BioC 3.3: CHECK report for metaX on morelia

Package: metaX

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaX_1.1.0.tar.gz

StartedAt: 2015-10-22 08:13:46 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 08:20:47 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 421.7 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_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/metaX.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.0’
* 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’
Undefined global functions or variables:
  ..density.. CV Component Freq ID Intensity Metrics Ratio SN Value
  batch breaks caretFuncs contains cv lessThan30 loessSpan maxOrder
  meanQC missPeaksN mzmed n n20 n30 name newOrder normCV npeaks outlier
  plot.roc ratio rfFuncs rfe rfeControl sdQC sig statistic total
  trainIndex val value valueNorm valuePredict x y
* 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 ... [257s/270s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
createModels      101.141  3.803 105.168
dataClean          15.532  0.094  15.650
plotIntDistr       10.808  0.305  11.368
plotHeatMap        10.027  0.330  10.606
plotMissValue       9.386  0.355   9.754
plotCV              9.161  0.400   9.567
plotTreeMap         8.402  0.366   8.790
plotPeakNumber      8.242  0.370   8.618
plotPeakSN          8.142  0.335   8.483
plotQCRLSC          8.356  0.049  14.206
normalize           7.790  0.342   8.717
autoRemoveOutlier   7.804  0.257   8.072
plotPCA             5.534  0.266   5.814
plotPLSDA           4.891  0.773   5.666
doQCRLSC            1.063  0.015   6.123
* 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
  ‘/Users/biocbuild/bbs-3.3-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'
** 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'
* DONE (metaX)

name	user	system	elapsed
addValueNorm	0.352	0.009	0.361
autoRemoveOutlier	7.804	0.257	8.072
calcAUROC	0.000	0.000	0.001
calcVIP	0.019	0.002	0.020
center	0.001	0.000	0.001
cor.network	2.680	0.089	2.775
createModels	101.141	3.803	105.168
dataClean	15.532	0.094	15.650
dir.case	0.001	0.000	0.001
dir.ctrl	0.001	0.000	0.001
doQCRLSC	1.063	0.015	6.123
filterPeaks	0.806	0.024	0.831
filterQCPeaks	0.432	0.016	0.448
filterQCPeaksByCV	0.781	0.025	0.806
getPeaksTable	0.516	0.028	0.543
group.bw	0.016	0.000	0.017
group.bw0	0.019	0.000	0.019
group.max	0.018	0.001	0.019
group.minfrac	0.018	0.000	0.019
group.minsamp	0.015	0.000	0.015
group.mzwid	0.014	0.000	0.015
group.mzwid0	0.015	0.001	0.016
group.sleep	0.014	0.000	0.014
hasQC	0.291	0.008	0.298
idres	0.014	0.001	0.015
kfold	0	0	0
makeDirectory	0.001	0.000	0.002
makeMetaboAnalystInput	1.165	0.040	1.210
metaXpipe	0.001	0.000	0.002
method	0.001	0.000	0.000
missValueImputeMethod	0.001	0.000	0.001
missingValueImpute	1.275	0.043	1.320
myCalcAUROC	0.000	0.000	0.001
myPLSDA	0.012	0.000	0.012
ncomp	0.001	0.000	0.000
normalize	7.790	0.342	8.717
nperm	0.000	0.000	0.001
outdir	0.001	0.000	0.001
pathwayAnalysis	0.000	0.001	0.000
peakFinder	0.001	0.000	0.000
peakStat	0.000	0.000	0.001
peaksData	0.360	0.014	0.374
plotCV	9.161	0.400	9.567
plotCorHeatmap	2.799	0.094	3.026
plotHeatMap	10.027	0.330	10.606
plotIntDistr	10.808	0.305	11.368
plotMissValue	9.386	0.355	9.754
plotNetwork	1.295	0.053	1.349
plotPCA	5.534	0.266	5.814
plotPLSDA	4.891	0.773	5.666
plotPeakBox	4.518	0.020	4.551
plotPeakNumber	8.242	0.370	8.618
plotPeakSN	8.142	0.335	8.483
plotPeakSumDist	0.979	0.028	1.013
plotQC	1.629	0.040	1.670
plotQCRLSC	8.356	0.049	14.206
plotTreeMap	8.402	0.366	8.790
powerAnalyst	0	0	0
preProcess	2.130	0.082	2.214
prefix	0.001	0.000	0.001
qcRlscSpan	0.019	0.000	0.019
ratioPairs	0.001	0.000	0.002
rawPeaks	0.020	0.001	0.021
reSetPeaksData	0.663	0.008	0.670
removeSample	0.300	0.009	0.309
retcor.method	0.021	0.000	0.022
retcor.plottype	0.020	0.001	0.021
retcor.profStep	0.018	0.000	0.019
sampleListFile	0.001	0.001	0.002
scale	0.001	0.000	0.001
selectBestComponent	2.379	0.096	2.475
t	0.000	0.000	0.001
transformation	0.947	0.039	0.985
validation	0	0	0
xcmsSet.fitgauss	0.015	0.001	0.015
xcmsSet.fwhm	0.016	0.000	0.016
xcmsSet.integrate	0.015	0.000	0.016
xcmsSet.max	0.016	0.000	0.017
xcmsSet.method	0.018	0.001	0.018
xcmsSet.mzCenterFun	0.014	0.000	0.014
xcmsSet.mzdiff	0.013	0.001	0.014
xcmsSet.nSlaves	0.015	0.000	0.016
xcmsSet.noise	0.015	0.000	0.014
xcmsSet.peakwidth	0.015	0.000	0.015
xcmsSet.polarity	0.015	0.000	0.014
xcmsSet.ppm	0.030	0.002	0.032
xcmsSet.prefilter	0.014	0.000	0.015
xcmsSet.profparam	0.014	0.000	0.015
xcmsSet.sleep	0.017	0.000	0.017
xcmsSet.snthresh	0.017	0.001	0.017
xcmsSet.step	0.02	0.00	0.02
xcmsSet.verbose.columns	0.015	0.000	0.015
xcmsSetObj	0.015	0.000	0.015
zero2NA	0.000	0.000	0.001