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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings variancePartition_1.39.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/variancePartition.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.39.1’
* 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 ‘variancePartition’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘lmerTest:::as_lmerModLT’
  See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
S3 methods shown with full name in Rd file 'residuals.MArrayLM2.Rd':
  ‘residuals.MArrayLM2’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
fitVarPartModel-method         28.766  0.056  28.824
fitExtractVarPartModel-method  22.222  0.136  22.359
getTreat-method                19.581  0.027  19.603
plotCompareP-method            15.068  0.005  15.073
extractVarPart                 13.938  0.175  14.115
varPartConfInf                  9.921  0.002   9.923
sortCols-method                 7.258  0.000   7.259
plotPercentBars-method          7.242  0.001   7.244
plotVarPart-method              6.955  0.003   6.959
residuals-VarParFitList-method  6.613  0.001   6.607
mvTest-method                   5.269  0.032  11.063
dream-method                    3.535  0.103   8.741
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  FAILURE in test_voomWithDreamWeights: Error in checkEquals(vobj1, vobj2) : 
    Length mismatch: comparison on first 4 components
  Component "weights": Mean relative difference: 0.06105003
  
  
  Test files with failing tests
  
     test_voomWithDreamWeights.R 
       test_reweigthing_voom 
       test_voomWithDreamWeights 
  
  
  Error in BiocGenerics:::testPackage("variancePartition") : 
    unit tests failed for package variancePartition
  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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/variancePartition.Rcheck/00check.log’
for details.