RUNIT TEST PROTOCOL--Sun Mar 04 04:41:21 2018

Number of test functions: 183

Number of errors: 0

Number of failures: 0

1 Test suite

Details

Test Suite: xcms unit testing

• Test file: runit.BiocParallel.R
  • test_BiocParallel: (3 checks) ... OK (5.81 seconds)
    
• Test file: runit.Chromatogram.R
  • test_deprecated_Chromatogram: (0 checks) ... OK (0.7 seconds)
    
  • test_extractChromatograms: (73 checks) ... OK (15 seconds)
    
• Test file: runit.Param-classes.R
  • test_CalibrantMassParam: (8 checks) ... OK (0.04 seconds)
    
  • test_CentWaveParam: (67 checks) ... OK (0.09 seconds)
    
  • test_CentWavePredIsoParam: (65 checks) ... OK (0.52 seconds)
    
  • test_FillChromPeaksParam: (15 checks) ... OK (0.03 seconds)
    
  • test_GenericParam: (3 checks) ... OK (0 seconds)
    
  • test_MSWParam: (47 checks) ... OK (0.12 seconds)
    
  • test_MassifquantParam: (44 checks) ... OK (0.11 seconds)
    
  • test_MzClustParam: (21 checks) ... OK (0.05 seconds)
    
  • test_NearestPeaksParam: (23 checks) ... OK (0.07 seconds)
    
  • test_ObiwarpParam: (60 checks) ... OK (0.08 seconds)
    
  • test_PeakDensityParam: (29 checks) ... OK (0.07 seconds)
    
  • test_PeakGroupsParam: (29 checks) ... OK (0.03 seconds)
    
  • test_matchedFilterParam: (45 checks) ... OK (0.07 seconds)
    
• Test file: runit.XCMSnExp.R
  • test_MS1_MS2_data: (20 checks) ... OK (4.06 seconds)
    
  • test_MsFeatureData_class_accessors: (12 checks) ... OK (0.07 seconds)
    
  • test_MsFeatureData_class_validation: (12 checks) ... OK (0.06 seconds)
    
  • test_XCMSnExp_class: (12 checks) ... OK (0.05 seconds)
    
  • test_XCMSnExp_class_accessors: (53 checks) ... OK (0.37 seconds)
    
  • test_XCMSnExp_droppers: (113 checks) ... OK (0.27 seconds)
    
  • test_XCMSnExp_filterFile: (59 checks) ... OK (0.7 seconds)
    
  • test_XCMSnExp_filterMz: (52 checks) ... OK (1.51 seconds)
    
  • test_XCMSnExp_filterRt: (88 checks) ... OK (1.42 seconds)
    
  • test_XCMSnExp_findChromPeaks: (11 checks) ... OK (8.61 seconds)
    
  • test_XCMSnExp_inherited_methods: (54 checks) ... OK (3.94 seconds)
    
  • test_XCMSnExp_intensity: (2 checks) ... OK (1.64 seconds)
    
  • test_XCMSnExp_mz: (2 checks) ... OK (1.98 seconds)
    
  • test_XCMSnExp_processHistory: (8 checks) ... OK (0.05 seconds)
    
  • test_XCMSnExp_rtime: (5 checks) ... OK (0.04 seconds)
    
  • test_XCMSnExp_spectra: (11 checks) ... OK (10.43 seconds)
    
  • test_adjustRtimePeakGroups: (5 checks) ... OK (0.13 seconds)
    
  • test_as_XCMSnExp_xcmsSet: (19 checks) ... OK (0.74 seconds)
    
  • test_chromatogram: (9 checks) ... OK (1.87 seconds)
    
  • test_extractMsData: (24 checks) ... OK (4.09 seconds)
    
  • test_featureValues: (2 checks) ... OK (0.58 seconds)
    
  • test_peakIndex: (2 checks) ... OK (0 seconds)
    
  • test_processHistory: (5 checks) ... OK (0 seconds)
    
  • test_signal_integration: (12 checks) ... OK (5.29 seconds)
    
  • test_spectrapply_spectra: (9 checks) ... OK (3.08 seconds)
    
  • test_split: (13 checks) ... OK (11.07 seconds)
    
• Test file: runit.absentPresent.R
  • testPresentAbsentSum: (8 checks) ... OK (1.92 seconds)
    
  • testPresentAbsentSumAfterFillPeaks: (8 checks) ... OK (0.55 seconds)
    
• Test file: runit.binning.R
  • test_binYonX_multi: (17 checks) ... OK (1.16 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 seconds)
    
  • test_imputation_lin: (14 checks) ... OK (0 seconds)
    
  • test_imputation_linbin: (8 checks) ... OK (0 seconds)
    
• Test file: runit.calibrate.R
  • test_calibrate_XCMSnExp: (14 checks) ... OK (0.3 seconds)
    
• Test file: runit.createProfileMatrix.R
  • test_createProfileMatrix: (7 checks) ... OK (0.23 seconds)
    
  • test_profMat: (4 checks) ... OK (2.05 seconds)
    
  • test_profMat_OnDiskMSnExp: (4 checks) ... OK (4.79 seconds)
    
  • test_profMethodReplace: (6 checks) ... OK (1.97 seconds)
    
  • test_profStepReplace: (4 checks) ... OK (0.03 seconds)
    
• Test file: runit.diffreport.R
  • testAnova: (0 checks) ... OK (0.88 seconds)
    
  • testDiffreport: (0 checks) ... OK (0.29 seconds)
    
  • testDiffreportMinSamples: (0 checks) ... OK (1.59 seconds)
    
• Test file: runit.do_adjustRtime.R
  • test_adjustRtime_PeakGroups: (32 checks) ... OK (1.6 seconds)
    
  • test_applyRtAdjustment: (2 checks) ... OK (1.41 seconds)
    
  • test_do_adjustRtime_peakGroups_implementation: (6 checks) ... OK (2.12 seconds)
    
  • test_getPeakGroupsRtMatrix: (3 checks) ... OK (0.02 seconds)
    
  • test_obiwarp: (13 checks) ... OK (18.87 seconds)
    
  • test_plotAdjustedRtime: (0 checks) ... OK (0.11 seconds)
    
• Test file: runit.do_findChromPeaks_MSW.R
  • test_do_findPeaks_MSW: (2 checks) ... OK (1.46 seconds)
    
  • test_findChromPeaks_MSW: (7 checks) ... OK (1.28 seconds)
    
• Test file: runit.do_findChromPeaks_centWave.R
  • test_do_findChromPeaks_centWave: (2 checks) ... OK (4.86 seconds)
    
  • test_findChromPeaks_centWave: (8 checks) ... OK (3.92 seconds)
    
  • test_findChromPeaks_centWave_peakIntensity: (4 checks) ... OK (4.43 seconds)
    
  • test_findChromPeaks_multiple_MS: (1 checks) ... OK (10.09 seconds)
    
• Test file: runit.do_findChromPeaks_centWave_isotopes.R
  • test_do_findChromPeaks_centWaveWithPredIsoROIs: (1 checks) ... OK (15.18 seconds)
    
  • test_findChromPeaks_centWaveWithPredIsoROIs: (8 checks) ... OK (21.1 seconds)
    
• Test file: runit.do_findChromPeaks_massifquant.R
  • test_do_findChromPeaks_massifquant: (4 checks) ... OK (11.62 seconds)
    
  • test_findChromPeaks_massifquant: (3 checks) ... OK (5.77 seconds)
    
• Test file: runit.do_findChromPeaks_matchedFilter.R
  • test_do_findChromPeaks_matchedFilter: (2 checks) ... OK (0.23 seconds)
    
  • test_findChromPeaks_matchedFilter: (3 checks) ... OK (2.21 seconds)
    
• Test file: runit.do_groupChromPeaks.R
  • test_do_groupChromPeaks_density: (1 checks) ... OK (2.58 seconds)
    
  • test_do_groupChromPeaks_nearest: (2 checks) ... OK (0.96 seconds)
    
  • test_do_groupPeaks_mzClust: (3 checks) ... OK (0.19 seconds)
    
  • test_featureValues_XCMSnExp: (3 checks) ... OK (0.6 seconds)
    
  • test_groupChromPeaks_NearestPeaksParam: (10 checks) ... OK (1.24 seconds)
    
  • test_groupChromPeaks_PeakDensityParam: (10 checks) ... OK (0.97 seconds)
    
  • test_groupPeaks_MzClustParam: (10 checks) ... OK (0.21 seconds)
    
• Test file: runit.fillChromPeaks.R
  • test_fillChromPeaks: (58 checks) ... OK (9.25 seconds)
    
  • test_fillChromPeaks_MSW: (11 checks) ... OK (2.52 seconds)
    
  • test_fillChromPeaks_matchedFilter: (18 checks) ... OK (9.38 seconds)
    
• Test file: runit.fillPeaks.R
  • test.fillPeaksColumns: (2 checks) ... OK (5.36 seconds)
    
  • test.getPeaks_implementation: (9 checks) ... OK (4.46 seconds)
    
  • testFilledFlag: (1 checks) ... OK (5.25 seconds)
    
• Test file: runit.findPeaksCentWave.R
  • test.findPeaksCentWaveResort: (1 checks) ... OK (2.86 seconds)
    
• Test file: runit.findPeaksCentWave.fitGauss.plot.R
  • test.findPeaksCentWave: (0 checks) ... OK (12.96 seconds)
    
• Test file: runit.findPeaksCentWaveWithIsotopeROIs.R
  • test.addPredictedIsotopeFeatures: (2 checks) ... OK (6.11 seconds)
    
• Test file: runit.findPeaksMassIfQuant.R
  • test.findPeaksMassIfQuant: (0 checks) ... OK (2.46 seconds)
    
• Test file: runit.functions-IO.R
  • test_mzRBackendFromFilecontent: (5 checks) ... OK (0.02 seconds)
    
  • test_mzRBackendFromFilename: (7 checks) ... OK (0 seconds)
    
  • test_mzRBackendFromFiletype: (7 checks) ... OK (0 seconds)
    
• Test file: runit.functions-XCMSnExp.R
  • test_applyAdjustedRtime: (8 checks) ... OK (0.1 seconds)
    
  • test_plotChromPeakDensity: (0 checks) ... OK (0.12 seconds)
    
  • test_plotChromPeakImage: (0 checks) ... OK (0.06 seconds)
    
  • test_plotChromPeaks: (0 checks) ... OK (0.83 seconds)
    
• Test file: runit.functions-normalization.R
  • test.fitModel: (1 checks) ... OK (0.03 seconds)
    
• Test file: runit.functions-utils.R
  • test_plotMsData: (0 checks) ... OK (0.52 seconds)
    
• Test file: runit.getEIC.R
  • test.getEICretcor: (0 checks) ... OK (3.79 seconds)
    
  • test.plotEIC: (0 checks) ... OK (0.08 seconds)
    
  • test_getEICxset: (5 checks) ... OK (15.64 seconds)
    
  • test_profEIC: (39 checks) ... OK (0.59 seconds)
    
• Test file: runit.getXcmsRaw.R
  • test.getXcmsRaw: (10 checks) ... OK (14.79 seconds)
    
  • test.getXcmsRawIssue44: (3 checks) ... OK (4.85 seconds)
    
• Test file: runit.group.R
  • testGroupDensityOnePeak: (0 checks) ... OK (0 seconds)
    
  • testGroupNearest: (1 checks) ... OK (10.07 seconds)
    
• Test file: runit.matchpeaks.R
  • test_matchpeaks: (0 checks) ... OK (1.8 seconds)
    
• Test file: runit.msms.R
  • test.msn2xcmsRaw: (3 checks) ... OK (1.42 seconds)
    
  • test.xcmsRawms1: (0 checks) ... OK (0.73 seconds)
    
  • test.xcmsRawms123: (4 checks) ... OK (2.26 seconds)
    
  • test.xcmsSetms2cw: (0 checks) ... OK (1.36 seconds)
    
  • test.xcmsSetms2mf: (0 checks) ... OK (1.25 seconds)
    
• Test file: runit.new_read_data.R
  • test_compare_readRawData: (7 checks) ... OK (7.81 seconds)
    
  • test_evaluate_xcmsSource: (6 checks) ... OK (4.58 seconds)
    
• Test file: runit.new_scanrange_subsetting.R
  • test_scanrange_centWave: (1 checks) ... OK (1.75 seconds)
    
  • test_scanrange_massifquant: (2 checks) ... OK (1 seconds)
    
  • test_scanrange_matchedFilter: (1 checks) ... OK (3.62 seconds)
    
  • test_scanrange_xcmsRaw: (6 checks) ... OK (1.85 seconds)
    
• Test file: runit.obiwarp.R
  • test.obiwarp.cor: (0 checks) ... OK (2.52 seconds)
    
  • test.obiwarp.cor_opt: (0 checks) ... OK (2.39 seconds)
    
  • test.obiwarp.cov: (0 checks) ... OK (2.56 seconds)
    
  • test.obiwarp.default: (0 checks) ... OK (2.32 seconds)
    
  • test.obiwarp.euc: (0 checks) ... OK (2.49 seconds)
    
  • test.obiwarp.local: (0 checks) ... OK (2.48 seconds)
    
  • test.obiwarp.prd: (0 checks) ... OK (2.39 seconds)
    
• Test file: runit.phenoData.R
  • testMultiFactor: (0 checks) ... OK (1.38 seconds)
    
  • testMultiFactorDiffreport: (1 checks) ... OK (5.8 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 (0.02 seconds)
    
  • test_showError: (6 checks) ... OK (0 seconds)
    
• Test file: runit.rawMat.R
  • test.rawMat: (10 checks) ... OK (1.06 seconds)
    
• Test file: runit.sampclass.R
  • test.sampclass: (5 checks) ... OK (5.45 seconds)
    
• Test file: runit.scanrage.R
  • test.xcmsRawScanrange.100: (1 checks) ... OK (0.91 seconds)
    
  • test.xcmsRawScanrange.first: (1 checks) ... OK (0.91 seconds)
    
  • test.xcmsRawScanrange.last: (1 checks) ... OK (0.9 seconds)
    
  • test.xcmsRawScanrange.none: (1 checks) ... OK (0.9 seconds)
    
• Test file: runit.snames.R
  • testAssignClass: (1 checks) ... OK (2.13 seconds)
    
  • testAssignNames: (2 checks) ... OK (2.11 seconds)
    
• Test file: runit.specDist.R
  • test.specDist: (3 checks) ... OK (0.08 seconds)
    
• Test file: runit.splitCombine.R
  • testCombine: (1 checks) ... OK (0.01 seconds)
    
  • testSplit: (1 checks) ... OK (0.04 seconds)
    
  • testSplitAll: (1 checks) ... OK (0.02 seconds)
    
  • testSplitFactorLongDrop: (6 checks) ... OK (0.02 seconds)
    
  • testSplitFactorShort: (6 checks) ... OK (0.01 seconds)
    
  • testSplitFirst: (1 checks) ... OK (0.02 seconds)
    
  • testSplitLast: (1 checks) ... OK (0.01 seconds)
    
  • testSplitMiddle: (1 checks) ... OK (0.02 seconds)
    
  • testSplitNone: (1 checks) ... OK (0 seconds)
    
  • testSplitPhenoData: (7 checks) ... OK (0.03 seconds)
    
  • testSubset: (70 checks) ... OK (3.12 seconds)
    
  • test_c_ProcessHistory: (8 checks) ... OK (0.09 seconds)
    
  • test_c_empty: (1 checks) ... OK (2.22 seconds)
    
  • test_getProcessHistory: (1 checks) ... OK (0.01 seconds)
    
  • test_split_ProcessHistory: (5 checks) ... OK (0.03 seconds)
    
• Test file: runit.splitRaw.R
  • testSplitRawEven: (3 checks) ... OK (0.01 seconds)
    
  • testSplitRawFirst: (1 checks) ... OK (0.02 seconds)
    
  • testSplitRawLast: (1 checks) ... OK (0.02 seconds)
    
  • testSplitRawNone: (3 checks) ... OK (0.02 seconds)
    
  • testSplitRawOdd: (3 checks) ... OK (0.02 seconds)
    
  • test_bracket_subset_xcmsRaw: (17 checks) ... OK (4.05 seconds)
    
• Test file: runit.unusedGroups.R
  • testGroup: (1 checks) ... OK (1.33 seconds)
    
• Test file: runit.updateObject.R
  • test_updateObject_xcmsSet: (2 checks) ... OK (0.02 seconds)
    
• Test file: runit.useOriginalCode.R
  • test_useOriginalCode: (0 checks) ... OK (0 seconds)
    
• Test file: runit.writecdf.R
  • test.write.cdf: (2 checks) ... OK (2.78 seconds)
    
• Test file: runit.writemzdata.R
  • test.write.mzdata: (2 checks) ... OK (3.39 seconds)
    
  • test.writeMS2.mzdata: (2 checks) ... OK (4.11 seconds)
    
  • test.writeMSn.mzdata: (2 checks) ... OK (1.39 seconds)
    
  • test.writePolarity.mzdata: (1 checks) ... OK (1.89 seconds)
    
• Test file: runit.writemzquantml.R
  • test.write.mzQuantML: (1 checks) ... OK (5.14 seconds)
    
• Test file: runit.xcmsRawCopy.R
  • test.rawMat: (2 checks) ... OK (0.93 seconds)
    
• Test file: runit.xcmsSet.R
  • test.findPeaksCentWave: (2 checks) ... OK (4 seconds)
    
  • test.findPeaksMatchedFilter: (2 checks) ... OK (5 seconds)
    
  • test.phenoDataFromPaths: (2 checks) ... OK (0 seconds)
    
  • test.xcmsSetParallel: (1 checks) ... OK (2.47 seconds)