BioC 3.2: CHECK report for metaX on perceval

Package: metaX

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaX_1.0.0.tar.gz

StartedAt: 2015-11-10 06:50:34 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 07:00:57 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 622.4 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_1.0.0.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 (2015-10-08 r69496)
* 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 ‘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 ... [20s/21s] 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 ... [388s/407s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
createModels        149.228  5.683 154.920
dataClean            21.932  0.135  23.505
plotIntDistr         15.014  0.706  15.736
plotPeakNumber       13.867  0.786  14.667
plotHeatMap          13.706  0.807  14.533
plotCV               13.480  0.600  14.094
plotTreeMap          12.800  0.536  13.337
autoRemoveOutlier    12.744  0.400  13.167
plotMissValue        12.121  0.712  12.847
normalize            11.813  0.595  12.923
plotPeakSN           11.729  0.647  12.377
plotQCRLSC           11.936  0.072  20.492
plotPLSDA             8.735  1.281  10.020
plotPCA               8.533  0.426   8.980
plotPeakBox           6.198  0.037   6.241
selectBestComponent   5.515  0.208   5.724
doQCRLSC              1.677  0.027  10.413
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/11s]
 [11s/11s] 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	0.892	0.017	0.910
autoRemoveOutlier	12.744	0.400	13.167
calcAUROC	0.001	0.000	0.001
calcVIP	0.062	0.001	0.063
center	0.002	0.000	0.002
cor.network	3.631	0.132	3.764
createModels	149.228	5.683	154.920
dataClean	21.932	0.135	23.505
dir.case	0.001	0.000	0.002
dir.ctrl	0.001	0.000	0.001
doQCRLSC	1.677	0.027	10.413
filterPeaks	1.189	0.036	1.226
filterQCPeaks	0.702	0.029	0.731
filterQCPeaksByCV	1.785	0.047	1.833
getPeaksTable	0.594	0.036	0.630
group.bw	0.045	0.000	0.047
group.bw0	0.046	0.001	0.046
group.max	0.045	0.001	0.046
group.minfrac	0.046	0.001	0.046
group.minsamp	0.050	0.000	0.051
group.mzwid	0.05	0.00	0.05
group.mzwid0	0.049	0.000	0.051
group.sleep	0.05	0.00	0.05
hasQC	0.444	0.021	0.466
idres	0.050	0.001	0.050
kfold	0.001	0.001	0.001
makeDirectory	0.002	0.000	0.002
makeMetaboAnalystInput	1.855	0.073	1.929
metaXpipe	0.001	0.000	0.002
method	0.001	0.000	0.001
missValueImputeMethod	0.002	0.001	0.001
missingValueImpute	1.553	0.063	1.615
myCalcAUROC	0.001	0.000	0.001
myPLSDA	0.012	0.000	0.012
ncomp	0.001	0.000	0.001
normalize	11.813	0.595	12.923
nperm	0.001	0.000	0.000
outdir	0.001	0.000	0.001
pathwayAnalysis	0	0	0
peakFinder	0.001	0.000	0.001
peakStat	0.001	0.001	0.000
peaksData	0.421	0.020	0.440
plotCV	13.480	0.600	14.094
plotCorHeatmap	3.741	0.156	3.912
plotHeatMap	13.706	0.807	14.533
plotIntDistr	15.014	0.706	15.736
plotMissValue	12.121	0.712	12.847
plotNetwork	2.267	0.114	2.382
plotPCA	8.533	0.426	8.980
plotPLSDA	8.735	1.281	10.020
plotPeakBox	6.198	0.037	6.241
plotPeakNumber	13.867	0.786	14.667
plotPeakSN	11.729	0.647	12.377
plotPeakSumDist	1.462	0.045	1.519
plotQC	2.602	0.088	2.690
plotQCRLSC	11.936	0.072	20.492
plotTreeMap	12.800	0.536	13.337
powerAnalyst	0.001	0.000	0.001
preProcess	4.386	0.142	4.528
prefix	0.001	0.000	0.002
qcRlscSpan	0.048	0.001	0.049
ratioPairs	0.001	0.000	0.001
rawPeaks	0.048	0.000	0.049
reSetPeaksData	0.901	0.016	0.917
removeSample	0.489	0.025	0.515
retcor.method	0.051	0.000	0.052
retcor.plottype	0.048	0.000	0.048
retcor.profStep	0.047	0.000	0.048
sampleListFile	0.001	0.001	0.001
scale	0.001	0.000	0.001
selectBestComponent	5.515	0.208	5.724
t	0.001	0.000	0.001
transformation	1.736	0.089	1.825
validation	0.001	0.000	0.001
xcmsSet.fitgauss	0.052	0.001	0.054
xcmsSet.fwhm	0.051	0.000	0.052
xcmsSet.integrate	0.052	0.000	0.052
xcmsSet.max	0.051	0.000	0.052
xcmsSet.method	0.051	0.001	0.052
xcmsSet.mzCenterFun	0.051	0.001	0.052
xcmsSet.mzdiff	0.052	0.001	0.052
xcmsSet.nSlaves	0.051	0.001	0.052
xcmsSet.noise	0.052	0.001	0.053
xcmsSet.peakwidth	0.052	0.000	0.053
xcmsSet.polarity	0.053	0.000	0.054
xcmsSet.ppm	0.052	0.000	0.052
xcmsSet.prefilter	0.053	0.000	0.053
xcmsSet.profparam	0.051	0.001	0.051
xcmsSet.sleep	0.054	0.001	0.054
xcmsSet.snthresh	0.055	0.001	0.056
xcmsSet.step	0.052	0.001	0.052
xcmsSet.verbose.columns	0.052	0.001	0.053
xcmsSetObj	0.051	0.001	0.052
zero2NA	0.001	0.000	0.001