# RUNIT TEST PROTOCOL--Tue Apr 25 04:25:44 2017

Number of test functions: 168

Number of errors: 0

Number of failures: 0

### 1 Test suite

Name | Test functions | Errors | Failures
--- | --- | --- | ---
xcms unit testing | 168 | 0 | 0

### Details

##### Test Suite: xcms unit testing

Test function regexp: ^test.+
Test file regexp: ^runit.+\.[rR]$
Involved directory:
C:/Users/biocbuild/bbs-3.5-bioc/meat/xcms.buildbin-libdir/xcms/unitTests

- Test file: runit.BiocParallel.R
  - test_BiocParallel: (3 checks) ... OK (5.22 seconds)
- Test file: runit.Chromatogram.R
  - test_Chromatogram_class: (32 checks) ... OK (0.06 seconds)
  - test_extractChromatograms: (52 checks) ... OK (16.75 seconds)
  - test_filterRt_Chromatogram: (7 checks) ... OK (0 seconds)
- Test file: runit.Param-classes.R
  - test_CentWaveParam: (67 checks) ... OK (0.08 seconds)
  - test_CentWavePredIsoParam: (65 checks) ... OK (0.39 seconds)
  - test_FillChromPeaksParam: (15 checks) ... OK (0.01 seconds)
  - test_GenericParam: (3 checks) ... OK (0 seconds)
  - test_MSWParam: (47 checks) ... OK (0.08 seconds)
  - test_MassifquantParam: (44 checks) ... OK (0.08 seconds)
  - test_MzClustParam: (21 checks) ... OK (0.03 seconds)
  - test_NearestPeaksParam: (23 checks) ... OK (0.04 seconds)
  - test_ObiwarpParam: (60 checks) ... OK (0.08 seconds)
  - test_PeakDensityParam: (25 checks) ... OK (0.03 seconds)
  - test_PeakGroupsParam: (29 checks) ... OK (0.03 seconds)
  - test_matchedFilterParam: (45 checks) ... OK (0.06 seconds)
- Test file: runit.XCMSnExp.R
  - test_MsFeatureData_class_accessors: (12 checks) ... OK (0.05 seconds)
  - test_MsFeatureData_class_validation: (12 checks) ... OK (0.07 seconds)
  - test_XCMSnExp_class: (12 checks) ... OK (0.05 seconds)
  - test_XCMSnExp_class_accessors: (52 checks) ... OK (0.99 seconds)
  - test_XCMSnExp_droppers: (99 checks) ... OK (0.19 seconds)
  - test_XCMSnExp_filterFile: (57 checks) ... OK (0.96 seconds)
  - test_XCMSnExp_filterMz: (52 checks) ... OK (2.48 seconds)
  - test_XCMSnExp_filterRt: (88 checks) ... OK (1.95 seconds)
  - test_XCMSnExp_findChromPeaks: (1 checks) ... OK (4.22 seconds)
  - test_XCMSnExp_inherited_methods: (34 checks) ... OK (4.36 seconds)
  - test_XCMSnExp_intensity: (2 checks) ... OK (4.31 seconds)
  - test_XCMSnExp_mz: (2 checks) ... OK (4.28 seconds)
  - test_XCMSnExp_processHistory: (8 checks) ... OK (0.03 seconds)
  - test_XCMSnExp_rtime: (5 checks) ... OK (0.05 seconds)
  - test_XCMSnExp_spectra: (7 checks) ... OK (11.26 seconds)
  - test_adjustRtimePeakGroups: (3 checks) ... OK (0 seconds)
  - test_as_XCMSnExp_xcmsSet: (19 checks) ... OK (0.67 seconds)
  - test_extractChromatograms: (11 checks) ... OK (5.17 seconds)
  - test_featureValues: (2 checks) ... OK (0.45 seconds)
  - test_peakIndex: (2 checks) ... OK (0 seconds)
  - test_signal_integration: (14 checks) ... OK (9.25 seconds)
- Test file: runit.absentPresent.R
  - testPresentAbsentSum: (8 checks) ... OK (1.61 seconds)
  - testPresentAbsentSumAfterFillPeaks: (8 checks) ... OK (16.94 seconds)
- Test file: runit.binning.R
  - test_binYonX_multi: (17 checks) ... OK (0.78 seconds)
  - test_binning_NA_handling: (5 checks) ... OK (0 seconds)
  - test_binning_max: (41 checks) ... OK (0.03 seconds)
  - test_binning_mean: (4 checks) ... OK (0 seconds)
  - test_binning_min: (10 checks) ... OK (0 seconds)
  - test_binning_sum: (9 checks) ... OK (0 seconds)
  - test_breaks: (12 checks) ... OK (0.02 seconds)
  - test_imputation_lin: (14 checks) ... OK (0 seconds)
  - test_imputation_linbin: (8 checks) ... OK (0 seconds)
- Test file: runit.createProfileMatrix.R
  - test_createProfileMatrix: (7 checks) ... OK (0.18 seconds)
  - test_profMat: (4 checks) ... OK (1.7 seconds)
  - test_profMat_OnDiskMSnExp: (4 checks) ... OK (6.68 seconds)
  - test_profMethodReplace: (6 checks) ... OK (1.64 seconds)
  - test_profStepReplace: (4 checks) ... OK (0.03 seconds)
- Test file: runit.diffreport.R
  - testAnova: (0 checks) ... OK (0.73 seconds)
  - testDiffreport: (0 checks) ... OK (0.24 seconds)
  - testDiffreportMinSamples: (0 checks) ... OK (1.32 seconds)
- Test file: runit.do_adjustRtime.R
  - test_adjustRtime_PeakGroups: (32 checks) ... OK (1.25 seconds)
  - test_applyRtAdjustment: (2 checks) ... OK (1.14 seconds)
  - test_do_adjustRtime_peakGroups_implementation: (6 checks) ... OK (1.72 seconds)
  - test_getPeakGroupsRtMatrix: (3 checks) ... OK (0 seconds)
  - test_obiwarp: (13 checks) ... OK (21.05 seconds)
  - test_plotAdjustedRtime: (0 checks) ... OK (0.12 seconds)
- Test file: runit.do_findChromPeaks_MSW.R
  - test_do_findPeaks_MSW: (2 checks) ... OK (1.07 seconds)
  - test_findChromPeaks_MSW: (6 checks) ... OK (2.75 seconds)
- Test file: runit.do_findChromPeaks_centWave.R
  - test_do_findChromPeaks_centWave: (2 checks) ... OK (2.28 seconds)
  - test_findChromPeaks_centWave: (7 checks) ... OK (4.86 seconds)
  - test_findChromPeaks_centWave_peakIntensity: (15 checks) ... OK (9.29 seconds)
- Test file: runit.do_findChromPeaks_centWave_isotopes.R
  - test_do_findChromPeaks_centWaveWithPredIsoROIs: (1 checks) ... OK (12.53 seconds)
  - test_findChromPeaks_centWaveWithPredIsoROIs: (7 checks) ... OK (18.49 seconds)
- Test file: runit.do_findChromPeaks_massifquant.R
  - test_do_findChromPeaks_massifquant: (4 checks) ... OK (8.89 seconds)
  - test_findChromPeaks_massifquant: (2 checks) ... OK (4.81 seconds)
- Test file: runit.do_findChromPeaks_matchedFilter.R
  - test_do_findChromPeaks_matchedFilter: (2 checks) ... OK (0.19 seconds)
  - test_findChromPeaks_matchedFilter: (2 checks) ... OK (2.05 seconds)
- Test file: runit.do_groupChromPeaks.R
  - test_do_groupChromPeaks_density: (1 checks) ... OK (2.11 seconds)
  - test_do_groupChromPeaks_nearest: (2 checks) ... OK (26.8 seconds)
  - test_do_groupPeaks_mzClust: (3 checks) ... OK (0.14 seconds)
  - test_featureValues_XCMSnExp: (3 checks) ... OK (0.48 seconds)
  - test_groupChromPeaks_NearestPeaksParam: (10 checks) ... OK (1.01 seconds)
  - test_groupChromPeaks_PeakDensityParam: (10 checks) ... OK (0.8 seconds)
  - test_groupPeaks_MzClustParam: (10 checks) ... OK (0.17 seconds)
- Test file: runit.fillChromPeaks.R
  - test_fillChromPeaks: (58 checks) ... OK (17.59 seconds)
  - test_fillChromPeaks_MSW: (11 checks) ... OK (3.08 seconds)
  - test_fillChromPeaks_matchedFilter: (18 checks) ... OK (18.69 seconds)
- Test file: runit.fillPeaks.R
  - test.fillPeaksColumns: (2 checks) ... OK (36.67 seconds)
  - test.fillPeaks_old_vs_new: (2 checks) ... OK (44.63 seconds)
  - test.getPeaks_implementation: (9 checks) ... OK (4.03 seconds)
  - testFillPeaksPar: (1 checks) ... OK (29.3 seconds)
  - testFilledFlag: (1 checks) ... OK (15.17 seconds)
- Test file: runit.findPeaksCentWave.R
  - test.findPeaksCentWaveResort: (1 checks) ... OK (2.32 seconds)
- Test file: runit.findPeaksCentWave.fitGauss.plot.R
  - test.findPeaksCentWave: (0 checks) ... OK (2.99 seconds)
- Test file: runit.findPeaksCentWaveWithIsotopeROIs.R
  - test.addPredictedIsotopeFeatures: (2 checks) ... OK (4.79 seconds)
- Test file: runit.findPeaksMassIfQuant.R
  - test.findPeaksMassIfQuant: (0 checks) ... OK (1.97 seconds)
- Test file: runit.getEIC.R
  - test.getEICretcor: (0 checks) ... OK (21.28 seconds)
  - test.issue7: (2 checks) ... OK (78.41 seconds)
  - test.plotEIC: (0 checks) ... OK (0 seconds)
  - test_getEICxset: (5 checks) ... OK (31.53 seconds)
  - test_profEIC: (39 checks) ... OK (0.47 seconds)
- Test file: runit.getXcmsRaw.R
  - test.getXcmsRaw: (10 checks) ... OK (31.93 seconds)
  - test.getXcmsRawIssue44: (3 checks) ... OK (4.23 seconds)
- Test file: runit.group.R
  - testGroupDensityOnePeak: (0 checks) ... OK (0 seconds)
  - testGroupNearest: (1 checks) ... OK (8.16 seconds)
- Test file: runit.msms.R
  - test.msn2xcmsRaw: (3 checks) ... OK (1.28 seconds)
  - test.xcmsRawms1: (0 checks) ... OK (0.61 seconds)
  - test.xcmsRawms123: (4 checks) ... OK (1.9 seconds)
  - test.xcmsSetms2cw: (0 checks) ... OK (1.11 seconds)
  - test.xcmsSetms2mf: (0 checks) ... OK (1.1 seconds)
- Test file: runit.new_read_data.R
  - test_compare_readRawData: (7 checks) ... OK (6.76 seconds)
  - test_evaluate_xcmsSource: (6 checks) ... OK (4.01 seconds)
- Test file: runit.new_scanrange_subsetting.R
  - test_scanrange_centWave: (1 checks) ... OK (1.46 seconds)
  - test_scanrange_massifquant: (2 checks) ... OK (0.8 seconds)
  - test_scanrange_matchedFilter: (1 checks) ... OK (3.26 seconds)
  - test_scanrange_xcmsRaw: (6 checks) ... OK (1.55 seconds)
- Test file: runit.obiwarp.R
  - test.obiwarp.cor: (0 checks) ... OK (13.43 seconds)
  - test.obiwarp.cor_opt: (0 checks) ... OK (12.95 seconds)
  - test.obiwarp.cov: (0 checks) ... OK (13.43 seconds)
  - test.obiwarp.default: (0 checks) ... OK (12.95 seconds)
  - test.obiwarp.euc: (0 checks) ... OK (13.47 seconds)
  - test.obiwarp.local: (0 checks) ... OK (12.97 seconds)
  - test.obiwarp.prd: (0 checks) ... OK (13.32 seconds)
- Test file: runit.phenoData.R
  - testMultiFactor: (0 checks) ... OK (1.1 seconds)
  - testMultiFactorDiffreport: (1 checks) ... OK (15.77 seconds)
- Test file: runit.processHistory.R
  - test_ProcessHistory_c_xcmsSet: (0 checks) ... OK (0 seconds)
  - test_ProcessHistory_class: (10 checks) ... OK (0.02 seconds)
  - test_XProcessHistory_class: (7 checks) ... OK (0.01 seconds)
  - test_showError: (6 checks) ... OK (0.03 seconds)
- Test file: runit.rawMat.R
  - test.rawMat: (10 checks) ... OK (0.86 seconds)
- Test file: runit.sampclass.R
  - test.sampclass: (5 checks) ... OK (4.41 seconds)
- Test file: runit.scanrage.R
  - test.xcmsRawScanrange.100: (1 checks) ... OK (0.76 seconds)
  - test.xcmsRawScanrange.first: (1 checks) ... OK (0.79 seconds)
  - test.xcmsRawScanrange.last: (1 checks) ... OK (0.76 seconds)
  - test.xcmsRawScanrange.none: (1 checks) ... OK (0.79 seconds)
- Test file: runit.snames.R
  - testAssignClass: (1 checks) ... OK (1.81 seconds)
  - testAssignNames: (2 checks) ... OK (1.81 seconds)
- Test file: runit.specDist.R
  - test.specDist: (3 checks) ... OK (0.07 seconds)
- Test file: runit.splitCombine.R
  - testCombine: (1 checks) ... OK (0.02 seconds)
  - testSplit: (1 checks) ... OK (0.05 seconds)
  - testSplitAll: (1 checks) ... OK (0.01 seconds)
  - testSplitFactorLongDrop: (6 checks) ... OK (0.02 seconds)
  - testSplitFactorShort: (6 checks) ... OK (0 seconds)
  - testSplitFirst: (1 checks) ... OK (0 seconds)
  - testSplitLast: (1 checks) ... OK (0.01 seconds)
  - testSplitMiddle: (1 checks) ... OK (0 seconds)
  - testSplitNone: (1 checks) ... OK (0 seconds)
  - testSplitPhenoData: (7 checks) ... OK (0.02 seconds)
  - testSubset: (70 checks) ... OK (2.59 seconds)
  - test_c_ProcessHistory: (8 checks) ... OK (0.08 seconds)
  - test_c_empty: (1 checks) ... OK (2.06 seconds)
  - test_getProcessHistory: (1 checks) ... OK (0 seconds)
  - test_split_ProcessHistory: (5 checks) ... OK (0.01 seconds)
- Test file: runit.splitRaw.R
  - testSplitRawEven: (3 checks) ... OK (0.01 seconds)
  - testSplitRawFirst: (1 checks) ... OK (0.02 seconds)
  - testSplitRawLast: (1 checks) ... OK (0.01 seconds)
  - testSplitRawNone: (3 checks) ... OK (0.01 seconds)
  - testSplitRawOdd: (3 checks) ... OK (0.02 seconds)
  - test_bracket_subset_xcmsRaw: (17 checks) ... OK (3.47 seconds)
- Test file: runit.unusedGroups.R
  - testGroup: (1 checks) ... OK (1.07 seconds)
- Test file: runit.updateObject.R
  - test_updateObject_xcmsSet: (2 checks) ... OK (0 seconds)
- Test file: runit.useOriginalCode.R
  - test_useOriginalCode: (0 checks) ... OK (0 seconds)
- Test file: runit.writecdf.R
  - test.write.cdf: (2 checks) ... OK (2.37 seconds)
- Test file: runit.writemzdata.R
  - test.write.mzdata: (2 checks) ... OK (2.83 seconds)
  - test.writeMS2.mzdata: (2 checks) ... OK (3.54 seconds)
  - test.writeMSn.mzdata: (2 checks) ... OK (1.22 seconds)
  - test.writePolarity.mzdata: (1 checks) ... OK (1.6 seconds)
- Test file: runit.writemzquantml.R
  - test.write.mzQuantML: (1 checks) ... OK (5.1 seconds)
- Test file: runit.xcmsRawCopy.R
  - test.rawMat: (2 checks) ... OK (0.93 seconds)
- Test file: runit.xcmsSet.R
  - test.findPeaksCentWave: (2 checks) ... OK (3.51 seconds)
  - test.findPeaksMatchedFilter: (2 checks) ... OK (4.44 seconds)
  - test.xcmsSetParallel: (1 checks) ... OK (2.23 seconds)

Name | Value
--- | ---
platform | x86_64-w64-mingw32
arch | x86_64
os | mingw32
system | x86_64, mingw32
status |
major | 3
minor | 4.0
year | 2017
month | 04
day | 21
svn rev | 72570
language | R
version.string | R version 3.4.0 (2017-04-21)
nickname | You Stupid Darkness
host | TOKAY2
compiler | NA