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CHECK report for ClassifyR on merida2

This page was generated on 2019-04-09 13:30:08 -0400 (Tue, 09 Apr 2019).

Package 275/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.3.6
Dario Strbenac
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: master
Last Commit: 8091e0b
Last Changed Date: 2019-01-22 19:41:20 -0400 (Tue, 22 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: ClassifyR
Version: 2.3.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClassifyR_2.3.6.tar.gz
StartedAt: 2019-04-08 23:55:22 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-09 00:01:04 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 342.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClassifyR_2.3.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ClassifyR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClassifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClassifyR’ version ‘2.3.6’
* 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 ‘ClassifyR’ 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
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.posterior_probs : <anonymous>: no visible global function definition
  for ‘dmvnorm’
kTSPclassifier,DataFrame : <anonymous>: no visible global function
  definition for ‘Pairs’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘measurement’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘..density..’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘legends grouping’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘key’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘value’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘ID’
rankingPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for ‘first’
rankingPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for ‘second’
rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘first’
rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘second’
runTest,DataFrame: no visible binding for global variable ‘setsNodes’
runTests,DataFrame: no visible binding for global variable ‘setsNodes’
samplesMetricMap,list: no visible binding for global variable ‘Class’
samplesMetricMap,list: no visible binding for global variable ‘Group’
samplesMetricMap,list: no visible binding for global variable
  ‘measurements’
samplesMetricMap,list: no visible binding for global variable ‘name’
samplesMetricMap,list: no visible binding for global variable ‘type’
samplesMetricMap,list: no visible binding for global variable ‘Metric’
samplesMetricMap,matrix: no visible binding for global variable ‘Class’
samplesMetricMap,matrix: no visible binding for global variable ‘Group’
samplesMetricMap,matrix: no visible binding for global variable
  ‘measurements’
samplesMetricMap,matrix: no visible binding for global variable ‘name’
samplesMetricMap,matrix: no visible binding for global variable ‘type’
samplesMetricMap,matrix: no visible binding for global variable
  ‘Metric’
selectionPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for ‘first’
selectionPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for ‘second’
selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for ‘first’
selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for ‘second’
selectionPlot,list: no visible binding for global variable ‘Freq’
Undefined global functions or variables:
  ..density.. Class Freq Group ID Metric Pairs dmvnorm first key
  legends grouping measurement measurements name second setsNodes type
  value
Consider adding
  importFrom("base", "grouping")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
ClassifyResult-class     116.139  6.175  32.923
elasticNetFeatures        45.949  3.911  19.084
elasticNetGLMinterface    45.276  3.667  18.904
distribution              19.397  6.206   9.357
samplesMetricMap          13.697  2.400   5.942
likelihoodRatioSelection   9.602  0.350  10.088
DMDselection               7.917  0.250   8.266
edgeRselection             6.121  0.320   6.499
previousTrained            3.709  2.041   2.856
previousSelection          3.412  1.724   2.861
runTests                   0.450  0.245   6.978
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.



Installation output

ClassifyR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ClassifyR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ClassifyR’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ClassifyR)

Tests output


Example timings

ClassifyR.Rcheck/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class116.139 6.175 32.923
DLDAinterface0.0610.0020.063
DMDselection7.9170.2508.266
FeatureSetCollection-class0.0080.0010.009
FeatureSetCollectionOrNULL-class0.0030.0010.003
KolmogorovSmirnovSelection2.6190.0322.696
KullbackLeiblerSelection1.3960.0081.425
NSCpredictInterface0.1160.0070.124
NSCselectionInterface0.0780.0020.080
NSCtrainInterface0.0870.0030.091
PredictParams-class0.0030.0000.003
ROCplot1.4960.0261.544
ResubstituteParams-class0.0020.0000.002
SVMinterface0.0590.0020.062
SelectParams-class0.0090.0010.011
SelectResult-class0.0010.0000.001
TrainParams-class0.0010.0000.001
TransformParams-class0.0010.0000.002
bartlettSelection1.8300.0191.870
calcPerformance0.0050.0000.006
characterOrDataFrame-class0.0110.0000.011
classifyInterface0.7010.1170.824
differentMeansSelection1.6780.0231.713
distribution19.397 6.206 9.357
edgeRselection6.1210.3206.499
edgesToHubNetworks0.0040.0000.005
elasticNetFeatures45.949 3.91119.084
elasticNetGLMinterface45.276 3.66718.904
featureSetSummary0.0040.0020.005
fisherDiscriminant0.1360.0290.168
forestFeatures0.1230.0220.146
functionOrList-class0.0110.0020.014
functionOrNULL-class0.0040.0000.004
getLocationsAndScales0.0500.0050.056
integerOrNumeric-class0.0190.0030.022
interactorDifferences0.0600.0070.070
kTSPclassifier0.1140.0160.130
knnInterface0.0410.0030.045
leveneSelection1.9590.1532.140
likelihoodRatioSelection 9.602 0.35010.088
limmaSelection0.6280.0260.659
mixmodels0.7790.0310.829
naiveBayesKernel0.5630.0150.595
networkCorrelationsSelection0.2050.0040.211
pairsDifferencesSelection0.3130.0010.322
performancePlot0.2760.0020.280
plotFeatureClasses3.5460.0123.589
previousSelection3.4121.7242.861
previousTrained3.7092.0412.856
randomForestInterface0.2850.0590.346
rankingPlot2.9490.8353.434
runTest0.8400.0420.886
runTests0.4500.2456.978
samplesMetricMap13.697 2.400 5.942
selectionPlot3.2830.4313.641
subtractFromLocation0.0020.0010.003