BioC 3.2: CHECK report for metaX on oaxaca

Package: metaX

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaX_1.0.3.tar.gz

StartedAt: 2016-04-23 01:58:49 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:08:04 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 555.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: metaX.Rcheck

Warnings: 1

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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_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/metaX.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.0.3’
* 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 ... [19s/23s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: Package 'metaX' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/metaX.Rcheck/00install.out’ for details.
* 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 ... [329s/347s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
createModels      142.026  5.783 148.115
dataClean          23.586  0.124  24.159
plotQCRLSC         12.712  0.078  20.212
autoRemoveOutlier  10.607  0.326  11.190
plotIntDistr       10.257  0.537  10.847
plotHeatMap         9.307  0.616   9.938
plotCV              9.032  0.513   9.558
plotMissValue       8.038  0.512   8.566
plotPeakNumber      7.962  0.513   8.490
plotPLSDA           7.053  1.162   8.219
normalize           7.405  0.596   8.788
plotTreeMap         7.439  0.515   7.979
plotPeakSN          6.868  0.508   7.381
plotPCA             6.340  0.354   6.713
plotPeakBox         6.275  0.030   6.328
doQCRLSC            2.037  0.019  10.105
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [10s/10s]
 [10s/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: 1 WARNING, 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: 'rgl_init' failed, running with rgl.useNULL = TRUE
** 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: 'rgl_init' failed, running with rgl.useNULL = TRUE
Warning: Package 'metaX' is deprecated and will be removed from Bioconductor
  version 3.3
* DONE (metaX)

name	user	system	elapsed
addValueNorm	0.824	0.018	0.842
autoRemoveOutlier	10.607	0.326	11.190
calcAUROC	0.000	0.000	0.001
calcVIP	0.038	0.001	0.038
center	0.002	0.000	0.002
cor.network	3.302	0.110	3.608
createModels	142.026	5.783	148.115
dataClean	23.586	0.124	24.159
dir.case	0.001	0.000	0.001
dir.ctrl	0.001	0.000	0.001
doQCRLSC	2.037	0.019	10.105
filterPeaks	0.878	0.029	0.909
filterQCPeaks	0.997	0.029	1.027
filterQCPeaksByCV	1.049	0.038	1.087
getPeaksTable	0.650	0.035	0.685
group.bw	0.027	0.000	0.027
group.bw0	0.025	0.000	0.025
group.max	0.024	0.001	0.024
group.minfrac	0.026	0.000	0.026
group.minsamp	0.022	0.001	0.022
group.mzwid	0.021	0.000	0.021
group.mzwid0	0.021	0.001	0.021
group.sleep	0.022	0.000	0.023
hasQC	0.437	0.016	0.452
idres	0.026	0.000	0.026
kfold	0.001	0.000	0.001
makeDirectory	0.002	0.000	0.002
makeMetaboAnalystInput	1.563	0.075	1.649
metaXpipe	0.001	0.000	0.001
method	0.001	0.000	0.001
missValueImputeMethod	0.001	0.000	0.001
missingValueImpute	1.542	0.074	1.616
myCalcAUROC	0.001	0.000	0.001
myPLSDA	0.012	0.000	0.013
ncomp	0.001	0.001	0.001
normalize	7.405	0.596	8.788
nperm	0.001	0.000	0.001
outdir	0.002	0.001	0.002
pathwayAnalysis	0	0	0
peakFinder	0.001	0.000	0.001
peakStat	0.001	0.000	0.001
peaksData	0.524	0.019	0.547
plotCV	9.032	0.513	9.558
plotCorHeatmap	3.496	0.139	3.664
plotHeatMap	9.307	0.616	9.938
plotIntDistr	10.257	0.537	10.847
plotMissValue	8.038	0.512	8.566
plotNetwork	1.852	0.114	1.999
plotPCA	6.340	0.354	6.713
plotPLSDA	7.053	1.162	8.219
plotPeakBox	6.275	0.030	6.328
plotPeakNumber	7.962	0.513	8.490
plotPeakSN	6.868	0.508	7.381
plotPeakSumDist	1.449	0.043	1.519
plotQC	2.326	0.066	2.393
plotQCRLSC	12.712	0.078	20.212
plotTreeMap	7.439	0.515	7.979
powerAnalyst	0.001	0.000	0.001
preProcess	2.353	0.112	2.465
prefix	0.002	0.000	0.001
qcRlscSpan	0.027	0.001	0.028
ratioPairs	0.001	0.000	0.001
rawPeaks	0.028	0.001	0.028
reSetPeaksData	0.522	0.019	0.540
removeSample	0.792	0.026	0.819
retcor.method	0.029	0.001	0.029
retcor.plottype	0.027	0.000	0.027
retcor.profStep	0.026	0.000	0.027
sampleListFile	0.002	0.000	0.001
scale	0.001	0.001	0.001
selectBestComponent	2.877	0.187	3.067
t	0.001	0.000	0.001
transformation	1.306	0.061	1.368
validation	0.001	0.000	0.001
xcmsSet.fitgauss	0.03	0.00	0.03
xcmsSet.fwhm	0.030	0.000	0.031
xcmsSet.integrate	0.031	0.001	0.032
xcmsSet.max	0.029	0.001	0.030
xcmsSet.method	0.028	0.000	0.028
xcmsSet.mzCenterFun	0.024	0.001	0.023
xcmsSet.mzdiff	0.025	0.000	0.026
xcmsSet.nSlaves	0.026	0.001	0.025
xcmsSet.noise	0.026	0.000	0.026
xcmsSet.peakwidth	0.029	0.000	0.030
xcmsSet.polarity	0.028	0.001	0.028
xcmsSet.ppm	0.035	0.001	0.035
xcmsSet.prefilter	0.028	0.000	0.028
xcmsSet.profparam	0.028	0.000	0.029
xcmsSet.sleep	0.028	0.001	0.028
xcmsSet.snthresh	0.03	0.00	0.03
xcmsSet.step	0.027	0.000	0.026
xcmsSet.verbose.columns	0.027	0.001	0.028
xcmsSetObj	0.029	0.001	0.029
zero2NA	0.000	0.000	0.001