BioC 3.2: CHECK report for metaX on oaxaca

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 05:28:44 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:38:12 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 568.1 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 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... [18s/19s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [345s/364s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
createModels      142.475  4.795 147.468
dataClean          21.431  0.118  21.928
plotHeatMap        13.147  0.392  13.556
plotIntDistr       12.932  0.424  13.365
plotPeakNumber     11.439  0.453  11.903
plotCV             10.954  0.432  11.429
plotMissValue      10.898  0.376  11.289
autoRemoveOutlier  10.759  0.348  11.118
plotTreeMap        10.599  0.398  11.146
plotQCRLSC         10.317  0.061  18.087
plotPeakSN          9.887  0.446  10.338
normalize           8.827  0.429   9.684
plotPLSDA           6.743  0.938   7.736
plotPCA             6.762  0.318   7.096
plotPeakBox         6.218  0.031   6.258
doQCRLSC            1.683  0.025   9.424
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [9s/9s] 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	0.790	0.011	0.801
autoRemoveOutlier	10.759	0.348	11.118
calcAUROC	0.001	0.000	0.001
calcVIP	0.034	0.001	0.036
center	0.001	0.000	0.002
cor.network	3.088	0.099	3.190
createModels	142.475	4.795	147.468
dataClean	21.431	0.118	21.928
dir.case	0.001	0.000	0.001
dir.ctrl	0.001	0.000	0.001
doQCRLSC	1.683	0.025	9.424
filterPeaks	1.006	0.027	1.035
filterQCPeaks	0.695	0.024	0.719
filterQCPeaksByCV	1.226	0.034	1.261
getPeaksTable	0.615	0.032	0.649
group.bw	0.024	0.001	0.024
group.bw0	0.024	0.000	0.024
group.max	0.027	0.001	0.027
group.minfrac	0.027	0.001	0.027
group.minsamp	0.026	0.000	0.027
group.mzwid	0.025	0.001	0.026
group.mzwid0	0.026	0.000	0.027
group.sleep	0.028	0.000	0.028
hasQC	0.527	0.010	0.538
idres	0.026	0.001	0.026
kfold	0.001	0.000	0.000
makeDirectory	0.001	0.000	0.002
makeMetaboAnalystInput	1.696	0.058	1.756
metaXpipe	0.001	0.001	0.001
method	0.001	0.000	0.001
missValueImputeMethod	0.002	0.000	0.001
missingValueImpute	1.509	0.055	1.565
myCalcAUROC	0.001	0.000	0.001
myPLSDA	0.01	0.00	0.01
ncomp	0.001	0.000	0.001
normalize	8.827	0.429	9.684
nperm	0.001	0.000	0.000
outdir	0.001	0.000	0.001
pathwayAnalysis	0.000	0.000	0.001
peakFinder	0.000	0.000	0.001
peakStat	0.001	0.000	0.001
peaksData	0.396	0.014	0.411
plotCV	10.954	0.432	11.429
plotCorHeatmap	3.488	0.103	3.601
plotHeatMap	13.147	0.392	13.556
plotIntDistr	12.932	0.424	13.365
plotMissValue	10.898	0.376	11.289
plotNetwork	2.101	0.090	2.194
plotPCA	6.762	0.318	7.096
plotPLSDA	6.743	0.938	7.736
plotPeakBox	6.218	0.031	6.258
plotPeakNumber	11.439	0.453	11.903
plotPeakSN	9.887	0.446	10.338
plotPeakSumDist	1.391	0.036	1.433
plotQC	2.676	0.077	2.757
plotQCRLSC	10.317	0.061	18.087
plotTreeMap	10.599	0.398	11.146
powerAnalyst	0.001	0.000	0.001
preProcess	2.735	0.101	2.837
prefix	0.002	0.000	0.001
qcRlscSpan	0.028	0.000	0.029
ratioPairs	0.001	0.000	0.002
rawPeaks	0.026	0.000	0.028
reSetPeaksData	0.543	0.013	0.556
removeSample	0.503	0.012	0.516
retcor.method	0.022	0.000	0.022
retcor.plottype	0.026	0.000	0.026
retcor.profStep	0.023	0.001	0.024
sampleListFile	0.002	0.000	0.002
scale	0.001	0.000	0.001
selectBestComponent	3.333	0.133	3.468
t	0	0	0
transformation	1.240	0.047	1.288
validation	0.001	0.000	0.001
xcmsSet.fitgauss	0.028	0.001	0.029
xcmsSet.fwhm	0.029	0.001	0.029
xcmsSet.integrate	0.025	0.000	0.025
xcmsSet.max	0.022	0.001	0.023
xcmsSet.method	0.022	0.000	0.021
xcmsSet.mzCenterFun	0.022	0.001	0.022
xcmsSet.mzdiff	0.022	0.000	0.022
xcmsSet.nSlaves	0.021	0.001	0.022
xcmsSet.noise	0.025	0.000	0.025
xcmsSet.peakwidth	0.030	0.001	0.030
xcmsSet.polarity	0.028	0.001	0.028
xcmsSet.ppm	0.026	0.000	0.027
xcmsSet.prefilter	0.023	0.001	0.023
xcmsSet.profparam	0.022	0.000	0.023
xcmsSet.sleep	0.044	0.002	0.045
xcmsSet.snthresh	0.029	0.001	0.030
xcmsSet.step	0.031	0.000	0.032
xcmsSet.verbose.columns	0.03	0.00	0.03
xcmsSetObj	0.030	0.001	0.031
zero2NA	0.001	0.000	0.000