Running ‘testthat.R’ [74s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PTXQC)
  Loading package PTXQC (version 0.92.0)
  > 
  > ##
  > ## 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
  
  getYAML with: PTXQC$ReportFilename$extended  default: TRUE 
   .. return default: TRUE 
  getYAML with: PTXQC$UseLocalMQPar  default: TRUE 
   .. return default: TRUE 
  getYAML with: File$Parameters$enabled  default: TRUE 
   .. return default: TRUE 
  getYAML with: PTXQC$NameLengthMax_num  default: 10 
   .. return default: 10 
  getYAML with: File$Summary$enabled  default: TRUE 
   .. return default: TRUE 
  getYAML with: File$Summary$IDRate$Thresh_bad_num  default: 20 
   .. return default: 20 
  getYAML with: File$Summary$IDRate$Thresh_great_num  default: 35 
   .. return default: 35 
  getYAML with: File$ProteinGroups$enabled  default: TRUE 
   .. return default: TRUE 
  getYAML with: File$ProteinGroups$RatioPlot$LabelIncThresh_num  default: 4 
   .. return default: 4 
  getYAML with: File$ProteinGroups$IntensityThreshLog2_num  default: 25 
   .. return default: 25 
  getYAML with: File$Evidence$enabled  default: TRUE 
   .. return default: TRUE 
  getYAML with: File$Evidence$ProteinCountThresh_num  default: 3500 
   .. return default: 3500 
  getYAML with: File$Evidence$IntensityThreshLog2_num  default: 23 
   .. return default: 23 
  getYAML with: File$Evidence$PeptideCountThresh_num  default: 15000 
   .. return default: 15000 
  getYAML with: File$Evidence$SpecialContaminants  default: c("MYCOPLASMA", "1") 
   .. return default: c("MYCOPLASMA", "1") 
  getYAML with: File$Evidence$MQpar_MatchingTimeWindow_num  default: 1 
   .. return default: 1 
  getYAML with: File$Evidence$MatchBetweenRuns_wA  default: auto 
   .. return default: auto 
  getYAML with: File$Evidence$MQpar_firstSearchTol_num  default: 20 
   .. return default: 20 
  getYAML with: File$Evidence$firstSearch_outOfCalWarnSD_num  default: 2 
   .. return default: 2 
  getYAML with: File$Evidence$MQpar_mainSearchTol_num  default: NA 
   .. return default: NA 
  getYAML with: File$MsMs$enabled  default: TRUE 
   .. return default: TRUE 
  getYAML with: File$MsMsScans$enabled  default: TRUE 
   .. return default: TRUE 
  getYAML with: File$MsMsScans$IonInjectionThresh_num  default: 10 
   .. return default: 10 
  getYAML with: PTXQC$OutputFormats  default: html 
   getYAML with: PTXQC$OutputFormats  default: plainPDF 
   .. return default: html 
    .. return default: plainPDF 
  getYAML with: PTXQC$PlainPDF$AddPageNumbers  default: on 
   .. return default: on 
  meta id:  qcMetric_PAR 
  getYAML with: order$qcMetric_PAR  default: 1 
   .. return default: 1 
  meta id:  qcMetric_PG_PCA 
  getYAML with: order$qcMetric_PG_PCA  default: 3 
   .. return default: 3 
  meta id:  qcMetric_EVD_Top5Cont 
  getYAML with: order$qcMetric_EVD_Top5Cont  default: 10 
   .. return default: 10 
  meta id:  qcMetric_PG_Ratio 
  getYAML with: order$qcMetric_PG_Ratio  default: 19 
   .. return default: 19 
  meta id:  qcMetric_EVD_UserContaminant 
  getYAML with: order$qcMetric_EVD_UserContaminant  default: 20 
   .. return default: 20 
  meta id:  qcMetric_EVD_PeptideInt 
  getYAML with: order$qcMetric_EVD_PeptideInt  default: 30 
   .. return default: 30 
  meta id:  qcMetric_PG_RawInt 
  getYAML with: order$qcMetric_PG_RawInt  default: 32 
   .. return default: 32 
  meta id:  qcMetric_PG_LFQInt 
  getYAML with: order$qcMetric_PG_LFQInt  default: 33 
   .. return default: 33 
  meta id:  qcMetric_PG_ITRAQInt 
  getYAML with: order$qcMetric_PG_ITRAQInt  default: 34 
   .. return default: 34 
  meta id:  qcMetric_MSMS_MissedCleavages 
  getYAML with: order$qcMetric_MSMS_MissedCleavages  default: 40 
   .. return default: 40 
  meta id:  qcMetric_EVD_Charge 
  getYAML with: order$qcMetric_EVD_Charge  default: 100 
   .. return default: 100 
  meta id:  qcMetric_PG_Cont 
  getYAML with: order$qcMetric_PG_Cont  default: 110 
   .. return default: 110 
  meta id:  qcMetric_MSMSScans_TopNoverRT 
  getYAML with: order$qcMetric_MSMSScans_TopNoverRT  default: 120 
   .. return default: 120 
  meta id:  qcMetric_EVD_IDoverRT 
  getYAML with: order$qcMetric_EVD_IDoverRT  default: 150 
   .. return default: 150 
  meta id:  qcMetric_EVD_RTPeakWidth 
  getYAML with: order$qcMetric_EVD_RTPeakWidth  default: 170 
   .. return default: 170 
  meta id:  qcMetric_EVD_MBRAlign 
  getYAML with: order$qcMetric_EVD_MBRAlign  default: 210 
   .. return default: 210 
  meta id:  qcMetric_EVD_MBRIdTransfer 
  getYAML with: order$qcMetric_EVD_MBRIdTransfer  default: 220 
   .. return default: 220 
  meta id:  qcMetric_EVD_MBRaux 
  getYAML with: order$qcMetric_EVD_MBRaux  default: 221 
   .. return default: 221 
  meta id:  qcMetric_MSMSScans_IonInjTime 
  getYAML with: order$qcMetric_MSMSScans_IonInjTime  default: 240 
   .. return default: 240 
  meta id:  qcMetric_MSMSScans_MSMSIntensity 
  getYAML with: order$qcMetric_MSMSScans_MSMSIntensity  default: 245 
   .. return default: 245 
  meta id:  qcMetric_EVD_MS2OverSampling 
  getYAML with: order$qcMetric_EVD_MS2OverSampling  default: 250 
   .. return default: 250 
  meta id:  qcMetric_EVD_PreCal 
  getYAML with: order$qcMetric_EVD_PreCal  default: 260 
   .. return default: 260 
  meta id:  qcMetric_EVD_PostCal 
  getYAML with: order$qcMetric_EVD_PostCal  default: 270 
   .. return default: 270 
  meta id:  qcMetric_MSMS_MSMSDecal 
  getYAML with: order$qcMetric_MSMS_MSMSDecal  default: 280 
   .. return default: 280 
  meta id:  qcMetric_SM_MSMSIdRate 
  getYAML with: order$qcMetric_SM_MSMSIdRate  default: 300 
   .. return default: 300 
  meta id:  qcMetric_MSMSScans_TopN 
  getYAML with: order$qcMetric_MSMSScans_TopN  default: 350 
   .. return val: 120 
  meta id:  qcMetric_MSMSScans_TopNID 
  getYAML with: order$qcMetric_MSMSScans_TopNID  default: 380 
   .. return default: 380 
  meta id:  qcMetric_MSMSScans_DepPep 
  getYAML with: order$qcMetric_MSMSScans_DepPep  default: 383 
   .. return default: 383 
  meta id:  qcMetric_EVD_MissingValues 
  getYAML with: order$qcMetric_EVD_MissingValues  default: 390 
   .. return default: 390 
  meta id:  qcMetric_EVD_PeptideCount 
  getYAML with: order$qcMetric_EVD_PeptideCount  default: 400 
   .. return default: 400 
  meta id:  qcMetric_EVD_ProteinCount 
  getYAML with: order$qcMetric_EVD_ProteinCount  default: 450 
   .. return default: 450 
  meta id:  qcMetric_AverageQualOverall 
  getYAML with: order$qcMetric_AverageQualOverall  default: 9999 
   .. return default: 9999 
  Reading file /tmp/RtmpUikp3K/txt/parameters.txt ...
  Read 61 entries from /tmp/RtmpUikp3K/txt/parameters.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Starting to work on PAR: MQ Parameters ...
  
  Memory [MB] prior|after|max(diff) : 52.5 | 54.1 | 100.5 (48)
  
  Duration: 1 s
  
  ... PAR: MQ Parameters  done
  Reading file /tmp/RtmpUikp3K/txt/summary.txt ...
  Read 5 entries from /tmp/RtmpUikp3K/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) : 54.3 | 55.7 | 78.3 (24)
  
  Duration: 0 s
  
  ... SM: MS^2 ID rate (">%1.0f")  done
  Reading file /tmp/RtmpUikp3K/txt/proteinGroups.txt ...
  Read 1128 entries from /tmp/RtmpUikp3K/txt/proteinGroups.txt.
  Updating colnames
  Simplifying contaminants
  Simplifying reverse
  Starting to work on PG: Contaminants ...
  
  Memory [MB] prior|after|max(diff) : 57.4 | 58 | 76.9 (20)
  
  Duration: 0 s
  
  ... PG: Contaminants  done
  Starting to work on PG: raw intensity ...
  
  Memory [MB] prior|after|max(diff) : 58 | 59.3 | 94 (36)
  
  Duration: 0 s
  
  ... PG: raw intensity  done
  Starting to work on PG: LFQ intensity ...
  
  Memory [MB] prior|after|max(diff) : 59.3 | 59.9 | 103.5 (44)
  
  Duration: 1 s
  
  ... PG: LFQ intensity  done
  Starting to work on PG: Principal Component ...
  
  Memory [MB] prior|after|max(diff) : 59.9 | 60.7 | 104.2 (44)
  
  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) : 60.7 | 62.2 | 90.1 (29)
  
  Duration: 0 s
  
  ... PG: Ratio  done
  Reading file /tmp/RtmpUikp3K/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'!
  Keeping 19 of 69 columns!
  Read 15505 entries from /tmp/RtmpUikp3K/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) : 65.9 | 65.9 | 69.2 (3)
  
  Duration: 0 s
  
  ... EVD:Contaminant (%s)  done
  Starting to work on EVD: Pep Intensity (">%1.1f") ...
  
  Memory [MB] prior|after|max(diff) : 65.9 | 67.6 | 84.9 (19)
  
  Duration: 0 s
  
  ... EVD: Pep Intensity (">%1.1f")  done
  Starting to work on EVD: Prot Count (">%1.0f") ...
  
  Memory [MB] prior|after|max(diff) : 67.7 | 67.8 | 88.1 (20)
  
  Duration: 0 s
  
  ... EVD: Prot Count (">%1.0f")  done
  Starting to work on EVD: Pep Count (">%1.0f") ...
  
  Memory [MB] prior|after|max(diff) : 67.8 | 67.9 | 90.7 (23)
  
  Duration: 0 s
  
  ... EVD: Pep Count (">%1.0f")  done
  Starting to work on EVD: RT Peak Width ...
  
  Memory [MB] prior|after|max(diff) : 67.9 | 68.2 | 99.9 (32)
  
  Duration: 0 s
  
  ... EVD: RT Peak Width  done
  Starting to work on EVD: MBR Align ...
  
  Memory [MB] prior|after|max(diff) : 68.2 | 68.8 | 119.2 (51)
  
  Duration: 4 s
  
  ... EVD: MBR Align  done
  Starting to work on EVD: MBR ID-Transfer ...
  
  Memory [MB] prior|after|max(diff) : 68.8 | 69.4 | 121 (52)
  
  Duration: 17 s
  
  ... EVD: MBR ID-Transfer  done
  Starting to work on EVD: MBR auxilliary ...
  
  Memory [MB] prior|after|max(diff) : 69.4 | 70.7 | 113.9 (44)
  
  Duration: 1 s
  
  ... EVD: MBR auxilliary  done
  Starting to work on EVD: Charge ...
  
  Memory [MB] prior|after|max(diff) : 70.7 | 70.8 | 79.7 (9)
  
  Duration: 0 s
  
  ... EVD: Charge  done
  Starting to work on EVD: ID rate over RT ...
  
  Memory [MB] prior|after|max(diff) : 70.8 | 71 | 94.2 (23)
  
  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) : 71 | 71.7 | 92.4 (21)
  
  Duration: 0 s
  
  ... EVD: MS Cal-Pre (%1.1f)  done
  Starting to work on EVD: MS Cal-Post ...
  
  Memory [MB] prior|after|max(diff) : 71.7 | 72.4 | 107.1 (35)
  
  Duration: 0 s
  
  ... EVD: MS Cal-Post  done
  Starting to work on EVD: Contaminants ...
  
  Memory [MB] prior|after|max(diff) : 72.4 | 73.1 | 101.8 (29)
  
  Duration: 0 s
  
  ... EVD: Contaminants  done
  Starting to work on EVD: MS^2 Oversampling ...
  
  Memory [MB] prior|after|max(diff) : 73.1 | 73.3 | 90.8 (18)
  
  Duration: 0 s
  
  ... EVD: MS^2 Oversampling  done
  Starting to work on EVD: Pep Missing Values ...
  
  Memory [MB] prior|after|max(diff) : 73.3 | 74.8 | 121.8 (48)
  
  Duration: 1 s
  
  ... EVD: Pep Missing Values  done
  Reading file /tmp/RtmpUikp3K/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/RtmpUikp3K/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) : 75.7 | 76.4 | 108.9 (33)
  
  Duration: 0 s
  
  ... MSMS: MS^2 Cal (%s)  done
  Starting to work on MSMS: %s ...
  
  Memory [MB] prior|after|max(diff) : 76.4 | 76.5 | 81.4 (5)
  
  Duration: 0 s
  
  ... MSMS: %s  done
  Reading file /tmp/RtmpUikp3K/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/RtmpUikp3K/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) : 77.8 | 79.6 | 89.6 (12)
  
  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) : 79.5 | 79.9 | 87.3 (8)
  
  Duration: 0 s
  
  ... MS^2*Scans: Ion Inj Time  done
  Starting to work on MS^2*Scans: Intensity ...
  
  Memory [MB] prior|after|max(diff) : 79.7 | 81.7 | 105.5 (26)
  
  Duration: 0 s
  
  ... MS^2*Scans: Intensity  done
  Starting to work on MS^2*Scans: TopN high ...
  
  Memory [MB] prior|after|max(diff) : 81.5 | 81.6 | 96.1 (15)
  
  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) : 81.5 | 81.6 | 92.2 (11)
  
  Duration: 0 s
  
  ... MS^2*Scans: TopN ID over N  done
  [1] "#Metrics: "
  [1] 32
  Starting to work on Average Overall Quality ...
  
  Memory [MB] prior|after|max(diff) : 81.6 | 81.6 | 82.3 (1)
  
  Duration: 0 s
  
  ... Average Overall Quality  done
  Creating Report file ...  ordinary text without R code
  
  label: setup (with options) 
  List of 1
   $ include: logi FALSE
  
     inline R code fragments
  
  label: MQparams (with options) 
  List of 2
   $ echo   : logi FALSE
   $ results: chr "asis"
  
    ordinary text without R code
  
  label: nameMapping (with options) 
  List of 2
   $ echo   : logi FALSE
   $ results: chr "asis"
  
    ordinary text without R code
  
  label: metrics (with options) 
  List of 2
   $ echo   : logi FALSE
   $ results: chr "asis"
  
    ordinary text without R code
  
  ── 1. Error: createReport (@test_computeQC.R#34)  ─────────────────────────
  cannot open the connection
  1: createReport(txt_folder, yaml_obj) at testthat/test_computeQC.R:34
  2: render(html_template, output_file = rprt_fns$report_file_HTML)
  3: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding)
  4: writeLines(if (encoding == "") res else native_encode(res, to = encoding), con = output, 
         useBytes = encoding != "")
  5: file(con, "w")
  
  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) : 77.1 | 76.9 | 78.8 (2)
  
  Duration: 0 s
  
  ... MS/MS Peak shape  done
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 141 SKIPPED: 0 FAILED: 1
  1. Error: createReport (@test_computeQC.R#34) 
  
  Error: testthat unit tests failed
  Execution halted