BioC 3.2: CHECK report for metaX on linux1.bioconductor.org

Package: metaX

Version: 1.0.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metaX_1.0.0.tar.gz

StartedAt: 2015-10-27 05:32:21 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:39:20 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 418.3 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_1.0.0.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 ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘metaX’ can be installed ... [15s/15s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [255s/269s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
createModels      107.503  0.068 107.632
dataClean          16.872  0.032  16.926
autoRemoveOutlier   9.827  0.036   9.865
plotQCRLSC          9.556  0.060  17.072
plotIntDistr        8.734  0.356   9.094
plotHeatMap         7.705  0.336   8.051
plotPeakSN          7.300  0.372   7.680
plotPCA             7.180  0.012   7.200
plotCV              7.028  0.132   7.332
plotMissValue       6.651  0.264   6.919
normalize           6.215  0.332   6.548
plotPLSDA           6.452  0.028   6.488
plotPeakNumber      6.225  0.180   6.412
plotTreeMap         5.657  0.224   5.885
doQCRLSC            1.065  0.032   7.428
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/7s] 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	0.937	0.024	0.963
autoRemoveOutlier	9.827	0.036	9.865
calcAUROC	0.000	0.000	0.001
calcVIP	0.034	0.000	0.034
center	0.001	0.000	0.001
cor.network	3.134	0.028	3.162
createModels	107.503	0.068	107.632
dataClean	16.872	0.032	16.926
dir.case	0.001	0.000	0.001
dir.ctrl	0.000	0.000	0.001
doQCRLSC	1.065	0.032	7.428
filterPeaks	0.534	0.000	0.534
filterQCPeaks	0.528	0.000	0.528
filterQCPeaksByCV	0.705	0.000	0.706
getPeaksTable	0.608	0.000	0.608
group.bw	0.03	0.00	0.03
group.bw0	0.025	0.000	0.025
group.max	0.023	0.000	0.023
group.minfrac	0.024	0.000	0.024
group.minsamp	0.024	0.000	0.024
group.mzwid	0.02	0.00	0.02
group.mzwid0	0.021	0.000	0.020
group.sleep	0.02	0.00	0.02
hasQC	0.565	0.000	0.564
idres	0.023	0.000	0.023
kfold	0.001	0.000	0.000
makeDirectory	0.002	0.000	0.002
makeMetaboAnalystInput	1.643	0.036	1.681
metaXpipe	0.001	0.000	0.001
method	0.000	0.000	0.001
missValueImputeMethod	0	0	0
missingValueImpute	1.214	0.008	1.225
myCalcAUROC	0.001	0.000	0.000
myPLSDA	0.008	0.000	0.009
ncomp	0.001	0.000	0.000
normalize	6.215	0.332	6.548
nperm	0.001	0.000	0.001
outdir	0.001	0.000	0.002
pathwayAnalysis	0.001	0.000	0.000
peakFinder	0.001	0.000	0.001
peakStat	0.000	0.004	0.001
peaksData	0.547	0.000	0.550
plotCV	7.028	0.132	7.332
plotCorHeatmap	2.187	0.028	2.217
plotHeatMap	7.705	0.336	8.051
plotIntDistr	8.734	0.356	9.094
plotMissValue	6.651	0.264	6.919
plotNetwork	2.076	0.008	2.084
plotPCA	7.180	0.012	7.200
plotPLSDA	6.452	0.028	6.488
plotPeakBox	4.801	0.008	4.816
plotPeakNumber	6.225	0.180	6.412
plotPeakSN	7.300	0.372	7.680
plotPeakSumDist	1.503	0.000	1.736
plotQC	2.534	0.000	2.602
plotQCRLSC	9.556	0.060	17.072
plotTreeMap	5.657	0.224	5.885
powerAnalyst	0.001	0.000	0.001
preProcess	2.193	0.000	2.194
prefix	0.000	0.000	0.001
qcRlscSpan	0.016	0.000	0.016
ratioPairs	0.001	0.000	0.001
rawPeaks	0.015	0.000	0.015
reSetPeaksData	0.381	0.000	0.381
removeSample	0.873	0.004	0.882
retcor.method	0.022	0.000	0.022
retcor.plottype	0.02	0.00	0.02
retcor.profStep	0.02	0.00	0.02
sampleListFile	0.002	0.000	0.002
scale	0.001	0.000	0.001
selectBestComponent	2.734	0.020	2.755
t	0.001	0.000	0.000
transformation	1.497	0.000	1.503
validation	0.001	0.000	0.001
xcmsSet.fitgauss	0.021	0.000	0.022
xcmsSet.fwhm	0.023	0.000	0.023
xcmsSet.integrate	0.020	0.000	0.021
xcmsSet.max	0.019	0.000	0.020
xcmsSet.method	0.021	0.000	0.021
xcmsSet.mzCenterFun	0.019	0.000	0.020
xcmsSet.mzdiff	0.019	0.000	0.019
xcmsSet.nSlaves	0.019	0.000	0.019
xcmsSet.noise	0.022	0.000	0.022
xcmsSet.peakwidth	0.019	0.000	0.019
xcmsSet.polarity	0.018	0.000	0.019
xcmsSet.ppm	0.019	0.000	0.019
xcmsSet.prefilter	0.021	0.000	0.021
xcmsSet.profparam	0.028	0.000	0.028
xcmsSet.sleep	0.025	0.000	0.025
xcmsSet.snthresh	0.023	0.000	0.025
xcmsSet.step	0.021	0.000	0.022
xcmsSet.verbose.columns	0.028	0.000	0.028
xcmsSetObj	0.021	0.000	0.022
zero2NA	0.000	0.000	0.001