BioC 3.2: CHECK report for metaX on moscato1

Package: metaX

Version: 0.99.16

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_0.99.16.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_0.99.16.tar.gz

StartedAt: 2015-08-20 06:58:35 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 07:19:32 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 1256.6 seconds

RetCode: 0

Status:  OK

CheckDir: metaX.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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_0.99.16.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_0.99.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/metaX.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '0.99.16'
* 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' ... [446s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
createModels      152.78   2.49  155.28
dataClean          24.75   0.08   24.98
autoRemoveOutlier  15.82   0.14   17.80
plotIntDistr       15.19   0.58   15.98
plotTreeMap        14.77   0.39   15.18
plotCV             14.47   0.57   15.14
plotHeatMap        14.40   0.34   15.68
plotPeakNumber     14.04   0.56   14.60
plotQCRLSC         12.81   0.04   21.22
plotPeakSN         12.31   0.46   12.76
plotMissValue      12.26   0.45   14.13
normalize          11.92   0.70   27.46
plotPLSDA          11.84   0.43   12.27
plotPCA            10.33   0.11   10.44
plotPeakBox         6.88   0.03    6.91
doQCRLSC            2.14   0.00   12.83
** running examples for arch 'x64' ... [473s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
createModels        181.15   1.27  182.45
dataClean            28.14   0.11   28.56
plotCV               15.89   1.33   17.22
plotTreeMap          16.09   0.94   17.11
plotIntDistr         15.67   1.34   17.02
plotPeakNumber       14.77   1.40   16.18
plotQCRLSC           15.91   0.03   25.34
plotMissValue        14.80   1.00   15.82
plotHeatMap          14.44   0.99   15.43
plotPeakSN           13.64   0.89   14.52
normalize            13.20   1.01   15.35
autoRemoveOutlier    12.70   0.12   13.00
plotPLSDA            11.29   0.51   11.81
plotPCA               8.66   0.06    8.73
plotPeakBox           7.83   0.05    7.88
selectBestComponent   5.08   0.10    5.21
doQCRLSC              2.64   0.00   13.20
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [10s]
 [11s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [13s]
 [13s] 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
  '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
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_0.99.16.zip
* DONE (metaX)

name	user	system	elapsed
addValueNorm	1.05	0.05	1.09
autoRemoveOutlier	15.82	0.14	17.80
calcAUROC	0	0	0
calcVIP	0.03	0.00	0.04
center	0	0	0
cor.network	4.65	0.05	4.69
createModels	152.78	2.49	155.28
dataClean	24.75	0.08	24.98
dir.case	0.01	0.00	0.02
dir.ctrl	0	0	0
doQCRLSC	2.14	0.00	12.83
filterPeaks	1.48	0.03	1.52
filterQCPeaks	1.06	0.00	1.06
filterQCPeaksByCV	1.45	0.03	1.49
getPeaksTable	1.29	0.00	1.29
group.bw	0.05	0.00	0.05
group.bw0	0.03	0.00	0.03
group.max	0.03	0.02	0.05
group.minfrac	0.02	0.00	0.01
group.minsamp	0.03	0.00	0.03
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	0.53	0.03	0.56
idres	0.01	0.00	0.02
kfold	0	0	0
makeDirectory	0	0	0
makeMetaboAnalystInput	3.01	0.03	3.05
metaXpipe	0.02	0.00	0.01
method	0	0	0
missValueImputeMethod	0	0	0
missingValueImpute	2.48	0.05	2.53
myCalcAUROC	0	0	0
myPLSDA	0.01	0.00	0.01
ncomp	0	0	0
normalize	11.92	0.70	27.46
nperm	0	0	0
outdir	0	0	0
pathwayAnalysis	0	0	0
peakFinder	0	0	0
peakStat	0	0	0
peaksData	0.56	0.01	0.58
plotCV	14.47	0.57	15.14
plotCorHeatmap	4.29	0.04	4.32
plotHeatMap	14.40	0.34	15.68
plotIntDistr	15.19	0.58	15.98
plotMissValue	12.26	0.45	14.13
plotNetwork	2.61	0.00	2.60
plotPCA	10.33	0.11	10.44
plotPLSDA	11.84	0.43	12.27
plotPeakBox	6.88	0.03	6.91
plotPeakNumber	14.04	0.56	14.60
plotPeakSN	12.31	0.46	12.76
plotPeakSumDist	1.71	0.01	1.73
plotQC	3.06	0.03	3.08
plotQCRLSC	12.81	0.04	21.22
plotTreeMap	14.77	0.39	15.18
powerAnalyst	0	0	0
preProcess	3.91	0.02	3.93
prefix	0	0	0
qcRlscSpan	0.03	0.00	0.03
ratioPairs	0	0	0
rawPeaks	0.02	0.02	0.03
reSetPeaksData	0.83	0.01	0.84
removeSample	0.57	0.00	0.58
retcor.method	0.03	0.00	0.03
retcor.plottype	0.02	0.00	0.01
retcor.profStep	0.03	0.00	0.03
sampleListFile	0.01	0.00	0.02
scale	0	0	0
selectBestComponent	4.73	0.03	4.77
t	0	0	0
transformation	1.9	0.0	1.9
validation	0	0	0
xcmsSet.fitgauss	0.01	0.00	0.02
xcmsSet.fwhm	0.04	0.00	0.03
xcmsSet.integrate	0.03	0.00	0.03
xcmsSet.max	0.03	0.00	0.03
xcmsSet.method	0.03	0.00	0.03
xcmsSet.mzCenterFun	0.03	0.00	0.03
xcmsSet.mzdiff	0.03	0.00	0.03
xcmsSet.nSlaves	0.02	0.00	0.02
xcmsSet.noise	0.02	0.00	0.02
xcmsSet.peakwidth	0.01	0.02	0.03
xcmsSet.polarity	0.05	0.00	0.05
xcmsSet.ppm	0.06	0.00	0.06
xcmsSet.prefilter	0.03	0.00	0.03
xcmsSet.profparam	0.04	0.00	0.03
xcmsSet.sleep	0.03	0.00	0.03
xcmsSet.snthresh	0.03	0.00	0.04
xcmsSet.step	0.03	0.00	0.03
xcmsSet.verbose.columns	0.05	0.00	0.04
xcmsSetObj	0.03	0.00	0.03
zero2NA	0	0	0

name	user	system	elapsed
addValueNorm	1.14	0.00	1.14
autoRemoveOutlier	12.70	0.12	13.00
calcAUROC	0	0	0
calcVIP	0.03	0.00	0.18
center	0	0	0
cor.network	3.96	0.04	4.00
createModels	181.15	1.27	182.45
dataClean	28.14	0.11	28.56
dir.case	0.02	0.00	0.02
dir.ctrl	0	0	0
doQCRLSC	2.64	0.00	13.20
filterPeaks	1.54	0.00	1.54
filterQCPeaks	1.03	0.03	1.06
filterQCPeaksByCV	1.83	0.01	1.84
getPeaksTable	0.74	0.02	0.77
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	0.03	0.00	0.04
group.minsamp	0.04	0.00	0.03
group.mzwid	0.03	0.00	0.03
group.mzwid0	0.03	0.00	0.04
group.sleep	0.03	0.01	0.05
hasQC	0.74	0.00	0.73
idres	0.04	0.00	0.05
kfold	0	0	0
makeDirectory	0.02	0.00	0.01
makeMetaboAnalystInput	2.08	0.05	2.12
metaXpipe	0	0	0
method	0	0	0
missValueImputeMethod	0	0	0
missingValueImpute	2.17	0.11	2.28
myCalcAUROC	0	0	0
myPLSDA	0.02	0.00	0.02
ncomp	0	0	0
normalize	13.20	1.01	15.35
nperm	0	0	0
outdir	0.01	0.00	0.02
pathwayAnalysis	0	0	0
peakFinder	0	0	0
peakStat	0.02	0.00	0.01
peaksData	0.97	0.00	0.97
plotCV	15.89	1.33	17.22
plotCorHeatmap	4.06	0.15	4.21
plotHeatMap	14.44	0.99	15.43
plotIntDistr	15.67	1.34	17.02
plotMissValue	14.80	1.00	15.82
plotNetwork	2.73	0.03	2.82
plotPCA	8.66	0.06	8.73
plotPLSDA	11.29	0.51	11.81
plotPeakBox	7.83	0.05	7.88
plotPeakNumber	14.77	1.40	16.18
plotPeakSN	13.64	0.89	14.52
plotPeakSumDist	2.20	0.05	2.25
plotQC	3.04	0.03	3.07
plotQCRLSC	15.91	0.03	25.34
plotTreeMap	16.09	0.94	17.11
powerAnalyst	0	0	0
preProcess	3.54	0.03	3.57
prefix	0.02	0.00	0.01
qcRlscSpan	0.03	0.00	0.04
ratioPairs	0	0	0
rawPeaks	0.03	0.00	0.03
reSetPeaksData	0.64	0.03	0.67
removeSample	1.29	0.00	1.30
retcor.method	0.03	0.00	0.03
retcor.plottype	0.03	0.00	0.04
retcor.profStep	0.05	0.00	0.04
sampleListFile	0	0	0
scale	0	0	0
selectBestComponent	5.08	0.10	5.21
t	0	0	0
transformation	2.14	0.01	2.16
validation	0	0	0
xcmsSet.fitgauss	0.03	0.00	0.03
xcmsSet.fwhm	0.03	0.00	0.03
xcmsSet.integrate	0.03	0.00	0.03
xcmsSet.max	0.05	0.00	0.05
xcmsSet.method	0.04	0.00	0.05
xcmsSet.mzCenterFun	0.05	0.00	0.05
xcmsSet.mzdiff	0.05	0.00	0.04
xcmsSet.nSlaves	0.04	0.00	0.05
xcmsSet.noise	0.05	0.00	0.05
xcmsSet.peakwidth	0.05	0.00	0.04
xcmsSet.polarity	0.01	0.00	0.02
xcmsSet.ppm	0.01	0.00	0.02
xcmsSet.prefilter	0.01	0.00	0.02
xcmsSet.profparam	0.04	0.00	0.03
xcmsSet.sleep	0.04	0.00	0.05
xcmsSet.snthresh	0.03	0.00	0.03
xcmsSet.step	0.02	0.02	0.03
xcmsSet.verbose.columns	0.03	0.00	0.03
xcmsSetObj	0.03	0.00	0.03
zero2NA	0	0	0