Last updated on 2020-01-28 05:50:26 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 16.12 | 204.02 | 220.14 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 16.21 | 151.54 | 167.75 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 258.38 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 250.56 | OK | |||
| r-devel-windows-ix86+x86_64 | 1.0.0 | 35.00 | 216.00 | 251.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.0 | 49.00 | 284.00 | 333.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.0 | OK | ||||
| r-patched-solaris-x86 | 1.0.0 | 271.00 | ERROR | |||
| r-release-linux-x86_64 | 1.0.0 | 12.98 | 178.23 | 191.21 | OK | |
| r-release-windows-ix86+x86_64 | 1.0.0 | 32.00 | 195.00 | 227.00 | NOTE | |
| r-release-osx-x86_64 | 1.0.0 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.0 | 46.00 | 248.00 | 294.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.0.0 | ERROR |
Version: 1.0.0
Check: installed package size
Result: NOTE
installed size is 8.5Mb
sub-directories of 1Mb or more:
doc 4.7Mb
examples 2.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, 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: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [80s/107s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(PTXQC)
Loading package PTXQC (version 1.0.0)
>
> ##
> ## 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 /tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/txt/parameters.txt ...
Read 61 entries from /tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/txt/parameters.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Starting to work on PAR: MQ Parameters ...
Memory [MB] prior|after|max(diff) : 40.7 | 41.7 | 67.4 (27)
Duration: 1 s
... PAR: MQ Parameters done
Reading file /tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/txt/summary.txt ...
Read 5 entries from /tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/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) : 41.9 | 43.3 | 47.6 (6)
Duration: 1 s
... SM: MS^2 ID rate (">%1.0f") done
Reading file /tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/txt/proteinGroups.txt ...
Read 1128 entries from /tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/txt/proteinGroups.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Starting to work on PG: Contaminants ...
Memory [MB] prior|after|max(diff) : 44.8 | 45.1 | 48.2 (3)
Duration: 1 s
... PG: Contaminants done
Starting to work on PG: Raw intensity ...
Memory [MB] prior|after|max(diff) : 45.1 | 46.2 | 54.8 (10)
Duration: 1 s
... PG: Raw intensity done
Starting to work on PG: LFQ intensity ...
Memory [MB] prior|after|max(diff) : 46.2 | 46.6 | 54 (8)
Duration: 1 s
... PG: LFQ intensity done
Starting to work on PG: Principal Component ...
Memory [MB] prior|after|max(diff) : 46.6 | 47.3 | 59.9 (13)
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) : 47.3 | 49.2 | 80.6 (33)
Duration: 2 s
... PG: Ratio done
Reading file /tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/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/RtmpGHaWYp/working_dir/RtmpXNaiOS/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) : 55.4 | 55.4 | 55.4 (0)
Duration: 1 s
Starting to work on EVD: Peptide Intensity (">%1.1f") ...
Memory [MB] prior|after|max(diff) : 55.4 | 56.5 | 68 (13)
Duration: 0 s
... EVD: Peptide Intensity (">%1.1f") done
Starting to work on EVD: Reporter intensity ...
Memory [MB] prior|after|max(diff) : 56.5 | 56.5 | 56.6 (0)
Duration: 0 s
Starting to work on EVD: Protein Count (">%1.0f") ...
Memory [MB] prior|after|max(diff) : 56.5 | 56.6 | 65.8 (9)
Duration: 1 s
... EVD: Protein Count (">%1.0f") done
Starting to work on EVD: Peptide Count (">%1.0f") ...
Memory [MB] prior|after|max(diff) : 56.6 | 56.8 | 62.8 (6)
Duration: 0 s
... EVD: Peptide Count (">%1.0f") done
Starting to work on EVD: RT Peak Width ...
Memory [MB] prior|after|max(diff) : 56.8 | 57 | 74.7 (18)
Duration: 1 s
... EVD: RT Peak Width done
Starting to work on EVD: MBR Align ...
Memory [MB] prior|after|max(diff) : 57 | 57.4 | 94.9 (38)
Duration: 4 s
... EVD: MBR Align done
Starting to work on EVD: MBR ID-Transfer ...
Memory [MB] prior|after|max(diff) : 57.4 | 57.9 | 124.6 (67)
Duration: 19 s
... EVD: MBR ID-Transfer done
Starting to work on EVD: MBR auxilliary ...
Memory [MB] prior|after|max(diff) : 57.9 | 58.9 | 86.8 (29)
Duration: 1 s
... EVD: MBR auxilliary done
Starting to work on EVD: Charge ...
Memory [MB] prior|after|max(diff) : 58.9 | 59 | 65.4 (6)
Duration: 0 s
... EVD: Charge done
Starting to work on EVD: ID rate over RT ...
Memory [MB] prior|after|max(diff) : 59 | 59.1 | 68.4 (9)
Duration: 1 s
... EVD: ID rate over RT done
Starting to work on EVD: UpSet ...
Memory [MB] prior|after|max(diff) : 59.1 | 62.2 | 96.4 (37)
Duration: 3 s
... EVD: UpSet done
Starting to work on EVD: MS Cal-Pre (%1.1f) ...
Memory [MB] prior|after|max(diff) : 62.2 | 62.7 | 75.9 (14)
Duration: 1 s
... EVD: MS Cal-Pre (%1.1f) done
Starting to work on EVD: MS Cal-Post ...
Memory [MB] prior|after|max(diff) : 62.7 | 63.2 | 76 (13)
Duration: 0 s
... EVD: MS Cal-Post done
Starting to work on EVD: Contaminants ...
Memory [MB] prior|after|max(diff) : 63.2 | 63.7 | 74.9 (12)
Duration: 0 s
... EVD: Contaminants done
Starting to work on EVD: MS^2 Oversampling ...
Memory [MB] prior|after|max(diff) : 63.7 | 63.8 | 73.6 (10)
Duration: 1 s
... EVD: MS^2 Oversampling done
Starting to work on EVD: Pep Missing Values ...
Memory [MB] prior|after|max(diff) : 63.8 | 64.9 | 103.4 (40)
Duration: 1 s
... EVD: Pep Missing Values done
Reading file /tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/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/RtmpGHaWYp/working_dir/RtmpXNaiOS/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) : 65.7 | 66.7 | 88.2 (22)
Duration: 1 s
... MSMS: MS^2 Cal (%s) done
Starting to work on MSMS: %s ...
Memory [MB] prior|after|max(diff) : 66.7 | 66.7 | 69.7 (3)
Duration: 1 s
... MSMS: %s done
Reading file /tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/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$' using case-INsensitive matching.
Keeping 2 of 41 columns!
Read 35113 entries from /tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/txt/msmsScans.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Adding fc.raw.file column ... done
Starting to work on MS^2*Scans: TopN over RT ...
Memory [MB] prior|after|max(diff) : 67.7 | 68.9 | 76.1 (8)
Duration: 1 s
... MS^2*Scans: TopN over RT done
Starting to work on MS^2*Scans: Ion Inj Time ...
Memory [MB] prior|after|max(diff) : 68.8 | 69.1 | 75.9 (7)
Duration: 1 s
... MS^2*Scans: Ion Inj Time done
Starting to work on MS^2*Scans: Intensity ...
Memory [MB] prior|after|max(diff) : 68.9 | 70.7 | 86.7 (18)
Duration: 1 s
... MS^2*Scans: Intensity done
Starting to work on MS^2*Scans: TopN high ...
Memory [MB] prior|after|max(diff) : 70.6 | 70.6 | 77.8 (7)
Duration: 0 s
... MS^2*Scans: TopN high done
Starting to work on MS^2*Scans: TopN ID over N ...
Memory [MB] prior|after|max(diff) : 70.6 | 70.6 | 76.8 (6)
Duration: 1 s
... MS^2*Scans: TopN ID over N done
[1] "#Metrics: "
[1] 35
Starting to work on Average Overall Quality ...
Memory [MB] prior|after|max(diff) : 70.6 | 70.6 | 71 (0)
Duration: 1 s
... Average Overall Quality done
Creating Report file ...[[1]]
done
Report file created at
/tmp/RtmpGHaWYp/working_dir/RtmpXNaiOS/txt/report_v1.0.0_RtmpXNaiOS.*
Time elapsed: 1.5 min
── 1. Failure: createReport (@test_computeQC.R#46) ────────────────────────────
all(file.exists(rep_files)) not equal to TRUE.
1 element mismatch
── 2. Failure: createReport (@test_computeQC.R#47) ────────────────────────────
all(file.info(rep_files)$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) : 54.7 | 54.6 | 56 (1)
Duration: 1 s
... MS/MS Peak shape done
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 119 | SKIPPED: 0 | WARNINGS: 123 | FAILED: 2 ]
1. Failure: createReport (@test_computeQC.R#46)
2. Failure: createReport (@test_computeQC.R#47)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [47s/45s]
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) : 93.8 | 93.8 | 3877684 (3877590)
Duration: 0 s
... MS/MS Peak shape done
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 119 | SKIPPED: 0 | WARNINGS: 123 | FAILED: 2 ]
1. Failure: createReport (@test_computeQC.R#46)
2. Failure: createReport (@test_computeQC.R#47)
Error: testthat unit tests failed
Execution halted
Flavor: r-release-osx-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [47s/45s]
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) : 100.4 | 100.2 | 4293140 (4293040)
Duration: 0 s
... MS/MS Peak shape done
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 119 | SKIPPED: 0 | WARNINGS: 123 | FAILED: 2 ]
1. Failure: createReport (@test_computeQC.R#46)
2. Failure: createReport (@test_computeQC.R#47)
Error: testthat unit tests failed
Execution halted
Flavor: r-oldrel-osx-x86_64