BioC 3.2: CHECK report for metaX on zin1

Package: metaX

Version: 0.99.16

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metaX_0.99.16.tar.gz

StartedAt: 2015-08-24 01:30:34 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:37:49 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 435.5 seconds

RetCode: 0

Status:  OK

CheckDir: metaX.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metaX_0.99.16.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/metaX.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘metaX’ can be installed ... [14s/14s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [269s/284s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
createModels      105.251  0.048 107.746
dataClean          16.583  0.020  16.624
plotIntDistr       11.504  0.112  11.621
plotHeatMap         9.906  0.152  10.049
plotCV              9.867  0.128  10.072
autoRemoveOutlier   9.709  0.024   9.795
plotPeakSN          9.357  0.168   9.522
normalize           9.196  0.152   9.366
plotPeakNumber      9.152  0.156   9.309
plotMissValue       9.201  0.080   9.310
plotQCRLSC          9.163  0.050  15.286
plotTreeMap         8.916  0.116   9.025
plotPCA             6.339  0.004   6.369
plotPLSDA           5.585  0.020   5.628
doQCRLSC            1.230  0.021   7.324
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/metaX.Rcheck/00check.log’
for details.

* 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.
* DONE (metaX)

name	user	system	elapsed
addValueNorm	0.686	0.012	0.697
autoRemoveOutlier	9.709	0.024	9.795
calcAUROC	0	0	0
calcVIP	0.029	0.000	0.029
center	0.001	0.000	0.001
cor.network	2.580	0.044	2.622
createModels	105.251	0.048	107.746
dataClean	16.583	0.020	16.624
dir.case	0.001	0.000	0.001
dir.ctrl	0	0	0
doQCRLSC	1.230	0.021	7.324
filterPeaks	0.642	0.000	0.641
filterQCPeaks	0.617	0.004	0.621
filterQCPeaksByCV	1.083	0.024	1.106
getPeaksTable	0.509	0.000	0.509
group.bw	0.022	0.000	0.022
group.bw0	0.017	0.000	0.017
group.max	0.017	0.000	0.017
group.minfrac	0.017	0.000	0.017
group.minsamp	0.018	0.000	0.018
group.mzwid	0.017	0.000	0.017
group.mzwid0	0.018	0.000	0.017
group.sleep	0.017	0.000	0.018
hasQC	0.432	0.000	0.431
idres	0.021	0.000	0.021
kfold	0.000	0.000	0.001
makeDirectory	0.002	0.000	0.001
makeMetaboAnalystInput	1.484	0.004	1.492
metaXpipe	0.001	0.000	0.001
method	0.001	0.000	0.001
missValueImputeMethod	0.001	0.000	0.000
missingValueImpute	1.360	0.004	1.369
myCalcAUROC	0.000	0.000	0.001
myPLSDA	0.011	0.000	0.011
ncomp	0.001	0.000	0.000
normalize	9.196	0.152	9.366
nperm	0.000	0.000	0.001
outdir	0.001	0.000	0.001
pathwayAnalysis	0.000	0.000	0.001
peakFinder	0	0	0
peakStat	0.000	0.000	0.001
peaksData	0.394	0.004	0.399
plotCV	9.867	0.128	10.072
plotCorHeatmap	2.252	0.020	2.270
plotHeatMap	9.906	0.152	10.049
plotIntDistr	11.504	0.112	11.621
plotMissValue	9.201	0.080	9.310
plotNetwork	1.867	0.004	1.879
plotPCA	6.339	0.004	6.369
plotPLSDA	5.585	0.020	5.628
plotPeakBox	4.867	0.003	4.895
plotPeakNumber	9.152	0.156	9.309
plotPeakSN	9.357	0.168	9.522
plotPeakSumDist	1.080	0.000	1.079
plotQC	2.157	0.016	2.204
plotQCRLSC	9.163	0.050	15.286
plotTreeMap	8.916	0.116	9.025
powerAnalyst	0.001	0.000	0.000
preProcess	2.162	0.000	2.160
prefix	0.001	0.000	0.001
qcRlscSpan	0.018	0.000	0.019
ratioPairs	0.001	0.000	0.001
rawPeaks	0.021	0.000	0.022
reSetPeaksData	0.645	0.000	0.644
removeSample	0.392	0.000	0.392
retcor.method	0.02	0.00	0.02
retcor.plottype	0.018	0.000	0.021
retcor.profStep	0.017	0.000	0.017
sampleListFile	0.001	0.000	0.001
scale	0.001	0.000	0.000
selectBestComponent	2.907	0.012	2.917
t	0.001	0.000	0.001
transformation	1.381	0.000	1.381
validation	0.001	0.000	0.001
xcmsSet.fitgauss	0.018	0.004	0.023
xcmsSet.fwhm	0.025	0.000	0.024
xcmsSet.integrate	0.014	0.004	0.018
xcmsSet.max	0.017	0.000	0.018
xcmsSet.method	0.018	0.000	0.018
xcmsSet.mzCenterFun	0.024	0.000	0.024
xcmsSet.mzdiff	0.025	0.000	0.025
xcmsSet.nSlaves	0.021	0.000	0.022
xcmsSet.noise	0.021	0.000	0.020
xcmsSet.peakwidth	0.020	0.000	0.021
xcmsSet.polarity	0.020	0.000	0.032
xcmsSet.ppm	0.018	0.000	0.018
xcmsSet.prefilter	0.018	0.000	0.017
xcmsSet.profparam	0.018	0.000	0.018
xcmsSet.sleep	0.015	0.000	0.018
xcmsSet.snthresh	0.017	0.000	0.019
xcmsSet.step	0.022	0.004	0.022
xcmsSet.verbose.columns	0.019	0.000	0.021
xcmsSetObj	0.018	0.000	0.018
zero2NA	0	0	0