##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings xcms_1.48.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/xcms.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘1.48.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xcms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
GPL (>= 2) + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘Biobase’ ‘BiocGenerics’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘mzR:::rampCloseAll’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Calls with DUP:
.C("ColMax", x, as.integer(n), as.integer(prod(dn)), double(prod(dn)),
DUP = FALSE, PACKAGE = "xcms")
.C("continuousPtsAboveThreshold", y, as.integer(istart - 1),
length(y), threshold = as.double(threshold), num = as.integer(num),
n = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("continuousPtsAboveThresholdIdx", y, as.integer(istart - 1),
length(y), threshold = as.double(threshold), num = as.integer(num),
n = integer(length(y)), DUP = FALSE, PACKAGE = "xcms")
.C("DescendMin", y, length(y), as.integer(istart - 1), ilower = integer(1),
iupper = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("DescendValue", y, length(y), as.integer(istart - 1), as.double(value),
ilower = integer(1), iupper = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("DescendZero", y, length(y), as.integer(istart - 1), ilower = integer(1),
iupper = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualGreater", x, length(x), as.double(value), index = integer(1),
DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualGreaterM", x, length(x), values, length(values),
index = integer(length(values)), DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualGreaterUnsorted", x, length(x), as.double(value),
index = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualLess", x, length(x), as.double(value), index = integer(1),
DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualGreater", x, length(x), as.double(values[1]), integer(1),
NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualLess", x, length(x), as.double(values[2]), integer(1),
NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
.C("MedianFilter", x, as.integer(dimx[1]), as.integer(dimx[2]),
as.integer(mrad), as.integer(nrad), out = doubleMatrix(dimx[1],
dimx[2]), DUP = FALSE, PACKAGE = "xcms")
.C("R_mzClust_hclust", x = as.double(x), num = N, d = as.double(d),
g = integer(length = N), eppm = as.double(eppm), eabs = as.double(eabs),
DUP = FALSE, NAOK = TRUE)
.C("NetCDFMSPoints", as.integer(ncid), as.integer(length(scanIndex)),
scanIndex, as.integer(len), massValues = double(len), intensityValues = double(len),
status = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("NetCDFVarDouble", as.integer(ncid), as.integer(var), data = double(len),
status = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("NetCDFVarInt", as.integer(ncid), as.integer(var), data = integer(len),
status = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("ProfBin", x, y, as.integer(length(x)), as.double(xstart),
as.double(xend), as.integer(num), out = double(num), DUP = FALSE,
PACKAGE = "xcms")
.C("ProfBinLin", x, y, as.integer(length(x)), as.double(xstart),
as.double(xend), as.integer(num), out = double(num), DUP = FALSE,
PACKAGE = "xcms")
.C("ProfBinLinBase", x, y, as.integer(length(x)), as.double(baselevel),
as.double(basespace), as.double(xstart), as.double(xend),
as.integer(num), out = double(num), DUP = FALSE, PACKAGE = "xcms")
.C("ProfBinLinBaseM", x, y, as.integer(length(x)), as.integer(zidx),
as.integer(length(zidx)), as.double(baselevel), as.double(basespace),
as.double(xstart), as.double(xend), as.integer(num), out = doubleMatrix(num,
length(zidx)), NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
.C("ProfBinLinM", x, y, as.integer(length(x)), as.integer(zidx),
as.integer(length(zidx)), as.double(xstart), as.double(xend),
as.integer(num), out = doubleMatrix(num, length(zidx)), NAOK = NAOK,
DUP = FALSE, PACKAGE = "xcms")
.C("ProfBinM", x, y, as.integer(length(x)), as.integer(zidx),
as.integer(length(zidx)), as.double(xstart), as.double(xend),
as.integer(num), out = doubleMatrix(num, length(zidx)), NAOK = NAOK,
DUP = FALSE, PACKAGE = "xcms")
.C("ProfIntLin", x, y, as.integer(length(x)), as.double(xstart),
as.double(xend), as.integer(num), out = double(num), DUP = FALSE,
PACKAGE = "xcms")
.C("ProfIntLinM", x, y, as.integer(length(x)), as.integer(zidx),
as.integer(length(zidx)), as.double(xstart), as.double(xend),
as.integer(num), out = doubleMatrix(num, length(zidx)), NAOK = NAOK,
DUP = FALSE, PACKAGE = "xcms")
.C("ProfMaxIdx", x, y, as.integer(length(x)), as.double(xstart),
as.double(xend), as.integer(num), out = integer(num), DUP = FALSE,
PACKAGE = "xcms")
.C("ProfMaxIdxM", x, y, as.integer(length(x)), as.integer(zidx),
as.integer(length(zidx)), as.double(xstart), as.double(xend),
as.integer(num), out = matrix(as.integer(0), num, length(zidx)),
NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
.C("RectUnique", m, as.integer(order - 1), nr, nc, as.double(xdiff),
as.double(ydiff), logical(nrow(m)), DUP = FALSE, PACKAGE = "xcms")
.C("RowMax", x, as.integer(prod(dn)), as.integer(p), double(prod(dn)),
DUP = FALSE, PACKAGE = "xcms")
.C("WhichColMax", x, as.integer(n), as.integer(prod(dn)), integer(prod(dn)),
DUP = FALSE, PACKAGE = "xcms")
.C("WhichRowMax", x, as.integer(prod(dn)), as.integer(p), integer(prod(dn)),
DUP = FALSE, PACKAGE = "xcms")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
joinOverlappingPeaks: warning in which(upper.tri(matrix(0, Ngp, Ngp)),
arr = TRUE): partial argument match of 'arr' to 'arr.ind'
joinOverlappingPeaks: warning in which(upper.tri(matrix(0, lcc, lcc)),
arr = TRUE): partial argument match of 'arr' to 'arr.ind'
plotQC: warning in apply(deviation_mzs[, sampOrder], MAR = 2, FUN =
function(x) median(x, na.rm = TRUE)): partial argument match of 'MAR'
to 'MARGIN'
plotQC: warning in apply(deviation_rts[, sampOrder], MAR = 2, FUN =
function(x) median(x, na.rm = TRUE)): partial argument match of 'MAR'
to 'MARGIN'
findPeaks.centWave,xcmsRaw: warning in which(m == max(m), arr = T):
partial argument match of 'arr' to 'arr.ind'
findPeaks.centWave,xcmsRaw: warning in matrix(c(1, 2, 3), nr = 3, nc =
1, byrow = T): partial argument match of 'nr' to 'nrow'
findPeaks.centWave,xcmsRaw: warning in matrix(c(1, 2, 3), nr = 3, nc =
1, byrow = T): partial argument match of 'nc' to 'ncol'
group.nearest,xcmsSet: warning in assign("peakmat", peakmat, env =
mplenv): partial argument match of 'env' to 'envir'
.onLoad : <anonymous>: no visible global function definition for
‘mpi.comm.size’
.onLoad : <anonymous>: no visible global function definition for
‘mpi.close.Rslaves’
.onLoad : <anonymous>: no visible global function definition for
‘mpi.finalize’
.write.metaboanalyst: no visible global function definition for
‘write.table’
.xcmsFragments.plotTree: no visible global function definition for
‘edgemode<-’
.xcmsFragments.plotTree: no visible global function definition for
‘addEdge’
.xcmsFragments.show: no visible global function definition for
‘object.size’
MSW.cwt: no visible global function definition for ‘convolve’
MSW.extendNBase: no visible global function definition for ‘nextn’
buildAnalysisSummary: no visible global function definition for
‘newXMLNode’
buildAssayList : <anonymous>: no visible global function definition for
‘newXMLNode’
buildAssayList: no visible global function definition for ‘newXMLNode’
buildAuditCollection: no visible global function definition for
‘newXMLNode’
buildCVlist: no visible global function definition for ‘newXMLNode’
buildCVlist: no visible global function definition for ‘addChildren’
buildCvParams : <anonymous>: no visible global function definition for
‘newXMLNode’
buildDataProcessingList: no visible global function definition for
‘newXMLNode’
buildFeatureList : <anonymous>: no visible global function definition
for ‘newXMLNode’
buildInputFiles : <anonymous>: no visible global function definition
for ‘newXMLNode’
buildInputFiles: no visible global function definition for ‘newXMLNode’
buildMzq: no visible global function definition for ‘xmlTree’
buildSmallMoleculeList : <anonymous>: no visible global function
definition for ‘newXMLNode’
buildSmallMoleculeList: no visible global function definition for
‘newXMLNode’
buildSoftwareList: no visible global function definition for
‘newXMLNode’
buildSoftwareList: no visible global function definition for
‘packageVersion’
buildStudyVariableList : <anonymous>: no visible global function
definition for ‘newXMLNode’
buildStudyVariableList : <anonymous> : <anonymous>: no visible global
function definition for ‘newXMLNode’
buildStudyVariableList: no visible global function definition for
‘newXMLNode’
defineColAndTy: no visible global function definition for ‘palette’
defineColAndTy: no visible global function definition for ‘rainbow’
estimate: no visible global function definition for ‘lm’
fillPeaksChromPar: no visible binding for global variable ‘i’
fillPeaksChromPar: no visible binding for global variable ‘object’
filtfft: no visible global function definition for ‘fft’
fitGauss: no visible global function definition for ‘nls’
getLocalNoiseEstimate: no visible global function definition for ‘sd’
joinOverlappingPeaks: no visible global function definition for
‘weighted.mean’
medianFilter: no visible binding for global variable ‘runmed’
msgfun.featureDetection: no visible global function definition for
‘flush.console’
msgfunGeneric: no visible global function definition for
‘flush.console’
mzCenter.wMean: no visible global function definition for
‘weighted.mean’
mzCenter.wMeanApex3: no visible global function definition for
‘weighted.mean’
mzClustGeneric : makeBin: no visible global function definition for
‘flush.console’
mzClustGeneric: no visible global function definition for
‘flush.console’
mzClust_hclust: no visible global function definition for ‘dist’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
patternVsRowScore: no visible global function definition for ‘nn2’
phenoDataFromPaths: no visible global function definition for ‘tail’
plot.xcmsEIC: no visible global function definition for ‘palette’
plot.xcmsEIC: no visible global function definition for ‘rainbow’
plot.xcmsEIC: no visible global function definition for ‘col2rgb’
plot.xcmsEIC: no visible global function definition for ‘rgb’
plot.xcmsEIC: no visible global function definition for ‘points’
plot.xcmsEIC: no visible global function definition for ‘legend’
plotQC: no visible global function definition for ‘rainbow’
plotQC: no visible global function definition for ‘hist’
plotQC: no visible global function definition for ‘na.omit’
plotQC: no visible global function definition for ‘loess’
plotQC: no visible global function definition for ‘lines’
plotQC: no visible global function definition for ‘predict’
plotQC: no visible global function definition for ‘legend’
plotQC: no visible global function definition for ‘barplot’
plotQC : <anonymous>: no visible global function definition for
‘median’
plotSpecWindow: no visible global function definition for ‘par’
plotSpecWindow: no visible global function definition for ‘lines’
plotSpecWindow: no visible global function definition for ‘title’
plotSpecWindow: no visible global function definition for ‘legend’
pval: no visible binding for global variable ‘sd’
pval: no visible global function definition for ‘pt’
rampRawData: no visible global function definition for
‘rampScanHeaders’
rampRawData: no visible global function definition for ‘rampSIPeaks’
rampRawDataMSn: no visible global function definition for
‘rampScanHeaders’
rampRawDataMSn: no visible global function definition for ‘rampSIPeaks’
read.mascot: no visible global function definition for ‘read.csv’
running: multiple local function definitions for ‘funct’ with different
formal arguments
specNoise: no visible global function definition for ‘quantile’
specNoise: no visible global function definition for ‘weighted.mean’
verify.mzQuantML: no visible global function definition for
‘xmlTreeParse’
verify.mzQuantML: no visible global function definition for
‘xmlInternalTreeParse’
verify.mzQuantML: no visible global function definition for
‘xmlSchemaValidate’
xcmsBoxPlot: no visible global function definition for ‘png’
xcmsBoxPlot: no visible global function definition for ‘pdf’
xcmsBoxPlot: no visible global function definition for ‘boxplot’
xcmsBoxPlot: no visible global function definition for ‘dev.off’
xcmsClusterApply: no visible global function definition for
‘checkCluster’
xcmsClusterApply : submit: no visible global function definition for
‘sendCall’
xcmsClusterApply: no visible global function definition for
‘recvOneResult’
xcmsClusterApply: no visible global function definition for
‘checkForRemoteErrors’
xcmsFragments.makeXS: no visible global function definition for
‘write.csv’
xcmsPapply: no visible global function definition for ‘mpi.comm.size’
xcmsPapply: no visible global function definition for
‘mpi.spawn.Rslaves’
xcmsPapply: no visible global function definition for ‘mpi.comm.rank’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.send.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.recv.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.any.source’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.any.tag’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for
‘mpi.bcast.Robj2slave’
xcmsPapply: no visible global function definition for ‘mpi.bcast.cmd’
xcmsPapply: no visible global function definition for ‘mpi.recv.Robj’
xcmsPapply: no visible global function definition for ‘mpi.any.source’
xcmsPapply: no visible global function definition for ‘mpi.any.tag’
xcmsPapply: no visible global function definition for
‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for ‘flush.console’
xcmsPapply: no visible global function definition for ‘mpi.send.Robj’
xcmsParallelSetup: no visible global function definition for
‘mpi.spawn.Rslaves’
xcmsParallelSetup: no visible global function definition for
‘mpi.comm.size’
xcmsParallelSetup: no visible global function definition for
‘mpi.comm.rank’
xcmsParallelSetup: no visible global function definition for
‘makeCluster’
xcmsSet: no visible global function definition for ‘mpi.close.Rslaves’
xcmsSet: no visible global function definition for ‘stopCluster’
AutoLockMass,xcmsRaw: no visible global function definition for
‘density’
AutoLockMass,xcmsRaw: no visible global function definition for
‘quantile’
AutoLockMass,xcmsRaw: no visible global function definition for ‘hist’
AutoLockMass,xcmsRaw: no visible global function definition for
‘median’
calibrate,xcmsSet: no visible global function definition for ‘abline’
calibrate,xcmsSet: no visible global function definition for ‘lines’
diffreport,xcmsSet: no visible global function definition for
‘mt.teststat’
diffreport,xcmsSet: no visible global function definition for ‘aov’
diffreport,xcmsSet: no visible global function definition for
‘write.table’
diffreport,xcmsSet: no visible global function definition for ‘png’
diffreport,xcmsSet: no visible global function definition for ‘pdf’
diffreport,xcmsSet: no visible global function definition for ‘dev.off’
fillPeaks.MSW,xcmsSet: no visible binding for global variable ‘median’
fillPeaks.MSW,xcmsSet: no visible global function definition for
‘flush.console’
fillPeaks.MSW,xcmsSet: no visible global function definition for
‘median’
fillPeaks.chrom,xcmsSet: no visible binding for global variable
‘median’
fillPeaks.chrom,xcmsSet: no visible global function definition for
‘mpi.close.Rslaves’
fillPeaks.chrom,xcmsSet: no visible global function definition for
‘stopCluster’
findPeaks.MSW,xcmsRaw: no visible global function definition for
‘peakDetectionCWT’
findPeaks.MSW,xcmsRaw: no visible global function definition for
‘tuneInPeakInfo’
findPeaks.centWave,xcmsRaw: no visible global function definition for
‘flush.console’
findPeaks.centWave,xcmsRaw: no visible global function definition for
‘par’
findPeaks.centWave,xcmsRaw: no visible global function definition for
‘layout’
findPeaks.centWave,xcmsRaw: no visible global function definition for
‘title’
findPeaks.centWave,xcmsRaw: no visible global function definition for
‘terrain.colors’
findPeaks.centWave,xcmsRaw: no visible global function definition for
‘lines’
findPeaks.centWave,xcmsRaw: no visible global function definition for
‘abline’
findPeaks.centWave,xcmsRaw: no visible global function definition for
‘na.omit’
findPeaks.massifquant,xcmsRaw: no visible global function definition
for ‘flush.console’
findPeaks.matchedFilter,xcmsRaw: no visible global function definition
for ‘nextn’
findPeaks.matchedFilter,xcmsRaw: no visible global function definition
for ‘deriv3’
findPeaks.matchedFilter,xcmsRaw: no visible global function definition
for ‘fft’
findPeaks.matchedFilter,xcmsRaw: no visible global function definition
for ‘flush.console’
findPeaks.matchedFilter,xcmsRaw: no visible global function definition
for ‘weighted.mean’
findPeaks.matchedFilter,xcmsRaw: no visible global function definition
for ‘points’
findPeaks.matchedFilter,xcmsRaw: no visible global function definition
for ‘abline’
getEIC,xcmsSet: no visible global function definition for
‘flush.console’
getEICNew,xcmsRaw: no visible binding for global variable ‘mclapply’
getPeaks,xcmsRaw: no visible global function definition for
‘weighted.mean’
getSpec,xcmsRaw: no visible global function definition for ‘approx’
getXcmsRaw,xcmsSet: no visible binding for global variable ‘mclapply’
group.density,xcmsSet: no visible global function definition for
‘flush.console’
group.density,xcmsSet: no visible global function definition for
‘density’
group.density,xcmsSet: no visible global function definition for
‘median’
group.density,xcmsSet: no visible global function definition for
‘points’
group.density,xcmsSet: no visible global function definition for
‘abline’
group.nearest,xcmsSet : <anonymous>: no visible binding for global
variable ‘coreList’
group.nearest,xcmsSet : <anonymous>: no visible binding for global
variable ‘peakIdxList’
group.nearest,xcmsSet: no visible global function definition for
‘median’
groupval,xcmsSet: no visible global function definition for ‘median’
image,xcmsRaw: no visible global function definition for ‘rainbow’
isCentroided,xcmsRaw: no visible global function definition for
‘quantile’
levelplot,xcmsRaw: no visible global function definition for
‘colorRampPalette’
levelplot,xcmsSet: no visible global function definition for
‘colorRampPalette’
peakTable,xcmsSet: no visible global function definition for
‘write.table’
plotChrom,xcmsRaw: no visible global function definition for ‘abline’
plotChrom,xcmsRaw: no visible global function definition for ‘nls’
plotChrom,xcmsRaw: no visible global function definition for ‘points’
plotChrom,xcmsRaw: no visible global function definition for ‘fitted’
plotChrom,xcmsRaw: no visible global function definition for ‘identify’
plotPeaks,xcmsRaw: no visible global function definition for
‘split.screen’
plotPeaks,xcmsRaw: no visible global function definition for
‘close.screen’
plotPeaks,xcmsRaw: no visible global function definition for ‘screen’
plotPeaks,xcmsRaw: no visible global function definition for ‘par’
plotPeaks,xcmsRaw: no visible global function definition for ‘abline’
plotRaw,xcmsRaw: no visible global function definition for
‘terrain.colors’
plotScan,xcmsRaw: no visible global function definition for ‘identify’
plotSpec,xcmsRaw: no visible global function definition for ‘abline’
plotSpec,xcmsRaw: no visible global function definition for ‘identify’
plotSurf,xcmsRaw: no visible global function definition for
‘terrain.colors’
plotSurf,xcmsRaw: no visible global function definition for ‘rgl.clear’
plotSurf,xcmsRaw: no visible global function definition for
‘rgl.surface’
plotSurf,xcmsRaw: no visible global function definition for
‘rgl.points’
plotSurf,xcmsRaw: no visible global function definition for ‘rgl.bbox’
plotTIC,xcmsRaw: no visible global function definition for ‘dev.cur’
plotTIC,xcmsRaw: no visible global function definition for ‘dev.list’
plotTIC,xcmsRaw: no visible global function definition for ‘identify’
plotTIC,xcmsRaw: no visible global function definition for ‘dev.set’
plotTree,xcmsFragments: no visible global function definition for
‘edgemode<-’
plotTree,xcmsFragments: no visible global function definition for
‘addEdge’
plotrt,xcmsSet: no visible global function definition for
‘split.screen’
plotrt,xcmsSet: no visible global function definition for ‘screen’
plotrt,xcmsSet: no visible global function definition for ‘par’
plotrt,xcmsSet: no visible global function definition for ‘legend’
plotrt,xcmsSet: no visible global function definition for ‘points’
plotrt,xcmsSet: no visible global function definition for ‘density’
plotrt,xcmsSet: no visible global function definition for ‘abline’
plotrt,xcmsSet: no visible global function definition for
‘close.screen’
retcor.obiwarp,xcmsSet: no visible global function definition for
‘median’
retcor.obiwarp,xcmsSet: no visible global function definition for
‘layout’
retcor.obiwarp,xcmsSet: no visible global function definition for ‘par’
retcor.obiwarp,xcmsSet: no visible global function definition for
‘points’
retcor.obiwarp,xcmsSet: no visible global function definition for
‘plot.new’
retcor.obiwarp,xcmsSet: no visible global function definition for
‘plot.window’
retcor.obiwarp,xcmsSet: no visible global function definition for
‘legend’
retcor.obiwarp,xcmsSet: no visible global function definition for
‘stepfun’
retcor.peakgroups,xcmsSet: no visible binding for global variable
‘median’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘na.omit’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘loess’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘predict’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘quantile’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘approx’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘tail’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘lsfit’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘head’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘split.screen’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘screen’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘par’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘legend’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘points’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘density’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘abline’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘close.screen’
retcor.peakgroups,xcmsSet: no visible global function definition for
‘stepfun’
show,xcmsEIC: no visible global function definition for ‘object.size’
show,xcmsFragments: no visible global function definition for
‘object.size’
show,xcmsRaw: no visible global function definition for ‘object.size’
show,xcmsSet: no visible global function definition for ‘object.size’
stitch.xml,xcmsRaw: no visible global function definition for ‘na.omit’
write.cdf,xcmsRaw: no visible global function definition for
‘ncdim_def’
write.cdf,xcmsRaw: no visible global function definition for
‘ncvar_def’
write.cdf,xcmsRaw: no visible global function definition for
‘nc_create’
write.cdf,xcmsRaw: no visible global function definition for
‘ncvar_put’
write.cdf,xcmsRaw: no visible global function definition for
‘ncatt_put’
write.cdf,xcmsRaw: no visible global function definition for ‘nc_close’
write.mzQuantML,xcmsSet: no visible global function definition for
‘saveXML’
write.mzdata,xcmsRaw: no visible global function definition for
‘base64encode’
Undefined global functions or variables:
abline addChildren addEdge aov approx barplot base64encode boxplot
checkCluster checkForRemoteErrors close.screen col2rgb
colorRampPalette convolve cor coreList density deriv3 dev.cur
dev.list dev.off dev.set dist edgemode<- fft fitted flush.console
head hist i identify layout legend lines lm loess lsfit makeCluster
mclapply median mpi.any.source mpi.any.tag mpi.bcast.Robj2slave
mpi.bcast.cmd mpi.close.Rslaves mpi.comm.rank mpi.comm.size
mpi.finalize mpi.get.sourcetag mpi.recv.Robj mpi.send.Robj
mpi.spawn.Rslaves mt.teststat na.omit nc_close nc_create ncatt_put
ncdim_def ncvar_def ncvar_put newXMLNode nextn nls nn2 object
object.size packageVersion palette par pdf peakDetectionCWT
peakIdxList plot.new plot.window png points predict pt quantile
rainbow rampSIPeaks rampScanHeaders read.csv recvOneResult rgb
rgl.bbox rgl.clear rgl.points rgl.surface runmed saveXML screen sd
sendCall split.screen stepfun stopCluster strwidth tail
terrain.colors text title tuneInPeakInfo weighted.mean write.csv
write.table xmlInternalTreeParse xmlSchemaValidate xmlTree
xmlTreeParse
Consider adding
importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.cur",
"dev.list", "dev.off", "dev.set", "palette", "pdf", "png",
"rainbow", "rgb", "terrain.colors")
importFrom("graphics", "abline", "barplot", "boxplot", "close.screen",
"hist", "identify", "layout", "legend", "lines", "par",
"plot.new", "plot.window", "points", "screen",
"split.screen", "strwidth", "text", "title")
importFrom("stats", "aov", "approx", "convolve", "cor", "density",
"deriv3", "dist", "fft", "fitted", "lm", "loess", "lsfit",
"median", "na.omit", "nextn", "nls", "predict", "pt",
"quantile", "runmed", "sd", "stepfun", "weighted.mean")
importFrom("utils", "flush.console", "head", "object.size",
"packageVersion", "read.csv", "tail", "write.csv",
"write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: split.xcmsRaw.Rd:18-20: Dropping empty section \usage
prepare_Rd: split.xcmsSet.Rd:19-21: Dropping empty section \usage
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘xcms/libs/xcms.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘massifquant/TrMgr.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
findPeaks.massifquant-methods 22.987 0.064 23.161
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 6 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/xcms.Rcheck/00check.log’
for details.
