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: 2015-10-27 09:46:36 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:57:06 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 629.9 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_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 ... [393s/411s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
createModels        147.783  5.927 153.798
dataClean            22.235  0.119  22.374
plotIntDistr         15.131  0.707  15.857
plotHeatMap          15.010  0.588  15.614
plotPeakNumber       14.561  0.751  15.326
plotMissValue        13.714  0.660  14.385
plotCV               13.256  0.558  13.824
plotPeakSN           13.040  0.633  13.673
autoRemoveOutlier    12.583  0.377  12.968
normalize            11.960  0.549  12.726
plotTreeMap          11.535  0.731  12.266
plotQCRLSC           12.180  0.067  20.784
plotPLSDA            10.070  1.318  11.388
plotPCA               8.562  0.436   9.018
plotPeakBox           6.647  0.049   6.733
selectBestComponent   5.024  0.212   5.237
doQCRLSC              1.556  0.026  10.112
* 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	0.871	0.015	0.887
autoRemoveOutlier	12.583	0.377	12.968
calcAUROC	0.001	0.000	0.001
calcVIP	0.058	0.001	0.060
center	0.001	0.000	0.001
cor.network	3.661	0.141	3.825
createModels	147.783	5.927	153.798
dataClean	22.235	0.119	22.374
dir.case	0.001	0.000	0.001
dir.ctrl	0.001	0.001	0.001
doQCRLSC	1.556	0.026	10.112
filterPeaks	0.794	0.033	0.827
filterQCPeaks	0.769	0.025	0.794
filterQCPeaksByCV	1.830	0.038	1.869
getPeaksTable	0.632	0.041	0.674
group.bw	0.050	0.000	0.051
group.bw0	0.050	0.000	0.051
group.max	0.051	0.001	0.051
group.minfrac	0.052	0.001	0.052
group.minsamp	0.051	0.001	0.051
group.mzwid	0.053	0.001	0.053
group.mzwid0	0.049	0.001	0.049
group.sleep	0.049	0.000	0.050
hasQC	0.483	0.016	0.500
idres	0.059	0.001	0.060
kfold	0.001	0.000	0.001
makeDirectory	0.001	0.000	0.002
makeMetaboAnalystInput	1.845	0.097	1.942
metaXpipe	0.001	0.000	0.001
method	0.001	0.000	0.001
missValueImputeMethod	0.001	0.000	0.001
missingValueImpute	1.680	0.071	1.751
myCalcAUROC	0.001	0.001	0.001
myPLSDA	0.013	0.000	0.013
ncomp	0.000	0.000	0.001
normalize	11.960	0.549	12.726
nperm	0.001	0.000	0.000
outdir	0.001	0.000	0.001
pathwayAnalysis	0.001	0.000	0.000
peakFinder	0.001	0.000	0.001
peakStat	0.001	0.000	0.001
peaksData	0.482	0.022	0.506
plotCV	13.256	0.558	13.824
plotCorHeatmap	3.821	0.143	3.985
plotHeatMap	15.010	0.588	15.614
plotIntDistr	15.131	0.707	15.857
plotMissValue	13.714	0.660	14.385
plotNetwork	2.285	0.121	2.408
plotPCA	8.562	0.436	9.018
plotPLSDA	10.070	1.318	11.388
plotPeakBox	6.647	0.049	6.733
plotPeakNumber	14.561	0.751	15.326
plotPeakSN	13.040	0.633	13.673
plotPeakSumDist	1.520	0.044	1.572
plotQC	2.688	0.085	2.773
plotQCRLSC	12.180	0.067	20.784
plotTreeMap	11.535	0.731	12.266
powerAnalyst	0.001	0.000	0.001
preProcess	4.395	0.138	4.533
prefix	0.002	0.000	0.002
qcRlscSpan	0.050	0.001	0.050
ratioPairs	0.002	0.000	0.002
rawPeaks	0.050	0.000	0.051
reSetPeaksData	0.521	0.014	0.535
removeSample	0.921	0.032	0.953
retcor.method	0.051	0.000	0.051
retcor.plottype	0.051	0.001	0.051
retcor.profStep	0.050	0.001	0.051
sampleListFile	0.001	0.000	0.002
scale	0	0	0
selectBestComponent	5.024	0.212	5.237
t	0.001	0.000	0.001
transformation	1.842	0.076	1.919
validation	0.001	0.000	0.001
xcmsSet.fitgauss	0.058	0.001	0.059
xcmsSet.fwhm	0.049	0.001	0.050
xcmsSet.integrate	0.054	0.001	0.054
xcmsSet.max	0.052	0.001	0.052
xcmsSet.method	0.056	0.000	0.056
xcmsSet.mzCenterFun	0.051	0.000	0.052
xcmsSet.mzdiff	0.052	0.000	0.052
xcmsSet.nSlaves	0.053	0.000	0.052
xcmsSet.noise	0.052	0.001	0.053
xcmsSet.peakwidth	0.052	0.001	0.053
xcmsSet.polarity	0.051	0.001	0.051
xcmsSet.ppm	0.05	0.00	0.05
xcmsSet.prefilter	0.051	0.000	0.051
xcmsSet.profparam	0.049	0.001	0.050
xcmsSet.sleep	0.049	0.001	0.049
xcmsSet.snthresh	0.049	0.001	0.050
xcmsSet.step	0.051	0.000	0.051
xcmsSet.verbose.columns	0.049	0.000	0.049
xcmsSetObj	0.048	0.000	0.048
zero2NA	0.001	0.000	0.001