##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:tidySingleCellExperiment.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings tidySingleCellExperiment_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/tidySingleCellExperiment.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘tidySingleCellExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidySingleCellExperiment’ version ‘1.19.0’
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tidySingleCellExperiment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... NOTE
nest.SingleCellExperiment: no visible global function definition for
  ‘n’
aggregate_cells,SingleCellExperiment: no visible binding for global
  variable ‘my_id_to_split_by___’
aggregate_cells,SingleCellExperiment: no visible binding for global
  variable ‘assay_name’
aggregate_cells,SingleCellExperiment: no visible binding for global
  variable ‘.feature’
Undefined global functions or variables:
  .feature assay_name my_id_to_split_by___ n
* checking Rd files ... NOTE
prepare_Rd: group_by.Rd:98-100: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  formatting.Rd: tbl_format_setup
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘tidySingleCellExperiment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arrange
> ### Title: Order rows using column values
> ### Aliases: arrange arrange.SingleCellExperiment
> 
> ### ** Examples
> 
> data(pbmc_small)
> pbmc_small |> 
+     arrange(nFeature_RNA)
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: arrange ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9. │         ├─methods::callNextMethod()
   10. │         └─SummarizedExperiment (local) .nextMethod(object = object)
   11. │           ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
   12. │           └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
   13. │             ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
   14. │             └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
   15. │               └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
   16. └─methods:::.extendsForS3(`<chr>`)
   17.   └─methods::extends(Class, maybe = FALSE)
   18.     └─methods::getClassDef(class1)
   19.       └─methods:::.requirePackage(package)
  
  [ FAIL 9 | WARN 1 | SKIP 0 | PASS 135 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from introduction.Rmd:86-88 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─tools::buildVignettes(...)
  2. │ ├─base::tryCatch(...)
  3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
  7. │   └─knitr:::vweave_rmarkdown(...)
  8. │     └─rmarkdown::render(...)
  9. │       └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10. │         └─knitr:::process_file(text, output)
 11. │           ├─xfun:::handle_error(...)
 12. │           ├─base::withCallingHandlers(...)
 13. │           └─knitr:::process_group(group)
 14. │             └─knitr:::call_block(x)
 15. │               └─knitr:::block_exec(params)
 16. │                 └─knitr:::eng_r(options)
 17. │                   ├─knitr:::in_input_dir(...)
 18. │                   │ └─knitr:::in_dir(input_dir(), expr)
 19. │                   └─knitr (local) evaluate(...)
 20. │                     └─evaluate::evaluate(...)
 21. │                       ├─base::withRestarts(...)
 22. │                       │ └─base (local) withRestartList(expr, restarts)
 23. │                       │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 24. │                       │   │ └─base (local) doWithOneRestart(return(expr), restart)
 25. │                       │   └─base (local) withRestartList(expr, restarts[-nr])
 26. │                       │     └─base (local) withOneRestart(expr, restarts[[1L]])
 27. │                       │       └─base (local) doWithOneRestart(return(expr), restart)
 28. │                       ├─evaluate:::with_handlers(...)
 29. │                       │ ├─base::eval(call)
 30. │                       │ │ └─base::eval(call)
 31. │                       │ └─base::withCallingHandlers(...)
 32. │                       └─watcher$print_value(ev$value, ev$visible, envir)
 33. │                         ├─base::withVisible(handle_value(handler, value, visible, envir))
 34. │                         └─evaluate:::handle_value(handler, value, visible, envir)
 35. │                           └─handler$value(value, visible)
 36. │                             └─knitr (local) fun(x, options = options)
 37. │                               ├─base::withVisible(knit_print(x, ...))
 38. │                               ├─knitr::knit_print(x, ...)
 39. │                               └─knitr:::knit_print.default(x, ...)
 40. │                                 └─knitr::normal_print(x)
 41. │                                   ├─methods::show(x)
 42. │                                   └─methods::show(x)
 43. │                                     ├─base::print(object)
 44. │                                     └─tidySingleCellExperiment:::print.SingleCellExperiment(object)
 45. │                                       ├─... %>% print()
 46. │                                       ├─vctrs::new_data_frame(...)
 47. │                                       ├─tibble::as_tibble(x, n_dimensions_to_return = 5)
 48. │                                       └─tidySingleCellExperiment:::as_tibble.SingleCellExperiment(...)
 49. │                                         ├─SingleCellExperiment::reducedDims(x)
 50. │                                         └─SingleCellExperiment::reducedDims(x)
 51. │                                           └─SingleCellExperiment (local) .local(x, ...)
 52. │                                             └─SingleCellExperiment:::.get_internal_all(...)
 53. │                                               ├─BiocGenerics::updateObject(x)
 54. │                                               └─SingleCellExperiment::updateObject(x)
 55. │                                                 ├─methods::callNextMethod()
 56. │                                                 └─SummarizedExperiment (local) .nextMethod(object = object)
 57. │                                                   ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 58. │                                                   └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 59. │                                                     ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 60. │                                                     └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 61. │                                                       └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 62. ├─base::print(.)
 63. ├─tidySingleCellExperiment:::add_attr(., assayNames(x), "assay_names")
 64. ├─tidySingleCellExperiment:::add_attr(., nrow(x), "number_of_features")
 65. └─methods:::.extendsForS3(`<chr>`)
 66.   └─methods::extends(Class, maybe = FALSE)
 67.     └─methods::getClassDef(class1)
 68.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- 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 ... OK
* DONE

Status: 3 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/tidySingleCellExperiment.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL tidySingleCellExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘tidySingleCellExperiment’ ...
** this is package ‘tidySingleCellExperiment’ version ‘1.19.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tidySingleCellExperiment)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(tidySingleCellExperiment)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'tidySingleCellExperiment'

The following object is masked from 'package:generics':

    tidy

> 
> test_check("tidySingleCellExperiment")
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
[ FAIL 9 | WARN 1 | SKIP 0 | PASS 135 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-dplyr_methods.R:241:5'): slice_sample() ────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-dplyr_methods.R:241:5
  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 = 0))
  5. ├─dplyr::slice_sample(pbmc_small, n = 0)
  6. ├─tidySingleCellExperiment:::slice_sample.SingleCellExperiment(...)
  7. │ ├─.data[, pull(new_meta, !!c_(.data)$symbol)]
  8. │ └─.data[, pull(new_meta, !!c_(.data)$symbol)]
  9. │   ├─BiocGenerics::updateObject(x)
 10. │   └─SingleCellExperiment::updateObject(x)
 11. │     ├─methods::callNextMethod()
 12. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 13. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 14. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 16. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 18. └─methods:::.extendsForS3(`<chr>`)
 19.   └─methods::extends(Class, maybe = FALSE)
 20.     └─methods::getClassDef(class1)
 21.       └─methods:::.requirePackage(package)
── Error ('test-dplyr_methods.R:252:5'): slice_head() ──────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_equal(ncol(slice_head(pbmc_small, n = 0)), 0) at test-dplyr_methods.R:252:5
  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 = 0))
  5. ├─dplyr::slice_head(pbmc_small, n = 0)
  6. ├─tidySingleCellExperiment:::slice_head.SingleCellExperiment(...)
  7. │ ├─.data[, idx]
  8. │ └─.data[, idx]
  9. │   ├─BiocGenerics::updateObject(x)
 10. │   └─SingleCellExperiment::updateObject(x)
 11. │     ├─methods::callNextMethod()
 12. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 13. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 14. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 16. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 18. └─methods:::.extendsForS3(`<chr>`)
 19.   └─methods::extends(Class, maybe = FALSE)
 20.     └─methods::getClassDef(class1)
 21.       └─methods:::.requirePackage(package)
── Error ('test-dplyr_methods.R:267:5'): slice_tail() ──────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_equal(ncol(slice_tail(pbmc_small, n = 0)), 0) at test-dplyr_methods.R:267:5
  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 = 0))
  5. ├─dplyr::slice_tail(pbmc_small, n = 0)
  6. ├─tidySingleCellExperiment:::slice_tail.SingleCellExperiment(...)
  7. │ ├─.data[, idx]
  8. │ └─.data[, idx]
  9. │   ├─BiocGenerics::updateObject(x)
 10. │   └─SingleCellExperiment::updateObject(x)
 11. │     ├─methods::callNextMethod()
 12. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 13. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 14. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 16. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 18. └─methods:::.extendsForS3(`<chr>`)
 19.   └─methods::extends(Class, maybe = FALSE)
 20.     └─methods::getClassDef(class1)
 21.       └─methods:::.requirePackage(package)
── Error ('test-dplyr_methods.R:282:5'): slice_min() ───────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-dplyr_methods.R:282:5
  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 = 0))
  5. ├─dplyr::slice_min(pbmc_small, nFeature_RNA, n = 0)
  6. ├─tidySingleCellExperiment:::slice_min.SingleCellExperiment(...)
  7. │ ├─.data[, idx]
  8. │ └─.data[, idx]
  9. │   ├─BiocGenerics::updateObject(x)
 10. │   └─SingleCellExperiment::updateObject(x)
 11. │     ├─methods::callNextMethod()
 12. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 13. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 14. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 16. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 18. └─methods:::.extendsForS3(`<chr>`)
 19.   └─methods::extends(Class, maybe = FALSE)
 20.     └─methods::getClassDef(class1)
 21.       └─methods:::.requirePackage(package)
── Error ('test-dplyr_methods.R:299:5'): slice_max() ───────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-dplyr_methods.R:299:5
  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 = 0))
  5. ├─dplyr::slice_max(pbmc_small, nFeature_RNA, n = 0)
  6. ├─tidySingleCellExperiment:::slice_max.SingleCellExperiment(...)
  7. │ ├─.data[, idx]
  8. │ └─.data[, idx]
  9. │   ├─BiocGenerics::updateObject(x)
 10. │   └─SingleCellExperiment::updateObject(x)
 11. │     ├─methods::callNextMethod()
 12. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 13. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 14. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 16. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 18. └─methods:::.extendsForS3(`<chr>`)
 19.   └─methods::extends(Class, maybe = FALSE)
 20.     └─methods::getClassDef(class1)
 21.       └─methods:::.requirePackage(package)
── Error ('test-dplyr_methods.R:316:3'): slice_min() slice_max() tibble input for order_by ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-dplyr_methods.R:316:3
  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. ├─tidySingleCellExperiment:::slice_min.SingleCellExperiment(...)
  7. │ ├─.data[, idx]
  8. │ └─.data[, idx]
  9. │   ├─BiocGenerics::updateObject(x)
 10. │   └─SingleCellExperiment::updateObject(x)
 11. │     ├─methods::callNextMethod()
 12. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 13. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 14. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 16. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 18. └─methods:::.extendsForS3(`<chr>`)
 19.   └─methods::extends(Class, maybe = FALSE)
 20.     └─methods::getClassDef(class1)
 21.       └─methods:::.requirePackage(package)
── Error ('test-methods.R:5:5'): show() ────────────────────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─utils::capture.output(show(df)) at test-methods.R:5:5
  2. │ └─base::withVisible(...elt(i))
  3. ├─methods::show(df)
  4. ├─tidySingleCellExperiment (local) show(df)
  5. │ ├─base::print(object)
  6. │ └─tidySingleCellExperiment:::print.SingleCellExperiment(object)
  7. │   ├─... %>% print()
  8. │   ├─vctrs::new_data_frame(...)
  9. │   ├─tibble::as_tibble(x, n_dimensions_to_return = 5)
 10. │   └─tidySingleCellExperiment:::as_tibble.SingleCellExperiment(...)
 11. │     ├─SingleCellExperiment::reducedDims(x)
 12. │     └─SingleCellExperiment::reducedDims(x)
 13. │       └─SingleCellExperiment (local) .local(x, ...)
 14. │         └─SingleCellExperiment:::.get_internal_all(...)
 15. │           ├─BiocGenerics::updateObject(x)
 16. │           └─SingleCellExperiment::updateObject(x)
 17. │             ├─methods::callNextMethod()
 18. │             └─SummarizedExperiment (local) .nextMethod(object = object)
 19. │               ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 20. │               └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 21. │                 ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 22. │                 └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 23. │                   └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 24. ├─base::print(.)
 25. ├─tidySingleCellExperiment:::add_attr(., assayNames(x), "assay_names")
 26. ├─tidySingleCellExperiment:::add_attr(., nrow(x), "number_of_features")
 27. └─methods:::.extendsForS3(`<chr>`)
 28.   └─methods::extends(Class, maybe = FALSE)
 29.     └─methods::getClassDef(class1)
 30.       └─methods:::.requirePackage(package)
── Error ('test-methods.R:16:5'): join_features() ──────────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─ttservice::join_features(df, gs, shape = "long") at test-methods.R:16:5
  2. ├─tidySingleCellExperiment::join_features(df, gs, shape = "long")
  3. │ ├─base::suppressMessages(...)
  4. │ │ └─base::withCallingHandlers(...)
  5. │ └─... %>% ...
  6. ├─dplyr::select(...)
  7. ├─dplyr::left_join(...)
  8. ├─tidySingleCellExperiment:::left_join.SingleCellExperiment(...)
  9. │ ├─dplyr (local) fun(as_tibble(x), y, by = by, copy = copy, suffix = suffix, ...)
 10. │ ├─tibble::as_tibble(x)
 11. │ └─tidySingleCellExperiment:::as_tibble.SingleCellExperiment(x)
 12. │   ├─SingleCellExperiment::reducedDims(x)
 13. │   └─SingleCellExperiment::reducedDims(x)
 14. │     └─SingleCellExperiment (local) .local(x, ...)
 15. │       └─SingleCellExperiment:::.get_internal_all(...)
 16. │         ├─BiocGenerics::updateObject(x)
 17. │         └─SingleCellExperiment::updateObject(x)
 18. │           ├─methods::callNextMethod()
 19. │           └─SummarizedExperiment (local) .nextMethod(object = object)
 20. │             ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 21. │             └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 22. │               ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 23. │               └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 24. │                 └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 25. └─methods:::.extendsForS3(`<chr>`)
 26.   └─methods::extends(Class, maybe = FALSE)
 27.     └─methods::getClassDef(class1)
 28.       └─methods:::.requirePackage(package)
── Error ('test-methods.R:33:5'): as_tibble() ──────────────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─tibble::as_tibble(df) at test-methods.R:33:5
  2. ├─tidySingleCellExperiment:::as_tibble.SingleCellExperiment(df)
  3. │ ├─SingleCellExperiment::reducedDims(x)
  4. │ └─SingleCellExperiment::reducedDims(x)
  5. │   └─SingleCellExperiment (local) .local(x, ...)
  6. │     └─SingleCellExperiment:::.get_internal_all(...)
  7. │       ├─BiocGenerics::updateObject(x)
  8. │       └─SingleCellExperiment::updateObject(x)
  9. │         ├─methods::callNextMethod()
 10. │         └─SummarizedExperiment (local) .nextMethod(object = object)
 11. │           ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 12. │           └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 13. │             ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 14. │             └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 15. │               └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 16. └─methods:::.extendsForS3(`<chr>`)
 17.   └─methods::extends(Class, maybe = FALSE)
 18.     └─methods::getClassDef(class1)
 19.       └─methods:::.requirePackage(package)

[ FAIL 9 | WARN 1 | SKIP 0 | PASS 135 ]
Error: Test failures
Execution halted