CRAN Package Check Results for Package PTXQC

Last updated on 2018-05-24 12:47:45 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.92.3 12.01 305.43 317.44 OK
r-devel-linux-x86_64-debian-gcc 0.92.3 11.58 249.12 260.70 OK
r-devel-linux-x86_64-fedora-clang 0.92.3 412.74 NOTE
r-devel-linux-x86_64-fedora-gcc 0.92.3 391.95 NOTE
r-devel-windows-ix86+x86_64 0.92.3 20.00 311.00 331.00 NOTE
r-patched-linux-x86_64 0.92.3 17.95 318.22 336.17 OK
r-patched-solaris-x86 0.92.3 411.80 ERROR
r-release-linux-x86_64 0.92.3 17.77 332.99 350.76 OK
r-release-windows-ix86+x86_64 0.92.3 45.00 455.00 500.00 NOTE
r-release-osx-x86_64 0.92.3 ERROR
r-oldrel-windows-ix86+x86_64 0.92.3 22.00 484.00 506.00 NOTE
r-oldrel-osx-x86_64 0.92.3 ERROR

Check Details

Version: 0.92.3
Check: installed package size
Result: NOTE
     installed size is 8.2Mb
     sub-directories of 1Mb or more:
     doc 4.6Mb
     examples 2.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.92.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [62s/76s]
    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/Rtmp8Ba42n/txt/parameters.txt ...
     Read 61 entries from /tmp/Rtmp8Ba42n/txt/parameters.txt.
     Updating colnames
     Simplifying contaminants
     Simplifying reverse
     Starting to work on PAR: MQ Parameters ...
    
     Memory [MB] prior|after|max(diff) : 38.8 | 40 | 72.6 (34)
    
     Duration: 1 s
    
     ... PAR: MQ Parameters done
     Reading file /tmp/Rtmp8Ba42n/txt/summary.txt ...
     Read 5 entries from /tmp/Rtmp8Ba42n/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) : 40 | 41.3 | 44.9 (5)
    
     Duration: 0 s
    
     ... SM: MS^2 ID rate (">%1.0f") done
     Reading file /tmp/Rtmp8Ba42n/txt/proteinGroups.txt ...
     Read 1128 entries from /tmp/Rtmp8Ba42n/txt/proteinGroups.txt.
     Updating colnames
     Simplifying contaminants
     Simplifying reverse
     Starting to work on PG: Contaminants ...
    
     Memory [MB] prior|after|max(diff) : 42.7 | 43.1 | 45.9 (3)
    
     Duration: 0 s
    
     ... PG: Contaminants done
     Starting to work on PG: raw intensity ...
    
     Memory [MB] prior|after|max(diff) : 43.1 | 44.1 | 52.4 (9)
    
     Duration: 0 s
    
     ... PG: raw intensity done
     Starting to work on PG: LFQ intensity ...
    
     Memory [MB] prior|after|max(diff) : 44.1 | 44.4 | 51.7 (8)
    
     Duration: 0 s
    
     ... PG: LFQ intensity done
     Starting to work on PG: Principal Component ...
    
     Memory [MB] prior|after|max(diff) : 44.4 | 45 | 55.5 (11)
    
     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) : 45 | 45.9 | 55.7 (11)
    
     Duration: 0 s
    
     ... PG: Ratio done
     Reading file /tmp/Rtmp8Ba42n/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/Rtmp8Ba42n/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) : 49.1 | 49.1 | 50.7 (2)
    
     Duration: 0 s
    
     ... EVD:Contaminant (%s) done
     Starting to work on EVD: Pep Intensity (">%1.1f") ...
    
     Memory [MB] prior|after|max(diff) : 49.1 | 50.5 | 63 (14)
    
     Duration: 0 s
    
     ... EVD: Pep Intensity (">%1.1f") done
     Starting to work on EVD: Prot Count (">%1.0f") ...
    
     Memory [MB] prior|after|max(diff) : 50.5 | 50.6 | 58.9 (8)
    
     Duration: 0 s
    
     ... EVD: Prot Count (">%1.0f") done
     Starting to work on EVD: Pep Count (">%1.0f") ...
    
     Memory [MB] prior|after|max(diff) : 50.6 | 50.7 | 55.8 (5)
    
     Duration: 0 s
    
     ... EVD: Pep Count (">%1.0f") done
     Starting to work on EVD: RT Peak Width ...
    
     Memory [MB] prior|after|max(diff) : 50.7 | 50.8 | 72.1 (21)
    
     Duration: 0 s
    
     ... EVD: RT Peak Width done
     Starting to work on EVD: MBR Align ...
    
     Memory [MB] prior|after|max(diff) : 50.8 | 51.3 | 87.7 (37)
    
     Duration: 4 s
    
     ... EVD: MBR Align done
     Starting to work on EVD: MBR ID-Transfer ...
    
     Memory [MB] prior|after|max(diff) : 51.3 | 51.6 | 91.1 (40)
    
     Duration: 14 s
    
     ... EVD: MBR ID-Transfer done
     Starting to work on EVD: MBR auxilliary ...
    
     Memory [MB] prior|after|max(diff) : 51.6 | 52.6 | 87.6 (36)
    
     Duration: 1 s
    
     ... EVD: MBR auxilliary done
     Starting to work on EVD: Charge ...
    
     Memory [MB] prior|after|max(diff) : 52.6 | 52.7 | 59.1 (6)
    
     Duration: 0 s
    
     ... EVD: Charge done
     Starting to work on EVD: ID rate over RT ...
    
     Memory [MB] prior|after|max(diff) : 52.7 | 52.8 | 62.6 (10)
    
     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) : 52.8 | 53.4 | 68 (15)
    
     Duration: 0 s
    
     ... EVD: MS Cal-Pre (%1.1f) done
     Starting to work on EVD: MS Cal-Post ...
    
     Memory [MB] prior|after|max(diff) : 53.4 | 53.9 | 67.9 (14)
    
     Duration: 0 s
    
     ... EVD: MS Cal-Post done
     Starting to work on EVD: Contaminants ...
    
     Memory [MB] prior|after|max(diff) : 53.9 | 54.5 | 66.6 (13)
    
     Duration: 1 s
    
     ... EVD: Contaminants done
     Starting to work on EVD: MS^2 Oversampling ...
    
     Memory [MB] prior|after|max(diff) : 54.5 | 54.6 | 65.2 (11)
    
     Duration: 0 s
    
     ... EVD: MS^2 Oversampling done
     Starting to work on EVD: Pep Missing Values ...
    
     Memory [MB] prior|after|max(diff) : 54.6 | 55.7 | 93.3 (39)
    
     Duration: 1 s
    
     ... EVD: Pep Missing Values done
     Reading file /tmp/Rtmp8Ba42n/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/Rtmp8Ba42n/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) : 56.6 | 57.1 | 74.5 (18)
    
     Duration: 0 s
    
     ... MSMS: MS^2 Cal (%s) done
     Starting to work on MSMS: %s ...
    
     Memory [MB] prior|after|max(diff) : 57.1 | 57.1 | 59.9 (3)
    
     Duration: 0 s
    
     ... MSMS: %s done
     Reading file /tmp/Rtmp8Ba42n/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/Rtmp8Ba42n/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) : 58.2 | 59.4 | 66.6 (8)
    
     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) : 59.4 | 59.5 | 64.5 (5)
    
     Duration: 0 s
    
     ... MS^2*Scans: Ion Inj Time done
     Starting to work on MS^2*Scans: Intensity ...
    
     Memory [MB] prior|after|max(diff) : 59.4 | 61.1 | 79.6 (20)
    
     Duration: 0 s
    
     ... MS^2*Scans: Intensity done
     Starting to work on MS^2*Scans: TopN high ...
    
     Memory [MB] prior|after|max(diff) : 60.9 | 61.1 | 67.7 (7)
    
     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) : 61 | 61.1 | 67.2 (6)
    
     Duration: 0 s
    
     ... MS^2*Scans: TopN ID over N done
     [1] "#Metrics: "
     [1] 33
     Starting to work on Average Overall Quality ...
    
     Memory [MB] prior|after|max(diff) : 61.1 | 61.1 | 61.5 (0)
    
     Duration: 0 s
    
     ... Average Overall Quality done
     Creating Report file ...[[1]]
    
     done
     Report file created at
    
     /tmp/Rtmp8Ba42n/txt/report_v0.92.3_Rtmp8Ba42n.*
    
    
    
     Time elapsed: 1.1 min
    
     ── 1. Failure: createReport (@test_computeQC.R#39) ────────────────────────────
     all(file.exists(rep_files)) not equal to TRUE.
     1 element mismatch
    
     ── 2. Failure: createReport (@test_computeQC.R#40) ────────────────────────────
     all(file.info(rep_files)$size > 100 * 1024) not equal to TRUE.
     'is.NA' value mismatch: 0 in current 1 in target
    
     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) : 55.9 | 55.7 | 56.7 (1)
    
     Duration: 0 s
    
     ... MS/MS Peak shape done
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 252 SKIPPED: 0 FAILED: 2
     1. Failure: createReport (@test_computeQC.R#39)
     2. Failure: createReport (@test_computeQC.R#40)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86

Version: 0.92.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [54s/84s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     jurkat_06_100731121305
     Starting to work on MS/MS Peak shape ...
    
     Memory [MB] prior|after|max(diff) : 91.9 | 91.6 | 4204302 (4204210)
    
     Duration: 1 s
    
     ... MS/MS Peak shape done
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 252 SKIPPED: 0 FAILED: 2
     1. Failure: createReport (@test_computeQC.R#39)
     2. Failure: createReport (@test_computeQC.R#40)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-osx-x86_64

Version: 0.92.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [43s/44s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     jurkat_06_100731121305
     Starting to work on MS/MS Peak shape ...
    
     Memory [MB] prior|after|max(diff) : 77.9 | 77.6 | 79.6 (2)
    
     Duration: 0 s
    
     ... MS/MS Peak shape done
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 252 SKIPPED: 0 FAILED: 2
     1. Failure: createReport (@test_computeQC.R#39)
     2. Failure: createReport (@test_computeQC.R#40)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-oldrel-osx-x86_64