Last updated on 2017-12-20 00:47:09 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.92.0 | 5.23 | 340.11 | 345.34 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.92.0 | ERROR | ||||
| r-devel-linux-x86_64-fedora-clang | 0.92.0 | 411.40 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.92.0 | 408.44 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 0.92.0 | 13.00 | 356.00 | 369.00 | NOTE | |
| r-patched-linux-x86_64 | 0.92.0 | 6.56 | 387.95 | 394.51 | OK | |
| r-patched-solaris-x86 | 0.92.0 | 406.60 | ERROR | |||
| r-release-linux-x86_64 | 0.92.0 | 6.12 | 390.18 | 396.30 | OK | |
| r-release-windows-ix86+x86_64 | 0.92.0 | 15.00 | 368.00 | 383.00 | NOTE | |
| r-release-osx-x86_64 | 0.92.0 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 0.92.0 | 20.00 | 462.00 | 482.00 | NOTE | |
| r-oldrel-osx-x86_64 | 0.92.0 | ERROR |
Version: 0.92.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [60s/99s]
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$SpecialContaminants default: c(name = "MYCOPLASMA", threshold = "1")
.. return default: c(name = "MYCOPLASMA", threshold = "1")
getYAML with: File$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/Rtmp1plk0B/txt/parameters.txt ...
Read 61 entries from /tmp/Rtmp1plk0B/txt/parameters.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Starting to work on PAR: MQ Parameters ...
Memory [MB] prior|after|max(diff) : 52.1 | 53.9 | 90.1 (38)
Duration: 1 s
... PAR: MQ Parameters done
Reading file /tmp/Rtmp1plk0B/txt/summary.txt ...
Read 5 entries from /tmp/Rtmp1plk0B/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 | 55.4 | 78.3 (24)
Duration: 0 s
... SM: MS^2 ID rate (">%1.0f") done
Reading file /tmp/Rtmp1plk0B/txt/proteinGroups.txt ...
Read 1128 entries from /tmp/Rtmp1plk0B/txt/proteinGroups.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Starting to work on PG: Contaminants ...
Memory [MB] prior|after|max(diff) : 57.1 | 57.7 | 77.4 (20)
Duration: 0 s
... PG: Contaminants done
Starting to work on PG: raw intensity ...
Memory [MB] prior|after|max(diff) : 57.7 | 59 | 94.1 (36)
Duration: 0 s
... PG: raw intensity done
Starting to work on PG: LFQ intensity ...
Memory [MB] prior|after|max(diff) : 59.1 | 59.6 | 93.3 (34)
Duration: 1 s
... PG: LFQ intensity done
Starting to work on PG: Principal Component ...
Memory [MB] prior|after|max(diff) : 59.6 | 60.4 | 92.7 (33)
Duration: 1 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) : 60.4 | 61.8 | 90 (30)
Duration: 1 s
... PG: Ratio done
Reading file /tmp/Rtmp1plk0B/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/Rtmp1plk0B/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) : 65.5 | 65.5 | 69 (4)
Duration: 0 s
... EVD:Contaminant (%s) done
Starting to work on EVD: Pep Intensity (">%1.1f") ...
Memory [MB] prior|after|max(diff) : 65.5 | 67.3 | 84.2 (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) : 67.4 | 67.5 | 87.7 (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) : 67.5 | 67.6 | 90.4 (23)
Duration: 0 s
... EVD: Pep Count (">%1.0f") done
Starting to work on EVD: RT Peak Width ...
Memory [MB] prior|after|max(diff) : 67.6 | 67.9 | 98.5 (31)
Duration: 0 s
... EVD: RT Peak Width done
Starting to work on EVD: MBR Align ...
Memory [MB] prior|after|max(diff) : 67.9 | 68.5 | 132.6 (65)
Duration: 3 s
... EVD: MBR Align done
Starting to work on EVD: MBR ID-Transfer ...
Memory [MB] prior|after|max(diff) : 68.5 | 69 | 137.8 (69)
Duration: 16 s
... EVD: MBR ID-Transfer done
Starting to work on EVD: MBR auxilliary ...
Memory [MB] prior|after|max(diff) : 69 | 70.3 | 133.2 (64)
Duration: 0 s
... EVD: MBR auxilliary done
Starting to work on EVD: Charge ...
Memory [MB] prior|after|max(diff) : 70.3 | 70.4 | 79.2 (9)
Duration: 0 s
... EVD: Charge done
Starting to work on EVD: ID rate over RT ...
Memory [MB] prior|after|max(diff) : 70.4 | 70.7 | 92.1 (22)
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) : 70.7 | 71.3 | 89.9 (19)
Duration: 0 s
... EVD: MS Cal-Pre (%1.1f) done
Starting to work on EVD: MS Cal-Post ...
Memory [MB] prior|after|max(diff) : 71.3 | 72 | 106.1 (35)
Duration: 0 s
... EVD: MS Cal-Post done
Starting to work on EVD: Contaminants ...
Memory [MB] prior|after|max(diff) : 72 | 72.7 | 101.4 (29)
Duration: 0 s
... EVD: Contaminants done
Starting to work on EVD: MS^2 Oversampling ...
Memory [MB] prior|after|max(diff) : 72.7 | 72.8 | 88.8 (16)
Duration: 0 s
... EVD: MS^2 Oversampling done
Starting to work on EVD: Pep Missing Values ...
Memory [MB] prior|after|max(diff) : 72.8 | 74.4 | 139.4 (67)
Duration: 1 s
... EVD: Pep Missing Values done
Reading file /tmp/Rtmp1plk0B/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/Rtmp1plk0B/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) : 75.4 | 76 | 111.6 (36)
Duration: 1 s
... MSMS: MS^2 Cal (%s) done
Starting to work on MSMS: %s ...
Memory [MB] prior|after|max(diff) : 76 | 76.1 | 80.9 (5)
Duration: 0 s
... MSMS: %s done
Reading file /tmp/Rtmp1plk0B/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/Rtmp1plk0B/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) : 77.3 | 79.2 | 89.2 (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) : 79.1 | 79.5 | 86.8 (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) : 79.3 | 81.3 | 105.1 (26)
Duration: 0 s
... MS^2*Scans: Intensity done
Starting to work on MS^2*Scans: TopN high ...
Memory [MB] prior|after|max(diff) : 81.1 | 81.1 | 95.8 (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) : 81.1 | 81.1 | 91.6 (10)
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) : 81.2 | 81.2 | 81.9 (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) : 76.7 | 76.5 | 78.4 (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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.92.0
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
trying URL ‘ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip’
Content type 'unknown' length 83554226 bytes (79.7 MB)
==================================================
Quitting from lines 62-63 (PTXQC_report_template.Rmd)
Error: processing vignette ‘PTXQC-Basic_Guide_for_R_users.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.92.0
Check: installed package size
Result: NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
doc 3.8Mb
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: 0.92.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [69s/85s]
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/Rtmpuoa46j/txt/parameters.txt ...
Read 61 entries from /tmp/Rtmpuoa46j/txt/parameters.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Starting to work on PAR: MQ Parameters ...
Memory [MB] prior|after|max(diff) : 27.8 | 28.7 | 46.4 (19)
Duration: 1 s
... PAR: MQ Parameters done
Reading file /tmp/Rtmpuoa46j/txt/summary.txt ...
Read 5 entries from /tmp/Rtmpuoa46j/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) : 28.8 | 29.5 | 41.4 (13)
Duration: 0 s
... SM: MS^2 ID rate (">%1.0f") done
Reading file /tmp/Rtmpuoa46j/txt/proteinGroups.txt ...
Read 1128 entries from /tmp/Rtmpuoa46j/txt/proteinGroups.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Starting to work on PG: Contaminants ...
Memory [MB] prior|after|max(diff) : 30.9 | 31.2 | 41 (10)
Duration: 0 s
... PG: Contaminants done
Starting to work on PG: raw intensity ...
Memory [MB] prior|after|max(diff) : 31.2 | 32 | 51.3 (20)
Duration: 0 s
... PG: raw intensity done
Starting to work on PG: LFQ intensity ...
Memory [MB] prior|after|max(diff) : 32 | 32.3 | 50.1 (18)
Duration: 1 s
... PG: LFQ intensity done
Starting to work on PG: Principal Component ...
Memory [MB] prior|after|max(diff) : 32.3 | 32.9 | 49.3 (17)
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) : 32.9 | 33.7 | 49 (16)
Duration: 0 s
... PG: Ratio done
Reading file /tmp/Rtmpuoa46j/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/Rtmpuoa46j/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) : 36.8 | 36.8 | 38.6 (2)
Duration: 0 s
... EVD:Contaminant (%s) done
Starting to work on EVD: Pep Intensity (">%1.1f") ...
Memory [MB] prior|after|max(diff) : 36.8 | 38.1 | 51 (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) : 38.2 | 38.2 | 49.8 (12)
Duration: 0 s
... EVD: Prot Count (">%1.0f") done
Starting to work on EVD: Pep Count (">%1.0f") ...
Memory [MB] prior|after|max(diff) : 38.2 | 38.3 | 50.9 (13)
Duration: 0 s
... EVD: Pep Count (">%1.0f") done
Starting to work on EVD: RT Peak Width ...
Memory [MB] prior|after|max(diff) : 38.3 | 38.4 | 55.4 (17)
Duration: 1 s
... EVD: RT Peak Width done
Starting to work on EVD: MBR Align ...
Memory [MB] prior|after|max(diff) : 38.4 | 38.7 | 69.2 (31)
Duration: 4 s
... EVD: MBR Align done
Starting to work on EVD: MBR ID-Transfer ...
Memory [MB] prior|after|max(diff) : 38.7 | 39.1 | 74.2 (36)
Duration: 14 s
... EVD: MBR ID-Transfer done
Starting to work on EVD: MBR auxilliary ...
Memory [MB] prior|after|max(diff) : 39.1 | 40 | 67.7 (29)
Duration: 1 s
... EVD: MBR auxilliary done
Starting to work on EVD: Charge ...
Memory [MB] prior|after|max(diff) : 40 | 40.1 | 46.6 (7)
Duration: 0 s
... EVD: Charge done
Starting to work on EVD: ID rate over RT ...
Memory [MB] prior|after|max(diff) : 40.1 | 40.1 | 56.1 (16)
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) : 40.1 | 40.7 | 56.2 (16)
Duration: 0 s
... EVD: MS Cal-Pre (%1.1f) done
Starting to work on EVD: MS Cal-Post ...
Memory [MB] prior|after|max(diff) : 40.7 | 41.2 | 63.7 (23)
Duration: 0 s
... EVD: MS Cal-Post done
Starting to work on EVD: Contaminants ...
Memory [MB] prior|after|max(diff) : 41.2 | 41.7 | 59.5 (18)
Duration: 0 s
... EVD: Contaminants done
Starting to work on EVD: MS^2 Oversampling ...
Memory [MB] prior|after|max(diff) : 41.7 | 41.7 | 53.5 (12)
Duration: 0 s
... EVD: MS^2 Oversampling done
Starting to work on EVD: Pep Missing Values ...
Memory [MB] prior|after|max(diff) : 41.7 | 42.8 | 74.2 (32)
Duration: 1 s
... EVD: Pep Missing Values done
Reading file /tmp/Rtmpuoa46j/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/Rtmpuoa46j/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) : 43.6 | 44.1 | 64.7 (21)
Duration: 0 s
... MSMS: MS^2 Cal (%s) done
Starting to work on MSMS: %s ...
Memory [MB] prior|after|max(diff) : 44.1 | 44.2 | 47 (3)
Duration: 0 s
... MSMS: %s done
Reading file /tmp/Rtmpuoa46j/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/Rtmpuoa46j/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) : 45.3 | 46.2 | 52.9 (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) : 46.2 | 46.4 | 51.1 (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) : 46.3 | 47.8 | 64.6 (18)
Duration: 0 s
... MS^2*Scans: Intensity done
Starting to work on MS^2*Scans: TopN high ...
Memory [MB] prior|after|max(diff) : 47.8 | 47.9 | 56.1 (8)
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) : 47.8 | 47.9 | 53.6 (6)
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) : 47.8 | 47.8 | 48.3 (0)
Duration: 0 s
... Average Overall Quality done
Creating Report file ...[[1]]
done
Report file created at
/tmp/Rtmpuoa46j/txt/report_v0.92.0_Rtmpuoa46j.*
Time elapsed: 1.2 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) : 42.4 | 42.3 | 43.2 (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: 0.92.0
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) : 76.8 | 76.6 | 78.6 (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-release-osx-x86_64
Version: 0.92.0
Check: tests
Result: ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Memory [MB] prior|after|max(diff) : 62.4 | 62.1 | 64.1 (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