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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings variancePartition_1.36.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/variancePartition.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.36.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Codoc mismatches from Rd file 'eBayes-method.Rd':
\S4method{eBayes}{MArrayLM2}
  Code: function(fit, proportion = 0.01, stdev.coef.lim = c(0.1, 4),
                 trend = FALSE, robust = FALSE, winsor.tail.p = c(0.05,
                 0.1), legacy = NULL)
  Docs: function(fit, proportion = 0.01, stdev.coef.lim = c(0.1, 4),
                 trend = FALSE, robust = FALSE, winsor.tail.p = c(0.05,
                 0.1))
  Argument names in code not in docs:
    legacy

* 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         24.094  0.139  24.234
fitExtractVarPartModel-method  19.089  0.185  19.278
getTreat-method                16.503  0.056  16.563
plotCompareP-method            12.971  0.510  13.482
extractVarPart                 12.182  0.151  12.334
varPartConfInf                  7.894  0.053   7.947
sortCols-method                 6.243  0.048   6.291
plotPercentBars-method          6.160  0.089   6.249
plotVarPart-method              6.033  0.067   6.101
residuals-VarParFitList-method  5.674  0.054   5.728
mvTest-method                   4.930  0.061  10.111
dream-method                    2.953  0.104   7.499
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/variancePartition.Rcheck/00check.log’
for details.