* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘SMITIDstruct’ ...
** this is package ‘SMITIDstruct’ version ‘0.0.5’
** package ‘SMITIDstruct’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘SMITIDstruct’
    finding HTML links ... done
    Host                                    html  
    SMITIDstruct-package                    html  
    ViralPop-class                          html  
    addHost                                 html  
    addIndex                                html  
    addViralObs                             html  
    addcode                                 html  
    alleleCount                             html  
    concatViralPop                          html  
    createAViralPop                         html  
    createHost                              html  
    createIndex                             html  
    demo.SMITIDstruct.run                   html  
    diversity.pDistance                     html  
    diversity.sfs                           html  
    getCov                                  html  
    getDate                                 html  
    getDiversity.pDistance                  html  
    getDiversity.sfs                        html  
    getInfosByHostAndTime                   html  
    getStates                               html  
    getTimeLine                             html  
    getTimestamp                            html  
    getTransmissionTree                     html  
    is.StringDate                           html  
    is.juliendate                           html  
    is.timestamp                            html  
    isInCode                                html  
    loadCoords                              html  
    loadCovs                                html  
    loadHost                                html  
    loadStates                              html  
    loadTree                                html  
    loadTreeDF                              html  
    loadViralObs                            html  
    loadViralPop                            html  
    loadViralPopSet                         html  
    mergeCode                               html  
    plotDiversity.pDistance                 html  
    plotDiversity.sfs                       html  
    setStates                               html  
    simulateStates                          html  
** building package indices
** 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 (SMITIDstruct)