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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:codelink.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings codelink_1.63.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/codelink.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'codelink/DESCRIPTION' ... OK
* this is package 'codelink' version '1.63.0'
* 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 'codelink' 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 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... 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: OK

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL codelink
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'codelink' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'codelink'
    finding HTML links ... done
    Codelink-class                          html  
    CodelinkSet-class                       html  
    finding level-2 HTML links ... done

    CodelinkSetUnique-class                 html  
    Nondocumented-objects                   html  
    SNR                                     html  
    arrayNew                                html  
    arraySize                               html  
    as.matrix.Codelink                      html  
    averageProbes                           html  
    bkgdCorrect                             html  
    codPlot                                 html  
    codelink.example                        html  
    codset                                  html  
    createWeights                           html  
    cutCV                                   html  
    decDetect                               html  
    dim.Codelink                            html  
    fc2Cond                                 html  
    imageCodelink                           html  
    logCodelink                             html  
    mergeArray                              html  
    na2false                                html  
    normalize                               html  
    plotCV                                  html  
    plotCorrelation                         html  
    plotDensities                           html  
    plotMA                                  html  
    printHead                               html  
    readCodelink                            html  
    readHeader                              html  
    readHeaderXLS                           html  
    reportCodelink                          html  
    selCV                                   html  
    writeCodelink                           html  
** 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 (codelink)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'easyRNASeq' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'OTUbase' is missing or broken
 done