BioC 3.2: CHECK report for metaX on moscato1

Package: metaX

Version: 1.0.3

Command: rm -rf metaX.buildbin-libdir metaX.Rcheck && mkdir metaX.buildbin-libdir metaX.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaX.buildbin-libdir metaX_1.0.3.tar.gz >metaX.Rcheck\00install.out 2>&1 && cp metaX.Rcheck\00install.out metaX-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=metaX.buildbin-libdir --install="check:metaX-install.out" --force-multiarch --no-vignettes --timings metaX_1.0.3.tar.gz

StartedAt: 2016-04-23 04:33:00 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:53:16 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 1216.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: metaX.Rcheck

Warnings: 1

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### Running command:
###
###   rm -rf metaX.buildbin-libdir metaX.Rcheck && mkdir metaX.buildbin-libdir metaX.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaX.buildbin-libdir metaX_1.0.3.tar.gz >metaX.Rcheck\00install.out 2>&1 && cp metaX.Rcheck\00install.out metaX-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=metaX.buildbin-libdir --install="check:metaX-install.out" --force-multiarch --no-vignettes --timings metaX_1.0.3.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/metaX.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metaX/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaX' version '1.0.3'
* 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 whether package 'metaX' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'metaX' is deprecated and will be removed from Bioconductor
See 'D:/biocbld/bbs-3.2-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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.
* 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'
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'
plotCorHeatmap: no visible binding for global variable 'ID'
powerAnalyst: no visible binding for global variable 'ID'
powerAnalyst: no visible binding for global variable 'statistic'
powerAnalyst: no visible binding for global variable 'x'
powerAnalyst: no visible binding for global variable 'y'
rfSelection: no visible global function definition for 'rfeControl'
rfSelection: no visible binding for global variable 'rfFuncs'
rfSelection: no visible global function definition for 'rfe'
selectBestComponent: no visible binding for global variable 'Component'
selectBestComponent: no visible binding for global variable 'Value'
selectBestComponent: no visible binding for global variable 'Metrics'
svmRadialSelection: no visible global function definition for
  'rfeControl'
svmRadialSelection: no visible binding for global variable 'caretFuncs'
svmRadialSelection: no visible global function definition for 'rfe'
autoRemoveOutlier,metaXpara: no visible binding for global variable 'y'
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 binding for global variable 'val'
dataClean,metaXpara: no visible binding for global variable 'batch'
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 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'
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 'value'
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'
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'
plotIntDistr,metaXpara: no visible binding for global variable 'value'
plotIntDistr,metaXpara: no visible binding for global variable
  'valueNorm'
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'
plotPCA,metaXpara: no visible binding for global variable 'y'
plotPLSDA,metaXpara: no visible binding for global variable 'x'
plotPLSDA,metaXpara: no visible binding for global variable 'y'
plotPeakBox,metaXpara: no visible binding for global variable 'ID'
plotPeakBox,metaXpara : <anonymous>: no visible binding for global
  variable 'valueNorm'
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'
plotPeakSN,metaXpara: no visible binding for global variable 'SN'
plotPeakSN,metaXpara: no visible binding for global variable 'Ratio'
plotPeakSumDist,metaXpara: no visible binding for global variable
  'batch'
plotPeakSumDist,metaXpara: no visible binding for global variable
  'outlier'
plotQCRLSC,metaXpara: no visible binding for global variable
  'Intensity'
plotQCRLSC,metaXpara: no visible binding for global variable 'batch'
* checking Rd files ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [435s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
createModels      153.66   3.49  157.17
dataClean          30.11   0.07   30.26
plotCV             15.99   0.58   16.57
autoRemoveOutlier  15.96   0.17   16.94
normalize          14.61   0.98   19.02
plotTreeMap        14.66   0.52   15.99
plotHeatMap        14.62   0.52   15.24
plotIntDistr       14.52   0.54   15.12
plotQCRLSC         14.51   0.04   23.68
plotMissValue      13.03   0.63   14.34
plotPeakSN         12.61   0.33   12.94
plotPeakNumber     11.08   0.69   11.77
plotPLSDA           9.30   0.56   10.45
plotPCA             8.24   0.06    8.30
plotPeakBox         7.08   0.00    7.84
cor.network         5.75   0.06    5.82
doQCRLSC            2.65   0.02   11.28
** running examples for arch 'x64' ... [440s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
createModels      169.34   3.11  172.47
dataClean          27.00   0.03   27.87
plotQCRLSC         19.17   0.07   29.37
plotIntDistr       14.01   1.41   15.51
autoRemoveOutlier  14.20   0.29   14.98
plotHeatMap        12.45   0.92   13.40
plotPeakSN         11.84   0.86   12.70
plotCV             11.70   0.85   12.54
plotTreeMap        11.25   1.26   12.61
normalize          10.07   1.06   11.43
plotMissValue      10.06   1.06   11.12
plotPeakNumber      9.79   0.76   10.56
plotPLSDA           9.49   0.79   10.28
plotPCA             8.21   0.09    8.72
plotPeakBox         7.88   0.02    8.10
doQCRLSC            2.48   0.01   11.26
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [9s]
 [9s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [12s]
 [12s] 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: 1 WARNING, 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/metaX.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'metaX' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'metaX' is deprecated and will be removed from Bioconductor
  version 3.3

install for x64

* installing *source* package 'metaX' ...
** testing if installed package can be loaded
Warning: Package 'metaX' is deprecated and will be removed from Bioconductor
  version 3.3
* MD5 sums
packaged installation of 'metaX' as metaX_1.0.3.zip
* DONE (metaX)

name	user	system	elapsed
addValueNorm	0.86	0.00	0.85
autoRemoveOutlier	15.96	0.17	16.94
calcAUROC	0	0	0
calcVIP	0.05	0.00	0.05
center	0	0	0
cor.network	5.75	0.06	5.82
createModels	153.66	3.49	157.17
dataClean	30.11	0.07	30.26
dir.case	0	0	0
dir.ctrl	0	0	0
doQCRLSC	2.65	0.02	11.28
filterPeaks	1.09	0.01	1.10
filterQCPeaks	1.02	0.00	1.02
filterQCPeaksByCV	1.46	0.02	1.48
getPeaksTable	0.83	0.04	1.49
group.bw	0.05	0.00	0.04
group.bw0	0.03	0.00	0.03
group.max	0.03	0.00	0.03
group.minfrac	0.05	0.00	0.05
group.minsamp	0.05	0.00	0.05
group.mzwid	0.03	0.00	0.03
group.mzwid0	0.02	0.01	0.03
group.sleep	0.03	0.00	0.03
hasQC	0.67	0.02	0.69
idres	0.03	0.00	0.03
kfold	0	0	0
makeDirectory	0	0	0
makeMetaboAnalystInput	2.07	0.00	2.07
metaXpipe	0	0	0
method	0	0	0
missValueImputeMethod	0	0	0
missingValueImpute	1.39	0.03	1.42
myCalcAUROC	0	0	0
myPLSDA	0.02	0.00	0.02
ncomp	0.01	0.00	0.01
normalize	14.61	0.98	19.02
nperm	0	0	0
outdir	0	0	0
pathwayAnalysis	0	0	0
peakFinder	0.01	0.00	0.02
peakStat	0	0	0
peaksData	0.83	0.00	0.82
plotCV	15.99	0.58	16.57
plotCorHeatmap	4.29	0.09	4.38
plotHeatMap	14.62	0.52	15.24
plotIntDistr	14.52	0.54	15.12
plotMissValue	13.03	0.63	14.34
plotNetwork	1.99	0.03	2.03
plotPCA	8.24	0.06	8.30
plotPLSDA	9.30	0.56	10.45
plotPeakBox	7.08	0.00	7.84
plotPeakNumber	11.08	0.69	11.77
plotPeakSN	12.61	0.33	12.94
plotPeakSumDist	1.52	0.00	1.51
plotQC	2.93	0.00	2.93
plotQCRLSC	14.51	0.04	23.68
plotTreeMap	14.66	0.52	15.99
powerAnalyst	0	0	0
preProcess	3.54	0.00	3.54
prefix	0	0	0
qcRlscSpan	0.03	0.00	0.03
ratioPairs	0	0	0
rawPeaks	0.05	0.00	0.05
reSetPeaksData	0.68	0.00	0.68
removeSample	0.77	0.00	0.77
retcor.method	0.03	0.00	0.03
retcor.plottype	0.05	0.00	0.05
retcor.profStep	0.03	0.00	0.03
sampleListFile	0	0	0
scale	0	0	0
selectBestComponent	4.18	0.03	4.37
t	0	0	0
transformation	1.62	0.00	1.62
validation	0	0	0
xcmsSet.fitgauss	0.03	0.00	0.03
xcmsSet.fwhm	0.03	0.00	0.04
xcmsSet.integrate	0.02	0.00	0.01
xcmsSet.max	0.04	0.00	0.05
xcmsSet.method	0.04	0.00	0.03
xcmsSet.mzCenterFun	0.01	0.00	0.01
xcmsSet.mzdiff	0.01	0.00	0.02
xcmsSet.nSlaves	0.03	0.00	0.03
xcmsSet.noise	0.02	0.00	0.01
xcmsSet.peakwidth	0.01	0.00	0.01
xcmsSet.polarity	0.02	0.02	0.03
xcmsSet.ppm	0.03	0.00	0.04
xcmsSet.prefilter	0.01	0.00	0.01
xcmsSet.profparam	0.03	0.00	0.03
xcmsSet.sleep	0.04	0.00	0.03
xcmsSet.snthresh	0.01	0.00	0.02
xcmsSet.step	0.03	0.00	0.03
xcmsSet.verbose.columns	0.03	0.00	0.03
xcmsSetObj	0.03	0.00	0.03
zero2NA	0	0	0

name	user	system	elapsed
addValueNorm	1.22	0.03	1.41
autoRemoveOutlier	14.20	0.29	14.98
calcAUROC	0	0	0
calcVIP	0.05	0.00	0.05
center	0	0	0
cor.network	4.52	0.07	4.60
createModels	169.34	3.11	172.47
dataClean	27.00	0.03	27.87
dir.case	0.02	0.00	0.01
dir.ctrl	0	0	0
doQCRLSC	2.48	0.01	11.26
filterPeaks	1.12	0.02	1.14
filterQCPeaks	1.42	0.02	1.44
filterQCPeaksByCV	1.45	0.03	1.48
getPeaksTable	1.33	0.01	1.36
group.bw	0.03	0.00	0.03
group.bw0	0.03	0.02	0.05
group.max	0.05	0.00	0.04
group.minfrac	0.05	0.00	0.05
group.minsamp	0.04	0.00	0.05
group.mzwid	0.03	0.00	0.03
group.mzwid0	0.03	0.00	0.03
group.sleep	0.04	0.00	0.03
hasQC	0.57	0.00	0.58
idres	0.03	0.00	0.03
kfold	0	0	0
makeDirectory	0	0	0
makeMetaboAnalystInput	1.84	0.05	1.89
metaXpipe	0	0	0
method	0	0	0
missValueImputeMethod	0.02	0.00	0.01
missingValueImpute	2.45	0.03	2.48
myCalcAUROC	0	0	0
myPLSDA	0.02	0.00	0.02
ncomp	0	0	0
normalize	10.07	1.06	11.43
nperm	0	0	0
outdir	0	0	0
pathwayAnalysis	0	0	0
peakFinder	0	0	0
peakStat	0	0	0
peaksData	1.00	0.01	1.01
plotCV	11.70	0.85	12.54
plotCorHeatmap	4.57	0.10	4.68
plotHeatMap	12.45	0.92	13.40
plotIntDistr	14.01	1.41	15.51
plotMissValue	10.06	1.06	11.12
plotNetwork	1.95	0.02	3.49
plotPCA	8.21	0.09	8.72
plotPLSDA	9.49	0.79	10.28
plotPeakBox	7.88	0.02	8.10
plotPeakNumber	9.79	0.76	10.56
plotPeakSN	11.84	0.86	12.70
plotPeakSumDist	2.28	0.02	2.29
plotQC	3.35	0.04	3.40
plotQCRLSC	19.17	0.07	29.37
plotTreeMap	11.25	1.26	12.61
powerAnalyst	0	0	0
preProcess	4.18	0.02	4.20
prefix	0	0	0
qcRlscSpan	0.05	0.00	0.05
ratioPairs	0	0	0
rawPeaks	0.06	0.00	0.06
reSetPeaksData	1.06	0.00	1.06
removeSample	0.69	0.00	0.69
retcor.method	0.03	0.00	0.03
retcor.plottype	0.03	0.00	0.03
retcor.profStep	0.03	0.00	0.03
sampleListFile	0	0	0
scale	0	0	0
selectBestComponent	4.84	0.07	4.95
t	0	0	0
transformation	2.62	0.04	2.67
validation	0	0	0
xcmsSet.fitgauss	0.03	0.00	0.03
xcmsSet.fwhm	0.03	0.00	0.03
xcmsSet.integrate	0.01	0.00	0.01
xcmsSet.max	0.03	0.00	0.03
xcmsSet.method	0.05	0.00	0.04
xcmsSet.mzCenterFun	0.05	0.00	0.05
xcmsSet.mzdiff	0.06	0.00	0.06
xcmsSet.nSlaves	0.04	0.00	0.05
xcmsSet.noise	0.04	0.01	0.05
xcmsSet.peakwidth	0.04	0.00	0.04
xcmsSet.polarity	0.05	0.00	0.05
xcmsSet.ppm	0.01	0.00	0.03
xcmsSet.prefilter	0.03	0.00	0.03
xcmsSet.profparam	0.03	0.00	0.03
xcmsSet.sleep	0.03	0.00	0.03
xcmsSet.snthresh	0.04	0.00	0.03
xcmsSet.step	0.03	0.00	0.03
xcmsSet.verbose.columns	0.04	0.00	0.05
xcmsSetObj	0.05	0.00	0.05
zero2NA	0	0	0