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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:AUCell.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings AUCell_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/AUCell.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-29 01:49:38 UTC
* checking for file ‘AUCell/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AUCell’ version ‘1.34.0’
* 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 ‘AUCell’ 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 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
plotEmb_rgb : <anonymous>: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  rgb
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AUCell_buildRankings.Rd: RangedSummarizedExperiment
  AUCell_calcAUC.Rd: GeneSet, GeneSetCollection
  AUCell_run.Rd: RangedSummarizedExperiment, GeneSet, GeneSetCollection
  GeneSet-methods.Rd: GeneSet, GeneSetCollection
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 ‘AUCell.Rmd’ using rmarkdown
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60361/suppl/GSE60361_C1-3005-Expression.txt.gz'
Content type 'application/x-gzip' length 11239106 bytes (10.7 MB)
==================================================
downloaded 10.7 MB


Quitting from AUCell.Rmd:176-180 [randomSamples]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'i' in selecting a method for function '[': cannot take a sample larger than the population when 'replace = FALSE'
---
Backtrace:
    ▆
 1. ├─...[]
 2. ├─methods (local) sample(rownames(mouseBrainExprMatrix), 5000)
 3. ├─methods (local) sample(rownames(mouseBrainExprMatrix), 5000)
 4. │ └─base::sample(x, size, replace = replace, prob = prob, ...)
 5. │   └─base::sample.int(length(x), size, replace, prob)
 6. └─base::.handleSimpleError(...)
 7.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'AUCell.Rmd' failed with diagnostics:
error in evaluating the argument 'i' in selecting a method for function '[': cannot take a sample larger than the population when 'replace = FALSE'
--- failed re-building ‘AUCell.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/AUCell.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL AUCell
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘AUCell’ ...
** this is package ‘AUCell’ version ‘1.34.0’
** using staged installation
** R
** 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 (AUCell)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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(AUCell)
> 
> test_check("AUCell")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 56 ]
> 
> proc.time()
   user  system elapsed 
 15.428   0.814  16.231