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BioC 3.2: CHECK report for metaX on windows1.bioconductor.org

This page was generated on 2015-10-27 17:32:28 -0400 (Tue, 27 Oct 2015).

Package 628/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaX 1.0.0
Bo Wen
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/metaX
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: metaX
Version: 1.0.0
Command: rm -rf metaX.buildbin-libdir metaX.Rcheck && mkdir metaX.buildbin-libdir metaX.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaX.buildbin-libdir metaX_1.0.0.tar.gz >metaX.Rcheck\00install.out 2>&1 && cp metaX.Rcheck\00install.out metaX-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=metaX.buildbin-libdir --install="check:metaX-install.out" --force-multiarch --no-vignettes --timings metaX_1.0.0.tar.gz
StartedAt: 2015-10-27 03:27:36 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 03:40:17 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 761.0 seconds
RetCode: 0
Status:  OK  
CheckDir: metaX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf metaX.buildbin-libdir metaX.Rcheck && mkdir metaX.buildbin-libdir metaX.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaX.buildbin-libdir metaX_1.0.0.tar.gz >metaX.Rcheck\00install.out 2>&1 && cp metaX.Rcheck\00install.out metaX-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=metaX.buildbin-libdir --install="check:metaX-install.out" --force-multiarch --no-vignettes --timings metaX_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/metaX.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'metaX' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [259s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
createModels      93.06   3.39   96.47
dataClean         15.88   0.10   15.96
plotIntDistr       9.88   0.41   10.28
plotCV             9.18   0.74    9.90
normalize          9.12   0.57    9.70
plotHeatMap        8.44   0.39    8.83
plotMissValue      8.26   0.50    8.77
autoRemoveOutlier  8.31   0.18    8.50
plotPeakNumber     8.09   0.30    8.39
plotTreeMap        7.80   0.35    8.20
plotPeakSN         7.53   0.28    7.81
plotQCRLSC         7.51   0.04   12.61
plotPLSDA          6.74   0.19    6.92
plotPCA            5.48   0.05    5.53
doQCRLSC           1.12   0.03    6.35
** running examples for arch 'x64' ... [298s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
createModels      108.21   2.78  110.99
dataClean          16.61   0.05   16.65
plotPeakNumber     11.72   0.87   12.59
plotIntDistr       11.19   1.05   12.25
plotMissValue      10.78   0.73   11.51
plotCV             10.45   0.95   11.41
plotHeatMap         9.93   0.86   10.80
plotTreeMap         9.93   0.83   10.75
normalize           8.82   0.75    9.56
plotPeakSN          8.66   0.84    9.50
plotQCRLSC          8.90   0.06   14.84
plotPLSDA           7.75   0.95    8.71
autoRemoveOutlier   7.59   0.16    7.75
plotPCA             5.66   0.07    5.72
doQCRLSC            1.26   0.03    7.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [7s]
 [7s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [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
  'C:/biocbld/bbs-3.2-bioc/meat/metaX.Rcheck/00check.log'
for details.


metaX.Rcheck/00install.out:


install for i386

* installing *source* package 'metaX' ...
** R
** inst
** preparing package for lazy loading
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
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.

install for x64

* installing *source* package 'metaX' ...
** testing if installed package can be loaded
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.
* MD5 sums
packaged installation of 'metaX' as metaX_1.0.0.zip
* DONE (metaX)

metaX.Rcheck/examples_i386/metaX-Ex.timings:

nameusersystemelapsed
addValueNorm0.640.000.64
autoRemoveOutlier8.310.188.50
calcAUROC000
calcVIP0.030.000.03
center000
cor.network3.020.073.10
createModels93.06 3.3996.47
dataClean15.88 0.1015.96
dir.case000
dir.ctrl000
doQCRLSC1.120.036.35
filterPeaks0.580.000.58
filterQCPeaks0.580.000.58
filterQCPeaksByCV0.850.000.84
getPeaksTable0.680.000.69
group.bw0.040.000.03
group.bw00.010.000.02
group.max0.030.000.03
group.minfrac0.020.000.02
group.minsamp0.010.000.01
group.mzwid0.030.000.03
group.mzwid00.020.000.02
group.sleep0.030.000.03
hasQC0.490.000.48
idres0.010.000.02
kfold000
makeDirectory000
makeMetaboAnalystInput1.390.031.43
metaXpipe000
method000
missValueImputeMethod000
missingValueImpute1.190.021.20
myCalcAUROC000
myPLSDA000
ncomp000
normalize9.120.579.70
nperm000
outdir000
pathwayAnalysis000
peakFinder000
peakStat000
peaksData0.400.000.41
plotCV9.180.749.90
plotCorHeatmap2.070.142.22
plotHeatMap8.440.398.83
plotIntDistr 9.88 0.4110.28
plotMissValue8.260.508.77
plotNetwork1.520.011.53
plotPCA5.480.055.53
plotPLSDA6.740.196.92
plotPeakBox4.590.014.61
plotPeakNumber8.090.308.39
plotPeakSN7.530.287.81
plotPeakSumDist1.050.021.07
plotQC2.020.002.01
plotQCRLSC 7.51 0.0412.61
plotTreeMap7.800.358.20
powerAnalyst000
preProcess2.040.012.06
prefix000
qcRlscSpan0.020.000.02
ratioPairs000
rawPeaks0.010.000.02
reSetPeaksData0.640.000.64
removeSample0.360.000.36
retcor.method0.020.000.01
retcor.plottype0.020.000.02
retcor.profStep0.020.000.01
sampleListFile0.010.000.02
scale000
selectBestComponent2.440.042.48
t000
transformation1.330.001.32
validation000
xcmsSet.fitgauss0.010.000.02
xcmsSet.fwhm0.010.000.01
xcmsSet.integrate0.020.000.02
xcmsSet.max0.030.000.03
xcmsSet.method0.020.000.01
xcmsSet.mzCenterFun0.010.000.02
xcmsSet.mzdiff0.030.000.03
xcmsSet.nSlaves0.020.000.01
xcmsSet.noise0.030.000.03
xcmsSet.peakwidth0.020.000.02
xcmsSet.polarity0.020.000.02
xcmsSet.ppm0.030.000.03
xcmsSet.prefilter0.010.000.02
xcmsSet.profparam0.040.000.03
xcmsSet.sleep0.010.000.01
xcmsSet.snthresh0.020.000.02
xcmsSet.step0.020.000.01
xcmsSet.verbose.columns0.030.000.03
xcmsSetObj0.010.000.02
zero2NA000

metaX.Rcheck/examples_x64/metaX-Ex.timings:

nameusersystemelapsed
addValueNorm0.670.000.67
autoRemoveOutlier7.590.167.75
calcAUROC000
calcVIP0.030.000.03
center000
cor.network3.060.083.14
createModels108.21 2.78110.99
dataClean16.61 0.0516.65
dir.case000
dir.ctrl000
doQCRLSC1.260.037.39
filterPeaks0.640.000.64
filterQCPeaks0.680.010.69
filterQCPeaksByCV101
getPeaksTable0.820.000.82
group.bw0.020.010.04
group.bw00.010.000.01
group.max0.040.000.03
group.minfrac0.010.000.02
group.minsamp0.020.000.01
group.mzwid0.010.000.01
group.mzwid00.020.000.02
group.sleep0.010.000.02
hasQC0.350.020.36
idres0.010.000.02
kfold000
makeDirectory0.020.000.01
makeMetaboAnalystInput1.200.031.24
metaXpipe000
method000
missValueImputeMethod000
missingValueImpute1.170.081.25
myCalcAUROC000
myPLSDA000
ncomp000
normalize8.820.759.56
nperm000
outdir000
pathwayAnalysis000
peakFinder000
peakStat000
peaksData0.350.000.34
plotCV10.45 0.9511.41
plotCorHeatmap2.580.062.64
plotHeatMap 9.93 0.8610.80
plotIntDistr11.19 1.0512.25
plotMissValue10.78 0.7311.51
plotNetwork1.690.061.75
plotPCA5.660.075.72
plotPLSDA7.750.958.71
plotPeakBox4.930.024.95
plotPeakNumber11.72 0.8712.59
plotPeakSN8.660.849.50
plotPeakSumDist0.980.041.02
plotQC1.940.041.99
plotQCRLSC 8.90 0.0614.84
plotTreeMap 9.93 0.8310.75
powerAnalyst000
preProcess2.110.132.23
prefix000
qcRlscSpan0.020.000.02
ratioPairs000
rawPeaks0.020.000.02
reSetPeaksData0.70.00.7
removeSample0.360.030.39
retcor.method0.030.000.03
retcor.plottype0.020.000.01
retcor.profStep0.030.000.04
sampleListFile000
scale000
selectBestComponent2.750.102.84
t000
transformation1.310.061.37
validation000
xcmsSet.fitgauss0.020.000.02
xcmsSet.fwhm0.030.000.03
xcmsSet.integrate0.030.000.03
xcmsSet.max0.010.000.02
xcmsSet.method0.040.000.03
xcmsSet.mzCenterFun0.010.000.02
xcmsSet.mzdiff0.030.000.03
xcmsSet.nSlaves0.020.000.01
xcmsSet.noise0.030.000.03
xcmsSet.peakwidth0.010.000.02
xcmsSet.polarity0.040.000.03
xcmsSet.ppm0.030.000.03
xcmsSet.prefilter0.010.000.02
xcmsSet.profparam0.020.020.03
xcmsSet.sleep0.030.000.03
xcmsSet.snthresh0.030.000.03
xcmsSet.step0.020.000.02
xcmsSet.verbose.columns0.020.000.02
xcmsSetObj0.030.000.03
zero2NA000