Running ‘testthat.R’ [52s/89s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PTXQC)
  Loading package PTXQC (version 1.1.0)
  > 
  > ##
  > ## calls all code in PTXQC/tests/testthat/test*.R
  > ##
  > test_check("PTXQC")
  YAML: PTXQC$ReportFilename$extended def: TRUE
  Fri Mar  1 17:51:25 2024: Starting QC computation on report '/home/hornik/tmp/scratch/RtmpYui6FS/txt/report_v1.1.0_RtmpYui6FS'
  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/RtmpYui6FS/txt/report_v1.1.0_RtmpYui6FS_filename_sort.txt ' not possible!Reading file /home/hornik/tmp/scratch/RtmpYui6FS/txt/parameters.txt ...
  Read 61 entries from /home/hornik/tmp/scratch/RtmpYui6FS/txt/parameters.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Starting to work on PAR: MQ Parameters ...
  
  Memory [MB] prior|after|max(diff) : 94.8 | 97.5 | 177.9 (83)
  
  Duration: 1 s
  
  ... PAR: MQ Parameters  done
  Reading file /home/hornik/tmp/scratch/RtmpYui6FS/txt/summary.txt ...
  Read 5 entries from /home/hornik/tmp/scratch/RtmpYui6FS/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) : 98 | 106.9 | 140.4 (42)
  
  Duration: 1 s
  
  ... SM: MS^2 ID rate (">%1.0f")  done
  Reading file /home/hornik/tmp/scratch/RtmpYui6FS/txt/proteinGroups.txt ...
  Read 1128 entries from /home/hornik/tmp/scratch/RtmpYui6FS/txt/proteinGroups.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Starting to work on PG: Contaminants ...
  
  Memory [MB] prior|after|max(diff) : 108.6 | 109.4 | 118.3 (10)
  
  Duration: 0 s
  
  ... PG: Contaminants  done
  Starting to work on PG: Raw intensity ...
  
  Memory [MB] prior|after|max(diff) : 109.4 | 111.3 | 128.7 (19)
  
  Duration: 0 s
  
  ... PG: Raw intensity  done
  Starting to work on PG: LFQ intensity ...
  
  Memory [MB] prior|after|max(diff) : 111.3 | 111.8 | 127.5 (16)
  
  Duration: 0 s
  
  ... PG: LFQ intensity  done
  Starting to work on PG: Principal Component ...
  
  Memory [MB] prior|after|max(diff) : 111.9 | 113.1 | 137.2 (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) : 113.1 | 116.3 | 149.6 (36)
  
  Duration: 0 s
  
  ... PG: Ratio  done
  Reading file /home/hornik/tmp/scratch/RtmpYui6FS/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/RtmpYui6FS/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) : 124.1 | 124.1 | 124.1 (0)
  
  Duration: 0 s
  
  Starting to work on EVD: Peptide Intensity (">%1.1f") ...
  
  Memory [MB] prior|after|max(diff) : 124.1 | 125.9 | 145.6 (22)
  
  Duration: 0 s
  
  ... EVD: Peptide Intensity (">%1.1f")  done
  Starting to work on EVD: Reporter intensity ...
  
  Memory [MB] prior|after|max(diff) : 125.9 | 125.9 | 125.9 (0)
  
  Duration: 0 s
  
  Starting to work on EVD: Peptide VarMod ...
  
  Memory [MB] prior|after|max(diff) : 125.9 | 128.8 | 147.7 (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 8389 bytes
  ==================================================
  downloaded 8389 bytes
  
  trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.142/psi-ms.obo'
  Content type 'application/octet-stream' length 978630 bytes (955 KB)
  ==================================================
  downloaded 955 KB
  
  
  Memory [MB] prior|after|max(diff) : 128.6 | 137.1 | 238.5 (110)
  
  Duration: 8 s
  
  ... EVD: Protein Count (">%1.0f")  done
  Starting to work on EVD: Peptide Count (">%1.0f") ...
  
  Memory [MB] prior|after|max(diff) : 137.1 | 137.4 | 149.3 (12)
  
  Duration: 0 s
  
  ... EVD: Peptide Count (">%1.0f")  done
  Starting to work on EVD: RT Peak Width ...
  
  Memory [MB] prior|after|max(diff) : 137.4 | 137.7 | 162.9 (26)
  
  Duration: 0 s
  
  ... EVD: RT Peak Width  done
  Starting to work on EVD: MBR Align ...
  
  Memory [MB] prior|after|max(diff) : 137.7 | 138.7 | 204.8 (67)
  
  Duration: 3 s
  
  ... EVD: MBR Align  done
  Starting to work on EVD: MBR ID-Transfer ...
  
  Memory [MB] prior|after|max(diff) : 138.7 | 140 | 238.4 (100)
  
  Duration: 18 s
  
  ... EVD: MBR ID-Transfer  done
  Starting to work on EVD: MBR auxilliary ...
  
  Memory [MB] prior|after|max(diff) : 140 | 141.8 | 206.8 (67)
  
  Duration: 1 s
  
  ... EVD: MBR auxilliary  done
  Starting to work on EVD: Charge ...
  
  Memory [MB] prior|after|max(diff) : 141.8 | 141.9 | 151.6 (10)
  
  Duration: 0 s
  
  ... EVD: Charge  done
  Starting to work on EVD: ID rate over RT ...
  
  Memory [MB] prior|after|max(diff) : 141.9 | 142.2 | 156.8 (15)
  
  Duration: 0 s
  
  ... EVD: ID rate over RT  done
  Starting to work on EVD: UpSet ...
  
  Memory [MB] prior|after|max(diff) : 142.2 | 147.3 | 256.8 (115)
  
  Duration: 4 s
  
  ... EVD: UpSet  done
  Starting to work on EVD: MS Cal-Pre (%1.1f) ...
  
  Memory [MB] prior|after|max(diff) : 147.3 | 148.2 | 167.7 (20)
  
  Duration: 0 s
  
  ... EVD: MS Cal-Pre (%1.1f)  done
  Starting to work on EVD: MS Cal-Post ...
  
  Memory [MB] prior|after|max(diff) : 148.2 | 148.9 | 167.6 (19)
  
  Duration: 1 s
  
  ... EVD: MS Cal-Post  done
  Starting to work on EVD: Contaminants ...
  
  Memory [MB] prior|after|max(diff) : 148.9 | 149.7 | 170.4 (22)
  
  Duration: 0 s
  
  ... EVD: Contaminants  done
  Starting to work on EVD: MS^2 Oversampling ...
  
  Memory [MB] prior|after|max(diff) : 149.7 | 149.8 | 166.9 (17)
  
  Duration: 0 s
  
  ... EVD: MS^2 Oversampling  done
  Starting to work on EVD: Pep Missing Values ...
  
  Memory [MB] prior|after|max(diff) : 149.8 | 151.4 | 219.8 (70)
  
  Duration: 1 s
  
  ... EVD: Pep Missing Values  done
  Reading file /home/hornik/tmp/scratch/RtmpYui6FS/txt/msms.txt ...
  Requiring column(s) 'missed.cleavages' to be of type 'numeric'!
  Requiring column(s) 'evidence.id' to be of type 'numeric'!
  Keeping 2 of 59 columns!
  Read 1000 entries from /home/hornik/tmp/scratch/RtmpYui6FS/txt/msms.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Adding fc.raw.file column ... done
  Starting to work on MSMS: MS^2 Cal (%s) ...
  
  Memory [MB] prior|after|max(diff) : 152.4 | 153.7 | 181.3 (29)
  
  Duration: 1 s
  
  ... MSMS: MS^2 Cal (%s)  done
  Starting to work on MSMS: Missed Cleavages%s ...
  
  Memory [MB] prior|after|max(diff) : 153.7 | 153.8 | 160.4 (7)
  
  Duration: 1 s
  
  ... MSMS: Missed Cleavages%s  done
  Starting to work on MSMS: Missed Cleavages%s ...
  
  Memory [MB] prior|after|max(diff) : 153.9 | 154 | 168 (14)
  
  Duration: 0 s
  
  ... MSMS: Missed Cleavages%s  done
  Reading file /home/hornik/tmp/scratch/RtmpYui6FS/txt/msmsScans.txt ...
  Requiring column(s) 'ion.injection.time' to be of type 'numeric'!
  Requiring column(s) 'retention.time' to be of type 'numeric'!
  Requiring column(s) 'scan.event.number' to be of type 'numeric'!
  Requiring column(s) 'scan.index', 'ms.scan.index' to be of type 'numeric'!
  Requiring column(s) 'ms.scan.index' to be of type 'numeric'!
  WARNING: Could not find column regex '^dp.aa$' using case-INsensitive matching.
  WARNING: Could not find column regex '^dp.modification$' using case-INsensitive matching.
  Keeping 5 of 41 columns!
  Read 35113 entries from /home/hornik/tmp/scratch/RtmpYui6FS/txt/msmsScans.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Adding fc.raw.file column ... done
  Starting to work on MS^2*Scans: TopN over RT ...
  
  Memory [MB] prior|after|max(diff) : 155.8 | 156 | 175.8 (20)
  
  Duration: 0 s
  
  ... MS^2*Scans: TopN over RT  done
  Starting to work on MS^2*Scans: Ion Inj Time ...
  
  Memory [MB] prior|after|max(diff) : 155.9 | 156.3 | 166.9 (11)
  
  Duration: 0 s
  
  ... MS^2*Scans: Ion Inj Time  done
  Starting to work on MS^2*Scans: Intensity ...
  
  Memory [MB] prior|after|max(diff) : 156.1 | 158.2 | 179.9 (24)
  
  Duration: 1 s
  
  ... MS^2*Scans: Intensity  done
  Starting to work on MS^2*Scans: TopN high ...
  
  Memory [MB] prior|after|max(diff) : 158 | 158.1 | 169.6 (12)
  
  Duration: 0 s
  
  ... MS^2*Scans: TopN high  done
  Starting to work on MS^2*Scans: TopN ID over N ...
  
  Memory [MB] prior|after|max(diff) : 158 | 158.2 | 173 (15)
  
  Duration: 0 s
  
  ... MS^2*Scans: TopN ID over N  done
  [1] "#Metrics: "
  [1] 37
  Starting to work on Average Overall Quality ...
  
  Memory [MB] prior|after|max(diff) : 159.4 | 159.4 | 160.1 (1)
  
  Duration: 0 s
  
  ... Average Overall Quality  done
  Creating Report file ...HTML TEMPLATE: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PTXQC/./reportTemplate/PTXQC_report_template.Rmd
  Error in as.vector(x, "character") : 
    cannot coerce type 'environment' to vector of type 'character'
  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) : 144.1 | 143.6 | 146.6 (2)
  
  Duration: 0 s
  
  ... MS/MS Peak shape  done
  [ FAIL 1 | WARN 24 | SKIP 0 | PASS 131 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_computeQC.R:51:3'): createReport ───────────────────────────────
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
       ▆
    1. ├─PTXQC::createReport(txt_folder, NULL, yaml_obj) at test_computeQC.R:51:3
    2. │ ├─rmarkdown::render(html_template, output_file = rprt_fns$report_file_HTML)
    3. │ │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    4. │ │   └─knitr:::process_file(text, output)
    5. │ │     ├─knitr:::handle_error(...)
    6. │ │     │ └─base::withCallingHandlers(...)
    7. │ │     ├─base::withCallingHandlers(...)
    8. │ │     ├─knitr:::process_group(group)
    9. │ │     └─knitr:::process_group.block(group)
   10. │ │       └─knitr:::call_block(x)
   11. │ │         └─knitr:::block_exec(params)
   12. │ │           └─knitr:::eng_r(options)
   13. │ │             ├─knitr:::in_input_dir(...)
   14. │ │             │ └─knitr:::in_dir(input_dir(), expr)
   15. │ │             └─knitr (local) evaluate(...)
   16. │ │               └─evaluate::evaluate(...)
   17. │ │                 └─evaluate:::evaluate_call(...)
   18. │ │                   ├─evaluate (local) timing_fn(...)
   19. │ │                   ├─base (local) handle(...)
   20. │ │                   ├─base::withCallingHandlers(...)
   21. │ │                   ├─base::withVisible(...)
   22. │ │                   └─evaluate:::eval_with_user_handlers(expr, envir, enclos, user_handlers)
   23. │ │                     └─base::eval(expr, envir, enclos)
   24. │ │                       └─base::eval(expr, envir, enclos)
   25. │ ├─base::print(plots[[i]])
   26. │ └─ggplot2:::print.ggplot(plots[[i]])
   27. │   ├─ggplot2::ggplot_gtable(data)
   28. │   └─ggplot2:::ggplot_gtable.ggplot_built(data)
   29. │     └─plot$guides$assemble(theme)
   30. │       └─ggplot2 (local) assemble(..., self = self)
   31. │         └─self$draw(theme, default_position, theme$legend.direction)
   32. │           └─ggplot2 (local) draw(..., self = self)
   33. │             └─guides[[i]]$draw(...)
   34. │               └─ggplot2 (local) draw(..., self = self)
   35. │                 └─self$build_title(params$title, elems, params)
   36. │                   └─ggplot2 (local) build_title(...)
   37. │                     ├─ggplot2:::ggname(...)
   38. │                     │ └─grid::grobName(grob, prefix)
   39. │                     ├─ggplot2::element_grob(...)
   40. │                     └─ggplot2:::element_grob.element_text(...)
   41. │                       └─ggplot2:::titleGrob(...)
   42. │                         └─grid::textGrob(...)
   43. │                           └─grid::grob(...)
   44. │                             ├─grid:::validGrob(g)
   45. │                             └─grid:::validGrob.grob(g)
   46. │                               ├─grid::validDetails(x)
   47. │                               └─grid:::validDetails.text(x)
   48. │                                 ├─base::as.character(x$label)
   49. │                                 └─base::as.character.default(x$label)
   50. ├─base::.handleSimpleError(...)
   51. │ └─knitr (local) h(simpleError(msg, call))
   52. │   └─rlang::entrace(e)
   53. │     └─rlang::cnd_signal(entraced)
   54. │       └─rlang:::signal_abort(cnd)
   55. │         └─base::signalCondition(cnd)
   56. └─knitr (local) `<fn>`(`<rlng_rrr>`)
   57.   ├─base::message(one_string(handler(e, loc)))
   58.   ├─knitr:::one_string(handler(e, loc))
   59.   │ └─base::paste(x, ..., collapse = "\n")
   60.   └─knitr (local) handler(e, loc)
   61.     └─xfun::write_utf8(res, output %n% stdout())
   62.       └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
   63.         └─base::file(con, "w")
  
  [ FAIL 1 | WARN 24 | SKIP 0 | PASS 131 ]
  Error: Test failures
  Execution halted