##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DOtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DOtools_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/DOtools.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DOtools/DESCRIPTION’ ... OK
* this is package ‘DOtools’ version ‘1.1.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DOtools’ 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DOtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DO.BoxPlot
> ### Title: Box Graph with wilcox test on single cell level
> ### Aliases: DO.BoxPlot
> 
> ### ** Examples
> 
> sce_data <-
+     readRDS(system.file("extdata", "sce_data.rds", package = "DOtools"))
> 
> set.seed(123)
> sce_data$orig.ident <-
+     sample(rep(c("A", "B", "C"), length.out = ncol(sce_data)))
> 
> ListTest <- list()
> ListTest[[1]] <- c("healthy", "disease")
> 
> DO.BoxPlot(
+     sce_object = sce_data,
+     Feature = "NKG7",
+     sample.column = "orig.ident",
+     ListTest = ListTest,
+     group.by = "condition",
+     ctrl.condition = "healthy",
+ )
Using group, cluster as id variables
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
     ▆
  1. ├─DOtools::DO.BoxPlot(...)
  2. │ └─SCpubr::do_BoxPlot(...)
  3. │   └─SCpubr:::get_data_column_in_context(...)
  4. │     └─... %>% tibble::as_tibble()
  5. ├─tibble::as_tibble(.)
  6. ├─dplyr::left_join(...)
  7. ├─dplyr:::left_join.data.frame(...)
  8. │ └─dplyr::auto_copy(x, y, copy = copy)
  9. │   ├─dplyr::same_src(x, y)
 10. │   └─dplyr:::same_src.data.frame(x, y)
 11. │     └─base::is.data.frame(y)
 12. ├─SCpubr:::get_data_column(...)
 13. │ ├─base::suppressWarnings(...)
 14. │ │ └─base::withCallingHandlers(...)
 15. │ ├─... %>% dplyr::rename(feature = dplyr::all_of(c(feature)))
 16. │ ├─SeuratObject::GetAssayData(object = sample, assay = assay, slot = slot)
 17. │ └─SeuratObject:::GetAssayData.Seurat(...)
 18. │   └─SeuratObject::.Deprecate(...)
 19. │     └─lifecycle::deprecate_stop(...)
 20. │       └─lifecycle:::deprecate_stop0(msg)
 21. │         └─rlang::cnd_signal(...)
 22. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
 23. ├─tibble::rownames_to_column(., var = "cell")
 24. ├─base::as.data.frame(.)
 25. ├─base::t(.)
 26. └─base::as.matrix(.)
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:
   17. │ └─SeuratObject:::GetAssayData.Seurat(...)
   18. │   └─SeuratObject::.Deprecate(...)
   19. │     └─lifecycle::deprecate_stop(...)
   20. │       └─lifecycle:::deprecate_stop0(msg)
   21. │         └─rlang::cnd_signal(...)
   22. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
   23. ├─tibble::rownames_to_column(., var = "cell")
   24. ├─base::as.data.frame(.)
   25. ├─base::t(.)
   26. └─base::as.matrix(.)
  
  [ FAIL 12 | WARN 87 | SKIP 1 | PASS 216 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/DOtools.Rcheck/00check.log’
for details.