BioC 3.3: CHECK report for metaX on linux2.bioconductor.org

Package: metaX

Version: 1.1.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings metaX_1.1.0.tar.gz

StartedAt: 2015-10-27 05:39:38 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:47:05 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 446.4 seconds

RetCode: 0

Status:  OK

CheckDir: metaX.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings metaX_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/metaX.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.1.0’
* 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 ... [16s/16s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [274s/286s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
createModels      104.230  0.112 105.255
dataClean          16.374  0.016  16.534
plotIntDistr       12.063  0.152  12.236
plotPeakNumber     10.470  0.208  10.678
plotPeakSN         10.315  0.124  10.445
autoRemoveOutlier  10.292  0.020  10.342
plotMissValue      10.120  0.140  10.264
normalize          10.015  0.116  10.141
plotTreeMap         9.890  0.168  10.078
plotHeatMap         9.698  0.092   9.790
plotCV              8.798  0.196   9.003
plotQCRLSC          8.296  0.052  14.023
plotPLSDA           6.804  0.036   6.841
plotPCA             6.020  0.008   6.028
doQCRLSC            1.285  0.036   7.160
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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
* DONE (metaX)

name	user	system	elapsed
addValueNorm	0.911	0.011	0.931
autoRemoveOutlier	10.292	0.020	10.342
calcAUROC	0.000	0.000	0.001
calcVIP	0.03	0.00	0.03
center	0.001	0.000	0.001
cor.network	3.569	0.040	3.619
createModels	104.230	0.112	105.255
dataClean	16.374	0.016	16.534
dir.case	0.001	0.000	0.001
dir.ctrl	0	0	0
doQCRLSC	1.285	0.036	7.160
filterPeaks	1.045	0.028	1.072
filterQCPeaks	0.469	0.000	0.469
filterQCPeaksByCV	0.957	0.000	0.957
getPeaksTable	0.507	0.004	0.511
group.bw	0.016	0.000	0.016
group.bw0	0.015	0.000	0.016
group.max	0.016	0.000	0.015
group.minfrac	0.024	0.000	0.023
group.minsamp	0.016	0.000	0.016
group.mzwid	0.013	0.000	0.013
group.mzwid0	0.014	0.000	0.013
group.sleep	0.013	0.000	0.013
hasQC	0.560	0.000	0.562
idres	0.015	0.000	0.015
kfold	0.001	0.000	0.001
makeDirectory	0.002	0.000	0.002
makeMetaboAnalystInput	1.766	0.004	1.770
metaXpipe	0.000	0.000	0.001
method	0.001	0.000	0.001
missValueImputeMethod	0.001	0.000	0.001
missingValueImpute	1.708	0.008	1.716
myCalcAUROC	0.001	0.000	0.001
myPLSDA	0.012	0.000	0.012
ncomp	0.001	0.000	0.000
normalize	10.015	0.116	10.141
nperm	0	0	0
outdir	0.001	0.000	0.001
pathwayAnalysis	0	0	0
peakFinder	0.001	0.000	0.001
peakStat	0.001	0.000	0.001
peaksData	0.294	0.000	0.294
plotCV	8.798	0.196	9.003
plotCorHeatmap	2.211	0.012	2.223
plotHeatMap	9.698	0.092	9.790
plotIntDistr	12.063	0.152	12.236
plotMissValue	10.120	0.140	10.264
plotNetwork	1.925	0.000	1.925
plotPCA	6.020	0.008	6.028
plotPLSDA	6.804	0.036	6.841
plotPeakBox	4.122	0.004	4.126
plotPeakNumber	10.470	0.208	10.678
plotPeakSN	10.315	0.124	10.445
plotPeakSumDist	1.365	0.000	1.364
plotQC	1.734	0.020	1.754
plotQCRLSC	8.296	0.052	14.023
plotTreeMap	9.890	0.168	10.078
powerAnalyst	0.000	0.000	0.001
preProcess	2.018	0.000	2.019
prefix	0.000	0.000	0.001
qcRlscSpan	0.017	0.000	0.017
ratioPairs	0.001	0.000	0.001
rawPeaks	0.015	0.000	0.015
reSetPeaksData	0.681	0.000	0.682
removeSample	0.367	0.000	0.368
retcor.method	0.019	0.000	0.018
retcor.plottype	0.017	0.000	0.018
retcor.profStep	0.018	0.000	0.018
sampleListFile	0.002	0.000	0.001
scale	0.001	0.000	0.001
selectBestComponent	3.603	0.004	3.612
t	0.001	0.000	0.001
transformation	1.221	0.000	1.223
validation	0.001	0.000	0.001
xcmsSet.fitgauss	0.356	0.004	0.360
xcmsSet.fwhm	0.025	0.000	0.024
xcmsSet.integrate	0.022	0.000	0.023
xcmsSet.max	0.018	0.000	0.017
xcmsSet.method	0.021	0.000	0.021
xcmsSet.mzCenterFun	0.021	0.000	0.021
xcmsSet.mzdiff	0.013	0.004	0.018
xcmsSet.nSlaves	0.017	0.000	0.018
xcmsSet.noise	0.017	0.000	0.017
xcmsSet.peakwidth	0.017	0.004	0.021
xcmsSet.polarity	0.017	0.004	0.020
xcmsSet.ppm	0.02	0.00	0.02
xcmsSet.prefilter	0.018	0.000	0.018
xcmsSet.profparam	0.02	0.00	0.02
xcmsSet.sleep	0.024	0.000	0.025
xcmsSet.snthresh	0.018	0.000	0.018
xcmsSet.step	0.019	0.000	0.019
xcmsSet.verbose.columns	0.017	0.000	0.018
xcmsSetObj	0.021	0.004	0.024
zero2NA	0	0	0