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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no DOtools_0.99.11.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/DOtools.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
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘DOtools/DESCRIPTION’ ... OK
* this is package ‘DOtools’ version ‘0.99.11’
* 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 ... WARNING
Found the following files with non-portable file names:
  vignettes/DOtools_files/figure-html/Clustering and UMAP-1.png
  vignettes/DOtools_files/figure-html/Clustering and UMAP-2.png
  vignettes/DOtools_files/figure-html/Manual annotation-1.png
  vignettes/DOtools_files/figure-html/Manual annotation-2.png
  vignettes/DOtools_files/figure-html/cell populations-1.png
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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 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 ... 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 ... SKIPPED
* 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’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘test-DO.BarplotWilcox.R’
  Running ‘test-DO.Dotplot.R’
  Running ‘test-DO.MultiDGE.R’
  Running ‘test-DO.SplitBarGSEA.R’
  Running ‘test-DO.scVI.R’
 ERROR
Running the tests in ‘longtests/test-DO.BarplotWilcox.R’ failed.
Last 13 lines of output:
  **************************************************|
  ── Error: DO.BarplotWilcox returns ggplot and list correctly ───────────────────
  Error in `DO.BarplotWilcox(sce_object = seurat_obj, Feature = "gene1", 
      ListTest = list(c("A", "B")), returnValues = FALSE, ctrl.condition = "A", 
      group.by = "condition")`: could not find function "DO.BarplotWilcox"
  
  Error:
  ! Test failed
  Backtrace:
      ▆
   1. ├─testthat::test_that(...)
   2. │ └─withr (local) `<fn>`()
   3. └─reporter$stop_if_needed()
   4.   └─rlang::abort("Test failed", call = NULL)
  Execution halted
Running the tests in ‘longtests/test-DO.SplitBarGSEA.R’ failed.
Last 13 lines of output:
    9.   └─basilisk::basiliskRun(...)
   10.     └─basilisk::basiliskStart(...)
   11.       └─basilisk::obtainEnvironmentPath(env)
   12.         └─dir.expiry::lockDirectory(envdir, exclusive = !file.exists(envpath))
   13.           └─filelock::lock(plock, exclusive = FALSE)
  
  Error:
  ! Test failed
  Backtrace:
      ▆
   1. ├─testthat::test_that(...)
   2. │ └─withr (local) `<fn>`()
   3. └─reporter$stop_if_needed()
   4.   └─rlang::abort("Test failed", call = NULL)
  Execution halted
Running the tests in ‘longtests/test-DO.scVI.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─testthat::with_mocked_bindings(...)
   2. └─mockery::stub(DO.scVI, "as.Seurat", mock_as_seurat)
   3.   └─mockery:::build_function_tree(test_env, where, where_name, depth)
  
  Error:
  ! Test failed
  Backtrace:
      ▆
   1. ├─testthat::test_that(...)
   2. │ └─withr (local) `<fn>`()
   3. └─reporter$stop_if_needed()
   4.   └─rlang::abort("Test failed", call = NULL)
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/DOtools.Rcheck/00check.log’
for details.