BioC 3.2: CHECK report for metaX on windows1.bioconductor.org

Package: metaX

Version: 1.0.0

Command: rm -rf metaX.buildbin-libdir metaX.Rcheck && mkdir metaX.buildbin-libdir metaX.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaX.buildbin-libdir metaX_1.0.0.tar.gz >metaX.Rcheck\00install.out 2>&1 && cp metaX.Rcheck\00install.out metaX-install.out && C:\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_1.0.0.tar.gz

StartedAt: 2015-10-27 03:27:36 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:40:17 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 761.0 seconds

RetCode: 0

Status:  OK

CheckDir: metaX.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf metaX.buildbin-libdir metaX.Rcheck && mkdir metaX.buildbin-libdir metaX.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaX.buildbin-libdir metaX_1.0.0.tar.gz >metaX.Rcheck\00install.out 2>&1 && cp metaX.Rcheck\00install.out metaX-install.out  && C:\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_1.0.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/metaX.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.0.0'
* 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 whether package 'metaX' can be installed ... OK
* 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' ... [259s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
createModels      93.06   3.39   96.47
dataClean         15.88   0.10   15.96
plotIntDistr       9.88   0.41   10.28
plotCV             9.18   0.74    9.90
normalize          9.12   0.57    9.70
plotHeatMap        8.44   0.39    8.83
plotMissValue      8.26   0.50    8.77
autoRemoveOutlier  8.31   0.18    8.50
plotPeakNumber     8.09   0.30    8.39
plotTreeMap        7.80   0.35    8.20
plotPeakSN         7.53   0.28    7.81
plotQCRLSC         7.51   0.04   12.61
plotPLSDA          6.74   0.19    6.92
plotPCA            5.48   0.05    5.53
doQCRLSC           1.12   0.03    6.35
** running examples for arch 'x64' ... [298s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
createModels      108.21   2.78  110.99
dataClean          16.61   0.05   16.65
plotPeakNumber     11.72   0.87   12.59
plotIntDistr       11.19   1.05   12.25
plotMissValue      10.78   0.73   11.51
plotCV             10.45   0.95   11.41
plotHeatMap         9.93   0.86   10.80
plotTreeMap         9.93   0.83   10.75
normalize           8.82   0.75    9.56
plotPeakSN          8.66   0.84    9.50
plotQCRLSC          8.90   0.06   14.84
plotPLSDA           7.75   0.95    8.71
autoRemoveOutlier   7.59   0.16    7.75
plotPCA             5.66   0.07    5.72
doQCRLSC            1.26   0.03    7.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [7s]
 [7s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [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: 2 NOTEs
See
  'C:/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
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'metaX' ...
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'metaX' as metaX_1.0.0.zip
* DONE (metaX)

name	user	system	elapsed
addValueNorm	0.64	0.00	0.64
autoRemoveOutlier	8.31	0.18	8.50
calcAUROC	0	0	0
calcVIP	0.03	0.00	0.03
center	0	0	0
cor.network	3.02	0.07	3.10
createModels	93.06	3.39	96.47
dataClean	15.88	0.10	15.96
dir.case	0	0	0
dir.ctrl	0	0	0
doQCRLSC	1.12	0.03	6.35
filterPeaks	0.58	0.00	0.58
filterQCPeaks	0.58	0.00	0.58
filterQCPeaksByCV	0.85	0.00	0.84
getPeaksTable	0.68	0.00	0.69
group.bw	0.04	0.00	0.03
group.bw0	0.01	0.00	0.02
group.max	0.03	0.00	0.03
group.minfrac	0.02	0.00	0.02
group.minsamp	0.01	0.00	0.01
group.mzwid	0.03	0.00	0.03
group.mzwid0	0.02	0.00	0.02
group.sleep	0.03	0.00	0.03
hasQC	0.49	0.00	0.48
idres	0.01	0.00	0.02
kfold	0	0	0
makeDirectory	0	0	0
makeMetaboAnalystInput	1.39	0.03	1.43
metaXpipe	0	0	0
method	0	0	0
missValueImputeMethod	0	0	0
missingValueImpute	1.19	0.02	1.20
myCalcAUROC	0	0	0
myPLSDA	0	0	0
ncomp	0	0	0
normalize	9.12	0.57	9.70
nperm	0	0	0
outdir	0	0	0
pathwayAnalysis	0	0	0
peakFinder	0	0	0
peakStat	0	0	0
peaksData	0.40	0.00	0.41
plotCV	9.18	0.74	9.90
plotCorHeatmap	2.07	0.14	2.22
plotHeatMap	8.44	0.39	8.83
plotIntDistr	9.88	0.41	10.28
plotMissValue	8.26	0.50	8.77
plotNetwork	1.52	0.01	1.53
plotPCA	5.48	0.05	5.53
plotPLSDA	6.74	0.19	6.92
plotPeakBox	4.59	0.01	4.61
plotPeakNumber	8.09	0.30	8.39
plotPeakSN	7.53	0.28	7.81
plotPeakSumDist	1.05	0.02	1.07
plotQC	2.02	0.00	2.01
plotQCRLSC	7.51	0.04	12.61
plotTreeMap	7.80	0.35	8.20
powerAnalyst	0	0	0
preProcess	2.04	0.01	2.06
prefix	0	0	0
qcRlscSpan	0.02	0.00	0.02
ratioPairs	0	0	0
rawPeaks	0.01	0.00	0.02
reSetPeaksData	0.64	0.00	0.64
removeSample	0.36	0.00	0.36
retcor.method	0.02	0.00	0.01
retcor.plottype	0.02	0.00	0.02
retcor.profStep	0.02	0.00	0.01
sampleListFile	0.01	0.00	0.02
scale	0	0	0
selectBestComponent	2.44	0.04	2.48
t	0	0	0
transformation	1.33	0.00	1.32
validation	0	0	0
xcmsSet.fitgauss	0.01	0.00	0.02
xcmsSet.fwhm	0.01	0.00	0.01
xcmsSet.integrate	0.02	0.00	0.02
xcmsSet.max	0.03	0.00	0.03
xcmsSet.method	0.02	0.00	0.01
xcmsSet.mzCenterFun	0.01	0.00	0.02
xcmsSet.mzdiff	0.03	0.00	0.03
xcmsSet.nSlaves	0.02	0.00	0.01
xcmsSet.noise	0.03	0.00	0.03
xcmsSet.peakwidth	0.02	0.00	0.02
xcmsSet.polarity	0.02	0.00	0.02
xcmsSet.ppm	0.03	0.00	0.03
xcmsSet.prefilter	0.01	0.00	0.02
xcmsSet.profparam	0.04	0.00	0.03
xcmsSet.sleep	0.01	0.00	0.01
xcmsSet.snthresh	0.02	0.00	0.02
xcmsSet.step	0.02	0.00	0.01
xcmsSet.verbose.columns	0.03	0.00	0.03
xcmsSetObj	0.01	0.00	0.02
zero2NA	0	0	0

name	user	system	elapsed
addValueNorm	0.67	0.00	0.67
autoRemoveOutlier	7.59	0.16	7.75
calcAUROC	0	0	0
calcVIP	0.03	0.00	0.03
center	0	0	0
cor.network	3.06	0.08	3.14
createModels	108.21	2.78	110.99
dataClean	16.61	0.05	16.65
dir.case	0	0	0
dir.ctrl	0	0	0
doQCRLSC	1.26	0.03	7.39
filterPeaks	0.64	0.00	0.64
filterQCPeaks	0.68	0.01	0.69
filterQCPeaksByCV	1	0	1
getPeaksTable	0.82	0.00	0.82
group.bw	0.02	0.01	0.04
group.bw0	0.01	0.00	0.01
group.max	0.04	0.00	0.03
group.minfrac	0.01	0.00	0.02
group.minsamp	0.02	0.00	0.01
group.mzwid	0.01	0.00	0.01
group.mzwid0	0.02	0.00	0.02
group.sleep	0.01	0.00	0.02
hasQC	0.35	0.02	0.36
idres	0.01	0.00	0.02
kfold	0	0	0
makeDirectory	0.02	0.00	0.01
makeMetaboAnalystInput	1.20	0.03	1.24
metaXpipe	0	0	0
method	0	0	0
missValueImputeMethod	0	0	0
missingValueImpute	1.17	0.08	1.25
myCalcAUROC	0	0	0
myPLSDA	0	0	0
ncomp	0	0	0
normalize	8.82	0.75	9.56
nperm	0	0	0
outdir	0	0	0
pathwayAnalysis	0	0	0
peakFinder	0	0	0
peakStat	0	0	0
peaksData	0.35	0.00	0.34
plotCV	10.45	0.95	11.41
plotCorHeatmap	2.58	0.06	2.64
plotHeatMap	9.93	0.86	10.80
plotIntDistr	11.19	1.05	12.25
plotMissValue	10.78	0.73	11.51
plotNetwork	1.69	0.06	1.75
plotPCA	5.66	0.07	5.72
plotPLSDA	7.75	0.95	8.71
plotPeakBox	4.93	0.02	4.95
plotPeakNumber	11.72	0.87	12.59
plotPeakSN	8.66	0.84	9.50
plotPeakSumDist	0.98	0.04	1.02
plotQC	1.94	0.04	1.99
plotQCRLSC	8.90	0.06	14.84
plotTreeMap	9.93	0.83	10.75
powerAnalyst	0	0	0
preProcess	2.11	0.13	2.23
prefix	0	0	0
qcRlscSpan	0.02	0.00	0.02
ratioPairs	0	0	0
rawPeaks	0.02	0.00	0.02
reSetPeaksData	0.7	0.0	0.7
removeSample	0.36	0.03	0.39
retcor.method	0.03	0.00	0.03
retcor.plottype	0.02	0.00	0.01
retcor.profStep	0.03	0.00	0.04
sampleListFile	0	0	0
scale	0	0	0
selectBestComponent	2.75	0.10	2.84
t	0	0	0
transformation	1.31	0.06	1.37
validation	0	0	0
xcmsSet.fitgauss	0.02	0.00	0.02
xcmsSet.fwhm	0.03	0.00	0.03
xcmsSet.integrate	0.03	0.00	0.03
xcmsSet.max	0.01	0.00	0.02
xcmsSet.method	0.04	0.00	0.03
xcmsSet.mzCenterFun	0.01	0.00	0.02
xcmsSet.mzdiff	0.03	0.00	0.03
xcmsSet.nSlaves	0.02	0.00	0.01
xcmsSet.noise	0.03	0.00	0.03
xcmsSet.peakwidth	0.01	0.00	0.02
xcmsSet.polarity	0.04	0.00	0.03
xcmsSet.ppm	0.03	0.00	0.03
xcmsSet.prefilter	0.01	0.00	0.02
xcmsSet.profparam	0.02	0.02	0.03
xcmsSet.sleep	0.03	0.00	0.03
xcmsSet.snthresh	0.03	0.00	0.03
xcmsSet.step	0.02	0.00	0.02
xcmsSet.verbose.columns	0.02	0.00	0.02
xcmsSetObj	0.03	0.00	0.03
zero2NA	0	0	0