Running ‘testthat.R’ [31s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PTXQC)
  Loading package PTXQC (version 0.92.3)
  > 
  > ##
  > ## calls all code in PTXQC/tests/testthat/test*.R
  > ##
  > test_check("PTXQC")
  trying URL 'https://raw.githubusercontent.com/cbielow/PTXQC_data/master/txt_Ecoli.zip'
  Content type 'application/zip' length 4975702 bytes (4.7 MB)
  ==================================================
  downloaded 4.7 MB
  
  YAML: PTXQC$ReportFilename$extended def: TRUE
  YAML: PTXQC$UseLocalMQPar def: TRUE
  YAML: File$Parameters$enabled def: TRUE
  YAML: PTXQC$NameLengthMax_num def: 10
  YAML: File$Summary$enabled def: TRUE
  YAML: File$Summary$IDRate$Thresh_bad_num def: 20
  YAML: File$Summary$IDRate$Thresh_great_num def: 35
  YAML: File$ProteinGroups$enabled def: TRUE
  YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4
  YAML: File$ProteinGroups$IntensityThreshLog2_num def: 25
  YAML: File$Evidence$enabled def: TRUE
  YAML: File$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$MQpar_mainSearchTol_num def: NA
  YAML: File$MsMs$enabled def: TRUE
  YAML: File$MsMsScans$enabled def: TRUE
  YAML: File$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_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$qcMetric_PG_Cont def: 110
  YAML: order$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_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_AverageQualOverall def: 9999
  Reading file /tmp/RtmpwtHaOD/txt/parameters.txt ...
  Read 61 entries from /tmp/RtmpwtHaOD/txt/parameters.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Starting to work on PAR: MQ Parameters ...
  
  Memory [MB] prior|after|max(diff) : 65.3 | 67.3 | 123.6 (58)
  
  Duration: 1 s
  
  ... PAR: MQ Parameters  done
  Reading file /tmp/RtmpwtHaOD/txt/summary.txt ...
  Read 5 entries from /tmp/RtmpwtHaOD/txt/summary.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Adding fc.raw.file column ... done
  Starting to work on SM: MS^2 ID rate (">%1.0f") ...
  
  Memory [MB] prior|after|max(diff) : 67.4 | 69.5 | 74.9 (8)
  
  Duration: 0 s
  
  ... SM: MS^2 ID rate (">%1.0f")  done
  Reading file /tmp/RtmpwtHaOD/txt/proteinGroups.txt ...
  Read 1128 entries from /tmp/RtmpwtHaOD/txt/proteinGroups.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Starting to work on PG: Contaminants ...
  
  Memory [MB] prior|after|max(diff) : 71.2 | 71.8 | 76.5 (5)
  
  Duration: 0 s
  
  ... PG: Contaminants  done
  Starting to work on PG: raw intensity ...
  
  Memory [MB] prior|after|max(diff) : 71.8 | 73.4 | 85.2 (13)
  
  Duration: 0 s
  
  ... PG: raw intensity  done
  Starting to work on PG: LFQ intensity ...
  
  Memory [MB] prior|after|max(diff) : 73.4 | 73.8 | 84.5 (11)
  
  Duration: 0 s
  
  ... PG: LFQ intensity  done
  Starting to work on PG: Principal Component ...
  
  Memory [MB] prior|after|max(diff) : 73.8 | 74.6 | 91.6 (18)
  
  Duration: 0 s
  
  ... PG: Principal Component  done
  Starting to work on PG: Ratio ...
  Maximum ratio (log2) was 0.695274100751481, NOT reaching the threshold of 2 for label-incorporation computation.
  Skipping ratios ...
  
  Memory [MB] prior|after|max(diff) : 74.6 | 76.3 | 91.5 (17)
  
  Duration: 0 s
  
  ... PG: Ratio  done
  Reading file /tmp/RtmpwtHaOD/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$' using case-INsensitive matching.
  Requiring column(s) 'k.count', 'r.count' to be of type 'numeric'!
  Requiring column(s) 'charge' to be of type 'numeric'!
  Requiring column(s) 'mass' to be of type 'numeric'!
  WARNING: Could not find column regex '^protein.names$' 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.
  Keeping 19 of 69 columns!
  Read 15505 entries from /tmp/RtmpwtHaOD/txt/evidence.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Adding fc.raw.file column ... done
  Starting to work on EVD:Contaminant (%s) ...
  
  Memory [MB] prior|after|max(diff) : 80 | 80 | 82.8 (3)
  
  Duration: 0 s
  
  ... EVD:Contaminant (%s)  done
  Starting to work on EVD: Pep Intensity (">%1.1f") ...
  
  Memory [MB] prior|after|max(diff) : 80 | 81.8 | 97.6 (18)
  
  Duration: 0 s
  
  ... EVD: Pep Intensity (">%1.1f")  done
  Starting to work on EVD: Prot Count (">%1.0f") ...
  
  Memory [MB] prior|after|max(diff) : 81.8 | 81.9 | 94.6 (13)
  
  Duration: 0 s
  
  ... EVD: Prot Count (">%1.0f")  done
  Starting to work on EVD: Pep Count (">%1.0f") ...
  
  Memory [MB] prior|after|max(diff) : 81.9 | 82.1 | 89.5 (8)
  
  Duration: 0 s
  
  ... EVD: Pep Count (">%1.0f")  done
  Starting to work on EVD: RT Peak Width ...
  
  Memory [MB] prior|after|max(diff) : 82.1 | 82.3 | 108.9 (27)
  
  Duration: 0 s
  
  ... EVD: RT Peak Width  done
  Starting to work on EVD: MBR Align ...
  
  Memory [MB] prior|after|max(diff) : 82.3 | 83.1 | 140 (58)
  
  Duration: 4 s
  
  ... EVD: MBR Align  done
  Starting to work on EVD: MBR ID-Transfer ...
  
  Memory [MB] prior|after|max(diff) : 83.1 | 83.6 | 144.2 (61)
  
  Duration: 14 s
  
  ... EVD: MBR ID-Transfer  done
  Starting to work on EVD: MBR auxilliary ...
  
  Memory [MB] prior|after|max(diff) : 83.6 | 85 | 136.6 (53)
  
  Duration: 1 s
  
  ... EVD: MBR auxilliary  done
  Starting to work on EVD: Charge ...
  
  Memory [MB] prior|after|max(diff) : 85 | 85.1 | 93.3 (8)
  
  Duration: 0 s
  
  ... EVD: Charge  done
  Starting to work on EVD: ID rate over RT ...
  
  Memory [MB] prior|after|max(diff) : 85.1 | 85.4 | 97.6 (12)
  
  Duration: 0 s
  
  ... EVD: ID rate over RT  done
  Starting to work on EVD: MS Cal-Pre (%1.1f) ...
  
  Memory [MB] prior|after|max(diff) : 85.4 | 86.1 | 103.7 (18)
  
  Duration: 0 s
  
  ... EVD: MS Cal-Pre (%1.1f)  done
  Starting to work on EVD: MS Cal-Post ...
  
  Memory [MB] prior|after|max(diff) : 86.1 | 86.8 | 103.9 (18)
  
  Duration: 0 s
  
  ... EVD: MS Cal-Post  done
  Starting to work on EVD: Contaminants ...
  
  Memory [MB] prior|after|max(diff) : 86.8 | 87.6 | 104.1 (17)
  
  Duration: 0 s
  
  ... EVD: Contaminants  done
  Starting to work on EVD: MS^2 Oversampling ...
  
  Memory [MB] prior|after|max(diff) : 87.6 | 87.7 | 103.1 (15)
  
  Duration: 0 s
  
  ... EVD: MS^2 Oversampling  done
  Starting to work on EVD: Pep Missing Values ...
  
  Memory [MB] prior|after|max(diff) : 87.7 | 89.3 | 148.8 (61)
  
  Duration: 0 s
  
  ... EVD: Pep Missing Values  done
  Reading file /tmp/RtmpwtHaOD/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/RtmpwtHaOD/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) : 90.2 | 91 | 114.5 (24)
  
  Duration: 0 s
  
  ... MSMS: MS^2 Cal (%s)  done
  Starting to work on MSMS: %s ...
  
  Memory [MB] prior|after|max(diff) : 91 | 91.1 | 95.4 (4)
  
  Duration: 0 s
  
  ... MSMS: %s  done
  Reading file /tmp/RtmpwtHaOD/txt/msmsScans.txt ...
  Requiring column(s) 'ion.injection.time' to be of type 'numeric'!
  Requiring column(s) 'retention.time' 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 2 of 41 columns!
  Read 35113 entries from /tmp/RtmpwtHaOD/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 ...
  ── 1. Error: createReport (@test_computeQC.R#34)  ──────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: createReport(txt_folder, yaml_obj) at testthat/test_computeQC.R:34
  2: lst_qcMetrics[["qcMetric_MSMSScans_TopNoverRT"]]$setData(df_msmsScan)
  3: workerFcn(.self, ...)
  4: dd[, {
         idx = which(getMaxima(scan.event.number, thresh_rel = 0))
         maxSE = scan.event.number[idx]
         RTbin = rRT[idx]
         list(maxSE = maxSE, rRT = RTbin)
     }, by = "fc.raw.file"]
  5: `[.data.table`(dd, , {
         idx = which(getMaxima(scan.event.number, thresh_rel = 0))
         maxSE = scan.event.number[idx]
         RTbin = rRT[idx]
         list(maxSE = maxSE, rRT = RTbin)
     }, by = "fc.raw.file")
  
  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) : 77.5 | 77.4 | 79 (2)
  
  Duration: 0 s
  
  ... MS/MS Peak shape  done
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 121 SKIPPED: 0 FAILED: 1
  1. Error: createReport (@test_computeQC.R#34) 
  
  Error: testthat unit tests failed
  Execution halted