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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch MSGFplus
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* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
* installing *source* package 'MSGFplus' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSGFplus'
    finding HTML links ... done
    MSGFplus-package                        html  
    chargeRange                             html  
    db                                      html  
    enzyme                                  html  
    fragmentation                           html  
    getMSGFpar                              html  
    instrument                              html  
    isotopeError                            html  
    lengthRange                             html  
    matches                                 html  
    mods                                    html  
    msgfAsync-class                         html  
    msgfPar-class                           html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSGFplus/man/msgfPar-class.Rd:121: missing link 'msgfParGUI'
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSGFplus/man/msgfPar-class.Rd:148: missing link 'msgfParGUI'
    msgfPar                                 html  
    msgfParChargeRange-class                html  
    msgfParEnzyme-class                     html  
    msgfParFragmentation-class              html  
    msgfParFromID                           html  
    msgfParInstrument-class                 html  
    msgfParIsotopeError-class               html  
    msgfParLengthRange-class                html  
    msgfParMatches-class                    html  
    msgfParModification-class               html  
    msgfParModificationList-class           html  
    msgfParNtt-class                        html  
    msgfParProtocol-class                   html  
    msgfParTda-class                        html  
    msgfParTolerance-class                  html  
    ntt                                     html  
    protocol                                html  
    runMSGF                                 html  
    tda                                     html  
    tolerance                               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 (MSGFplus)
Making 'packages.html' ... done