GNU Fortran (Debian 13.2.0-5) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘tidyseurat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidyseurat’ version ‘0.7.7’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/7s] Note_to_CRAN_maintainers
Maintainer: ‘Stefano Mangiola <mangiolastefano@gmail.com>’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tidyseurat’ can be installed ... [13s/13s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking whether startup messages can be suppressed ... [3s/3s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/15s] NOTE
join_features,Seurat: no visible binding for global variable ‘.feature’
Undefined global functions or variables:
  .feature
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] ERROR
Running examples in ‘tidyseurat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filter
> ### Title: Keep rows that match a condition
> ### Aliases: filter filter.Seurat
> 
> ### ** Examples
> 
> data("pbmc_small")
> pbmc_small |>  filter(groups == "g1")
Error in getClassDef(x@superClass, package = packageSlot(x))@virtual : 
  no applicable method for `@` applied to an object of class "NULL"
Calls: filter ... clean_seurat_object -> .hasSlot -> subset -> subset.Seurat
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [7s/7s] ERROR
  Running ‘testthat.R’ [7s/7s]
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 0.7.7
  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")
  [ FAIL 17 | WARN 9 | SKIP 0 | PASS 41 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-dplyr.R:9:3'): arrange ───────────────────────────────────────
  `arrange(pbmc_small, nFeature_RNA)` produced unexpected warnings.
  Expected match: arrange() is temporarly deprected
  Actual values:
  * `arrange()` was deprecated in tidyseurat 0.7.5.
  ℹ tidyseurat says: arrange() is temporarly deprected as it is not clear that
    Seurat allows reordering of cells.
  ── Error ('test-dplyr.R:46:3'): 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:46:3
    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:79:3'): 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:79:3
    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:86:3'): 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:86:3
    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:100:3'): 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:100:3
    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:107:3'): 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:107:3
    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:115:5'): 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:115:5
    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:126:3'): 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:126:3
    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:137:3'): 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:137:3
    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:148:3'): 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:148:3
    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:159:3'): 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:159:3
    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:170:3'): 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:170:3
    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:186:3'): 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:186:3
    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:211:3'): 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:211:3
    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-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 17 | WARN 9 | SKIP 0 | PASS 41 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [11s/11s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘figures_article.Rmd’ using knitr
--- finished re-building ‘figures_article.Rmd’

--- re-building ‘introduction.Rmd’ using knitr

Quitting from lines 184-190 [cluster] (./../man/fragments/intro.Rmd)

Quitting from lines 184-190 [unnamed-chunk-2] (./../man/fragments/intro.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid class "Graph" object: superclass "mMatrix" not defined in the environment of the object's class
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 ERRORs, 1 NOTE