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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:dorothea.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings dorothea_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/dorothea.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 ‘dorothea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dorothea’ version ‘1.21.0’
* 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 ‘dorothea’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 33.3Mb
  sub-directories of 1Mb or more:
    data       5.0Mb
    extdata   17.3Mb
    help       1.3Mb
    testdata   9.4Mb
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

Non-topic package-anchored link(s) in Rd file 'run_viper.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
run_viper 21.342   0.52  21.864
* 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:
    8. │       ├─methods::callNextMethod()
    9. │       └─SummarizedExperiment (local) .nextMethod(object = object)
   10. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
   11. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
   12. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
   13. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
   14. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
   15. └─methods:::.extendsForS3(`<chr>`)
   16.   └─methods::extends(Class, maybe = FALSE)
   17.     └─methods::getClassDef(class1)
   18.       └─methods:::.requirePackage(package)
  
  [ FAIL 1 | WARN 11 | SKIP 0 | PASS 15 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/dorothea.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL dorothea
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘dorothea’ ...
** this is package ‘dorothea’ version ‘1.21.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (dorothea)

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(dorothea)
> 
> test_check("dorothea")
Failed with error:  'there is no package called 'GenomeInfoDb''
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 15 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-viper_wrapper.R:107:3'): test run_viper with sce as input ──────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─dorothea::run_viper(...) at test-viper_wrapper.R:107:3
  2. ├─dorothea:::run_viper.SingleCellExperiment(...)
  3. │ ├─SingleCellExperiment::`altExp<-`(`*tmp*`, "dorothea", value = dorothea_se)
  4. │ └─SingleCellExperiment::`altExp<-`(`*tmp*`, "dorothea", value = dorothea_se)
  5. │   └─SingleCellExperiment:::.set_internal_character(...)
  6. │     ├─BiocGenerics::updateObject(x)
  7. │     └─SingleCellExperiment::updateObject(x)
  8. │       ├─methods::callNextMethod()
  9. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 10. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 11. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 12. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 13. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 14. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 15. └─methods:::.extendsForS3(`<chr>`)
 16.   └─methods::extends(Class, maybe = FALSE)
 17.     └─methods::getClassDef(class1)
 18.       └─methods:::.requirePackage(package)

[ FAIL 1 | WARN 11 | SKIP 0 | PASS 15 ]
Error: Test failures
Execution halted