BioC 3.2: CHECK report for metaX on oaxaca

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 01:35:09 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:45:26 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 617.3 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 (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 ‘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 ... [20s/25s] 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 ... [346s/379s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
createModels      151.997  6.307 163.036
dataClean          22.915  0.100  25.129
plotQCRLSC         12.998  0.072  21.842
autoRemoveOutlier  11.669  0.363  13.023
plotIntDistr       10.362  0.623  11.051
plotHeatMap         9.080  0.618   9.736
plotCV              8.727  0.600   9.674
plotPeakNumber      8.408  0.576   9.069
plotPLSDA           7.726  1.054   8.796
plotMissValue       8.085  0.578   8.716
normalize           8.067  0.578   9.125
plotTreeMap         7.875  0.638   8.783
plotPCA             7.449  0.386   7.885
plotPeakSN          7.245  0.557   7.811
plotPeakBox         6.274  0.023   6.326
doQCRLSC            1.810  0.027  12.294
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/10s]
 [9s/10s] 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	0.951	0.017	1.082
autoRemoveOutlier	11.669	0.363	13.023
calcAUROC	0.000	0.000	0.001
calcVIP	0.037	0.001	0.038
center	0.002	0.000	0.002
cor.network	3.403	0.116	4.043
createModels	151.997	6.307	163.036
dataClean	22.915	0.100	25.129
dir.case	0.001	0.000	0.001
dir.ctrl	0.001	0.000	0.002
doQCRLSC	1.810	0.027	12.294
filterPeaks	0.885	0.025	0.910
filterQCPeaks	0.843	0.023	1.007
filterQCPeaksByCV	1.227	0.046	1.397
getPeaksTable	1.000	0.043	1.214
group.bw	0.027	0.001	0.029
group.bw0	0.027	0.000	0.029
group.max	0.027	0.000	0.028
group.minfrac	0.028	0.001	0.029
group.minsamp	0.029	0.001	0.029
group.mzwid	0.029	0.000	0.029
group.mzwid0	0.029	0.000	0.029
group.sleep	0.029	0.001	0.029
hasQC	0.565	0.023	0.592
idres	0.029	0.001	0.029
kfold	0.001	0.000	0.001
makeDirectory	0.002	0.000	0.002
makeMetaboAnalystInput	1.635	0.079	1.831
metaXpipe	0.001	0.000	0.001
method	0.001	0.000	0.001
missValueImputeMethod	0.002	0.000	0.001
missingValueImpute	1.446	0.068	1.518
myCalcAUROC	0.000	0.000	0.001
myPLSDA	0.013	0.000	0.013
ncomp	0.000	0.000	0.001
normalize	8.067	0.578	9.125
nperm	0.000	0.000	0.001
outdir	0.001	0.000	0.002
pathwayAnalysis	0.000	0.000	0.001
peakFinder	0.000	0.000	0.001
peakStat	0.001	0.000	0.001
peaksData	0.540	0.018	0.557
plotCV	8.727	0.600	9.674
plotCorHeatmap	3.988	0.144	4.242
plotHeatMap	9.080	0.618	9.736
plotIntDistr	10.362	0.623	11.051
plotMissValue	8.085	0.578	8.716
plotNetwork	1.829	0.114	2.048
plotPCA	7.449	0.386	7.885
plotPLSDA	7.726	1.054	8.796
plotPeakBox	6.274	0.023	6.326
plotPeakNumber	8.408	0.576	9.069
plotPeakSN	7.245	0.557	7.811
plotPeakSumDist	1.587	0.040	1.652
plotQC	2.590	0.086	2.701
plotQCRLSC	12.998	0.072	21.842
plotTreeMap	7.875	0.638	8.783
powerAnalyst	0.000	0.000	0.001
preProcess	2.645	0.139	2.846
prefix	0.001	0.000	0.001
qcRlscSpan	0.030	0.000	0.031
ratioPairs	0.002	0.000	0.001
rawPeaks	0.031	0.001	0.032
reSetPeaksData	0.878	0.018	0.909
removeSample	0.522	0.018	0.546
retcor.method	0.027	0.001	0.028
retcor.plottype	0.026	0.000	0.026
retcor.profStep	0.027	0.000	0.028
sampleListFile	0.001	0.000	0.001
scale	0.001	0.000	0.001
selectBestComponent	3.213	0.174	3.392
t	0.000	0.001	0.001
transformation	1.653	0.058	1.713
validation	0.001	0.000	0.001
xcmsSet.fitgauss	0.030	0.001	0.031
xcmsSet.fwhm	0.027	0.000	0.028
xcmsSet.integrate	0.027	0.000	0.027
xcmsSet.max	0.028	0.001	0.028
xcmsSet.method	0.023	0.000	0.023
xcmsSet.mzCenterFun	0.027	0.001	0.028
xcmsSet.mzdiff	0.027	0.000	0.027
xcmsSet.nSlaves	0.026	0.000	0.026
xcmsSet.noise	0.026	0.001	0.027
xcmsSet.peakwidth	0.027	0.000	0.027
xcmsSet.polarity	0.026	0.001	0.027
xcmsSet.ppm	0.027	0.000	0.028
xcmsSet.prefilter	0.028	0.000	0.028
xcmsSet.profparam	0.027	0.001	0.027
xcmsSet.sleep	0.027	0.000	0.027
xcmsSet.snthresh	0.026	0.001	0.027
xcmsSet.step	0.024	0.000	0.025
xcmsSet.verbose.columns	0.026	0.000	0.025
xcmsSetObj	0.026	0.001	0.026
zero2NA	0.001	0.000	0.001