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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings variancePartition_1.24.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/variancePartition.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'variancePartition/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'variancePartition' version '1.24.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
fitVarPartModel-method         28.38   0.05   28.44
fitExtractVarPartModel-method  25.67   0.08   25.75
getTreat-method                23.72   0.06   23.78
plotCompareP-method            20.63   0.03   20.67
varPartConfInf                 15.78   0.03   15.81
extractVarPart                 13.86   0.03   13.89
sortCols-method                 9.55   0.02    9.56
plotPercentBars-method          8.59   0.00    8.59
residuals-VarParFitList-method  8.23   0.05    8.28
plotVarPart-method              7.62   0.00    7.62
dream-method                    4.10   0.05   11.42
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
fitVarPartModel-method         29.86   0.12   29.98
fitExtractVarPartModel-method  25.89   0.06   25.95
getTreat-method                24.36   0.08   24.44
plotCompareP-method            20.77   0.04   20.82
extractVarPart                 15.13   0.05   15.18
varPartConfInf                 13.67   0.03   13.70
sortCols-method                10.81   0.05   10.86
plotPercentBars-method          8.83   0.01    8.84
plotVarPart-method              8.58   0.08    8.65
residuals-VarParFitList-method  6.31   0.03    6.34
dream-method                    3.87   0.06   11.25
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/variancePartition.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/variancePartition_1.24.1.tar.gz && rm -rf variancePartition.buildbin-libdir && mkdir variancePartition.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=variancePartition.buildbin-libdir variancePartition_1.24.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL variancePartition_1.24.1.zip && rm variancePartition_1.24.1.tar.gz variancePartition_1.24.1.zip
###
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100 7695k  100 7695k    0     0  1752k      0  0:00:04  0:00:04 --:--:-- 1880k

install for i386

* installing *source* package 'variancePartition' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'calcVarPart' with signature '"negbin"': no definition for class "negbin"
in method for 'checkModelStatus' with signature '"negbin"': no definition for class "negbin"
Creating a new generic function for 'classifyTestsF' in package 'variancePartition'
** help
Loading required namespace: variancePartition
*** installing help indices
  converting help for package 'variancePartition'
    finding HTML links ... done
    ESS-method                              html  
    FMT-class                               html  
    FMT                                     html  
    FMT.ZI                                  html  
    MArrayLM2-class                         html  
    VarParCIList-class                      html  
    VarParFitList-class                     html  
    applyQualityWeights                     html  
    as.data.frame.varPartResults            html  
    as.matrix-varPartResults-method         html  
    calcVarPart-method                      html  
    canCorPairs                             html  
    classifyTestsF-MArrayLM2-method         html  
    classifyTestsF                          html  
    colinearityScore                        html  
    dot-getAllUniContrasts                  html  
    dot-isMixedModelFormula                 html  
    dot-standard_transform                  html  
    dream-method                            html  
    dscchisq                                html  
    eBayes-method                           html  
    eBayesFMT                               html  
    extractVarPart                          html  
    fitExtractVarPartModel-method           html  
    fitVarPartModel-method                  html  
    getContrast-method                      html  
    getTreat-method                         html  
    get_prediction-method                   html  
    ggColorHue                              html  
    isRunableFormula                        html  
    makeContrastsDream                      html  
    plotCompareP-method                     html  
    plotContrasts                           html  
    plotCorrMatrix                          html  
    plotCorrStructure                       html  
    plotPercentBars-method                  html  
    plotStratify                            html  
    plotStratifyBy                          html  
    plotVarPart-method                      html  
    plotVarianceEstimates                   html  
    rdf.merMod                              html  
    rdf_from_matrices                       html  
    reOnly                                  html  
    residuals-MArrayLM-method               html  
    residuals-MArrayLM2-method              html  
    residuals-VarParFitList-method          html  
    residuals.MArrayLM2                     html  
    shrinkageMetric                         html  
    sortCols-method                         html  
    subset.MArrayLM2-method                 html  
    toptable-method                         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/variancePartition.buildbin-libdir/00LOCK-variancePartition/00new/variancePartition/help/toptable+2CFMT-method.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/variancePartition.buildbin-libdir/00LOCK-variancePartition/00new/variancePartition/help/toptable+2CMArrayLM2-method.html
    varParFrac-class                        html  
    varPartConfInf                          html  
    varPartDEdata                           html  
    varPartData                             html  
    varPartResults-class                    html  
    voomWithDreamWeights                    html  
*** 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

install for x64

* installing *source* package 'variancePartition' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'variancePartition' as variancePartition_1.24.1.zip
* DONE (variancePartition)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'variancePartition' successfully unpacked and MD5 sums checked