* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘PTXQC’ ...
** this is package ‘PTXQC’ version ‘1.1.3’
** package ‘PTXQC’ 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 ‘PTXQC’
    finding HTML links ... done
    CV                                      html  
    FilenameMapper-class                    html  
    LCS                                     html  
    LCSn                                    html  
    MQDataReader-class                      html  
    MzTabReader-class                       html  
    PTXQC-package                           html  
    PTXQC                                   html  
    QCMetaFilenames                         html  
    RSD                                     html  
    RTalignmentTree                         html  
    ScoreInAlignWindow                      html  
    YAMLClass-class                         html  
    alignmentCheck                          html  
    appendEnv                               html  
    assembleMZQC                            html  
    assignBlocks                            html  
    boxplotCompare                          html  
    brewer.pal.Safe                         html  
    byX                                     html  
    byXflex                                 html  
    checkEnglishLocale                      html  
    computeMatchRTFractions                 html  
    correctSetSize                          html  
    createReport                            html  
    createYaml                              html  
    darken                                  html  
    del0                                    html  
    delLCP                                  html  
    delLCS                                  html  
    findAlignReference                      html  
    fixCalibration                          html  
    flattenList                             html  
    getAbundanceClass                       html  
    getECDF                                 html  
    getFileEncoding                         html  
    getFragmentErrors                       html  
    getHTMLTable                            html  
    getMQPARValue                           html  
    getMaxima                               html  
    getMetaData                             html  
    getMetaFilenames                        html  
    getMetricsObjects                       html  
    getPCA                                  html  
    getPeptideCounts                        html  
    getProteinCounts                        html  
    getQCHeatMap                            html  
    getReportFilenames                      html  
    getRunQualityTemplate                   html  
    ggAxisLabels                            html  
    ggText                                  html  
    grapes-plus-grapes                      html  
    grepv                                   html  
    idTransferCheck                         html  
    inMatchWindow                           html  
    lcpCount                                html  
    lcsCount                                html  
    longestCommonPrefix                     html  
    longestCommonSuffix                     html  
    modsToTable                             html  
    modsToTableByRaw                        html  
    mosaicize                               html  
    pasten                                  html  
    pastet                                  html  
    peakSegmentation                        html  
    peakWidthOverTime                       html  
    plotTable                               html  
    plotTableRaw                            html  
    plot_CalibratedMSErr                    html  
    plot_Charge                             html  
    plot_ContEVD                            html  
    plot_ContUser                           html  
    plot_ContUserScore                      html  
    plot_ContsPG                            html  
    plot_CountData                          html  
    plot_DataOverRT                         html  
    plot_IDRate                             html  
    plot_IDsOverRT                          html  
    plot_IonInjectionTimeOverRT             html  
    plot_MBRAlign                           html  
    plot_MBRIDtransfer                      html  
    plot_MBRgain                            html  
    plot_MS2Decal                           html  
    plot_MS2Oversampling                    html  
    plot_MissedCleavages                    html  
    plot_RTPeakWidth                        html  
    plot_RatiosPG                           html  
    plot_ScanIDRate                         html  
    plot_TIC                                html  
    plot_TopN                               html  
    plot_TopNoverRT                         html  
    plot_UncalibratedMSErr                  html  
    plot_peptideMods                        html  
    pointsPutX                              html  
    print.PTXQC_table                       html  
    printWithFooter                         html  
    qcMetric-class                          html  
    qcMetric_MSMSScans_TopNoverRT-class     html  
    qualBestKS                              html  
    qualCentered                            html  
    qualCenteredRef                         html  
    qualGaussDev                            html  
    qualHighest                             html  
    qualLinThresh                           html  
    qualMedianDist                          html  
    qualUniform                             html  
    read.MQ                                 html  
    renameFile                              html  
    repEach                                 html  
    scale01linear                           html  
    scale_x_discrete_reverse                html  
    scale_y_discrete_reverse                html  
    shortenStrings                          html  
    simplifyNames                           html  
    supCount                                html  
    theme_blank                             html  
    thinOut                                 html  
    thinOutBatch                            html  
    wait_for_writable                       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 (PTXQC)