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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaX_1.3.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/metaX.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaX’ version ‘1.3.7’
* 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 ‘metaX’ can be installed ... [15s/16s] WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Warning: Package 'metaX' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/metaX.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘HotE’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.runFit2: no visible binding for global variable ‘loessSpan’
bootPLSDA: no visible binding for global variable ‘trainIndex’
checkPvaluePlot: no visible global function definition for ‘png’
checkPvaluePlot: no visible binding for global variable ‘ID’
checkPvaluePlot: no visible binding for global variable
‘t.test_p.value’
checkPvaluePlot: no visible binding for global variable
‘wilcox.test_p.value’
checkPvaluePlot: no visible binding for global variable
‘t.test_p.value_BHcorrect’
checkPvaluePlot: no visible binding for global variable
‘wilcox.test_p.value_BHcorrect’
checkPvaluePlot: no visible binding for global variable ‘pvalue’
checkPvaluePlot: no visible global function definition for ‘dev.off’
checkQCPlot: no visible global function definition for ‘png’
checkQCPlot: no visible binding for global variable ‘ratio’
checkQCPlot: no visible binding for global variable ‘t.test_p.value’
checkQCPlot: no visible binding for global variable ‘Compound.ID’
checkQCPlot: no visible binding for global variable ‘ID’
checkQCPlot: no visible global function definition for ‘dev.off’
cor.network: no visible global function definition for ‘pdf’
cor.network: no visible global function definition for ‘dev.off’
importDataFromQI: no visible global function definition for ‘png’
importDataFromQI: no visible global function definition for ‘dev.off’
metaboliteAnnotation: no visible binding for global variable ‘mzmed’
metaboliteAnnotation: no visible binding for global variable ‘name’
myCalcAUROC : myROC: no visible binding for global variable ‘ID’
permutePLSDA: no visible global function definition for ‘pdf’
permutePLSDA: no visible global function definition for ‘dev.off’
plotCorHeatmap: no visible binding for global variable ‘ID’
plotCorHeatmap: no visible global function definition for
‘colorRampPalette’
plotCorHeatmap: no visible global function definition for ‘pdf’
plotCorHeatmap: no visible global function definition for ‘dev.off’
plotCorHeatmap: no visible global function definition for ‘png’
plotNetwork: no visible global function definition for ‘pdf’
plotNetwork: no visible global function definition for ‘dev.off’
powerAnalyst: no visible binding for global variable ‘ID’
powerAnalyst: no visible binding for global variable ‘statistic’
powerAnalyst: no visible global function definition for ‘pdf’
powerAnalyst: no visible binding for global variable ‘x’
powerAnalyst: no visible binding for global variable ‘y’
powerAnalyst: no visible global function definition for ‘dev.off’
runPLSDA: no visible global function definition for ‘pdf’
runPLSDA: no visible global function definition for ‘dev.off’
selectBestComponent: no visible global function definition for ‘pdf’
selectBestComponent: no visible binding for global variable ‘Component’
selectBestComponent: no visible binding for global variable ‘Value’
selectBestComponent: no visible binding for global variable ‘Metrics’
selectBestComponent: no visible global function definition for
‘dev.off’
svmRadialSelection: no visible binding for global variable ‘caretFuncs’
autoRemoveOutlier,metaXpara: no visible global function definition for
‘pdf’
autoRemoveOutlier,metaXpara: no visible binding for global variable ‘y’
autoRemoveOutlier,metaXpara: no visible global function definition for
‘dev.off’
calcAUROC,numeric: no visible global function definition for ‘plot.roc’
dataClean,metaXpara: no visible binding for global variable ‘ID’
dataClean,metaXpara: no visible binding for global variable ‘meanQC’
dataClean,metaXpara: no visible binding for global variable ‘sdQC’
dataClean,metaXpara: no visible global function definition for ‘pdf’
dataClean,metaXpara: no visible binding for global variable ‘val’
dataClean,metaXpara: no visible binding for global variable ‘batch’
dataClean,metaXpara: no visible global function definition for
‘dev.off’
doQCRLSC,metaXpara: no visible binding for global variable ‘maxOrder’
doQCRLSC,metaXpara: no visible binding for global variable ‘newOrder’
doQCRLSC,metaXpara: no visible binding for global variable ‘ID’
doQCRLSC,metaXpara: no visible binding for global variable ‘value’
doQCRLSC,metaXpara: no visible binding for global variable
‘valuePredict’
doQCRLSC,metaXpara: no visible binding for global variable ‘batch’
doQCRLSC,metaXpara: no visible binding for global variable ‘valueNorm’
doQCRLSC,metaXpara: no visible binding for global variable ‘CV’
doQCRLSC,metaXpara: no visible binding for global variable ‘lessThan30’
doQCRLSC,metaXpara: no visible binding for global variable ‘total’
doQCRLSC,metaXpara: no visible global function definition for ‘pdf’
doQCRLSC,metaXpara: no visible global function definition for ‘dev.off’
doQCRLSC,metaXpara: no visible binding for global variable ‘normCV’
doQCRLSC,metaXpara: no visible binding for global variable ‘cv’
filterPeaks,metaXpara: no visible binding for global variable ‘ID’
filterPeaks,metaXpara: no visible binding for global variable ‘value’
filterQCPeaks,metaXpara: no visible binding for global variable ‘ID’
filterQCPeaks,metaXpara: no visible binding for global variable ‘value’
filterQCPeaksByCV,metaXpara: no visible binding for global variable
‘ID’
metaXpipe,metaXpara: no visible binding for global variable ‘batch’
metaXpipe,metaXpara: no visible binding for global variable ‘value’
peakFinder,metaXpara: no visible global function definition for ‘pdf’
peakFinder,metaXpara: no visible global function definition for
‘dev.off’
peakStat,metaXpara-plsDAPara: no visible global function definition for
‘pdf’
peakStat,metaXpara-plsDAPara : <anonymous>: no visible binding for
global variable ‘ID’
peakStat,metaXpara-plsDAPara : <anonymous>: no visible binding for
global variable ‘valueNorm’
peakStat,metaXpara-plsDAPara : <anonymous>: no visible binding for
global variable ‘x’
peakStat,metaXpara-plsDAPara : <anonymous>: no visible binding for
global variable ‘y’
peakStat,metaXpara-plsDAPara : <anonymous>: no visible binding for
global variable ‘sig’
peakStat,metaXpara-plsDAPara : <anonymous>: no visible binding for
global variable ‘..density..’
peakStat,metaXpara-plsDAPara: no visible binding for global variable
‘ID’
peakStat,metaXpara-plsDAPara: no visible global function definition for
‘contains’
peakStat,metaXpara-plsDAPara: no visible global function definition for
‘dev.off’
plotCV,metaXpara: no visible global function definition for ‘pdf’
plotCV,metaXpara: no visible binding for global variable ‘ID’
plotCV,metaXpara: no visible binding for global variable ‘value’
plotCV,metaXpara: no visible binding for global variable ‘cv’
plotCV,metaXpara: no visible binding for global variable ‘n30’
plotCV,metaXpara: no visible binding for global variable ‘n20’
plotCV,metaXpara: no visible binding for global variable ‘n’
plotCV,metaXpara: no visible binding for global variable ‘valueNorm’
plotCV,metaXpara: no visible global function definition for ‘dev.off’
plotCV,metaXpara: no visible global function definition for ‘png’
plotHeatMap,metaXpara: no visible global function definition for
‘colorRampPalette’
plotHeatMap,metaXpara: no visible global function definition for
‘heat.colors’
plotHeatMap,metaXpara: no visible global function definition for
‘topo.colors’
plotHeatMap,metaXpara: no visible global function definition for ‘pdf’
plotHeatMap,metaXpara: no visible global function definition for
‘dev.off’
plotHeatMap,metaXpara: no visible global function definition for ‘png’
plotIntDistr,metaXpara: no visible global function definition for ‘pdf’
plotIntDistr,metaXpara: no visible binding for global variable ‘value’
plotIntDistr,metaXpara: no visible binding for global variable
‘valueNorm’
plotIntDistr,metaXpara: no visible global function definition for
‘dev.off’
plotIntDistr,metaXpara: no visible global function definition for ‘png’
plotLoading,data.frame: no visible global function definition for ‘png’
plotLoading,data.frame: no visible binding for global variable ‘PC1’
plotLoading,data.frame: no visible binding for global variable ‘PC2’
plotLoading,data.frame: no visible binding for global variable
‘alllabel’
plotLoading,data.frame: no visible global function definition for
‘dev.off’
plotMissValue,metaXpara: no visible global function definition for
‘pdf’
plotMissValue,metaXpara: no visible binding for global variable ‘ID’
plotMissValue,metaXpara: no visible binding for global variable ‘value’
plotMissValue,metaXpara: no visible binding for global variable
‘breaks’
plotMissValue,metaXpara: no visible binding for global variable ‘Freq’
plotMissValue,metaXpara: no visible binding for global variable ‘ratio’
plotMissValue,metaXpara: no visible global function definition for
‘dev.off’
plotMissValue,metaXpara: no visible global function definition for
‘png’
plotPCA,metaXpara: no visible global function definition for ‘pdf’
plotPCA,metaXpara: no visible binding for global variable ‘y’
plotPCA,metaXpara: no visible global function definition for ‘dev.off’
plotPCA,metaXpara: no visible global function definition for ‘png’
plotPLSDA,metaXpara: no visible global function definition for ‘pdf’
plotPLSDA,metaXpara: no visible binding for global variable ‘x’
plotPLSDA,metaXpara: no visible binding for global variable ‘y’
plotPLSDA,metaXpara: no visible global function definition for
‘dev.off’
plotPeakBox,metaXpara: no visible global function definition for ‘pdf’
plotPeakBox,metaXpara: no visible binding for global variable ‘ID’
plotPeakBox,metaXpara : <anonymous>: no visible binding for global
variable ‘valueNorm’
plotPeakBox,metaXpara: no visible global function definition for
‘dev.off’
plotPeakNumber,metaXpara: no visible global function definition for
‘pdf’
plotPeakNumber,metaXpara: no visible binding for global variable
‘npeaks’
plotPeakNumber,metaXpara: no visible binding for global variable
‘batch’
plotPeakNumber,metaXpara: no visible binding for global variable
‘outlier’
plotPeakNumber,metaXpara: no visible binding for global variable
‘missPeaksN’
plotPeakNumber,metaXpara: no visible global function definition for
‘dev.off’
plotPeakNumber,metaXpara: no visible global function definition for
‘png’
plotPeakSN,metaXpara: no visible global function definition for ‘pdf’
plotPeakSN,metaXpara: no visible binding for global variable ‘SN’
plotPeakSN,metaXpara: no visible binding for global variable ‘Ratio’
plotPeakSN,metaXpara: no visible global function definition for
‘dev.off’
plotPeakSumDist,metaXpara: no visible binding for global variable
‘batch’
plotPeakSumDist,metaXpara: no visible global function definition for
‘pdf’
plotPeakSumDist,metaXpara: no visible binding for global variable
‘outlier’
plotPeakSumDist,metaXpara: no visible global function definition for
‘dev.off’
plotPeakSumDist,metaXpara: no visible global function definition for
‘png’
plotQC,metaXpara: no visible global function definition for ‘pdf’
plotQC,metaXpara: no visible global function definition for ‘dev.off’
plotQCRLSC,metaXpara: no visible global function definition for ‘pdf’
plotQCRLSC,metaXpara: no visible binding for global variable
‘Intensity’
plotQCRLSC,metaXpara: no visible binding for global variable ‘batch’
plotQCRLSC,metaXpara: no visible global function definition for ‘png’
plotQCRLSC,metaXpara: no visible global function definition for
‘dev.off’
plotTreeMap,metaXpara: no visible global function definition for ‘pdf’
plotTreeMap,metaXpara: no visible global function definition for
‘dev.off’
Undefined global functions or variables:
..density.. CV Component Compound.ID Freq ID Intensity Metrics PC1
PC2 Ratio SN Value alllabel batch breaks caretFuncs colorRampPalette
contains cv dev.off heat.colors lessThan30 loessSpan maxOrder meanQC
missPeaksN mzmed n n20 n30 name newOrder normCV npeaks outlier pdf
plot.roc png pvalue ratio sdQC sig statistic t.test_p.value
t.test_p.value_BHcorrect topo.colors total trainIndex val value
valueNorm valuePredict wilcox.test_p.value
wilcox.test_p.value_BHcorrect x y
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "heat.colors",
"pdf", "png", "topo.colors")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'addValueNorm<-' and siglist 'metaXpara,metaXpara'
generic 'autoRemoveOutlier' and siglist 'metaXpara'
generic 'calcVIP' and siglist 'ANY'
generic 'center<-' and siglist 'plsDAPara'
generic 'dataClean' and siglist 'metaXpara'
generic 'dir.case<-' and siglist 'metaXpara'
generic 'dir.ctrl<-' and siglist 'metaXpara'
generic 'doQCRLSC' and siglist 'metaXpara'
generic 'filterPeaks' and siglist 'metaXpara'
generic 'filterQCPeaks' and siglist 'metaXpara'
generic 'filterQCPeaksByCV' and siglist 'metaXpara'
generic 'getPeaksTable' and siglist 'metaXpara'
generic 'group.bw0<-' and siglist 'metaXpara'
generic 'group.bw<-' and siglist 'metaXpara'
generic 'group.max<-' and siglist 'metaXpara'
generic 'group.minfrac<-' and siglist 'metaXpara'
generic 'group.minsamp<-' and siglist 'metaXpara'
generic 'group.mzwid0<-' and siglist 'metaXpara'
generic 'group.mzwid<-' and siglist 'metaXpara'
generic 'group.sleep<-' and siglist 'metaXpara'
generic 'hasQC' and siglist 'metaXpara'
generic 'idres<-' and siglist 'metaXpara'
generic 'kfold<-' and siglist 'plsDAPara'
generic 'makeDirectory' and siglist 'metaXpara'
generic 'makeMetaboAnalystInput' and siglist 'metaXpara'
generic 'metaXpipe' and siglist 'metaXpara'
generic 'method<-' and siglist 'plsDAPara'
generic 'missValueImputeMethod<-' and siglist 'metaXpara'
generic 'missingValueImpute' and siglist 'data.frame'
generic 'missingValueImpute' and siglist 'metaXpara'
generic 'myPLSDA' and siglist 'ANY,ANY,ANY,ANY'
generic 'myPLSDA' and siglist 'ANY,ANY,logical,ANY'
generic 'myPLSDA' and siglist 'ANY,ANY,missing,logical'
generic 'ncomp<-' and siglist 'plsDAPara'
generic 'normalize' and siglist 'metaXpara'
generic 'nperm<-' and siglist 'plsDAPara'
generic 'outdir<-' and siglist 'metaXpara'
generic 'peakFinder' and siglist 'metaXpara'
generic 'peakStat' and siglist 'metaXpara,plsDAPara'
generic 'peaksData<-' and siglist 'metaXpara'
generic 'plotCV' and siglist 'metaXpara'
generic 'plotHeatMap' and siglist 'metaXpara'
generic 'plotIntDistr' and siglist 'metaXpara'
generic 'plotLoading' and siglist 'data.frame'
generic 'plotLoading' and siglist 'mvr'
generic 'plotLoading' and siglist 'pcaRes'
generic 'plotMissValue' and siglist 'metaXpara'
generic 'plotPCA' and siglist 'metaXpara'
generic 'plotPLSDA' and siglist 'metaXpara'
generic 'plotPeakBox' and siglist 'metaXpara'
generic 'plotPeakNumber' and siglist 'metaXpara'
generic 'plotPeakSN' and siglist 'metaXpara'
generic 'plotPeakSumDist' and siglist 'metaXpara'
generic 'plotQC' and siglist 'metaXpara'
generic 'plotQCRLSC' and siglist 'metaXpara'
generic 'plotTreeMap' and siglist 'metaXpara'
generic 'prefix<-' and siglist 'metaXpara'
generic 'qcRlscSpan<-' and siglist 'metaXpara'
generic 'ratioPairs<-' and siglist 'metaXpara'
generic 'rawPeaks<-' and siglist 'metaXpara'
generic 'reSetPeaksData' and siglist 'metaXpara'
generic 'removeSample' and siglist 'metaXpara'
generic 'retcor.method<-' and siglist 'metaXpara'
generic 'retcor.plottype<-' and siglist 'metaXpara'
generic 'retcor.profStep<-' and siglist 'metaXpara'
generic 'sampleListFile<-' and siglist 'metaXpara'
generic 'scale<-' and siglist 'plsDAPara'
generic 't<-' and siglist 'plsDAPara'
generic 'validation<-' and siglist 'plsDAPara'
generic 'xcmsSet.fitgauss<-' and siglist 'metaXpara'
generic 'xcmsSet.fwhm<-' and siglist 'metaXpara'
generic 'xcmsSet.integrate<-' and siglist 'metaXpara'
generic 'xcmsSet.max<-' and siglist 'metaXpara'
generic 'xcmsSet.method<-' and siglist 'metaXpara'
generic 'xcmsSet.mzCenterFun<-' and siglist 'metaXpara'
generic 'xcmsSet.mzdiff<-' and siglist 'metaXpara'
generic 'xcmsSet.nSlaves<-' and siglist 'metaXpara'
generic 'xcmsSet.noise<-' and siglist 'metaXpara'
generic 'xcmsSet.peakwidth<-' and siglist 'metaXpara'
generic 'xcmsSet.polarity<-' and siglist 'metaXpara'
generic 'xcmsSet.ppm<-' and siglist 'metaXpara'
generic 'xcmsSet.prefilter<-' and siglist 'metaXpara'
generic 'xcmsSet.profparam<-' and siglist 'metaXpara'
generic 'xcmsSet.sleep<-' and siglist 'metaXpara'
generic 'xcmsSet.snthresh<-' and siglist 'metaXpara'
generic 'xcmsSet.step<-' and siglist 'metaXpara'
generic 'xcmsSet.verbose.columns<-' and siglist 'metaXpara'
generic 'xcmsSetObj<-' and siglist 'metaXpara'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'checkPvaluePlot'
‘file’
Documented arguments not in \usage in documentation object 'checkPvaluePlot':
‘f1’
Documented arguments not in \usage in documentation object 'myPLSDA':
‘ncomp’ ‘validation’ ‘method’ ‘k’
Undocumented arguments in documentation object 'plotLoading'
‘fig’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [303s/319s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
createModels 127.247 5.385 134.113
dataClean 21.222 0.139 21.826
plotQCRLSC 11.037 0.063 17.284
plotIntDistr 9.421 0.602 10.054
autoRemoveOutlier 9.701 0.287 10.233
plotPeakNumber 8.100 0.535 8.658
plotCV 7.876 0.500 8.411
normalize 7.610 0.569 8.803
plotMissValue 7.396 0.535 7.947
plotHeatMap 7.367 0.539 7.911
plotPCA 7.271 0.385 7.719
plotPLSDA 6.420 1.120 7.552
plotLoading 7.098 0.373 7.510
plotPeakSN 6.736 0.477 7.221
plotPeakBox 6.868 0.033 6.999
plotTreeMap 5.934 0.434 6.373
doQCRLSC 1.692 0.019 8.168
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [7s/8s]
[8s/8s] 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: 3 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/metaX.Rcheck/00check.log’
for details.
