BioC 3.2: CHECK report for metaX on perceval

Package: metaX

Version: 0.99.16

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaX_0.99.16.tar.gz

StartedAt: 2015-08-24 02:33:22 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:44:38 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 675.9 seconds

RetCode: 0

Status:  OK

CheckDir: metaX.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaX_0.99.16.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/metaX.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [23s/23s] 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’
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’
plotPLSDA,metaXpara: no visible binding for global variable ‘x’
plotPLSDA,metaXpara: no visible binding for global variable ‘y’
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 ... [411s/435s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
createModels        163.201 11.484 177.727
dataClean            21.425  0.187  21.722
autoRemoveOutlier    14.038  0.659  14.736
plotIntDistr         13.007  0.942  13.962
plotTreeMap          12.736  1.156  13.903
plotPeakNumber       12.605  1.257  13.874
plotPLSDA            11.566  2.174  13.751
plotHeatMap          12.363  1.225  13.614
plotCV               12.571  0.906  13.511
plotMissValue        11.731  1.181  12.922
plotQCRLSC           12.372  0.110  22.414
normalize            11.075  0.916  12.163
plotPeakSN           10.866  0.996  11.869
plotPCA               8.313  0.686   9.016
plotPeakBox           6.534  0.062   6.609
selectBestComponent   5.576  0.367   5.949
doQCRLSC              1.531  0.035  11.350
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [12s/12s]
 [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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/metaX.Rcheck/00check.log’
for details.

* installing *source* package ‘metaX’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
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
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
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	1.096	0.030	1.126
autoRemoveOutlier	14.038	0.659	14.736
calcAUROC	0.001	0.000	0.000
calcVIP	0.073	0.002	0.074
center	0.001	0.000	0.001
cor.network	4.063	0.218	4.296
createModels	163.201	11.484	177.727
dataClean	21.425	0.187	21.722
dir.case	0.001	0.000	0.002
dir.ctrl	0.001	0.000	0.001
doQCRLSC	1.531	0.035	11.350
filterPeaks	0.731	0.053	0.783
filterQCPeaks	0.676	0.041	0.718
filterQCPeaksByCV	1.562	0.073	1.635
getPeaksTable	0.617	0.068	0.685
group.bw	0.057	0.001	0.058
group.bw0	0.059	0.001	0.059
group.max	0.060	0.001	0.060
group.minfrac	0.059	0.001	0.060
group.minsamp	0.062	0.001	0.062
group.mzwid	0.060	0.001	0.060
group.mzwid0	0.056	0.001	0.057
group.sleep	0.058	0.001	0.058
hasQC	0.458	0.034	0.492
idres	0.059	0.001	0.061
kfold	0.001	0.000	0.001
makeDirectory	0.002	0.000	0.001
makeMetaboAnalystInput	1.734	0.143	1.879
metaXpipe	0.001	0.001	0.002
method	0.001	0.000	0.001
missValueImputeMethod	0.002	0.001	0.002
missingValueImpute	1.872	0.143	2.018
myCalcAUROC	0.001	0.001	0.001
myPLSDA	0.022	0.001	0.023
ncomp	0.001	0.000	0.001
normalize	11.075	0.916	12.163
nperm	0.001	0.000	0.001
outdir	0.001	0.000	0.001
pathwayAnalysis	0.001	0.001	0.001
peakFinder	0.001	0.000	0.001
peakStat	0.001	0.000	0.001
peaksData	0.444	0.039	0.483
plotCV	12.571	0.906	13.511
plotCorHeatmap	3.966	0.264	4.244
plotHeatMap	12.363	1.225	13.614
plotIntDistr	13.007	0.942	13.962
plotMissValue	11.731	1.181	12.922
plotNetwork	1.884	0.177	2.064
plotPCA	8.313	0.686	9.016
plotPLSDA	11.566	2.174	13.751
plotPeakBox	6.534	0.062	6.609
plotPeakNumber	12.605	1.257	13.874
plotPeakSN	10.866	0.996	11.869
plotPeakSumDist	1.580	0.076	1.671
plotQC	2.910	0.141	3.062
plotQCRLSC	12.372	0.110	22.414
plotTreeMap	12.736	1.156	13.903
powerAnalyst	0.001	0.000	0.001
preProcess	4.290	0.296	4.589
prefix	0.001	0.000	0.001
qcRlscSpan	0.066	0.001	0.067
ratioPairs	0.001	0.000	0.002
rawPeaks	0.064	0.000	0.065
reSetPeaksData	0.593	0.032	0.624
removeSample	0.583	0.047	0.629
retcor.method	0.059	0.000	0.061
retcor.plottype	0.064	0.001	0.064
retcor.profStep	0.073	0.001	0.074
sampleListFile	0.001	0.001	0.002
scale	0.001	0.000	0.001
selectBestComponent	5.576	0.367	5.949
t	0.000	0.000	0.001
transformation	1.792	0.104	1.899
validation	0.001	0.000	0.001
xcmsSet.fitgauss	0.065	0.001	0.067
xcmsSet.fwhm	0.06	0.00	0.06
xcmsSet.integrate	0.062	0.000	0.063
xcmsSet.max	0.058	0.000	0.059
xcmsSet.method	0.058	0.000	0.059
xcmsSet.mzCenterFun	0.057	0.000	0.058
xcmsSet.mzdiff	0.065	0.000	0.065
xcmsSet.nSlaves	0.063	0.001	0.063
xcmsSet.noise	0.063	0.001	0.063
xcmsSet.peakwidth	0.062	0.001	0.062
xcmsSet.polarity	0.057	0.001	0.058
xcmsSet.ppm	0.066	0.001	0.067
xcmsSet.prefilter	0.066	0.000	0.067
xcmsSet.profparam	0.062	0.001	0.063
xcmsSet.sleep	0.063	0.001	0.064
xcmsSet.snthresh	0.069	0.001	0.070
xcmsSet.step	0.062	0.001	0.063
xcmsSet.verbose.columns	0.059	0.001	0.060
xcmsSetObj	0.061	0.001	0.061
zero2NA	0.000	0.000	0.001