R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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> ## unit tests will not be done if RUnit is not available
> if(require("RUnit", quietly=TRUE)) {
+
+ ## --- Setup ---
+
+ pkg <- "xcms" # <-- Change to package name!
+ if(Sys.getenv("RCMDCHECK") == "FALSE") {
+ ## Path to unit tests for standalone running under Makefile (not R CMD check)
+ ## PKG/tests/../inst/unitTests
+ path <- file.path(getwd(), "..", "inst", "unitTests")
+ } else {
+ ## Path to unit tests for R CMD check
+ ## PKG.Rcheck/tests/../PKG/unitTests
+ path <- system.file(package=pkg, "unitTests")
+ }
+ cat("\nRunning unit tests\n")
+ print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
+
+ library(package=pkg, character.only=TRUE)
+ library(package="faahKO", character.only=TRUE)
+
+ attr(faahko, "filepaths") <- sapply(as.list(basename(attr(faahko, "filepaths"))),
+ function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else "WT" ,x, package = "faahKO"))
+
+ library(BiocParallel)
+ if (.Platform$OS.type == "unix") {
+ prm <- MulticoreParam()
+ } else {
+ prm <- SnowParam()
+ }
+ register(bpstart(prm))
+
+ ## Create some objects we can re-use in different tests:
+ ## Needed in runit.XCMSnExp.R
+ faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+ system.file('cdf/KO/ko16.CDF', package = "faahKO"),
+ system.file('cdf/KO/ko18.CDF', package = "faahKO"))
+
+ ## An xcmsRaw for the first file:
+ faahko_xr_1 <- xcmsRaw(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+ profstep = 0)
+ faahko_od <- readMSData(faahko_3_files, mode = "onDisk")
+
+ faahko_xod <- findChromPeaks(faahko_od, param = CentWaveParam(noise = 10000,
+ snthresh = 40))
+ faahko_xs <- xcmsSet(faahko_3_files, profparam = list(step = 0),
+ method = "centWave", noise = 10000, snthresh = 40)
+
+ ## faahko_xod <- findChromPeaks(faahko_od, param = CentWaveParam(noise = 5000))
+ ## faahko_xs <- xcmsSet(faahko_3_files, profparam = list(step = 0),
+ ## method = "centWave", noise = 5000)
+ ## Doing also the retention time correction etc
+ od_x <- faahko_od
+ xod_x <- faahko_xod
+ xod_xg <- groupChromPeaks(
+ xod_x, param = PeakDensityParam(
+ sampleGroups = rep(1, length(fileNames(xod_x)))))
+ xod_xgr <- adjustRtime(xod_xg, param = PeakGroupsParam(span = 0.4))
+ xod_xgrg <- groupChromPeaks(
+ xod_xgr, param = PeakDensityParam(
+ sampleGroups = rep(1, length(fileNames(xod_x)))))
+
+ xod_r <- adjustRtime(as(od_x, "XCMSnExp"), param = ObiwarpParam())
+
+ faahko_grouped_filled <- fillPeaks(group(faahko))
+ faahko_grouped_retcor_filled <- fillPeaks(group(retcor(group(
+ updateObject(faahko)))))
+
+ ## microtofq
+ library(msdata)
+ microtofq_fs <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+ system.file("microtofq/MM8.mzML", package = "msdata"))
+ microtofq_xr <- xcmsRaw(microtofq_fs[1], profstep = 0)
+ microtofq_od <- readMSData(microtofq_fs, mode = "onDisk")
+
+ ## Direct injection data:
+ fticrf <- list.files(system.file("fticr", package = "msdata"),
+ recursive = TRUE, full.names = TRUE)
+ fticr <- readMSData(fticrf[1:2], msLevel. = 1, mode = "onDisk")
+ fticr_xod <- findChromPeaks(fticr, MSWParam(scales = c(1, 7),
+ peakThr = 80000, ampTh = 0.005,
+ SNR.method = "data.mean",
+ winSize.noise = 500))
+ fticr_xs <- xcmsSet(method="MSW", files=fticrf[1:2], scales=c(1,7),
+ SNR.method='data.mean' , winSize.noise=500,
+ peakThr=80000, amp.Th=0.005)
+
+ ## microtofq_xod <- findChromPeaks(microtofq_od, param = MSWParam())
+ ## If desired, load the name space to allow testing of private functions
+ ## if (is.element(pkg, loadedNamespaces()))
+ ## attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3)
+ ##
+ ## or simply call PKG:::myPrivateFunction() in tests
+
+ ## --- Testing ---
+
+ ## Define tests
+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
+ dirs=path)
+ ## Run
+ tests <- runTestSuite(testSuite)
+
+ ## Default report name
+ pathReport <- file.path(path, "report")
+
+ ## Report to stdout and text files
+ cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+ printTextProtocol(tests, showDetails=FALSE)
+ printTextProtocol(tests, showDetails=FALSE,
+ fileName=paste(pathReport, "Summary.txt", sep=""))
+ printTextProtocol(tests, showDetails=TRUE,
+ fileName=paste(pathReport, ".txt", sep=""))
+
+ ## Report to HTML file
+ printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
+
+ ## Return stop() to cause R CMD check stop in case of
+ ## - failures i.e. FALSE to unit tests or
+ ## - errors i.e. R errors
+ tmp <- getErrors(tests)
+ if(tmp$nFail > 0 | tmp$nErr > 0) {
+ stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
+ ", #R errors: ", tmp$nErr, ")\n\n", sep=""))
+ }
+ } else {
+ warning("cannot run unit tests -- package RUnit is not available")
+ }
Running unit tests
$pkg
[1] "xcms"
$getwd
[1] "/Users/biocbuild/bbs-3.6-bioc/meat/xcms.Rcheck/tests"
$pathToUnitTests
[1] "/Users/biocbuild/bbs-3.6-bioc/meat/xcms.Rcheck/xcms/unitTests"
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: ProtGenerics
This is MSnbase version 2.4.2
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
This is xcms version 3.0.2
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Processing 2572 mz slices ... OK
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
Processing 2572 mz slices ... OK
Sample number 2 used as center sample.
Aligning ko18.CDF against ko16.CDF ... OK
Aligning ko15.CDF against ko16.CDF ... OK
Processing 3195 mz slices ... OK
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt22.CDF
method: bin
step: 0.1
Processing 3195 mz slices ... OK
Performing retention time correction using 132 peak groups.
Processing 3195 mz slices ... OK
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
Executing test function test_BiocParallel ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 781 regions of interest ... OK: 46 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 75 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 75 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 781 regions of interest ... OK: 46 found.
done successfully.
Executing test function test_deprecated_Chromatogram ... done successfully.
Executing test function test_extractChromatograms ... Reverting retention times of identified peaks to original values ... OK
done successfully.
Executing test function test_CalibrantMassParam ... Error in validObject(p) :
invalid class "CalibrantMassParam" object: 'method' should be one of 'linear', 'shift' or 'edgeshift'.
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Error in validObject(p) :
invalid class "CalibrantMassParam" object: the mz values in 'mz' have to be increasingly ordered
done successfully.
Executing test function test_CentWaveParam ... Error in validObject(.Object) :
invalid class "CentWaveParam" object: 'ppm' has to be positive numeric of length 1.
Error in validObject(.Object) :
invalid class "CentWaveParam" object: 'prefilter' has to be a numeric of length 2.
Error in validObject(p) :
invalid class "CentWaveParam" object: 'mzCenterFun' has to be one of 'wMean', 'mean', 'apex', 'wMeanApex3', 'meanApex3'.
Error in (function (cl, name, valueClass) :
assignment of an object of class "character" is not valid for @'ppm' in an object of class "CentWaveParam"; is(value, "numeric") is not TRUE
Error in validObject(object) :
invalid class "CentWaveParam" object: 'peakwidth' has to be a numeric of length 2 with only positive values.
Error in validObject(object) :
invalid class "CentWaveParam" object: 'prefilter' has to be a numeric of length 2.
Error in validObject(object) :
invalid class "CentWaveParam" object: 'mzCenterFun' has to be one of 'wMean', 'mean', 'apex', 'wMeanApex3', 'meanApex3'.
Error in validObject(object) :
invalid class "CentWaveParam" object: 'integrate' has to be either 1 or 2.
Error in validObject(object) :
invalid class "CentWaveParam" object: 'mzdiff' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "CentWaveParam" object: 'fitgauss' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "CentWaveParam" object: 'noise' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "CentWaveParam" object: 'verboseColumns' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "CentWaveParam" object: 'firstBaselineCheck' has to be a numeric of length 1.
done successfully.
Executing test function test_CentWavePredIsoParam ... Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'ppm' has to be positive numeric of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'peakwidth' has to be a numeric of length 2 with only positive values.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'snthresh' has to be a positive numeric of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'prefilter' has to be a numeric of length 2.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'mzCenterFun' has to be one of 'wMean', 'mean', 'apex', 'wMeanApex3', 'meanApex3'.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'integrate' has to be either 1 or 2.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'mzdiff' has to be a numeric of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'fitgauss' has to be a numeric of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'noise' has to be a numeric of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'verboseColumns' has to be a numeric of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'firstBaselineCheck' has to be a numeric of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'snthreshIsoROIs' has to be a positive numeric of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'maxCharge' has to be a positive integer of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'maxIso' has to be a positive integer of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'mzIntervalExtension' has to be a logical of length 1.
Error in validObject(.Object) :
invalid class "CentWavePredIsoParam" object: 'polarity' has to be either 'positive', 'negative' or 'unknown'!
done successfully.
Executing test function test_FillChromPeaksParam ... Error in validObject(object) :
invalid class "FillChromPeaksParam" object: 'expandMz' has to be > -1 and of length 1
Error in validObject(object) :
invalid class "FillChromPeaksParam" object: 'expandMz' has to be > -1 and of length 1
Error in validObject(object) :
invalid class "FillChromPeaksParam" object: 'expandRt' has to be > -1 and of length 1
Error in validObject(object) :
invalid class "FillChromPeaksParam" object: 'expandRt' has to be > -1 and of length 1
Error in validObject(object) :
invalid class "FillChromPeaksParam" object: 'ppm' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "FillChromPeaksParam" object: 'ppm' has to be a positive numeric of length 1!
done successfully.
Executing test function test_GenericParam ... Error in validObject(.Object) :
invalid class "GenericParam" object: No function name specified in '@fun' but got '@args'
Error in validObject(.Object) :
invalid class "GenericParam" object: '@fun' has to be of length 1
done successfully.
Executing test function test_MSWParam ... Error in validObject(.Object) :
invalid class "MSWParam" object: 1: 'snthresh' has to be a positive numeric of length 1.
invalid class "MSWParam" object: 2: 'minNoiseLevel' has to be a positive numeric of length 1.
Error in validObject(.Object) :
invalid class "MSWParam" object: 'verboseColumns' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MSWParam" object: 'nearbyPeak' has to be a logical of length 1.
Error in validObject(object) :
invalid class "MSWParam" object: 'peakScaleRange' has to be a positive numeric of length 1.
Error in validObject(object) :
invalid class "MSWParam" object: 'ampTh' has to be a positive numeric of length 1.
Error in validObject(object) :
invalid class "MSWParam" object: 'minNoiseLevel' has to be a positive numeric of length 1.
Error in validObject(object) :
invalid class "MSWParam" object: 'ridgeLength' has to be a positive numeric of length 1.
Error in validObject(object) :
invalid class "MSWParam" object: 'peakThr' has to be a positive numeric of length 1.
Error in validObject(object) :
invalid class "MSWParam" object: 'tuneIn' has to be a logical of length 1.
done successfully.
Executing test function test_MassifquantParam ... Error in validObject(object) :
invalid class "MassifquantParam" object: 'ppm' has to be positive numeric of length 1.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'peakwidth' has to be a numeric of length 2 with only positive values.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'snthresh' has to be a positive numeric of length 1.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'prefilter' has to be a numeric of length 2.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'mzCenterFun' has to be one of 'wMean', 'mean', 'apex', 'wMeanApex3', 'meanApex3'.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'integrate' has to be either 1 or 2.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'mzdiff' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'fitgauss' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'noise' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'verboseColumns' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'criticalValue' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'consecMissedLimit' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MassifquantParam" object: 'unions' has to be either 0 or 1!
Error in validObject(object) :
invalid class "MassifquantParam" object: 'checkBack' has to be either 0 or 1!
Error in validObject(object) :
invalid class "MassifquantParam" object: 'withWave' has to be a numeric of length 1.
done successfully.
Executing test function test_MzClustParam ... Error in validObject(.Object) :
invalid class "MzClustParam" object: 'ppm' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "MzClustParam" object: 'absMz' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "MzClustParam" object: 'minFraction' has to be a single positive number between 0 and 1!
Error in validObject(object) :
invalid class "MzClustParam" object: 'minFraction' has to be a single positive number between 0 and 1!
Error in validObject(object) :
invalid class "MzClustParam" object: 'minFraction' has to be a single positive number between 0 and 1!
Error in validObject(.Object) :
invalid class "MzClustParam" object: 'minSamples' has to be a positive numeric of length 1!
done successfully.
Executing test function test_NearestPeaksParam ... Error in validObject(.Object) :
invalid class "NearestPeaksParam" object: 'mzVsRtBalance' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "NearestPeaksParam" object: 'mzVsRtBalance' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "NearestPeaksParam" object: 'absMz' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "NearestPeaksParam" object: 'absMz' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "NearestPeaksParam" object: 'absRt' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "NearestPeaksParam" object: 'absRt' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "NearestPeaksParam" object: 'kNN' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "NearestPeaksParam" object: 'kNN' has to be a positive numeric of length 1!
done successfully.
Executing test function test_ObiwarpParam ... Error in validObject(object) :
invalid class "ObiwarpParam" object: 'binSize' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'binSize' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'centerSample' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'centerSample' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'response' has to be a single integer from 1 to 100!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'response' has to be a single integer from 1 to 100!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'response' has to be a single integer from 1 to 100!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'distFun' has to be one of "cor", "cor_opt", "cov", "euc" or "prd"!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'distFun' has to be one of "cor", "cor_opt", "cov", "euc" or "prd"!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'gapInit' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'gapInit' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'gapExtend' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'gapExtend' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'factorDiag' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'factorDiag' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'factorGap' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'factorGap' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'localAlignment' has to be a logical of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'factorGap' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "ObiwarpParam" object: 'factorGap' has to be a positive numeric of length 1!
done successfully.
Executing test function test_PeakDensityParam ... Error in `sampleGroups<-`(`*tmp*`, value = NULL) :
'sampleGroups' should not contain any NAs and its length has to be >= 1
In addition: Warning message:
In is.na(value) : is.na() applied to non-(list or vector) of type 'NULL'
Error in `sampleGroups<-`(`*tmp*`, value = c(2, 2, NA)) :
'sampleGroups' should not contain any NAs and its length has to be >= 1
Error in PeakDensityParam() :
Argument 'sampleGroups' has to be defined. It should not contain 'NA's
Error in PeakDensityParam(sampleGroups = c(1, 1, NA)) :
Argument 'sampleGroups' has to be defined. It should not contain 'NA's
Error in validObject(.Object) :
invalid class "PeakDensityParam" object: 'bw' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "PeakDensityParam" object: 'minFraction' has to be a single positive number between 0 and 1!
Error in validObject(object) :
invalid class "PeakDensityParam" object: 'minFraction' has to be a single positive number between 0 and 1!
Error in validObject(object) :
invalid class "PeakDensityParam" object: 'minFraction' has to be a single positive number between 0 and 1!
Error in validObject(.Object) :
invalid class "PeakDensityParam" object: 'minSamples' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "PeakDensityParam" object: 'binSize' has to be a positive numeric of length 1!
Error in validObject(.Object) :
invalid class "PeakDensityParam" object: 'maxFeatures' has to be a positive numeric of length 1!
done successfully.
Executing test function test_PeakGroupsParam ... Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'minFraction' has to be a single number between 0 and 1!
Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'minFraction' has to be a single number between 0 and 1!
Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'minFraction' has to be a single number between 0 and 1!
Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'extraPeaks' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'extraPeaks' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'span' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'span' has to be a positive numeric of length 1!
Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'smooth' has to be either "loess" or "linear"!
Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'smooth' has to be either "loess" or "linear"!
Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'family' has to be either "gaussian" or "symmetric"!
Error in validObject(object) :
invalid class "PeakGroupsParam" object: 'family' has to be either "gaussian" or "symmetric"!
done successfully.
Executing test function test_matchedFilterParam ... Error in validObject(object) :
invalid class "MatchedFilterParam" object: 'binSize' has to be positive numeric of length 1.
Error in validObject(object) :
invalid class "MatchedFilterParam" object: Only values 'none', 'lin' and 'linbase' are allowed for'impute'
Error in validObject(object) :
invalid class "MatchedFilterParam" object: 'baseValue' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MatchedFilterParam" object: 'distance' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MatchedFilterParam" object: 'fwhm' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MatchedFilterParam" object: 'sigma' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MatchedFilterParam" object: 'max' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MatchedFilterParam" object: 'snthresh' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MatchedFilterParam" object: 'steps' has to be a numeric of length 1.
Error in validObject(object) :
invalid class "MatchedFilterParam" object: 'mzdiff' has to be a numeric of length 1.
Error in (function (cl, name, valueClass) :
assignment of an object of class "integer" is not valid for @'index' in an object of class "MatchedFilterParam"; is(value, "logical") is not TRUE
done successfully.
Processing 2572 mz slices ... OK
Performing retention time correction using 44 peak groups.
Processing 2572 mz slices ... OK
Executing test function test_MS1_MS2_data ... Sample number 2 used as center sample.
Aligning ko15.CDF against ko16.CDF ... OK
Aligning ko18.CDF against ko16.CDF ... OK
Apply retention time correction performed on MS1 to spectra from all MS levels
Sample number 2 used as center sample.
Aligning ko18.CDF against ko16.CDF ... OK
Aligning ko15.CDF against ko16.CDF ... OK
Sample number 2 used as center sample.
Aligning ko15.CDF against ko16.CDF ... OK
Aligning ko18.CDF against ko16.CDF ... OK
Apply retention time correction performed on MS1 to spectra from all MS levels
Applying retention time adjustment to the identified chromatographic peaks ... OK
Sample number 2 used as center sample.
Aligning ko18.CDF against ko16.CDF ... OK
Aligning ko15.CDF against ko16.CDF ... OK
done successfully.
Executing test function test_MsFeatureData_class_accessors ... Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
done successfully.
Executing test function test_MsFeatureData_class_validation ... done successfully.
Executing test function test_XCMSnExp_class ... Error in validObject(x) :
invalid class "XCMSnExp" object: Only 'ProcessHistory' objects are allowed in slot .processHistory!
Error in xod@msFeatureData$chromPeaks <- 3 :
cannot add bindings to a locked environment
Error in xod@msFeatureData$bla <- 4 :
cannot add bindings to a locked environment
done successfully.
Executing test function test_XCMSnExp_class_accessors ... Error in validObject(object) :
invalid class "MsFeatureData" object: 'chromPeaks' has to be a matrix or a data.frame!
Error in validObject(object) :
invalid class "XCMSnExp" object: The number of available samples does not match with the sample assignment of peaks in the 'chromPeaks' element of the msFeatureData slot!
Error in validObject(object) :
invalid class "XCMSnExp" object: The number of numeric vectors in the 'adjustedRtime' element of the msFeatureData slot does not match the number of samples!
done successfully.
Executing test function test_XCMSnExp_droppers ... Reverting retention times of identified peaks to original values ... OK
Reverting retention times of identified peaks to original values ... OK
done successfully.
Executing test function test_XCMSnExp_filterFile ... Error in tmp@msFeatureData$bla <- 3 :
cannot add bindings to a locked environment
Error in .local(object, ...) :
'file' has to be within 1 and the number of files in the object!
Error in .local(object, ...) :
'file' has to be within 1 and the number of files in the object!
Correspondence results (features) removed.
Reverting retention times of identified peaks to original values ... OK
Correspondence results (features) removed.
Reverting retention times of identified peaks to original values ... OK
Correspondence results (features) removed.
done successfully.
Executing test function test_XCMSnExp_filterMz ... done successfully.
Executing test function test_XCMSnExp_filterRt ... Error in res@msFeatureData$bla <- 3 :
cannot add bindings to a locked environment
done successfully.
Executing test function test_XCMSnExp_findChromPeaks ... Removed previously identified chromatographic peaks.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Removed feature definitions.
Removed previously identified chromatographic peaks.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Correspondence results (features) removed.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
done successfully.
Executing test function test_XCMSnExp_inherited_methods ... Error in xod_r[1, 1] : subsetting by columns ('j') not supported
Reverting retention times of identified peaks to original values ... OK
done successfully.
Executing test function test_XCMSnExp_intensity ... done successfully.
Executing test function test_XCMSnExp_mz ... done successfully.
Executing test function test_XCMSnExp_processHistory ... Error in .local(object, ...) :
'fileIndex' has to be within 1 and the number of samples!
In addition: Warning messages:
1: In xod_xgrg[idxs] : Removed preprocessing results
2: In xod_xgrg[idxs, keepAdjusted = TRUE] : Removed preprocessing results
done successfully.
Executing test function test_XCMSnExp_rtime ... done successfully.
Executing test function test_XCMSnExp_spectra ... done successfully.
Executing test function test_adjustRtimePeakGroups ... Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
done successfully.
Executing test function test_as_XCMSnExp_xcmsSet ... Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
Processing 2572 mz slices ... OK
Processing 2572 mz slices ... OK
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
Performing retention time correction using 19 peak groups.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
done successfully.
Executing test function test_chromatogram ... Correspondence results (features) removed.
done successfully.
Executing test function test_extractMsData ... Reverting retention times of identified peaks to original values ... OK
done successfully.
Executing test function test_featureValues ... Processing 2572 mz slices ... OK
Processing 2572 mz slices ... OK
done successfully.
Executing test function test_peakIndex ... done successfully.
Executing test function test_processHistory ... done successfully.
Executing test function test_signal_integration ... Correspondence results (features) removed.
Reverting retention times of identified peaks to original values ... OK
done successfully.
Executing test function test_spectrapply_spectra ... done successfully.
Executing test function test_split ... done successfully.
Executing test function testPresentAbsentSum ... Processing 3195 mz slices ... OK
done successfully.
Executing test function testPresentAbsentSumAfterFillPeaks ... done successfully.
Executing test function test_binYonX_multi ... Error in binYonX(X, X, nBins = 5L, fromIdx = 1, toIdx = c(2, 3)) :
'fromIdx' and 'toIdx' have to have the same length!
In addition: Warning message:
In .local(object, ...) : No aligned feature information available.
done successfully.
Executing test function test_binning_NA_handling ... done successfully.
Executing test function test_binning_max ... 'x' is not sorted, will sort 'x' and 'y'.
Error in binYonX(X, X, nBins = -4) : 'nBins' must be larger 1!
Error in binYonX(X, X, nBins = 0) : 'nBins' must be larger 1!
Error in binYonX(X, X, nBins = 4, fromIdx = 0) :
'fromIdx' and 'toIdx' have to be within 1 and lenght(x)!
Error in binYonX(X, X, nBins = 4, toIdx = 0) :
'fromIdx' and 'toIdx' have to be >= 0!
Error in binYonX(X, X, nBins = 4, fromIdx = 7, toIdx = 3) :
'fromIdx' has to be smaller than 'toIdx'!
Error in binYonX(X, X, nBins = 4, toIdx = 30) :
'fromIdx' and 'toIdx' have to be within 1 and lenght(x)!
done successfully.
Executing test function test_binning_mean ... done successfully.
Executing test function test_binning_min ... done successfully.
Executing test function test_binning_sum ... done successfully.
Executing test function test_breaks ... done successfully.
Executing test function test_imputation_lin ... done successfully.
Executing test function test_imputation_linbin ... done successfully.
Executing test function test_calibrate_XCMSnExp ... Error in .local(object, ...) :
The calibrate method for 'XCMSnExp' objects requires a 'CalibrantMassParam' object to be passed with argument 'param'
In addition: Warning message:
In .local(object, ...) :
Sample 1: only a single peak found, falling back to method = 'shift'
Error in .local(object, ...) :
Number of calibrant mz vectors differs from the number of samples
done successfully.
Executing test function test_createProfileMatrix ... done successfully.
Executing test function test_profMat ... Error in .local(object, ...) :
Can not calculate a profile matrix with step=0! Either provide a positive number with argument 'step' or use the 'profStep' method to set the step parameter for the xcmsSet.
Create profile matrix with method 'bin' and step 2 ... OK
Create profile matrix with method 'bin' and step 2 ... OK
Create profile matrix with method 'binlinbase' and step 2 ... OK
Create profile matrix with method 'binlinbase' and step 2 ... OK
done successfully.
Executing test function test_profMat_OnDiskMSnExp ... Create profile matrix with method 'bin' and step 2 ... OK
Create profile matrix with method 'bin' and step 2 ... OK
Create profile matrix with method 'binlin' and step 2 ... OK
done successfully.
Executing test function test_profMethodReplace ... Create profile matrix with method 'binlin' and step 2 ... OK
Create profile matrix with method 'binlin' and step 2 ... OK
Create profile matrix with method 'binlinbase' and step 2 ... OK
Create profile matrix with method 'binlinbase' and step 2 ... OK
done successfully.
Executing test function test_profStepReplace ... Create profile matrix with method 'bin' and step 2 ... OK
done successfully.
Processing 3195 mz slices ... OK
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
Executing test function testAnova ... done successfully.
Executing test function testDiffreport ... done successfully.
Executing test function testDiffreportMinSamples ... Too few samples per class, skipping t-test.
Too few samples per class, skipping t-test.
done successfully.
Executing test function test_adjustRtime_PeakGroups ... Processing 2572 mz slices ... OK
Processing 2572 mz slices ... OK
Performing retention time correction using 19 peak groups.
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
Processing 2572 mz slices ... OK
Processing 2572 mz slices ... OK
Performing retention time correction using 19 peak groups.
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
Performing retention time correction using 19 peak groups.
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
Performing retention time correction using 19 peak groups.
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
Reverting retention times of identified peaks to original values ... OK
done successfully.
Executing test function test_applyRtAdjustment ... Processing 3195 mz slices ... OK
Performing retention time correction using 132 peak groups.
done successfully.
Executing test function test_do_adjustRtime_peakGroups_implementation ... Processing 3195 mz slices ... OK
Performing retention time correction using 132 peak groups.
Performing retention time correction using 132 peak groups.
Performing retention time correction using 183 peak groups.
Performing retention time correction using 183 peak groups.
Performing retention time correction using 162 peak groups.
Performing retention time correction using 162 peak groups.
Performing retention time correction using 162 peak groups.
Performing retention time correction using 162 peak groups.
Performing retention time correction using 162 peak groups.
Performing retention time correction using 162 peak groups.
Performing retention time correction using 162 peak groups.
Performing retention time correction using 162 peak groups.
done successfully.
Executing test function test_getPeakGroupsRtMatrix ... done successfully.
Executing test function test_obiwarp ... center sample: ko16
Processing: ko15 Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
ko18 Create profile matrix with method 'bin' and step 1 ... OK
Sample number 2 used as center sample.
Aligning ko15.CDF against ko16.CDF ... OK
Aligning ko18.CDF against ko16.CDF ... OK
Sample number 2 used as center sample.
Aligning ko18.CDF against ko16.CDF ... OK
Aligning ko15.CDF against ko16.CDF ... OK
Sample number 2 used as center sample.
Aligning ko15.CDF against ko16.CDF ... OK
Aligning ko18.CDF against ko16.CDF ... OK
Applying retention time adjustment to the identified chromatographic peaks ... OK
Reverting retention times of identified peaks to original values ... OK
center sample: ko18
Processing: ko15 Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
ko16 Create profile matrix with method 'bin' and step 1 ... OK
Sample number 3 used as center sample.
Aligning ko15.CDF against ko18.CDF ... OK
Aligning ko16.CDF against ko18.CDF ... OK
center sample: ko18
Processing: ko15 Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
ko16 Create profile matrix with method 'bin' and step 1 ... OK
Sample number 3 used as center sample.
Aligning ko15.CDF against ko18.CDF ... OK
Aligning ko16.CDF against ko18.CDF ... OK
done successfully.
Executing test function test_plotAdjustedRtime ... done successfully.
Executing test function test_do_findPeaks_MSW ... done successfully.
Executing test function test_findChromPeaks_MSW ... Error in .local(object, param, ...) :
No MS level 2 spectra present to perform peak detection
In addition: Warning messages:
1: In plotAdjustedRtime(xod_x) :
No alignment/retention time correction results present.
2: In .local(object, ...) :
Adjusted retention times requested but none present. returning raw retention times instead.
3: In .local(object, ...) :
Adjusted retention times requested but none present. returning raw retention times instead.
4: In plotAdjustedRtime(xod_xg) :
No alignment/retention time correction results present.
5: In .local(object, ...) :
Adjusted retention times requested but none present. returning raw retention times instead.
6: In .local(object, ...) :
Adjusted retention times requested but none present. returning raw retention times instead.
done successfully.
Executing test function test_do_findChromPeaks_centWave ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 2814 regions of interest ... OK: 62 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 2814 regions of interest ... OK: 57 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1681 regions of interest ... OK: 102 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1681 regions of interest ... OK: 102 found.
done successfully.
Executing test function test_findChromPeaks_centWave ... Detecting mass traces at 40 ppm ... OK
Detecting chromatographic peaks in 78 regions of interest ... OK: 6 found.
Detecting mass traces at 40 ppm ... OK
Detecting chromatographic peaks in 78 regions of interest ... OK: 6 found.
Detecting mass traces at 40 ppm ... OK
Detecting chromatographic peaks in 78 regions of interest ... OK: 6 found.
Error in .local(object, param, ...) :
No MS level 2 spectra present to perform peak detection
Detecting mass traces at 40 ppm ... OK
Detecting chromatographic peaks in 78 regions of interest ... OK: 6 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
Detecting mass traces at 40 ppm ... OK
Detecting chromatographic peaks in 78 regions of interest ... OK: 6 found.
done successfully.
Executing test function test_findChromPeaks_centWave_peakIntensity ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 523 regions of interest ... OK: 176 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 523 regions of interest ...Correspondence results (features) removed.
Reverting retention times of identified peaks to original values ... OK
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... done successfully.
Executing test function test_findChromPeaks_multiple_MS ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 32539 regions of interest ... OK: 1568 found.
done successfully.
Executing test function test_do_findChromPeaks_centWaveWithPredIsoROIs ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 10673 regions of interest ... OK: 758 found.
Detecting chromatographic peaks in 3000 regions of interest ... OK: 147 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 10673 regions of interest ... OK: 758 found.
Detecting chromatographic peaks in 3000 regions of interest ... OK: 147 found.
done successfully.
Executing test function test_findChromPeaks_centWaveWithPredIsoROIs ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 5204 regions of interest ... OK: 274 found.
Detecting chromatographic peaks in 1123 regions of interest ... OK: 87 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 5204 regions of interest ... OK: 274 found.
Detecting chromatographic peaks in 1123 regions of interest ... OK: 87 found.
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 5204 regions of interest ... OK: 274 found.
Detecting chromatographic peaks in 1123 regions of interest ... OK: 87 found.
Error in .local(object, param, ...) :
No MS level 2 spectra present to perform peak detection
In addition: Warning message:
In .local(object, param, ...) :
Your data appears to be not centroided! CentWave works best on data in centroid mode.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 5204 regions of interest ... OK: 274 found.
Detecting chromatographic peaks in 1123 regions of interest ... OK: 87 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 5204 regions of interest ... OK: 274 found.
Detecting chromatographic peaks in 1123 regions of interest ... OK: 87 found.
done successfully.
Executing test function test_do_findChromPeaks_massifquant ...
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
1542 Peaks.
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
1542 Peaks.
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
Detecting chromatographic peaks in 1542 regions of interest ... OK: 66 found.
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
Detecting chromatographic peaks in 1542 regions of interest ... OK: 66 found.
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
559 Peaks.
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
559 Peaks.
done successfully.
Executing test function test_findChromPeaks_massifquant ...
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 20ppm ... OK
122 Peaks.
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 20ppm ... OK
122 Peaks.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
Error in .local(object, param, ...) :
No MS level 2 spectra present to perform peak detection
done successfully.
Executing test function test_do_findChromPeaks_matchedFilter ... done successfully.
Executing test function test_findChromPeaks_matchedFilter ... Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
Error in .local(object, param, ...) :
No MS level 2 spectra present to perform peak detection
done successfully.
Executing test function test_do_groupChromPeaks_density ... Processing 3195 mz slices ... OK
Processing 3195 mz slices ... OK
done successfully.
Executing test function test_do_groupChromPeaks_nearest ... Processing sample number 1 ... OK
Processing sample number 3 ... OK
Processing sample number 1 ... OK
Processing sample number 3 ... OK
Processing sample number 1 ... OK
Processing sample number 3 ... OK
done successfully.
Executing test function test_do_groupPeaks_mzClust ... 8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
8.00 16.00 28.00 32.00 40.00 64.00 80.00 96.00 100.00
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
done successfully.
Executing test function test_featureValues_XCMSnExp ... Processing 2572 mz slices ... OK
Processing 2572 mz slices ... OK
Error in .local(object, ...) :
Column 'bla' not present in the chromatographic peaks matrix!
done successfully.
Executing test function test_groupChromPeaks_NearestPeaksParam ... Processing sample number 1 ... OK
Processing sample number 3 ... OK
Processing sample number 1 ... OK
Processing sample number 3 ... OK
Processing sample number 1 ... OK
Processing sample number 3 ... OK
Processing sample number 1 ... OK
Processing sample number 3 ... OK
done successfully.
Executing test function test_groupChromPeaks_PeakDensityParam ... Processing 2572 mz slices ... OK
Processing 2572 mz slices ... OK
Processing 323 mz slices ... OK
Processing 323 mz slices ... OK
done successfully.
Executing test function test_groupPeaks_MzClustParam ... 8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
8.00 16.00 28.00 32.00 40.00 56.00 64.00 80.00 88.00 96.00 100.00
8.00 16.00 28.00 32.00 40.00 56.00 64.00 80.00 88.00 96.00 100.00
done successfully.
Executing test function test_fillChromPeaks ... Requesting 8 missing peaks from ko15.CDF ... got 7.
Requesting 10 missing peaks from ko16.CDF ... got 10.
Requesting 8 missing peaks from ko18.CDF ... got 7.
Correspondence results (features) removed.
Correspondence results (features) removed.
Correspondence results (features) removed.
Correspondence results (features) removed.
Correspondence results (features) removed.
Correspondence results (features) removed.
Requesting 87 missing peaks from ko15.CDF ... got 87.
Correspondence results (features) removed.
Requesting 100 missing peaks from ko16.CDF ... got 100.
Correspondence results (features) removed.
Requesting 61 missing peaks from ko18.CDF ... got 61.
Correspondence results (features) removed.
Requesting 8 missing peaks from ko15.CDF ... got 7.
Requesting 8 missing peaks from ko18.CDF ... got 7.
Requesting 10 missing peaks from ko16.CDF ... got 10.
Requesting 8 missing peaks from ko15.CDF ... got 7.
Requesting 10 missing peaks from ko16.CDF ... got 10.
Requesting 8 missing peaks from ko18.CDF ... got 7.
Requesting 10 missing peaks from ko16.CDF ... got 10.
Requesting 8 missing peaks from ko15.CDF ... got 8.
Requesting 8 missing peaks from ko18.CDF ... got 8.
Requesting 10 missing peaks from ko16.CDF ... got 10.
Requesting 8 missing peaks from ko18.CDF ... got 7.
Requesting 8 missing peaks from ko15.CDF ... got 7.
Correspondence results (features) removed.
done successfully.
Executing test function test_fillChromPeaks_MSW ... Empty 'sampleGroups' in 'param', assuming all samples to be in the same group.
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
Error in .local(object, param, ...) :
'object' does not provide feature definitions! Please run 'groupChromPeaks' first.
Requesting 5 missing peaks from HAM004_641fE_14-11-07--Exp1.extracted.mzdata ... got 5.
Requesting 4 missing peaks from HAM004_641fE_14-11-07--Exp2.extracted.mzdata ... got 4.
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
HAM004_641fE_14-11-07--Exp1.extracted HAM004_641fE_14-11-07--Exp2.extracted
Correspondence results (features) removed.
Requesting 17 missing peaks from HAM004_641fE_14-11-07--Exp1.extracted.mzdata ... got 17.
done successfully.
Executing test function test_fillChromPeaks_matchedFilter ... Processing 3195 mz slices ... OK
Requesting 45 missing peaks from ko15.CDF ... got 40.
Requesting 34 missing peaks from ko16.CDF ... got 33.
Requesting 39 missing peaks from ko18.CDF ... got 38.
Correspondence results (features) removed.
Requesting 470 missing peaks from ko15.CDF ... got 470.
Correspondence results (features) removed.
Requesting 556 missing peaks from ko16.CDF ... got 556.
Correspondence results (features) removed.
Requesting 418 missing peaks from ko18.CDF ... got 418.
Requesting 34 missing peaks from ko16.CDF ... got 34.
Requesting 45 missing peaks from ko15.CDF ... got 41.
Requesting 39 missing peaks from ko18.CDF ... got 39.
done successfully.
Executing test function test.fillPeaksColumns ... Processing 3195 mz slices ... OK
Processing 2572 mz slices ... OK
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
Processing 2572 mz slices ... OK
Processing 2572 mz slices ... OK
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
done successfully.
Executing test function test.getPeaks_implementation ... method: bin
step: 0.1
method: bin
step: 0.3
method: binlin
step: 0.2
method: binlinbase
step: 0.2
method: intlin
step: 0.2
done successfully.
Executing test function testFilledFlag ... Processing 3195 mz slices ... OK
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt22.CDF
method: bin
step: 0.1
done successfully.
Executing test function test.findPeaksCentWaveResort ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 292 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 292 found.
done successfully.
Executing test function test.findPeaksCentWave ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 272 found.
done successfully.
Executing test function test.addPredictedIsotopeFeatures ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 292 found.
Detecting chromatographic peaks in 1312 regions of interest ... OK: 112 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ...Detecting chromatographic peaks in 1312 regions of interest ... done successfully.
Executing test function test.findPeaksMassIfQuant ...
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
114 Peaks.
done successfully.
Executing test function test_mzRBackendFromFilecontent ... done successfully.
Executing test function test_mzRBackendFromFilename ... Error in xcms:::.mzRBackendFromFilename(c(1, 2)) :
parameter 'x' has to be of length 1
done successfully.
Executing test function test_mzRBackendFromFiletype ... Error in match.arg(tolower(x), c("mzml", "mzxml", "cdf", "netcdf", "mzdata")) :
'arg' must be of length 1
Error in match.arg(tolower(x), c("mzml", "mzxml", "cdf", "netcdf", "mzdata")) :
'arg' should be one of "mzml", "mzxml", "cdf", "netcdf", "mzdata"
done successfully.
Executing test function test_applyAdjustedRtime ... Error in applyAdjustedRtime(faahko_od) :
'object' has to be an 'XCMSnExp' object
done successfully.
Executing test function test_plotChromPeakDensity ... done successfully.
Executing test function test_plotChromPeakImage ... done successfully.
Executing test function test_plotChromPeaks ... done successfully.
Executing test function test.fitModel ... done successfully.
Executing test function test_plotMsData ... done successfully.
Executing test function test.getEICretcor ... Create profile matrix with method 'bin' and step 0.1 ... OK
Applying retention time correction to ko15.CDF.
Create profile matrix with method 'bin' and step 0.1 ... OK
Applying retention time correction to ko16.CDF.
done successfully.
Executing test function test.plotEIC ... done successfully.
Executing test function test_getEICxset ... No slot mslevel available, consider updating the object with the 'updateObject' method.
No slot scanrange available, consider updating the object with the 'updateObject' method.
Create profile matrix with method 'bin' and step 0.1 ... OK
No need to perform retention time correction, raw and corrected rt are identical for ko15.CDF.
No slot mslevel available, consider updating the object with the 'updateObject' method.
No slot scanrange available, consider updating the object with the 'updateObject' method.
Create profile matrix with method 'bin' and step 0.1 ... OK
No need to perform retention time correction, raw and corrected rt are identical for ko16.CDF.
No slot mslevel available, consider updating the object with the 'updateObject' method.
No slot scanrange available, consider updating the object with the 'updateObject' method.
Create profile matrix with method 'bin' and step 0.1 ... OK
No need to perform retention time correction, raw and corrected rt are identical for ko21.CDF.
No slot mslevel available, consider updating the object with the 'updateObject' method.
No slot scanrange available, consider updating the object with the 'updateObject' method.
Create profile matrix with method 'bin' and step 0.1 ... OK
No need to perform retention time correction, raw and corrected rt are identical for wt18.CDF.
No slot mslevel available, consider updating the object with the 'updateObject' method.
No slot scanrange available, consider updating the object with the 'updateObject' method.
Create profile matrix with method 'bin' and step 0.1 ... OK
Create profile matrix with method 'bin' and step 0.1 ... OK
No slot mslevel available, consider updating the object with the 'updateObject' method.
No slot scanrange available, consider updating the object with the 'updateObject' method.
Create profile matrix with method 'bin' and step 0.1 ... OK
No slot mslevel available, consider updating the object with the 'updateObject' method.
No slot scanrange available, consider updating the object with the 'updateObject' method.
Create profile matrix with method 'bin' and step 0.1 ... OK
Create profile matrix with method 'bin' and step 0.1 ... OK
Create profile matrix with method 'bin' and step 0.1 ... OK
done successfully.
Executing test function test_profEIC ... Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'binlinbase' and step 1 ... OK
Create profile matrix with method 'binlinbase' and step 0.2 ... OK
Create profile matrix with method 'intlin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 0.2 ... OK
Create profile matrix with method 'bin' and step 0.5 ... OK
Error in xcms:::profEIC(xraw, mzrange = mzr) :
'mzrange' number 1 (0, 14) is outside of the mz value range of 'object'
Error in profEIC(object, mzrange = mzrange, rtrange = rtrange, step = step) :
'mzrange' number 1 (0, 14) is outside of the mz value range of 'object'
Error in xcms:::profEIC(xraw, rtrange = c(6000, 6060)) :
'rtrange' number 1 (6000, 6060) is outside of the retention time range of 'object'
Error in profEIC(object, mzrange = mzrange, rtrange = rtrange, step = step) :
'rtrange' number 1 (6000, 6060) is outside of the retention time range of 'object'
Error in xcms:::profEIC(xraw, mzrange = c(1, 3, 5)) :
'mzrange' is supposed to be a two-column matrix with each row containing the min and max value specifying the mz range.
Error in profEIC(object, mzrange = mzrange, rtrange = rtrange, step = step) :
'mzrange' is supposed to be a two-column matrix with each row containing the min and max value specifying the mz range.
Error in xcms:::profEIC(xraw, rtrange = c(2, 4, 6)) :
'rtrange' is supposed to be a two-column matrix with each row containing the min and max value specifying the rt range.
Error in profEIC(object, mzrange = mzrange, rtrange = rtrange, step = step) :
'rtrange' is supposed to be a two-column matrix with each row containing the min and max value specifying the rt range.
done successfully.
Executing test function test.getXcmsRaw ... Create profile matrix with method 'bin' and step 0.1 ... OK
Applying retention time correction to ko15.CDF.
Create profile matrix with method 'bin' and step 0.1 ... OK
Create profile matrix with method 'bin' and step 0.1 ... OK
Create profile matrix with method 'bin' and step 0.1 ... OK
Create profile matrix with method 'bin' and step 0.1 ... OK
Create profile matrix with method 'bin' and step 0.1 ... OK
Applying retention time correction to ko15.CDF.
Applying retention time correction to ko16.CDF.
Applying retention time correction to ko18.CDF.
Applying retention time correction to ko19.CDF.
Create profile matrix with method 'bin' and step 2 ... OK
No need to perform retention time correction, raw and corrected rt are identical for ko15.CDF.
Create profile matrix with method 'bin' and step 2 ... OK
Create profile matrix with method 'bin' and step 2 ... OK
No need to perform retention time correction, raw and corrected rt are identical for ko15.CDF.
Create profile matrix with method 'bin' and step 2 ... OK
Create profile matrix with method 'bin' and step 2 ... OK
Create profile matrix with method 'bin' and step 2 ... OK
No need to perform retention time correction, raw and corrected rt are identical for ko15.CDF.
Create profile matrix with method 'bin' and step 2 ... OK
done successfully.
Executing test function test.getXcmsRawIssue44 ... Processing 3195 mz slices ... OK
center sample: ko15
Processing: ko16 Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 0.1 ... OK
Applying retention time correction to ko16.CDF.
done successfully.
Executing test function testGroupDensityOnePeak ... Processing 2 mz slices ... OK
done successfully.
Executing test function testGroupNearest ... Processing sample number 8 ... OK
Processing sample number 1 ... OK
Processing sample number 7 ... OK
Processing sample number 3 ... OK
Processing sample number 12 ... OK
Processing sample number 9 ... OK
Processing sample number 6 ... OK
Processing sample number 5 ... OK
Processing sample number 4 ... OK
Processing sample number 11 ... OK
Processing sample number 10 ... OK
done successfully.
Executing test function test_matchpeaks ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
done successfully.
Executing test function test.msn2xcmsRaw ... Create profile matrix with method 'bin' and step 1 ... OK
done successfully.
Executing test function test.xcmsRawms1 ... done successfully.
Executing test function test.xcmsRawms123 ... done successfully.
Executing test function test.xcmsSetms2cw ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 557 regions of interest ... OK: 107 found.
done successfully.
Executing test function test.xcmsSetms2mf ... done successfully.
Executing test function test_compare_readRawData ... done successfully.
Executing test function test_evaluate_xcmsSource ... done successfully.
Executing test function test_scanrange_centWave ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 292 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 382 regions of interest ... OK: 63 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 382 regions of interest ... OK: 63 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 588 regions of interest ... OK: 87 found.
done successfully.
Executing test function test_scanrange_massifquant ...
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
271 Peaks.
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
271 Peaks.
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
Detecting chromatographic peaks in 350 regions of interest ... OK: 23 found.
Massifquant, Copyright (C) 2013 Brigham Young University.
Massifquant comes with ABSOLUTELY NO WARRANTY. See LICENSE for details.
Detecting mass traces at 10ppm ... OK
Detecting chromatographic peaks in 350 regions of interest ... OK: 23 found.
done successfully.
Executing test function test_scanrange_matchedFilter ... Provided scanrange was adjusted to 901278
done successfully.
Executing test function test_scanrange_xcmsRaw ... done successfully.
Executing test function test.obiwarp.cor ... center sample: ko16
Processing: ko15 Create profile matrix with method 'bin' and step 10 ... OK
Create profile matrix with method 'bin' and step 10 ... OK
done successfully.
Executing test function test.obiwarp.cor_opt ... center sample: ko16
Processing: ko15 Create profile matrix with method 'bin' and step 10 ... OK
Create profile matrix with method 'bin' and step 10 ... OK
done successfully.
Executing test function test.obiwarp.cov ... center sample: ko16
Processing: ko15 Create profile matrix with method 'bin' and step 10 ... OK
Create profile matrix with method 'bin' and step 10 ... OK
done successfully.
Executing test function test.obiwarp.default ... center sample: ko16
Processing: ko15 Create profile matrix with method 'bin' and step 10 ... OK
Create profile matrix with method 'bin' and step 10 ... OK
done successfully.
Executing test function test.obiwarp.euc ... center sample: ko16
Processing: ko15 Create profile matrix with method 'bin' and step 10 ... OK
Create profile matrix with method 'bin' and step 10 ... OK
done successfully.
Executing test function test.obiwarp.local ... center sample: ko16
Processing: ko15 Create profile matrix with method 'bin' and step 10 ... OK
Create profile matrix with method 'bin' and step 10 ... OK
done successfully.
Executing test function test.obiwarp.prd ... center sample: ko16
Processing: ko15 Create profile matrix with method 'bin' and step 10 ... OK
Create profile matrix with method 'bin' and step 10 ... OK
done successfully.
Executing test function testMultiFactor ... Processing 3195 mz slices ... OK
done successfully.
Executing test function testMultiFactorDiffreport ... Processing 3195 mz slices ... OK
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/faahKO/cdf/WT/wt22.CDF
method: bin
step: 0.1
done successfully.
Executing test function test_ProcessHistory_c_xcmsSet ... done successfully.
Executing test function test_ProcessHistory_class ... Error in validObject(ph) :
invalid class "ProcessHistory" object: Got invalid type 'FAILURE'! Allowd are: "Unknown", "Peak detection", "Peak grouping", "Retention time correction", "Missing peak filling", "Calibration"
In addition: Warning messages:
1: In readRawData(fileName(object), includeMSn = includeMSn) :
MSn spectra requested but none present in the file.
2: In split.xcmsRaw(object, f = object@msnLevel == mslevel) :
MSn information will be dropped
3: In split.xcmsRaw(object, f = object@msnLevel == mslevel) :
MSn information will be dropped
4: In split.xcmsRaw(object, f = object@msnLevel == mslevel) :
MSn information will be dropped
5: In split.xcmsRaw(object, f = object@msnLevel == mslevel) :
MSn information will be dropped
Error in validObject(.Object) :
invalid class "ProcessHistory" object: Got invalid type 'any'! Allowd are: "Unknown", "Peak detection", "Peak grouping", "Retention time correction", "Missing peak filling", "Calibration"
Error in validObject(object) :
invalid class "ProcessHistory" object: Got invalid type 'OOOO'! Allowd are: "Unknown", "Peak detection", "Peak grouping", "Retention time correction", "Missing peak filling", "Calibration"
Error in validObject(object) :
invalid class "ProcessHistory" object: length of 'date' should not be larger than 1!
Error in validObject(object) :
invalid class "ProcessHistory" object: length of 'info' should not be larger than 1!
done successfully.
Executing test function test_XProcessHistory_class ... Error in validObject(ph) :
invalid class "XProcessHistory" object: Got invalid type 'other'! Allowd are: "Unknown", "Peak detection", "Peak grouping", "Retention time correction", "Missing peak filling", "Calibration"
done successfully.
Executing test function test_showError ... done successfully.
Executing test function test.rawMat ... done successfully.
Executing test function test.sampclass ... Processing 3195 mz slices ... OK
Processing 3195 mz slices ... OK
Processing 3195 mz slices ... OK
Processing 3195 mz slices ... OK
Setting the class labels as the interaction of the data.frame columns.
done successfully.
Executing test function test.xcmsRawScanrange.100 ... done successfully.
Executing test function test.xcmsRawScanrange.first ... done successfully.
Executing test function test.xcmsRawScanrange.last ... done successfully.
Executing test function test.xcmsRawScanrange.none ... done successfully.
Executing test function testAssignClass ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 292 found.
done successfully.
Executing test function testAssignNames ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 292 found.
done successfully.
Executing test function test.specDist ... done successfully.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 41 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 75 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 79 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 781 regions of interest ... OK: 46 found.
Executing test function testCombine ... done successfully.
Executing test function testSplit ... done successfully.
Executing test function testSplitAll ... done successfully.
Executing test function testSplitFactorLongDrop ... done successfully.
Executing test function testSplitFactorShort ... done successfully.
Executing test function testSplitFirst ... done successfully.
Executing test function testSplitLast ... done successfully.
Executing test function testSplitMiddle ... done successfully.
Executing test function testSplitNone ... done successfully.
Executing test function testSplitPhenoData ... No slot mslevel available, consider updating the object with the 'updateObject' method.
No slot scanrange available, consider updating the object with the 'updateObject' method.
done successfully.
Executing test function testSubset ... Comparing peaks...OK
Comparing peaks...OK
Processing 3195 mz slices ... OK
Performing retention time correction using 132 peak groups.
Processing 3195 mz slices ... OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
Error in xset[1, ] : Subsetting to rows is not supported!
Error in xset[, 20] : j has to be a numeric with values between 1 and 12!
Error in xset[, "not there"] :
j has to be a numeric with values between 1 and 12!
done successfully.
Executing test function test_c_ProcessHistory ... done successfully.
Executing test function test_c_empty ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 22 regions of interest ... FAIL: none found!
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 7 regions of interest ... FAIL: none found!
done successfully.
Executing test function test_getProcessHistory ... done successfully.
Executing test function test_split_ProcessHistory ... done successfully.
Executing test function testSplitRawEven ... done successfully.
Executing test function testSplitRawFirst ... done successfully.
Executing test function testSplitRawLast ... done successfully.
Executing test function testSplitRawNone ... done successfully.
Executing test function testSplitRawOdd ... done successfully.
Executing test function test_bracket_subset_xcmsRaw ... Create profile matrix with method 'bin' and step 20 ... OK
Create profile matrix with method 'bin' and step 20 ... OK
Create profile matrix with method 'bin' and step 20 ... OK
No need to perform retention time correction, raw and corrected rt are identical for ko15.CDF.
Create profile matrix with method 'bin' and step 20 ... OK
done successfully.
Executing test function testGroup ... Processing 3195 mz slices ... OK
done successfully.
Executing test function test_updateObject_xcmsSet ... done successfully.
Executing test function test_useOriginalCode ... done successfully.
Executing test function test.write.cdf ... Loading required package: ncdf4
Create profile matrix with method 'bin' and step 1 ... OK
done successfully.
Executing test function test.write.mzdata ... Loading required package: caTools
Attaching package: 'caTools'
The following object is masked from 'package:S4Vectors':
runmean
Create profile matrix with method 'bin' and step 1 ... OK
done successfully.
Executing test function test.writeMS2.mzdata ... Create profile matrix with method 'bin' and step 1 ... OK
done successfully.
Executing test function test.writeMSn.mzdata ... Create profile matrix with method 'bin' and step 1 ... OK
done successfully.
Executing test function test.writePolarity.mzdata ... Create profile matrix with method 'bin' and step 1 ... OK
done successfully.
Executing test function test.write.mzQuantML ... Processing 3195 mz slices ... OK
Loading required package: XML
done successfully.
Executing test function test.rawMat ... done successfully.
Executing test function test.findPeaksCentWave ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 392 regions of interest ... OK: 154 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 392 regions of interest ... OK: 154 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 323 regions of interest ... OK: 96 found.
done successfully.
Executing test function test.findPeaksMatchedFilter ... done successfully.
Executing test function test.phenoDataFromPaths ... done successfully.
Executing test function test.xcmsSetParallel ... Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 323 regions of interest ... OK: 96 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 323 regions of interest ... OK: 96 found.
done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Thu Apr 12 11:04:06 2018
***********************************************
Number of test functions: 183
Number of errors: 0
Number of failures: 0
1 Test Suite :
xcms unit testing - 183 test functions, 0 errors, 0 failures
Warning messages:
1: In .centWave_orig(mz = mz, int = int, scantime = scantime, valsPerSpect = valsPerSpect, :
No peaks found!
2: In xcmsSet(system.file("microtofq/MM14.mzML", package = "msdata"), :
No peaks found in sample MM14.
3: In xmlRoot.XMLInternalDocument(currentNodes[[1]]) : empty XML document
4: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, suppressNamespaceWarning) :
missing namespace definitions for prefix(es) xsi
5: In buildSmallMoleculeList(xs) :
xcmsSet still contains NA values, filling zero in. Better use fillPeaks() !
>
>
> proc.time()
user system elapsed
381.417 14.717 473.429
