Package: PTXQC
Check: examples
New result: ERROR
  Running examples in ‘PTXQC-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: qcMetric-class
  > ### Title: Class which can compute plots and generate mzQC output (usually
  > ###   for a single metric).
  > ### Aliases: qcMetric-class qcMetric
  > 
  > ### ** Examples
  > 
  > 
  > require(ggplot2)
  Loading required package: ggplot2
  > dd = data.frame(x=1:10, y=11:20)
  > a = qcMetric$new(helpText="small help text", 
  +                  ## arbitrary arguments, matched during setData()
  +                  workerFcn=function(.self, data, gtitle)
  +                  {
  +                    ## usually some code here to produce ggplots
  +                    pl = lapply(1:2, function(xx) {
  +                        ggplot(data) +
  +                          geom_point(aes(x=x*xx,y=y)) +
  +                          ggtitle(gtitle)
  +                      })
  +                      ## add mzQC metric for count of identified clusters
  +                      template_proteinCount = rmzqc::getQualityMetricTemplate("MS:1002406") 
  +                      mzqc = lapply(1:3, function(id){
  +                        out = template_proteinCount$copy();
  +                        out$value = id;
  +                        return(out) })
  +                      names(mzqc) = paste0("file", 1:3);
  +                    return(list(plots = pl, mzQC = mzqc))
  +                  }, 
  +                  qcCat="LC", 
  +                  qcName="MS/MS Peak shape", 
  +                  orderNr = 30)
  > ## test some output
  > a$setData(dd, "my title")
  Starting to work on MS/MS Peak shape ...
  trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
  Content type 'application/json; charset=utf-8' length 7655 bytes
  ==================================================
  downloaded 7655 bytes
  
  Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.195/psi-ms.obo' ...
  trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.195/psi-ms.obo'
  Content type 'application/octet-stream' length 1010702 bytes (987 KB)
  ==================================================
  downloaded 987 KB
  
  Error in template_proteinCount$copy() : attempt to apply non-function
  Calls: <Anonymous> -> workerFcn -> lapply -> FUN
  Execution halted

Package: PTXQC
Check: tests
New result: ERROR
    Running ‘testthat.R’ [9s/10s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(PTXQC)
    Loading package PTXQC (version 1.1.2)
    
    Attaching package: 'PTXQC'
    
    The following object is masked from 'package:base':
    
        grepv
    
    > 
    > ##
    > ## calls all code in PTXQC/tests/testthat/test*.R
    > ##
    > test_check("PTXQC")
    YAML: PTXQC$ReportFilename$extended def: TRUE
    Mon Jul 14 15:20:15 2025: Starting QC computation on report '/home/hornik/tmp/scratch/RtmpPVSS0W/txt/report_v1.1.2_RtmpPVSS0W'
    YAML: PTXQC$UseLocalMQPar def: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 25
    YAML: File$Evidence$ProteinCountThresh_num def: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10
    YAML: PTXQC$OutputFormats def: html,plainPDF
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on
    YAML: order$qcMetric_PAR def: 1
    YAML: order$qcMetric_PG_PCA def: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10
    YAML: order$qcMetric_PG_Ratio def: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20
    YAML: order$qcMetric_SM_TIC def: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31
    YAML: order$qcMetric_PG_RawInt def: 32
    YAML: order$qcMetric_PG_LFQInt def: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40
    YAML: order$qcMetric_EVD_Charge def: 100
    YAML: order$qcMetric_EVD_modTable def: 103
    YAML: order$qcMetric_PG_Cont def: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250
    YAML: order$qcMetric_EVD_PreCal def: 260
    YAML: order$qcMetric_EVD_PostCal def: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350 || new val: 120
    YAML: order$qcMetric_MSMSScans_TopNID def: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450
    YAML: order$qcMetric_EVD_UpSet def: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999
    No mapping found. Writing mapping file ' /home/hornik/tmp/scratch/RtmpPVSS0W/txt/report_v1.1.2_RtmpPVSS0W_filename_sort.txt ' not possible!Reading file /home/hornik/tmp/scratch/RtmpPVSS0W/txt/parameters.txt ...
    Read 61 entries from /home/hornik/tmp/scratch/RtmpPVSS0W/txt/parameters.txt.
    Updating colnames
    Simplifying contaminants
    Simplifying reverse
    Starting to work on PAR: MQ Parameters ...
    
    Memory [MB] prior|after|max(diff) : 86.7 | 89.2 | 166.8 (80)
    
    Duration: 0 s
    
    ... PAR: MQ Parameters  done
    Reading file /home/hornik/tmp/scratch/RtmpPVSS0W/txt/summary.txt ...
    Read 5 entries from /home/hornik/tmp/scratch/RtmpPVSS0W/txt/summary.txt.
    Updating colnames
    Simplifying contaminants
    Simplifying reverse
    Adding fc.raw.file column ...Created a new filename mapping:
                           from         to best.effort
    1 Toni_20120502_GM_Ecoli_01 ..Ecoli_01  ..Ecoli_01
    2 Toni_20120502_GM_Ecoli_02 ..Ecoli_02  ..Ecoli_02
     done
    Starting to work on SM: MS^2 ID rate (">%1.0f") ...
    
    Memory [MB] prior|after|max(diff) : 89.8 | 96.1 | 108.9 (19)
    
    Duration: 0 s
    
    ... SM: MS^2 ID rate (">%1.0f")  done
    Reading file /home/hornik/tmp/scratch/RtmpPVSS0W/txt/proteinGroups.txt ...
    Read 1128 entries from /home/hornik/tmp/scratch/RtmpPVSS0W/txt/proteinGroups.txt.
    Updating colnames
    Simplifying contaminants
    Simplifying reverse
    Starting to work on PG: Contaminants ...
    
    Memory [MB] prior|after|max(diff) : 97.9 | 100.2 | 115.5 (18)
    
    Duration: 0 s
    
    ... PG: Contaminants  done
    Starting to work on PG: Raw intensity ...
    
    Memory [MB] prior|after|max(diff) : 100.2 | 102.2 | 123.1 (23)
    
    Duration: 0 s
    
    ... PG: Raw intensity  done
    Starting to work on PG: LFQ intensity ...
    
    Memory [MB] prior|after|max(diff) : 102.2 | 102.7 | 118.8 (17)
    
    Duration: 0 s
    
    ... PG: LFQ intensity  done
    Starting to work on PG: Principal Component ...
    
    Memory [MB] prior|after|max(diff) : 102.9 | 103.7 | 127.7 (25)
    
    Duration: 0 s
    
    ... PG: Principal Component  done
    Starting to work on PG: Ratio ...
    Maximum ratio (log2) was 0.69527410075148, NOT reaching the threshold of 2 for label-incorporation computation.
    Skipping ratios ...
    
    Memory [MB] prior|after|max(diff) : 103.7 | 107.1 | 131.5 (28)
    
    Duration: 0 s
    
    ... PG: Ratio  done
    Reading file /home/hornik/tmp/scratch/RtmpPVSS0W/txt/evidence.txt ...
    Requiring column(s) 'retention.length' to be of type 'numeric'!
    Requiring column(s) 'retention.time.calibration' to be of type 'numeric'!
    Requiring column(s) 'retention.time', 'calibrated.retention.time' to be of type 'numeric'!
    Requiring column(s) 'match.time.difference' to be of type 'numeric'!
    Requiring column(s) 'intensity' to be of type 'numeric'!
    Requiring column(s) 'mass.error..ppm.', 'mass.error..da.', 'uncalibrated.mass.error..ppm.', 'uncalibrated.mass.error..da.' to be of type 'numeric'!
    Requiring column(s) 'uncalibrated...calibrated.m.z..ppm.', 'uncalibrated...calibrated.m.z..da.' to be of type 'numeric'!
    Requiring column(s) 'm.z' to be of type 'numeric'!
    Requiring column(s) 'score' to be of type 'numeric'!
    WARNING: Could not find column regex '^fraction$' using case-INsensitive matching.
    Requiring column(s) 'charge' to be of type 'numeric'!
    Requiring column(s) 'mass' to be of type 'numeric'!
    WARNING: Could not find column regex '^protein.names$' using case-INsensitive matching.
    Requiring column(s) 'ms.ms.count' to be of type 'numeric'!
    WARNING: Could not find column regex '^reporter.intensity.' using case-INsensitive matching.
    Requiring column(s) 'missed.cleavages' to be of type 'numeric'!
    Keeping 18 of 69 columns!
    Read 15505 entries from /home/hornik/tmp/scratch/RtmpPVSS0W/txt/evidence.txt.
    Updating colnames
    Simplifying contaminants
    Simplifying reverse
    Adding fc.raw.file column ... done
    Starting to work on EVD:User Contaminant (%s) ...
    
    Memory [MB] prior|after|max(diff) : 114.9 | 114.9 | 114.9 (0)
    
    Duration: 0 s
    
    Starting to work on EVD: Peptide Intensity (">%1.1f") ...
    
    Memory [MB] prior|after|max(diff) : 114.9 | 116.7 | 136.8 (22)
    
    Duration: 0 s
    
    ... EVD: Peptide Intensity (">%1.1f")  done
    Starting to work on EVD: Reporter intensity ...
    
    Memory [MB] prior|after|max(diff) : 116.7 | 116.7 | 116.7 (0)
    
    Duration: 0 s
    
    Starting to work on EVD: Peptide VarMod ...
    
    Memory [MB] prior|after|max(diff) : 116.7 | 119.6 | 138.7 (22)
    
    Duration: 0 s
    
    ... EVD: Peptide VarMod  done
    Starting to work on EVD: Protein Count (">%1.0f") ...
    trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
    Content type 'application/json; charset=utf-8' length 7655 bytes
    ==================================================
    downloaded 7655 bytes
    
    trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.195/psi-ms.obo'
    Content type 'application/octet-stream' length 1010702 bytes (987 KB)
    ==================================================
    downloaded 987 KB
    
    YAML: PTXQC$UseLocalMQPar def: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 25
    YAML: File$Evidence$ProteinCountThresh_num def: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10
    YAML: PTXQC$OutputFormats def: html,plainPDF
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on
    YAML: order$qcMetric_PAR def: 1
    YAML: order$qcMetric_PG_PCA def: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10
    YAML: order$qcMetric_PG_Ratio def: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20
    YAML: order$qcMetric_SM_TIC def: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31
    YAML: order$qcMetric_PG_RawInt def: 32
    YAML: order$qcMetric_PG_LFQInt def: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40
    YAML: order$qcMetric_EVD_Charge def: 100
    YAML: order$qcMetric_EVD_modTable def: 103
    YAML: order$qcMetric_PG_Cont def: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250
    YAML: order$qcMetric_EVD_PreCal def: 260
    YAML: order$qcMetric_EVD_PostCal def: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350 || new val: 120
    YAML: order$qcMetric_MSMSScans_TopNID def: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450
    YAML: order$qcMetric_EVD_UpSet def: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999
    YAML: PTXQC$UseLocalMQPar def: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 30
    YAML: File$Evidence$ProteinCountThresh_num def: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10
    YAML: PTXQC$OutputFormats def: html,plainPDF
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on
    YAML: order$qcMetric_PAR def: 1
    YAML: order$qcMetric_PG_PCA def: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10
    YAML: order$qcMetric_PG_Ratio def: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20
    YAML: order$qcMetric_SM_TIC def: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31
    YAML: order$qcMetric_PG_RawInt def: 32
    YAML: order$qcMetric_PG_LFQInt def: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40
    YAML: order$qcMetric_EVD_Charge def: 100
    YAML: order$qcMetric_EVD_modTable def: 103
    YAML: order$qcMetric_PG_Cont def: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250
    YAML: order$qcMetric_EVD_PreCal def: 260
    YAML: order$qcMetric_EVD_PostCal def: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350 || new val: 120
    YAML: order$qcMetric_MSMSScans_TopNID def: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450
    YAML: order$qcMetric_EVD_UpSet def: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999
    YAML: PTXQC$UseLocalMQPar def: TRUE || new val: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14 || new val: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20 || new val: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35 || new val: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4 || new val: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 30 || new val: 30
    YAML: File$Evidence$ProteinCountThresh_num def: 3500 || new val: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23 || new val: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000 || new val: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1") || new val: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1 || new val: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto || new val: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20 || new val: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2 || new val: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA || new val: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10 || new val: 10
    YAML: PTXQC$OutputFormats def: html,plainPDF || new val: html,plainPDF
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on || new val: on
    YAML: order$qcMetric_PAR def: 1 || new val: 1
    YAML: order$qcMetric_PG_PCA def: 3 || new val: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10 || new val: 10
    YAML: order$qcMetric_PG_Ratio def: 19 || new val: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20 || new val: 20
    YAML: order$qcMetric_SM_TIC def: 25 || new val: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30 || new val: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31 || new val: 31
    YAML: order$qcMetric_PG_RawInt def: 32 || new val: 32
    YAML: order$qcMetric_PG_LFQInt def: 33 || new val: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34 || new val: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40 || new val: 40
    YAML: order$qcMetric_EVD_Charge def: 100 || new val: 100
    YAML: order$qcMetric_EVD_modTable def: 103 || new val: 103
    YAML: order$qcMetric_PG_Cont def: 110 || new val: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120 || new val: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150 || new val: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170 || new val: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210 || new val: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220 || new val: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221 || new val: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240 || new val: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245 || new val: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250 || new val: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250 || new val: 250
    YAML: order$qcMetric_EVD_PreCal def: 260 || new val: 260
    YAML: order$qcMetric_EVD_PostCal def: 270 || new val: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280 || new val: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300 || new val: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350
    YAML: order$qcMetric_MSMSScans_TopNID def: 380 || new val: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383 || new val: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390 || new val: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400 || new val: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450 || new val: 450
    YAML: order$qcMetric_EVD_UpSet def: 500 || new val: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999 || new val: 9999
    YAML: PTXQC$UseLocalMQPar def: TRUE || new val: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14 || new val: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20 || new val: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35 || new val: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4 || new val: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 30 || new val: 30
    YAML: File$Evidence$ProteinCountThresh_num def: 3500 || new val: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23 || new val: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000 || new val: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1") || new val: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1 || new val: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto || new val: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20 || new val: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2 || new val: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA || new val: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10 || new val: 10
    YAML: PTXQC$OutputFormats def: html,plainPDF || new val: html,plainPDF
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on || new val: on
    YAML: order$qcMetric_PAR def: 1 || new val: 1
    YAML: order$qcMetric_PG_PCA def: 3 || new val: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10 || new val: 10
    YAML: order$qcMetric_PG_Ratio def: 19 || new val: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20 || new val: 20
    YAML: order$qcMetric_SM_TIC def: 25 || new val: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30 || new val: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31 || new val: 31
    YAML: order$qcMetric_PG_RawInt def: 32 || new val: 32
    YAML: order$qcMetric_PG_LFQInt def: 33 || new val: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34 || new val: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40 || new val: 40
    YAML: order$qcMetric_EVD_Charge def: 100 || new val: 100
    YAML: order$qcMetric_EVD_modTable def: 103 || new val: 103
    YAML: order$qcMetric_PG_Cont def: 110 || new val: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120 || new val: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150 || new val: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170 || new val: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210 || new val: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220 || new val: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221 || new val: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240 || new val: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245 || new val: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250 || new val: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250 || new val: 250
    YAML: order$qcMetric_EVD_PreCal def: 260 || new val: 260
    YAML: order$qcMetric_EVD_PostCal def: 270 || new val: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280 || new val: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300 || new val: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350 || new val: 350
    YAML: order$qcMetric_MSMSScans_TopNID def: 380 || new val: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383 || new val: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390 || new val: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400 || new val: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450 || new val: 450
    YAML: order$qcMetric_EVD_UpSet def: 500 || new val: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999 || new val: 9999
    YAML: PTXQC$UseLocalMQPar def: TRUE || new val: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14 || new val: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20 || new val: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35 || new val: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4 || new val: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 25 || new val: 30
    YAML: File$Evidence$ProteinCountThresh_num def: 3500 || new val: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23 || new val: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000 || new val: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1") || new val: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1 || new val: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto || new val: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20 || new val: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2 || new val: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA || new val: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10 || new val: 10
    YAML: PTXQC$OutputFormats def: html,plainPDF || new val: html,plainPDF
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on || new val: on
    YAML: order$qcMetric_PAR def: 1 || new val: 1
    YAML: order$qcMetric_PG_PCA def: 3 || new val: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10 || new val: 10
    YAML: order$qcMetric_PG_Ratio def: 19 || new val: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20 || new val: 20
    YAML: order$qcMetric_SM_TIC def: 25 || new val: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30 || new val: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31 || new val: 31
    YAML: order$qcMetric_PG_RawInt def: 32 || new val: 32
    YAML: order$qcMetric_PG_LFQInt def: 33 || new val: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34 || new val: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40 || new val: 40
    YAML: order$qcMetric_EVD_Charge def: 100 || new val: 100
    YAML: order$qcMetric_EVD_modTable def: 103 || new val: 103
    YAML: order$qcMetric_PG_Cont def: 110 || new val: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120 || new val: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150 || new val: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170 || new val: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210 || new val: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220 || new val: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221 || new val: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240 || new val: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245 || new val: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250 || new val: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250 || new val: 250
    YAML: order$qcMetric_EVD_PreCal def: 260 || new val: 260
    YAML: order$qcMetric_EVD_PostCal def: 270 || new val: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280 || new val: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300 || new val: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350 || new val: 350
    YAML: order$qcMetric_MSMSScans_TopNID def: 380 || new val: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383 || new val: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390 || new val: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400 || new val: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450 || new val: 450
    YAML: order$qcMetric_EVD_UpSet def: 500 || new val: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999 || new val: 9999
    YAML: PTXQC$UseLocalMQPar def: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 30
    YAML: File$Evidence$ProteinCountThresh_num def: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10
    YAML: PTXQC$OutputFormats def: txt
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on
    YAML: order$qcMetric_PAR def: 1
    YAML: order$qcMetric_PG_PCA def: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10
    YAML: order$qcMetric_PG_Ratio def: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20
    YAML: order$qcMetric_SM_TIC def: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31
    YAML: order$qcMetric_PG_RawInt def: 32
    YAML: order$qcMetric_PG_LFQInt def: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40
    YAML: order$qcMetric_EVD_Charge def: 100
    YAML: order$qcMetric_EVD_modTable def: 103
    YAML: order$qcMetric_PG_Cont def: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250
    YAML: order$qcMetric_EVD_PreCal def: 260
    YAML: order$qcMetric_EVD_PostCal def: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350 || new val: 120
    YAML: order$qcMetric_MSMSScans_TopNID def: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450
    YAML: order$qcMetric_EVD_UpSet def: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999
    YAML: PTXQC$UseLocalMQPar def: TRUE || new val: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14 || new val: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20 || new val: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35 || new val: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4 || new val: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 30 || new val: 30
    YAML: File$Evidence$ProteinCountThresh_num def: 3500 || new val: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23 || new val: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000 || new val: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1") || new val: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1 || new val: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto || new val: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20 || new val: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2 || new val: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA || new val: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10 || new val: 10
    YAML: PTXQC$OutputFormats def: txt || new val: txt
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on || new val: on
    YAML: order$qcMetric_PAR def: 1 || new val: 1
    YAML: order$qcMetric_PG_PCA def: 3 || new val: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10 || new val: 10
    YAML: order$qcMetric_PG_Ratio def: 19 || new val: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20 || new val: 20
    YAML: order$qcMetric_SM_TIC def: 25 || new val: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30 || new val: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31 || new val: 31
    YAML: order$qcMetric_PG_RawInt def: 32 || new val: 32
    YAML: order$qcMetric_PG_LFQInt def: 33 || new val: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34 || new val: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40 || new val: 40
    YAML: order$qcMetric_EVD_Charge def: 100 || new val: 100
    YAML: order$qcMetric_EVD_modTable def: 103 || new val: 103
    YAML: order$qcMetric_PG_Cont def: 110 || new val: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120 || new val: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150 || new val: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170 || new val: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210 || new val: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220 || new val: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221 || new val: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240 || new val: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245 || new val: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250 || new val: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250 || new val: 250
    YAML: order$qcMetric_EVD_PreCal def: 260 || new val: 260
    YAML: order$qcMetric_EVD_PostCal def: 270 || new val: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280 || new val: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300 || new val: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350
    YAML: order$qcMetric_MSMSScans_TopNID def: 380 || new val: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383 || new val: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390 || new val: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400 || new val: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450 || new val: 450
    YAML: order$qcMetric_EVD_UpSet def: 500 || new val: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999 || new val: 9999
    YAML: PTXQC$UseLocalMQPar def: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 25
    YAML: File$Evidence$ProteinCountThresh_num def: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10
    YAML: PTXQC$OutputFormats def: html,plainPDF
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on
    YAML: order$qcMetric_PAR def: 1
    YAML: order$qcMetric_PG_PCA def: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10
    YAML: order$qcMetric_PG_Ratio def: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20
    YAML: order$qcMetric_SM_TIC def: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31
    YAML: order$qcMetric_PG_RawInt def: 32
    YAML: order$qcMetric_PG_LFQInt def: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40
    YAML: order$qcMetric_EVD_Charge def: 100
    YAML: order$qcMetric_EVD_modTable def: 103
    YAML: order$qcMetric_PG_Cont def: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250
    YAML: order$qcMetric_EVD_PreCal def: 260
    YAML: order$qcMetric_EVD_PostCal def: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350 || new val: 120
    YAML: order$qcMetric_MSMSScans_TopNID def: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450
    YAML: order$qcMetric_EVD_UpSet def: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999
    YAML: PTXQC$UseLocalMQPar def: TRUE || new val: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14 || new val: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20 || new val: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35 || new val: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4 || new val: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 25 || new val: 25
    YAML: File$Evidence$ProteinCountThresh_num def: 3500 || new val: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23 || new val: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000 || new val: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1") || new val: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1 || new val: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto || new val: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20 || new val: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2 || new val: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA || new val: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10 || new val: 10
    YAML: PTXQC$OutputFormats def: html,plainPDF || new val: html,plainPDF
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on || new val: on
    YAML: order$qcMetric_PAR def: 1 || new val: 1
    YAML: order$qcMetric_PG_PCA def: 3 || new val: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10 || new val: 10
    YAML: order$qcMetric_PG_Ratio def: 19 || new val: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20 || new val: 20
    YAML: order$qcMetric_SM_TIC def: 25 || new val: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30 || new val: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31 || new val: 31
    YAML: order$qcMetric_PG_RawInt def: 32 || new val: 32
    YAML: order$qcMetric_PG_LFQInt def: 33 || new val: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34 || new val: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40 || new val: 40
    YAML: order$qcMetric_EVD_Charge def: 100 || new val: 100
    YAML: order$qcMetric_EVD_modTable def: 103 || new val: 103
    YAML: order$qcMetric_PG_Cont def: 110 || new val: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120 || new val: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150 || new val: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170 || new val: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210 || new val: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220 || new val: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221 || new val: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240 || new val: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245 || new val: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250 || new val: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250 || new val: 250
    YAML: order$qcMetric_EVD_PreCal def: 260 || new val: 260
    YAML: order$qcMetric_EVD_PostCal def: 270 || new val: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280 || new val: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300 || new val: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350
    YAML: order$qcMetric_MSMSScans_TopNID def: 380 || new val: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383 || new val: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390 || new val: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400 || new val: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450 || new val: 450
    YAML: order$qcMetric_EVD_UpSet def: 500 || new val: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999 || new val: 9999
    YAML: PTXQC$UseLocalMQPar def: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 30
    YAML: File$Evidence$ProteinCountThresh_num def: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10
    YAML: PTXQC$OutputFormats def: txt
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on
    YAML: order$qcMetric_PAR def: 1
    YAML: order$qcMetric_PG_PCA def: -1
    YAML: order$qcMetric_EVD_Top5Cont def: -1
    YAML: order$qcMetric_PG_Ratio def: -1
    YAML: order$qcMetric_EVD_UserContaminant def: -1
    YAML: order$qcMetric_SM_TIC def: -1
    YAML: order$qcMetric_EVD_PeptideInt def: -1
    YAML: order$qcMetric_EVD_ReporterInt def: -1
    YAML: order$qcMetric_PG_RawInt def: -1
    YAML: order$qcMetric_PG_LFQInt def: -1
    YAML: order$qcMetric_PG_ReporterInt def: -1
    YAML: order$qcMetric_MSMS_MissedCleavages def: -1
    YAML: order$qcMetric_EVD_Charge def: -1
    YAML: order$qcMetric_EVD_modTable def: -1
    YAML: order$qcMetric_PG_Cont def: -1
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: -1
    YAML: order$qcMetric_EVD_IDoverRT def: -1
    YAML: order$qcMetric_EVD_RTPeakWidth def: -1
    YAML: order$qcMetric_EVD_MBRAlign def: -1
    YAML: order$qcMetric_EVD_MBRIdTransfer def: -1
    YAML: order$qcMetric_EVD_MBRaux def: -1
    YAML: order$qcMetric_MSMSScans_IonInjTime def: -1
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: -1
    YAML: order$qcMetric_EVD_CarryOver def: -1
    YAML: order$qcMetric_EVD_MS2OverSampling def: -1
    YAML: order$qcMetric_EVD_PreCal def: -1
    YAML: order$qcMetric_EVD_PostCal def: -1
    YAML: order$qcMetric_MSMS_MSMSDecal def: -1
    YAML: order$qcMetric_SM_MSMSIdRate def: -1
    YAML: order$qcMetric_MSMSScans_TopN def: -1 || new val: -1
    YAML: order$qcMetric_MSMSScans_TopNID def: -1
    YAML: order$qcMetric_MSMSScans_DepPep def: -1
    YAML: order$qcMetric_EVD_MissingValues def: -1
    YAML: order$qcMetric_EVD_PeptideCount def: -1
    YAML: order$qcMetric_EVD_ProteinCount def: -1
    YAML: order$qcMetric_EVD_UpSet def: -1
    YAML: order$qcMetric_AverageQualOverall def: -1
    YAML: PTXQC$UseLocalMQPar def: TRUE || new val: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14 || new val: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20 || new val: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35 || new val: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4 || new val: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 30 || new val: 30
    YAML: File$Evidence$ProteinCountThresh_num def: 3500 || new val: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23 || new val: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000 || new val: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1") || new val: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1 || new val: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto || new val: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20 || new val: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2 || new val: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA || new val: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10 || new val: 10
    YAML: PTXQC$OutputFormats def: txt || new val: txt
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on || new val: on
    YAML: order$qcMetric_PAR def: 1 || new val: 1
    YAML: order$qcMetric_PG_PCA def: -1 || new val: -1
    YAML: order$qcMetric_EVD_Top5Cont def: -1 || new val: -1
    YAML: order$qcMetric_PG_Ratio def: -1 || new val: -1
    YAML: order$qcMetric_EVD_UserContaminant def: -1 || new val: -1
    YAML: order$qcMetric_SM_TIC def: -1 || new val: -1
    YAML: order$qcMetric_EVD_PeptideInt def: -1 || new val: -1
    YAML: order$qcMetric_EVD_ReporterInt def: -1 || new val: -1
    YAML: order$qcMetric_PG_RawInt def: -1 || new val: -1
    YAML: order$qcMetric_PG_LFQInt def: -1 || new val: -1
    YAML: order$qcMetric_PG_ReporterInt def: -1 || new val: -1
    YAML: order$qcMetric_MSMS_MissedCleavages def: -1 || new val: -1
    YAML: order$qcMetric_EVD_Charge def: -1 || new val: -1
    YAML: order$qcMetric_EVD_modTable def: -1 || new val: -1
    YAML: order$qcMetric_PG_Cont def: -1 || new val: -1
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: -1 || new val: -1
    YAML: order$qcMetric_EVD_IDoverRT def: -1 || new val: -1
    YAML: order$qcMetric_EVD_RTPeakWidth def: -1 || new val: -1
    YAML: order$qcMetric_EVD_MBRAlign def: -1 || new val: -1
    YAML: order$qcMetric_EVD_MBRIdTransfer def: -1 || new val: -1
    YAML: order$qcMetric_EVD_MBRaux def: -1 || new val: -1
    YAML: order$qcMetric_MSMSScans_IonInjTime def: -1 || new val: -1
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: -1 || new val: -1
    YAML: order$qcMetric_EVD_CarryOver def: -1 || new val: -1
    YAML: order$qcMetric_EVD_MS2OverSampling def: -1 || new val: -1
    YAML: order$qcMetric_EVD_PreCal def: -1 || new val: -1
    YAML: order$qcMetric_EVD_PostCal def: -1 || new val: -1
    YAML: order$qcMetric_MSMS_MSMSDecal def: -1 || new val: -1
    YAML: order$qcMetric_SM_MSMSIdRate def: -1 || new val: -1
    YAML: order$qcMetric_MSMSScans_TopN def: -1
    YAML: order$qcMetric_MSMSScans_TopNID def: -1 || new val: -1
    YAML: order$qcMetric_MSMSScans_DepPep def: -1 || new val: -1
    YAML: order$qcMetric_EVD_MissingValues def: -1 || new val: -1
    YAML: order$qcMetric_EVD_PeptideCount def: -1 || new val: -1
    YAML: order$qcMetric_EVD_ProteinCount def: -1 || new val: -1
    YAML: order$qcMetric_EVD_UpSet def: -1 || new val: -1
    YAML: order$qcMetric_AverageQualOverall def: -1 || new val: -1
    YAML: PTXQC$UseLocalMQPar def: TRUE
    YAML: PTXQC$NameLengthMax_num def: 14
    YAML: File$Summary$IDRate$Thresh_bad_num def: 20
    YAML: File$Summary$IDRate$Thresh_great_num def: 35
    YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4
    YAML: File$ProteinGroups$IntensityThreshLog2_num def: 25
    YAML: File$Evidence$ProteinCountThresh_num def: 3500
    YAML: File$Evidence$IntensityThreshLog2_num def: 23
    YAML: File$Evidence$PeptideCountThresh_num def: 15000
    YAML: File$Evidence$SpecialContaminants def: c(name = "MYCOPLASMA", threshold = "1")
    YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1
    YAML: File$Evidence$MatchBetweenRuns_wA def: auto
    YAML: File$Evidence$MQpar_firstSearchTol_num def: 20
    YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2
    YAML: File$Evidence$MQpar_mainSearchTol_num def: NA
    YAML: File$MsMsScans$IonInjectionThresh_num def: 10
    YAML: PTXQC$OutputFormats def: html,plainPDF
    YAML: PTXQC$PlainPDF$AddPageNumbers def: on
    YAML: order$qcMetric_PAR def: 1
    YAML: order$qcMetric_PG_PCA def: 3
    YAML: order$qcMetric_EVD_Top5Cont def: 10
    YAML: order$qcMetric_PG_Ratio def: 19
    YAML: order$qcMetric_EVD_UserContaminant def: 20
    YAML: order$qcMetric_SM_TIC def: 25
    YAML: order$qcMetric_EVD_PeptideInt def: 30
    YAML: order$qcMetric_EVD_ReporterInt def: 31
    YAML: order$qcMetric_PG_RawInt def: 32
    YAML: order$qcMetric_PG_LFQInt def: 33
    YAML: order$qcMetric_PG_ReporterInt def: 34
    YAML: order$qcMetric_MSMS_MissedCleavages def: 40
    YAML: order$qcMetric_EVD_Charge def: 100
    YAML: order$qcMetric_EVD_modTable def: 103
    YAML: order$qcMetric_PG_Cont def: 110
    YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120
    YAML: order$qcMetric_EVD_IDoverRT def: 150
    YAML: order$qcMetric_EVD_RTPeakWidth def: 170
    YAML: order$qcMetric_EVD_MBRAlign def: 210
    YAML: order$qcMetric_EVD_MBRIdTransfer def: 220
    YAML: order$qcMetric_EVD_MBRaux def: 221
    YAML: order$qcMetric_MSMSScans_IonInjTime def: 240
    YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245
    YAML: order$qcMetric_EVD_CarryOver def: 250
    YAML: order$qcMetric_EVD_MS2OverSampling def: 250
    YAML: order$qcMetric_EVD_PreCal def: 260
    YAML: order$qcMetric_EVD_PostCal def: 270
    YAML: order$qcMetric_MSMS_MSMSDecal def: 280
    YAML: order$qcMetric_SM_MSMSIdRate def: 300
    YAML: order$qcMetric_MSMSScans_TopN def: 350 || new val: 120
    YAML: order$qcMetric_MSMSScans_TopNID def: 380
    YAML: order$qcMetric_MSMSScans_DepPep def: 383
    YAML: order$qcMetric_EVD_MissingValues def: 390
    YAML: order$qcMetric_EVD_PeptideCount def: 400
    YAML: order$qcMetric_EVD_ProteinCount def: 450
    YAML: order$qcMetric_EVD_UpSet def: 500
    YAML: order$qcMetric_AverageQualOverall def: 9999
    The following labels will be shortened to ease plotting:
      jurkat_06_100731121305
    Starting to work on MS/MS Peak shape ...
    
    Memory [MB] prior|after|max(diff) : 116 | 115.6 | 119.1 (3)
    
    Duration: 0 s
    
    ... MS/MS Peak shape  done
    [ FAIL 1 | WARN 17 | SKIP 0 | PASS 131 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_computeQC.R:51:3'): createReport ───────────────────────────────
    Error in `FUN(X[[i]], ...)`: attempt to apply non-function
    Backtrace:
        ▆
     1. └─PTXQC::createReport(txt_folder, NULL, yaml_obj) at test_computeQC.R:51:3
     2.   └─lst_qcMetrics[["qcMetric_EVD_ProteinCount"]]$setData(...)
     3.     └─PTXQC (local) workerFcn(.self, df, ...)
     4.       └─base::lapply(...)
     5.         └─PTXQC (local) FUN(X[[i]], ...)
    
    [ FAIL 1 | WARN 17 | SKIP 0 | PASS 131 ]
    Error: Test failures
    Execution halted