CRAN Package Check Results for Package PTXQC

Last updated on 2024-02-28 00:56:29 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.0 21.67 208.29 229.96 ERROR
r-devel-linux-x86_64-debian-gcc 1.1.0 14.40 158.48 172.88 ERROR
r-devel-linux-x86_64-fedora-clang 1.1.0 193.37 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1.0 284.47 ERROR
r-devel-windows-x86_64 1.1.0 19.00 223.00 242.00 NOTE
r-patched-linux-x86_64 1.1.0 19.55 264.21 283.76 OK
r-release-linux-x86_64 1.1.0 14.33 204.12 218.45 ERROR
r-release-macos-arm64 1.1.0 110.00 NOTE
r-release-macos-x86_64 1.1.0 216.00 NOTE
r-release-windows-x86_64 1.1.0 26.00 233.00 259.00 ERROR
r-oldrel-macos-arm64 1.1.0 160.00 NOTE
r-oldrel-windows-x86_64 1.1.0 27.00 212.00 239.00 ERROR

Check Details

Version: 1.1.0
Check: examples
Result: ERROR Running examples in ‘PTXQC-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot_RatiosPG > ### Title: Plot ratios of labeled data (e.g. SILAC) from proteinGroups.txt > ### Aliases: plot_RatiosPG > > ### ** Examples > > > x1 = seq(-3, 3, by = 0.1) > y1 = dnorm(x1) > x2 = seq(-5, 1, by = 0.1) > y2 = dnorm(x2, mean = -1) > data = data.frame( x = c(x1,x2), + y = c(y1,y2), + col = c(rep("ok", length(x1)), rep("shifted", length(x2))), + ltype = c(rep("solid", length(x1)), rep("dotted", length(x2)))) > plot_RatiosPG(data, range(data$x), "Ratio plot", "red", "group") Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type 'character' Calls: <Anonymous> ... validDetails.text -> as.character -> as.character.default Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [66s/81s] 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 Mon Feb 26 20:30:51 2024: Starting QC computation on report '/tmp/Rtmpr1iumM/txt/report_v1.1.0_Rtmpr1iumM' 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 ' /tmp/Rtmpr1iumM/txt/report_v1.1.0_Rtmpr1iumM_filename_sort.txt ' not possible!Reading file /tmp/Rtmpr1iumM/txt/parameters.txt ... Read 61 entries from /tmp/Rtmpr1iumM/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 /tmp/Rtmpr1iumM/txt/summary.txt ... Read 5 entries from /tmp/Rtmpr1iumM/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 | 140.3 (42) Duration: 0 s ... SM: MS^2 ID rate (">%1.0f") done Reading file /tmp/Rtmpr1iumM/txt/proteinGroups.txt ... Read 1128 entries from /tmp/Rtmpr1iumM/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 | 149.5 (36) Duration: 0 s ... PG: Ratio done Reading file /tmp/Rtmpr1iumM/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 /tmp/Rtmpr1iumM/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 | 125.8 | 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) : 125.8 | 125.8 | 125.9 (0) Duration: 0 s Starting to work on EVD: Peptide VarMod ... Memory [MB] prior|after|max(diff) : 125.8 | 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 8388 bytes ================================================== downloaded 8388 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 | 238.4 (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 | 138.6 | 204.8 (67) Duration: 3 s ... EVD: MBR Align done Starting to work on EVD: MBR ID-Transfer ... Memory [MB] prior|after|max(diff) : 138.6 | 140 | 238.4 (100) Duration: 16 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 | 156.7 (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 | 256.7 (114) Duration: 3 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: 0 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 | 166.8 (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 /tmp/Rtmpr1iumM/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 /tmp/Rtmpr1iumM/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 | 181.2 (29) Duration: 0 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 | 160.3 (7) Duration: 0 s ... MSMS: Missed Cleavages%s done Starting to work on MSMS: Missed Cleavages%s ... Memory [MB] prior|after|max(diff) : 153.8 | 153.9 | 167.8 (14) Duration: 0 s ... MSMS: Missed Cleavages%s done Reading file /tmp/Rtmpr1iumM/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$' using case-INsensitive matching. Keeping 5 of 41 columns! Read 35113 entries from /tmp/Rtmpr1iumM/txt/msmsScans.txt. Updating colnames Simplifying contaminants Simplifying reverse Adding fc.raw.file column ... done Starting to work on MS^2*Scans: TopN over RT ... Memory [MB] prior|after|max(diff) : 155.7 | 156 | 175.8 (20) Duration: 0 s ... MS^2*Scans: TopN over RT done Starting to work on MS^2*Scans: Ion Inj Time ... Memory [MB] prior|after|max(diff) : 155.9 | 156.3 | 166.9 (11) Duration: 0 s ... MS^2*Scans: Ion Inj Time done Starting to work on MS^2*Scans: Intensity ... Memory [MB] prior|after|max(diff) : 156.1 | 158.2 | 179.9 (24) Duration: 0 s ... MS^2*Scans: Intensity done Starting to work on MS^2*Scans: TopN high ... Memory [MB] prior|after|max(diff) : 158 | 158 | 169.6 (12) Duration: 0 s ... MS^2*Scans: TopN high done Starting to work on MS^2*Scans: TopN ID over N ... Memory [MB] prior|after|max(diff) : 158 | 158.2 | 172.9 (15) Duration: 0 s ... MS^2*Scans: TopN ID over N done [1] "#Metrics: " [1] 37 Starting to work on Average Overall Quality ... Memory [MB] prior|after|max(diff) : 159.3 | 159.4 | 160 (1) Duration: 0 s ... Average Overall Quality done Creating Report file ...HTML TEMPLATE: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/PTXQC/./reportTemplate/PTXQC_report_template.Rmd Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type 'character' YAML: PTXQC$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 Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [51s/85s] 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 Mon Feb 26 17:39:37 2024: Starting QC computation on report '/home/hornik/tmp/scratch/Rtmp3jVZsB/txt/report_v1.1.0_Rtmp3jVZsB' 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/Rtmp3jVZsB/txt/report_v1.1.0_Rtmp3jVZsB_filename_sort.txt ' not possible!Reading file /home/hornik/tmp/scratch/Rtmp3jVZsB/txt/parameters.txt ... Read 61 entries from /home/hornik/tmp/scratch/Rtmp3jVZsB/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/Rtmp3jVZsB/txt/summary.txt ... Read 5 entries from /home/hornik/tmp/scratch/Rtmp3jVZsB/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 | 140.3 (42) Duration: 0 s ... SM: MS^2 ID rate (">%1.0f") done Reading file /home/hornik/tmp/scratch/Rtmp3jVZsB/txt/proteinGroups.txt ... Read 1128 entries from /home/hornik/tmp/scratch/Rtmp3jVZsB/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: 1 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: 1 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 | 149.5 (36) Duration: 1 s ... PG: Ratio done Reading file /home/hornik/tmp/scratch/Rtmp3jVZsB/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/Rtmp3jVZsB/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 | 125.8 | 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) : 125.8 | 125.8 | 125.9 (0) Duration: 0 s Starting to work on EVD: Peptide VarMod ... Memory [MB] prior|after|max(diff) : 125.8 | 128.8 | 147.7 (22) Duration: 1 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 8388 bytes ================================================== downloaded 8388 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 | 238.4 (110) Duration: 7 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: 1 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: 16 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 | 156.7 (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 | 256.7 (114) Duration: 3 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: 1 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: 0 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 | 166.8 (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/Rtmp3jVZsB/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/Rtmp3jVZsB/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 | 181.2 (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 | 160.3 (7) Duration: 0 s ... MSMS: Missed Cleavages%s done Starting to work on MSMS: Missed Cleavages%s ... Memory [MB] prior|after|max(diff) : 153.8 | 153.9 | 167.9 (14) Duration: 1 s ... MSMS: Missed Cleavages%s done Reading file /home/hornik/tmp/scratch/Rtmp3jVZsB/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$' using case-INsensitive matching. Keeping 5 of 41 columns! Read 35113 entries from /home/hornik/tmp/scratch/Rtmp3jVZsB/txt/msmsScans.txt. Updating colnames Simplifying contaminants Simplifying reverse Adding fc.raw.file column ... done Starting to work on MS^2*Scans: TopN over RT ... Memory [MB] prior|after|max(diff) : 155.7 | 156 | 175.8 (20) Duration: 1 s ... MS^2*Scans: TopN over RT done Starting to work on MS^2*Scans: Ion Inj Time ... Memory [MB] prior|after|max(diff) : 155.9 | 156.3 | 166.9 (11) Duration: 0 s ... MS^2*Scans: Ion Inj Time done Starting to work on MS^2*Scans: Intensity ... Memory [MB] prior|after|max(diff) : 156.1 | 158.2 | 179.9 (24) Duration: 0 s ... MS^2*Scans: Intensity done Starting to work on MS^2*Scans: TopN high ... Memory [MB] prior|after|max(diff) : 158 | 158 | 169.6 (12) Duration: 1 s ... MS^2*Scans: TopN high done Starting to work on MS^2*Scans: TopN ID over N ... Memory [MB] prior|after|max(diff) : 158 | 158.2 | 172.9 (15) Duration: 0 s ... MS^2*Scans: TopN ID over N done [1] "#Metrics: " [1] 37 Starting to work on Average Overall Quality ... Memory [MB] prior|after|max(diff) : 159.4 | 159.4 | 160 (1) Duration: 0 s ... Average Overall Quality done Creating Report file ...HTML TEMPLATE: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PTXQC/./reportTemplate/PTXQC_report_template.Rmd Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type 'character' YAML: PTXQC$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 Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.1.0
Check: installed package size
Result: NOTE installed size is 7.9Mb sub-directories of 1Mb or more: doc 4.0Mb examples 2.6Mb Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-windows-x86_64

Version: 1.1.0
Check: examples
Result: ERROR Running examples in ‘PTXQC-Ex.R’ failed The error most likely occurred in: > ### Name: plot_RatiosPG > ### Title: Plot ratios of labeled data (e.g. SILAC) from proteinGroups.txt > ### Aliases: plot_RatiosPG > > ### ** Examples > > > x1 = seq(-3, 3, by = 0.1) > y1 = dnorm(x1) > x2 = seq(-5, 1, by = 0.1) > y2 = dnorm(x2, mean = -1) > data = data.frame( x = c(x1,x2), + y = c(y1,y2), + col = c(rep("ok", length(x1)), rep("shifted", length(x2))), + ltype = c(rep("solid", length(x1)), rep("dotted", length(x2)))) > plot_RatiosPG(data, range(data$x), "Ratio plot", "red", "group") Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type 'character' Calls: <Anonymous> ... validDetails.text -> as.character -> as.character.default Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [46s/46s] 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 Tue Feb 27 04:12:36 2024: Starting QC computation on report '/tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/txt/report_v1.1.0_RtmpeHfA6G' 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 ' /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/txt/report_v1.1.0_RtmpeHfA6G_filename_sort.txt ' not possible!Reading file /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/txt/parameters.txt ... Read 61 entries from /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/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 /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/txt/summary.txt ... Read 5 entries from /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/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 | 140.3 (42) Duration: 0 s ... SM: MS^2 ID rate (">%1.0f") done Reading file /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/txt/proteinGroups.txt ... Read 1128 entries from /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/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 | 149.5 (36) Duration: 0 s ... PG: Ratio done Reading file /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/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 /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/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 | 125.8 | 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) : 125.8 | 125.8 | 125.9 (0) Duration: 0 s Starting to work on EVD: Peptide VarMod ... Memory [MB] prior|after|max(diff) : 125.8 | 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 8388 bytes ================================================== downloaded 8388 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 | 232.1 (104) Duration: 4 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 | 138.6 | 204.7 (67) Duration: 2 s ... EVD: MBR Align done Starting to work on EVD: MBR ID-Transfer ... Memory [MB] prior|after|max(diff) : 138.6 | 140 | 280.9 (142) Duration: 9 s ... EVD: MBR ID-Transfer done Starting to work on EVD: MBR auxilliary ... Memory [MB] prior|after|max(diff) : 140 | 141.8 | 207.6 (68) Duration: 0 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 | 156.7 (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 | 257.5 (115) Duration: 2 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: 0 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 | 166.8 (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 | 151.3 | 219.8 (70) Duration: 0 s ... EVD: Pep Missing Values done Reading file /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/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 /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/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: 0 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 | 160.3 (7) Duration: 0 s ... MSMS: Missed Cleavages%s done Starting to work on MSMS: Missed Cleavages%s ... Memory [MB] prior|after|max(diff) : 153.8 | 153.9 | 167.8 (14) Duration: 0 s ... MSMS: Missed Cleavages%s done Reading file /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/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$' using case-INsensitive matching. Keeping 5 of 41 columns! Read 35113 entries from /tmp/Rtmp3ADUkG/working_dir/RtmpeHfA6G/txt/msmsScans.txt. Updating colnames Simplifying contaminants Simplifying reverse Adding fc.raw.file column ... done Starting to work on MS^2*Scans: TopN over RT ... Memory [MB] prior|after|max(diff) : 155.7 | 156 | 175.8 (20) Duration: 0 s ... MS^2*Scans: TopN over RT done Starting to work on MS^2*Scans: Ion Inj Time ... Memory [MB] prior|after|max(diff) : 155.9 | 156.3 | 166.9 (11) Duration: 0 s ... MS^2*Scans: Ion Inj Time done Starting to work on MS^2*Scans: Intensity ... Memory [MB] prior|after|max(diff) : 156.1 | 158.2 | 179.9 (24) Duration: 0 s ... MS^2*Scans: Intensity done Starting to work on MS^2*Scans: TopN high ... Memory [MB] prior|after|max(diff) : 158 | 158 | 169.6 (12) Duration: 0 s ... MS^2*Scans: TopN high done Starting to work on MS^2*Scans: TopN ID over N ... Memory [MB] prior|after|max(diff) : 158 | 158.2 | 172.9 (15) Duration: 0 s ... MS^2*Scans: TopN ID over N done [1] "#Metrics: " [1] 37 Starting to work on Average Overall Quality ... Memory [MB] prior|after|max(diff) : 159.4 | 159.4 | 160 (1) Duration: 0 s ... Average Overall Quality done Creating Report file ...HTML TEMPLATE: /data/gannet/ripley/R/packages/tests-clang/PTXQC.Rcheck/PTXQC/./reportTemplate/PTXQC_report_template.Rmd Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type 'character' YAML: PTXQC$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$qcMetric_AverageQualOverall def: 9999 The following labels will be shortened to ease plotting: jurkat_06_100731121305 Starting to work on MS/MS Peak shape ... Memory [MB] prior|after|max(diff) : 143.9 | 143.4 | 146.3 (2) Duration: 0 s ... MS/MS Peak shape done [ FAIL 1 | WARN 23 | SKIP 0 | PASS 131 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_computeQC.R:51:3'): createReport ─────────────────────────────── Error in `as.vector(x, "character")`: cannot coerce type 'environment' to vector of type 'character' Backtrace: ▆ 1. └─PTXQC::createReport(txt_folder, NULL, yaml_obj) at test_computeQC.R:51:3 2. ├─rmarkdown::render(html_template, output_file = rprt_fns$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) [ FAIL 1 | WARN 23 | SKIP 0 | PASS 131 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [76s/94s] 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 Tue Feb 27 02:13:19 2024: Starting QC computation on report '/tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/txt/report_v1.1.0_RtmpMRhnH5' 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 ' /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/txt/report_v1.1.0_RtmpMRhnH5_filename_sort.txt ' not possible!Reading file /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/txt/parameters.txt ... Read 61 entries from /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/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 /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/txt/summary.txt ... Read 5 entries from /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/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 | 140.3 (42) Duration: 1 s ... SM: MS^2 ID rate (">%1.0f") done Reading file /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/txt/proteinGroups.txt ... Read 1128 entries from /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/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: 1 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 | 149.5 (36) Duration: 1 s ... PG: Ratio done Reading file /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/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 /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/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 | 125.8 | 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) : 125.8 | 125.8 | 125.9 (0) Duration: 0 s Starting to work on EVD: Peptide VarMod ... Memory [MB] prior|after|max(diff) : 125.8 | 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 8388 bytes ================================================== downloaded 8388 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 | 232 (103) Duration: 9 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: 1 s ... EVD: RT Peak Width done Starting to work on EVD: MBR Align ... Memory [MB] prior|after|max(diff) : 137.7 | 138.6 | 204.6 (67) Duration: 4 s ... EVD: MBR Align done Starting to work on EVD: MBR ID-Transfer ... Memory [MB] prior|after|max(diff) : 138.6 | 140 | 280.9 (142) Duration: 19 s ... EVD: MBR ID-Transfer done Starting to work on EVD: MBR auxilliary ... Memory [MB] prior|after|max(diff) : 140 | 141.8 | 207.6 (68) 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 | 156.7 (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 | 257.5 (115) Duration: 3 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: 1 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: 0 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: 1 s ... EVD: Contaminants done Starting to work on EVD: MS^2 Oversampling ... Memory [MB] prior|after|max(diff) : 149.7 | 149.8 | 166.8 (17) Duration: 1 s ... EVD: MS^2 Oversampling done Starting to work on EVD: Pep Missing Values ... Memory [MB] prior|after|max(diff) : 149.8 | 151.3 | 219.8 (70) Duration: 1 s ... EVD: Pep Missing Values done Reading file /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/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 /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/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 | 181.4 (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) : 153.8 | 153.9 | 167.9 (14) Duration: 0 s ... MSMS: Missed Cleavages%s done Reading file /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/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$' using case-INsensitive matching. Keeping 5 of 41 columns! Read 35113 entries from /tmp/RtmpFG47Pa/working_dir/RtmpMRhnH5/txt/msmsScans.txt. Updating colnames Simplifying contaminants Simplifying reverse Adding fc.raw.file column ... done Starting to work on MS^2*Scans: TopN over RT ... Memory [MB] prior|after|max(diff) : 155.7 | 156 | 175.8 (20) Duration: 0 s ... MS^2*Scans: TopN over RT done Starting to work on MS^2*Scans: Ion Inj Time ... Memory [MB] prior|after|max(diff) : 155.9 | 156.3 | 166.9 (11) Duration: 1 s ... MS^2*Scans: Ion Inj Time done Starting to work on MS^2*Scans: Intensity ... Memory [MB] prior|after|max(diff) : 156.1 | 158.2 | 179.9 (24) Duration: 0 s ... MS^2*Scans: Intensity done Starting to work on MS^2*Scans: TopN high ... Memory [MB] prior|after|max(diff) : 158 | 158 | 169.6 (12) Duration: 0 s ... MS^2*Scans: TopN high done Starting to work on MS^2*Scans: TopN ID over N ... Memory [MB] prior|after|max(diff) : 158 | 158.2 | 172.9 (15) Duration: 1 s ... MS^2*Scans: TopN ID over N done [1] "#Metrics: " [1] 37 Starting to work on Average Overall Quality ... Memory [MB] prior|after|max(diff) : 159.4 | 159.4 | 160.1 (1) Duration: 0 s ... Average Overall Quality done Creating Report file ...HTML TEMPLATE: /data/gannet/ripley/R/packages/tests-devel/PTXQC.Rcheck/PTXQC/./reportTemplate/PTXQC_report_template.Rmd Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type 'character' YAML: PTXQC$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$qcMetric_AverageQualOverall def: 9999 The following labels will be shortened to ease plotting: jurkat_06_100731121305 Starting to work on MS/MS Peak shape ... Memory [MB] prior|after|max(diff) : 143.9 | 143.4 | 146.3 (2) Duration: 0 s ... MS/MS Peak shape done [ FAIL 1 | WARN 23 | SKIP 0 | PASS 131 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_computeQC.R:51:3'): createReport ─────────────────────────────── Error in `as.vector(x, "character")`: cannot coerce type 'environment' to vector of type 'character' Backtrace: ▆ 1. └─PTXQC::createReport(txt_folder, NULL, yaml_obj) at test_computeQC.R:51:3 2. ├─rmarkdown::render(html_template, output_file = rprt_fns$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) [ FAIL 1 | WARN 23 | SKIP 0 | PASS 131 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [66s/79s] 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 Sun Feb 25 03:25:21 2024: Starting QC computation on report '/tmp/Rtmpr416ay/txt/report_v1.1.0_Rtmpr416ay' 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 ' /tmp/Rtmpr416ay/txt/report_v1.1.0_Rtmpr416ay_filename_sort.txt ' not possible!Reading file /tmp/Rtmpr416ay/txt/parameters.txt ... Read 61 entries from /tmp/Rtmpr416ay/txt/parameters.txt. Updating colnames Simplifying contaminants Simplifying reverse Starting to work on PAR: MQ Parameters ... Memory [MB] prior|after|max(diff) : 92.7 | 95.3 | 175.7 (83) Duration: 1 s ... PAR: MQ Parameters done Reading file /tmp/Rtmpr416ay/txt/summary.txt ... Read 5 entries from /tmp/Rtmpr416ay/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) : 95.9 | 104.7 | 138.1 (42) Duration: 1 s ... SM: MS^2 ID rate (">%1.0f") done Reading file /tmp/Rtmpr416ay/txt/proteinGroups.txt ... Read 1128 entries from /tmp/Rtmpr416ay/txt/proteinGroups.txt. Updating colnames Simplifying contaminants Simplifying reverse Starting to work on PG: Contaminants ... Memory [MB] prior|after|max(diff) : 106.5 | 107.2 | 116.1 (10) Duration: 0 s ... PG: Contaminants done Starting to work on PG: Raw intensity ... Memory [MB] prior|after|max(diff) : 107.2 | 109.2 | 126.4 (19) Duration: 0 s ... PG: Raw intensity done Starting to work on PG: LFQ intensity ... Memory [MB] prior|after|max(diff) : 109.2 | 109.6 | 125.3 (16) Duration: 0 s ... PG: LFQ intensity done Starting to work on PG: Principal Component ... Memory [MB] prior|after|max(diff) : 109.8 | 111 | 135 (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) : 111 | 114.2 | 147.3 (36) Duration: 0 s ... PG: Ratio done Reading file /tmp/Rtmpr416ay/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 /tmp/Rtmpr416ay/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) : 121.9 | 121.9 | 121.9 (0) Duration: 0 s Starting to work on EVD: Peptide Intensity (">%1.1f") ... Memory [MB] prior|after|max(diff) : 121.9 | 123.8 | 143.4 (22) Duration: 0 s ... EVD: Peptide Intensity (">%1.1f") done Starting to work on EVD: Reporter intensity ... Memory [MB] prior|after|max(diff) : 123.8 | 123.8 | 123.8 (0) Duration: 0 s Starting to work on EVD: Peptide VarMod ... Memory [MB] prior|after|max(diff) : 123.8 | 126.6 | 145.5 (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 8388 bytes ================================================== downloaded 8388 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) : 126.4 | 134.9 | 212.7 (86) Duration: 9 s ... EVD: Protein Count (">%1.0f") done Starting to work on EVD: Peptide Count (">%1.0f") ... Memory [MB] prior|after|max(diff) : 134.9 | 135.2 | 147.1 (12) Duration: 0 s ... EVD: Peptide Count (">%1.0f") done Starting to work on EVD: RT Peak Width ... Memory [MB] prior|after|max(diff) : 135.2 | 135.6 | 160.8 (26) Duration: 0 s ... EVD: RT Peak Width done Starting to work on EVD: MBR Align ... Memory [MB] prior|after|max(diff) : 135.6 | 136.6 | 198.3 (63) Duration: 4 s ... EVD: MBR Align done Starting to work on EVD: MBR ID-Transfer ... Memory [MB] prior|after|max(diff) : 136.6 | 137.9 | 232.5 (96) Duration: 15 s ... EVD: MBR ID-Transfer done Starting to work on EVD: MBR auxilliary ... Memory [MB] prior|after|max(diff) : 137.9 | 139.7 | 196.1 (58) Duration: 1 s ... EVD: MBR auxilliary done Starting to work on EVD: Charge ... Memory [MB] prior|after|max(diff) : 139.6 | 139.8 | 149.4 (10) Duration: 0 s ... EVD: Charge done Starting to work on EVD: ID rate over RT ... Memory [MB] prior|after|max(diff) : 139.8 | 140 | 154.6 (15) Duration: 0 s ... EVD: ID rate over RT done Starting to work on EVD: UpSet ... Memory [MB] prior|after|max(diff) : 140 | 145.2 | 200 (60) Duration: 3 s ... EVD: UpSet done Starting to work on EVD: MS Cal-Pre (%1.1f) ... Memory [MB] prior|after|max(diff) : 145.2 | 146 | 165.5 (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) : 146 | 146.8 | 165.5 (20) Duration: 0 s ... EVD: MS Cal-Post done Starting to work on EVD: Contaminants ... Memory [MB] prior|after|max(diff) : 146.8 | 147.5 | 168.3 (22) Duration: 0 s ... EVD: Contaminants done Starting to work on EVD: MS^2 Oversampling ... Memory [MB] prior|after|max(diff) : 147.5 | 147.6 | 164.6 (17) Duration: 0 s ... EVD: MS^2 Oversampling done Starting to work on EVD: Pep Missing Values ... Memory [MB] prior|after|max(diff) : 147.6 | 149.2 | 217.7 (70) Duration: 1 s ... EVD: Pep Missing Values done Reading file /tmp/Rtmpr416ay/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 /tmp/Rtmpr416ay/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) : 150.2 | 151.7 | 179.4 (29) Duration: 0 s ... MSMS: MS^2 Cal (%s) done Starting to work on MSMS: Missed Cleavages%s ... Memory [MB] prior|after|max(diff) : 151.7 | 151.8 | 158.2 (6) Duration: 0 s ... MSMS: Missed Cleavages%s done Starting to work on MSMS: Missed Cleavages%s ... Memory [MB] prior|after|max(diff) : 151.8 | 151.8 | 165.7 (14) Duration: 0 s ... MSMS: Missed Cleavages%s done Reading file /tmp/Rtmpr416ay/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$' using case-INsensitive matching. Keeping 5 of 41 columns! Read 35113 entries from /tmp/Rtmpr416ay/txt/msmsScans.txt. Updating colnames Simplifying contaminants Simplifying reverse Adding fc.raw.file column ... done Starting to work on MS^2*Scans: TopN over RT ... Memory [MB] prior|after|max(diff) : 153.6 | 153.9 | 173.7 (20) Duration: 0 s ... MS^2*Scans: TopN over RT done Starting to work on MS^2*Scans: Ion Inj Time ... Memory [MB] prior|after|max(diff) : 153.7 | 154.2 | 164.8 (11) Duration: 0 s ... MS^2*Scans: Ion Inj Time done Starting to work on MS^2*Scans: Intensity ... Memory [MB] prior|after|max(diff) : 154 | 156 | 177.8 (24) Duration: 0 s ... MS^2*Scans: Intensity done Starting to work on MS^2*Scans: TopN high ... Memory [MB] prior|after|max(diff) : 155.8 | 156 | 167.4 (12) Duration: 0 s ... MS^2*Scans: TopN high done Starting to work on MS^2*Scans: TopN ID over N ... Memory [MB] prior|after|max(diff) : 156 | 156 | 170.8 (15) Duration: 0 s ... MS^2*Scans: TopN ID over N done [1] "#Metrics: " [1] 37 Starting to work on Average Overall Quality ... Memory [MB] prior|after|max(diff) : 157.2 | 157.2 | 157.8 (1) Duration: 0 s ... Average Overall Quality done Creating Report file ...HTML TEMPLATE: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/PTXQC/./reportTemplate/PTXQC_report_template.Rmd Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type 'character' YAML: PTXQC$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$qcMetric_AverageQualOverall def: 9999 The following labels will be shortened to ease plotting: jurkat_06_100731121305 Starting to work on MS/MS Peak shape ... Memory [MB] prior|after|max(diff) : 141.8 | 141.4 | 144.3 (2) Duration: 0 s ... MS/MS Peak shape done [ FAIL 1 | WARN 24 | SKIP 0 | PASS 131 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_computeQC.R:51:3'): createReport ─────────────────────────────── Error in `file(con, "w")`: cannot open the connection Backtrace: ▆ 1. ├─PTXQC::createReport(txt_folder, NULL, yaml_obj) at test_computeQC.R:51:3 2. │ ├─rmarkdown::render(html_template, output_file = rprt_fns$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 Flavor: r-release-linux-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running 'testthat.R' [73s] 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 Tue Feb 27 07:34:58 2024: Starting QC computation on report 'D:\temp\RtmpSKHj0j/txt/report_v1.1.0_RtmpSKHj0j' 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 ' D:\temp\RtmpSKHj0j/txt/report_v1.1.0_RtmpSKHj0j_filename_sort.txt ' not possible!Reading file D:\temp\RtmpSKHj0j/txt/parameters.txt ... Read 61 entries from D:\temp\RtmpSKHj0j/txt/parameters.txt. Updating colnames Simplifying contaminants Simplifying reverse Starting to work on PAR: MQ Parameters ... Memory [MB] prior|after|max(diff) : 92.3 | 94.9 | 175.3 (83) Duration: 1 s ... PAR: MQ Parameters done Reading file D:\temp\RtmpSKHj0j/txt/summary.txt ... Read 5 entries from D:\temp\RtmpSKHj0j/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) : 95.5 | 104.3 | 137.7 (42) Duration: 0 s ... SM: MS^2 ID rate (">%1.0f") done Reading file D:\temp\RtmpSKHj0j/txt/proteinGroups.txt ... Read 1128 entries from D:\temp\RtmpSKHj0j/txt/proteinGroups.txt. Updating colnames Simplifying contaminants Simplifying reverse Starting to work on PG: Contaminants ... Memory [MB] prior|after|max(diff) : 106.1 | 106.8 | 115.7 (10) Duration: 0 s ... PG: Contaminants done Starting to work on PG: Raw intensity ... Memory [MB] prior|after|max(diff) : 106.8 | 108.7 | 126.1 (19) Duration: 0 s ... PG: Raw intensity done Starting to work on PG: LFQ intensity ... Memory [MB] prior|after|max(diff) : 108.7 | 109.2 | 124.9 (16) Duration: 0 s ... PG: LFQ intensity done Starting to work on PG: Principal Component ... Memory [MB] prior|after|max(diff) : 109.4 | 110.6 | 134.6 (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) : 110.6 | 113.8 | 146.9 (36) Duration: 1 s ... PG: Ratio done Reading file D:\temp\RtmpSKHj0j/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 D:\temp\RtmpSKHj0j/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) : 121.5 | 121.5 | 121.6 (0) Duration: 0 s Starting to work on EVD: Peptide Intensity (">%1.1f") ... Memory [MB] prior|after|max(diff) : 121.5 | 123.4 | 143 (22) Duration: 0 s ... EVD: Peptide Intensity (">%1.1f") done Starting to work on EVD: Reporter intensity ... Memory [MB] prior|after|max(diff) : 123.4 | 123.4 | 123.4 (0) Duration: 0 s Starting to work on EVD: Peptide VarMod ... Memory [MB] prior|after|max(diff) : 123.4 | 126.2 | 145.1 (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' downloaded 8388 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) : 126 | 134.5 | 211.8 (86) Duration: 5 s ... EVD: Protein Count (">%1.0f") done Starting to work on EVD: Peptide Count (">%1.0f") ... Memory [MB] prior|after|max(diff) : 134.5 | 134.8 | 146.8 (12) Duration: 0 s ... EVD: Peptide Count (">%1.0f") done Starting to work on EVD: RT Peak Width ... Memory [MB] prior|after|max(diff) : 134.8 | 135.2 | 160.4 (26) Duration: 0 s ... EVD: RT Peak Width done Starting to work on EVD: MBR Align ... Memory [MB] prior|after|max(diff) : 135.2 | 136.1 | 197.1 (62) Duration: 2 s ... EVD: MBR Align done Starting to work on EVD: MBR ID-Transfer ... Memory [MB] prior|after|max(diff) : 136.1 | 137.5 | 277.1 (141) Duration: 11 s ... EVD: MBR ID-Transfer done Starting to work on EVD: MBR auxilliary ... Memory [MB] prior|after|max(diff) : 137.5 | 139.3 | 205 (68) Duration: 1 s ... EVD: MBR auxilliary done Starting to work on EVD: Charge ... Memory [MB] prior|after|max(diff) : 139.3 | 139.4 | 149 (10) Duration: 0 s ... EVD: Charge done Starting to work on EVD: ID rate over RT ... Memory [MB] prior|after|max(diff) : 139.4 | 139.6 | 154.2 (15) Duration: 0 s ... EVD: ID rate over RT done Starting to work on EVD: UpSet ... Memory [MB] prior|after|max(diff) : 139.6 | 144.8 | 253.1 (114) Duration: 3 s ... EVD: UpSet done Starting to work on EVD: MS Cal-Pre (%1.1f) ... Memory [MB] prior|after|max(diff) : 144.8 | 145.6 | 165.1 (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) : 145.6 | 146.4 | 165.1 (20) Duration: 0 s ... EVD: MS Cal-Post done Starting to work on EVD: Contaminants ... Memory [MB] prior|after|max(diff) : 146.4 | 147.1 | 167.9 (22) Duration: 0 s ... EVD: Contaminants done Starting to work on EVD: MS^2 Oversampling ... Memory [MB] prior|after|max(diff) : 147.1 | 147.2 | 164.2 (17) Duration: 0 s ... EVD: MS^2 Oversampling done Starting to work on EVD: Pep Missing Values ... Memory [MB] prior|after|max(diff) : 147.2 | 148.8 | 217.3 (70) Duration: 1 s ... EVD: Pep Missing Values done Reading file D:\temp\RtmpSKHj0j/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 D:\temp\RtmpSKHj0j/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) : 149.8 | 151.2 | 178.7 (29) Duration: 0 s ... MSMS: MS^2 Cal (%s) done Starting to work on MSMS: Missed Cleavages%s ... Memory [MB] prior|after|max(diff) : 151.2 | 151.4 | 157.8 (7) Duration: 0 s ... MSMS: Missed Cleavages%s done Starting to work on MSMS: Missed Cleavages%s ... Memory [MB] prior|after|max(diff) : 151.4 | 151.4 | 165.3 (14) Duration: 0 s ... MSMS: Missed Cleavages%s done Reading file D:\temp\RtmpSKHj0j/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$' using case-INsensitive matching. Keeping 5 of 41 columns! Read 35113 entries from D:\temp\RtmpSKHj0j/txt/msmsScans.txt. Updating colnames Simplifying contaminants Simplifying reverse Adding fc.raw.file column ... done Starting to work on MS^2*Scans: TopN over RT ... Memory [MB] prior|after|max(diff) : 153.2 | 153.4 | 173.2 (20) Duration: 0 s ... MS^2*Scans: TopN over RT done Starting to work on MS^2*Scans: Ion Inj Time ... Memory [MB] prior|after|max(diff) : 153.3 | 153.8 | 164.4 (11) Duration: 0 s ... MS^2*Scans: Ion Inj Time done Starting to work on MS^2*Scans: Intensity ... Memory [MB] prior|after|max(diff) : 153.6 | 155.6 | 177.4 (24) Duration: 0 s ... MS^2*Scans: Intensity done Starting to work on MS^2*Scans: TopN high ... Memory [MB] prior|after|max(diff) : 155.4 | 155.6 | 167 (12) Duration: 0 s ... MS^2*Scans: TopN high done Starting to work on MS^2*Scans: TopN ID over N ... Memory [MB] prior|after|max(diff) : 155.5 | 155.6 | 170.4 (15) Duration: 0 s ... MS^2*Scans: TopN ID over N done [1] "#Metrics: " [1] 37 Starting to work on Average Overall Quality ... Memory [MB] prior|after|max(diff) : 156.7 | 156.7 | 157.4 (1) Duration: 0 s ... Average Overall Quality done Creating Report file ...HTML TEMPLATE: D:/RCompile/CRANpkg/lib/4.3/PTXQC/./reportTemplate/PTXQC_report_template.Rmd Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type 'character' YAML: PTXQC$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$qcMetric_AverageQualOverall def: 9999 The following labels will be shortened to ease plotting: jurkat_06_100731121305 Starting to work on MS/MS Peak shape ... Memory [MB] prior|after|max(diff) : 141.3 | 140.8 | 143.8 (2) Duration: 0 s ... MS/MS Peak shape done [ FAIL 1 | WARN 21 | SKIP 0 | PASS 131 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_computeQC.R:51:3'): createReport ─────────────────────────────── Error in `as.vector(x, "character")`: cannot coerce type 'environment' to vector of type 'character' Backtrace: ▆ 1. └─PTXQC::createReport(txt_folder, NULL, yaml_obj) at test_computeQC.R:51:3 2. ├─rmarkdown::render(html_template, output_file = rprt_fns$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) [ FAIL 1 | WARN 21 | SKIP 0 | PASS 131 ] Error: Test failures Execution halted Flavor: r-release-windows-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running 'testthat.R' [68s] 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 Mon Feb 26 14:42:30 2024: Starting QC computation on report 'D:\temp\Rtmp65r4oZ/txt/report_v1.1.0_Rtmp65r4oZ' 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 ' D:\temp\Rtmp65r4oZ/txt/report_v1.1.0_Rtmp65r4oZ_filename_sort.txt ' not possible!Reading file D:\temp\Rtmp65r4oZ/txt/parameters.txt ... Read 61 entries from D:\temp\Rtmp65r4oZ/txt/parameters.txt. Updating colnames Simplifying contaminants Simplifying reverse Starting to work on PAR: MQ Parameters ... Memory [MB] prior|after|max(diff) : 87.6 | 90.2 | 170.6 (83) Duration: 1 s ... PAR: MQ Parameters done Reading file D:\temp\Rtmp65r4oZ/txt/summary.txt ... Read 5 entries from D:\temp\Rtmp65r4oZ/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) : 90.8 | 99.7 | 133 (42) Duration: 0 s ... SM: MS^2 ID rate (">%1.0f") done Reading file D:\temp\Rtmp65r4oZ/txt/proteinGroups.txt ... Read 1128 entries from D:\temp\Rtmp65r4oZ/txt/proteinGroups.txt. Updating colnames Simplifying contaminants Simplifying reverse Starting to work on PG: Contaminants ... Memory [MB] prior|after|max(diff) : 101.4 | 102 | 111 (10) Duration: 0 s ... PG: Contaminants done Starting to work on PG: Raw intensity ... Memory [MB] prior|after|max(diff) : 102 | 104.1 | 121.4 (19) Duration: 0 s ... PG: Raw intensity done Starting to work on PG: LFQ intensity ... Memory [MB] prior|after|max(diff) : 104.1 | 104.6 | 120.2 (16) Duration: 0 s ... PG: LFQ intensity done Starting to work on PG: Principal Component ... Memory [MB] prior|after|max(diff) : 104.7 | 105.9 | 130 (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) : 105.9 | 109 | 142.3 (36) Duration: 0 s ... PG: Ratio done Reading file D:\temp\Rtmp65r4oZ/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 D:\temp\Rtmp65r4oZ/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) : 116.8 | 116.8 | 116.8 (0) Duration: 0 s Starting to work on EVD: Peptide Intensity (">%1.1f") ... Memory [MB] prior|after|max(diff) : 116.8 | 118.6 | 138.3 (22) Duration: 0 s ... EVD: Peptide Intensity (">%1.1f") done Starting to work on EVD: Reporter intensity ... Memory [MB] prior|after|max(diff) : 118.6 | 118.6 | 118.6 (0) Duration: 0 s Starting to work on EVD: Peptide VarMod ... Memory [MB] prior|after|max(diff) : 118.6 | 121.5 | 140.3 (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 8388 bytes ================================================== downloaded 8388 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) : 121.3 | 129.8 | 209.3 (88) Duration: 8 s ... EVD: Protein Count (">%1.0f") done Starting to work on EVD: Peptide Count (">%1.0f") ... Memory [MB] prior|after|max(diff) : 129.8 | 130.1 | 142 (12) Duration: 0 s ... EVD: Peptide Count (">%1.0f") done Starting to work on EVD: RT Peak Width ... Memory [MB] prior|after|max(diff) : 130.1 | 130.5 | 155.5 (25) Duration: 0 s ... EVD: RT Peak Width done Starting to work on EVD: MBR Align ... Memory [MB] prior|after|max(diff) : 130.5 | 131.4 | 192.6 (62) Duration: 2 s ... EVD: MBR Align done Starting to work on EVD: MBR ID-Transfer ... Memory [MB] prior|after|max(diff) : 131.4 | 132.8 | 271.1 (140) Duration: 11 s ... EVD: MBR ID-Transfer done Starting to work on EVD: MBR auxilliary ... Memory [MB] prior|after|max(diff) : 132.8 | 134.6 | 200.4 (68) Duration: 1 s ... EVD: MBR auxilliary done Starting to work on EVD: Charge ... Memory [MB] prior|after|max(diff) : 134.6 | 134.7 | 144.4 (10) Duration: 0 s ... EVD: Charge done Starting to work on EVD: ID rate over RT ... Memory [MB] prior|after|max(diff) : 134.7 | 135 | 149.5 (15) Duration: 0 s ... EVD: ID rate over RT done Starting to work on EVD: UpSet ... Memory [MB] prior|after|max(diff) : 135 | 140.1 | 245 (110) Duration: 3 s ... EVD: UpSet done Starting to work on EVD: MS Cal-Pre (%1.1f) ... Memory [MB] prior|after|max(diff) : 140.1 | 141 | 160.4 (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) : 141 | 141.6 | 160.4 (19) Duration: 0 s ... EVD: MS Cal-Post done Starting to work on EVD: Contaminants ... Memory [MB] prior|after|max(diff) : 141.6 | 142.5 | 163.1 (22) Duration: 0 s ... EVD: Contaminants done Starting to work on EVD: MS^2 Oversampling ... Memory [MB] prior|after|max(diff) : 142.5 | 142.6 | 159.6 (17) Duration: 0 s ... EVD: MS^2 Oversampling done Starting to work on EVD: Pep Missing Values ... Memory [MB] prior|after|max(diff) : 142.6 | 144.1 | 212.6 (70) Duration: 0 s ... EVD: Pep Missing Values done Reading file D:\temp\Rtmp65r4oZ/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 D:\temp\Rtmp65r4oZ/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) : 145.1 | 146.5 | 174 (29) Duration: 0 s ... MSMS: MS^2 Cal (%s) done Starting to work on MSMS: Missed Cleavages%s ... Memory [MB] prior|after|max(diff) : 146.5 | 146.6 | 153.1 (7) Duration: 0 s ... MSMS: Missed Cleavages%s done Starting to work on MSMS: Missed Cleavages%s ... Memory [MB] prior|after|max(diff) : 146.6 | 146.7 | 160.6 (14) Duration: 0 s ... MSMS: Missed Cleavages%s done Reading file D:\temp\Rtmp65r4oZ/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$' using case-INsensitive matching. Keeping 5 of 41 columns! Read 35113 entries from D:\temp\Rtmp65r4oZ/txt/msmsScans.txt. Updating colnames Simplifying contaminants Simplifying reverse Adding fc.raw.file column ... done Starting to work on MS^2*Scans: TopN over RT ... Memory [MB] prior|after|max(diff) : 148.5 | 148.8 | 168.6 (20) Duration: 0 s ... MS^2*Scans: TopN over RT done Starting to work on MS^2*Scans: Ion Inj Time ... Memory [MB] prior|after|max(diff) : 148.7 | 149.1 | 159.7 (11) Duration: 0 s ... MS^2*Scans: Ion Inj Time done Starting to work on MS^2*Scans: Intensity ... Memory [MB] prior|after|max(diff) : 148.8 | 151 | 172.7 (24) Duration: 0 s ... MS^2*Scans: Intensity done Starting to work on MS^2*Scans: TopN high ... Memory [MB] prior|after|max(diff) : 150.8 | 150.8 | 162.4 (12) Duration: 0 s ... MS^2*Scans: TopN high done Starting to work on MS^2*Scans: TopN ID over N ... Memory [MB] prior|after|max(diff) : 150.8 | 150.9 | 165.5 (15) Duration: 0 s ... MS^2*Scans: TopN ID over N done [1] "#Metrics: " [1] 37 Starting to work on Average Overall Quality ... Memory [MB] prior|after|max(diff) : 152 | 152 | 152.6 (1) Duration: 0 s ... Average Overall Quality done Creating Report file ...HTML TEMPLATE: D:/RCompile/CRANpkg/lib/4.2/PTXQC/./reportTemplate/PTXQC_report_template.Rmd Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type 'character' YAML: PTXQC$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$qcMetric_AverageQualOverall def: 9999 The following labels will be shortened to ease plotting: jurkat_06_100731121305 Starting to work on MS/MS Peak shape ... Memory [MB] prior|after|max(diff) : 136.6 | 136.1 | 139 (2) Duration: 0 s ... MS/MS Peak shape done [ FAIL 1 | WARN 21 | SKIP 0 | PASS 131 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_computeQC.R:51:3'): createReport ─────────────────────────────── Error in `as.vector(x, "character")`: cannot coerce type 'environment' to vector of type 'character' Backtrace: ▆ 1. └─PTXQC::createReport(txt_folder, NULL, yaml_obj) at test_computeQC.R:51:3 2. ├─rmarkdown::render(html_template, output_file = rprt_fns$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) [ FAIL 1 | WARN 21 | SKIP 0 | PASS 131 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64