BioC 3.2: CHECK report for metaX on zin1

Package: metaX

Version: 1.0.3

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metaX_1.0.3.tar.gz

StartedAt: 2016-04-23 02:43:25 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:50:16 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 410.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: metaX.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metaX_1.0.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/metaX.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ... [14s/14s] WARNING
Found the following significant warnings:
  Warning: Package 'metaX' is deprecated and will be removed from Bioconductor
See ‘/home/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 ... [243s/259s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
createModels      104.040  0.063 104.303
dataClean          16.724  0.028  16.820
autoRemoveOutlier   9.836  0.036   9.871
plotQCRLSC          9.113  0.044  15.213
plotIntDistr        7.755  0.276   8.029
plotHeatMap         6.710  0.300   7.005
plotPeakNumber      6.761  0.200   6.958
plotMissValue       6.635  0.231   7.004
plotCV              6.733  0.092   6.843
plotTreeMap         6.468  0.192   6.657
plotPeakSN          5.981  0.208   6.262
plotPCA             6.159  0.008   6.163
normalize           5.958  0.104   6.350
plotPLSDA           5.373  0.016   5.386
plotPeakBox         5.010  0.004   5.036
doQCRLSC            1.399  0.032   9.817
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [8s/8s] 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/metaX.Rcheck/00check.log’
for details.

* installing *source* package ‘metaX’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'metaX' is deprecated and will be removed from Bioconductor
  version 3.3
* DONE (metaX)

name	user	system	elapsed
addValueNorm	0.696	0.004	0.700
autoRemoveOutlier	9.836	0.036	9.871
calcAUROC	0.000	0.000	0.001
calcVIP	0.029	0.000	0.028
center	0.001	0.000	0.001
cor.network	2.895	0.011	2.939
createModels	104.040	0.063	104.303
dataClean	16.724	0.028	16.820
dir.case	0.001	0.000	0.001
dir.ctrl	0.000	0.000	0.001
doQCRLSC	1.399	0.032	9.817
filterPeaks	1.006	0.032	1.043
filterQCPeaks	0.609	0.004	0.612
filterQCPeaksByCV	0.818	0.000	0.818
getPeaksTable	0.485	0.008	0.493
group.bw	0.019	0.000	0.019
group.bw0	0.019	0.000	0.019
group.max	0.018	0.000	0.018
group.minfrac	0.021	0.000	0.021
group.minsamp	0.02	0.00	0.02
group.mzwid	0.018	0.000	0.018
group.mzwid0	0.02	0.00	0.02
group.sleep	0.022	0.000	0.021
hasQC	0.376	0.000	0.389
idres	0.014	0.004	0.019
kfold	0.001	0.000	0.000
makeDirectory	0.001	0.000	0.001
makeMetaboAnalystInput	1.243	0.000	1.245
metaXpipe	0.000	0.000	0.001
method	0.000	0.000	0.001
missValueImputeMethod	0.001	0.000	0.000
missingValueImpute	1.109	0.000	1.110
myCalcAUROC	0	0	0
myPLSDA	0.012	0.000	0.012
ncomp	0.001	0.000	0.001
normalize	5.958	0.104	6.350
nperm	0.001	0.000	0.001
outdir	0.001	0.000	0.001
pathwayAnalysis	0.001	0.000	0.000
peakFinder	0	0	0
peakStat	0.001	0.000	0.001
peaksData	0.363	0.000	0.363
plotCV	6.733	0.092	6.843
plotCorHeatmap	2.218	0.008	2.224
plotHeatMap	6.710	0.300	7.005
plotIntDistr	7.755	0.276	8.029
plotMissValue	6.635	0.231	7.004
plotNetwork	1.427	0.008	1.434
plotPCA	6.159	0.008	6.163
plotPLSDA	5.373	0.016	5.386
plotPeakBox	5.010	0.004	5.036
plotPeakNumber	6.761	0.200	6.958
plotPeakSN	5.981	0.208	6.262
plotPeakSumDist	1.114	0.000	1.116
plotQC	2.028	0.000	2.048
plotQCRLSC	9.113	0.044	15.213
plotTreeMap	6.468	0.192	6.657
powerAnalyst	0.001	0.000	0.000
preProcess	2.085	0.000	2.089
prefix	0.001	0.000	0.001
qcRlscSpan	0.024	0.000	0.024
ratioPairs	0.001	0.000	0.001
rawPeaks	0.026	0.000	0.026
reSetPeaksData	0.758	0.004	0.762
removeSample	0.378	0.000	0.387
retcor.method	0.027	0.000	0.040
retcor.plottype	0.023	0.000	0.023
retcor.profStep	0.022	0.000	0.024
sampleListFile	0.001	0.000	0.002
scale	0.000	0.000	0.001
selectBestComponent	2.438	0.012	2.486
t	0.001	0.000	0.000
transformation	1.300	0.004	1.304
validation	0.001	0.000	0.000
xcmsSet.fitgauss	0.015	0.004	0.020
xcmsSet.fwhm	0.019	0.000	0.018
xcmsSet.integrate	0.019	0.000	0.019
xcmsSet.max	0.021	0.000	0.022
xcmsSet.method	0.02	0.00	0.02
xcmsSet.mzCenterFun	0.024	0.000	0.023
xcmsSet.mzdiff	0.022	0.000	0.023
xcmsSet.nSlaves	0.023	0.000	0.022
xcmsSet.noise	0.023	0.000	0.023
xcmsSet.peakwidth	0.021	0.000	0.022
xcmsSet.polarity	0.024	0.000	0.024
xcmsSet.ppm	0.022	0.000	0.022
xcmsSet.prefilter	0.023	0.000	0.022
xcmsSet.profparam	0.025	0.000	0.025
xcmsSet.sleep	0.046	0.000	0.047
xcmsSet.snthresh	0.026	0.004	0.027
xcmsSet.step	0.026	0.000	0.027
xcmsSet.verbose.columns	0.028	0.000	0.028
xcmsSetObj	0.028	0.000	0.027
zero2NA	0	0	0