Running ‘testthat.R’ [5s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PTXQC)
  Loading package PTXQC (version 1.0.2)
  > 
  > ##
  > ## calls all code in PTXQC/tests/testthat/test*.R
  > ##
  > test_check("PTXQC")
  YAML: PTXQC$ReportFilename$extended def: TRUE
  YAML: PTXQC$UseLocalMQPar def: TRUE
  YAML: PTXQC$NameLengthMax_num def: 10
  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_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_EVD_UpSet def: 500
  YAML: order$qcMetric_AverageQualOverall def: 9999
  Reading file /home/hornik/tmp/scratch/RtmpPr5lby/txt/parameters.txt ...
  Read 61 entries from /home/hornik/tmp/scratch/RtmpPr5lby/txt/parameters.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Starting to work on PAR: MQ Parameters ...
  
  Memory [MB] prior|after|max(diff) : 74.2 | 76 | 95 (21)
  
  Duration: 0 s
  
  ... PAR: MQ Parameters  done
  Reading file /home/hornik/tmp/scratch/RtmpPr5lby/txt/summary.txt ...
  Read 5 entries from /home/hornik/tmp/scratch/RtmpPr5lby/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) : 76.4 | 79 | 84.8 (8)
  
  Duration: 0 s
  
  ... SM: MS^2 ID rate (">%1.0f")  done
  Reading file /home/hornik/tmp/scratch/RtmpPr5lby/txt/proteinGroups.txt ...
  Read 1128 entries from /home/hornik/tmp/scratch/RtmpPr5lby/txt/proteinGroups.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Starting to work on PG: Contaminants ...
  
  Memory [MB] prior|after|max(diff) : 80.8 | 81.4 | 85.5 (5)
  
  Duration: 0 s
  
  ... PG: Contaminants  done
  Starting to work on PG: Raw intensity ...
  ── 1. Error: createReport (@test_computeQC.R#41)  ──────────────────────────────
  class(data$group2) == "factor" is not TRUE
  Backtrace:
   1. PTXQC::createReport(txt_folder, NULL, yaml_obj)
   2. lst_qcMetrics[["qcMetric_PG_RawInt"]]$setData(...)
   3. PTXQC:::workerFcn(.self, df, ...)
   4. PTXQC::boxplotCompare(...)
   5. base::stopifnot(class(data$group2) == "factor")
  
  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) : 81.6 | 81.6 | 83.3 (2)
  
  Duration: 0 s
  
  ... MS/MS Peak shape  done
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 111 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: createReport (@test_computeQC.R#41) 
  
  Error: testthat unit tests failed
  Execution halted