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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings variancePartition_1.28.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/variancePartition.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.28.9’
* 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 R 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 ... 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 documentation object 'residuals.MArrayLM2':
  ‘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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
fitVarPartModel-method         26.113  0.104  26.216
fitExtractVarPartModel-method  23.930  0.211  24.141
getTreat-method                21.699  0.044  21.743
plotCompareP-method            16.845  0.064  16.909
extractVarPart                 14.168  0.220  14.389
varPartConfInf                 14.222  0.036  14.259
sortCols-method                 9.297  0.036   9.334
plotVarPart-method              7.391  0.024   7.417
plotPercentBars-method          7.320  0.000   7.319
residuals-VarParFitList-method  5.966  0.000   5.966
dream-method                    3.217  0.107   9.327
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘FAQ.Rmd’ using ‘UTF-8’... OK
  ‘additional_visualization.Rmd’ using ‘UTF-8’... OK
  ‘dream.Rmd’ using ‘UTF-8’... OK
  ‘theory_practice_random_effects.Rmd’ using ‘UTF-8’... OK
  ‘variancePartition.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/variancePartition.Rcheck/00check.log’
for details.