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CHECK report for ClassifyR on malbec1

This page was generated on 2021-05-06 12:27:09 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ClassifyR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 308/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.10.0  (landing page)
Dario Strbenac
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: RELEASE_3_12
Last Commit: 37bf4a2
Last Changed Date: 2020-10-27 10:58:03 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ClassifyR
Version: 2.10.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ClassifyR_2.10.0.tar.gz
StartedAt: 2021-05-06 00:06:47 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:12:22 -0400 (Thu, 06 May 2021)
EllapsedTime: 334.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ClassifyR_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ClassifyR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘2.10.0’
* 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 ‘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’
easyHardClassifierPredict,EasyHardClassifier-MultiAssayExperiment: no
  visible binding for global variable ‘measurements’
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’
runTestEasyHard,MultiAssayExperiment: no visible binding for global
  variable ‘setsNodes’
runTests,DataFrame: no visible binding for global variable ‘setsNodes’
runTestsEasyHard,MultiAssayExperiment: no visible binding for global
  variable ‘setsNodes’
runTestsEasyHard,MultiAssayExperiment: no visible binding for global
  variable ‘.iteration’
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.. .iteration 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 (user + system) or elapsed time > 5s
                            user system elapsed
ClassifyResult-class     115.032  3.796  38.681
elasticNetFeatures        40.304  1.544  16.490
runTests                  29.884  6.332  13.051
elasticNetGLMinterface    22.800  1.072  14.083
distribution              16.188  1.808   7.423
fisherDiscriminant        13.788  0.440   0.265
likelihoodRatioSelection   6.920  0.040   6.977
runTest                    6.348  0.160   6.521
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.



Installation output

ClassifyR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ClassifyR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ClassifyR’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ClassifyR)

Tests output


Example timings

ClassifyR.Rcheck/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class115.032 3.796 38.681
DLDAinterface0.0600.0000.061
DMDselection4.8720.0764.954
EasyHardClassifier-class0.0240.0000.021
FeatureSetCollection-class0.0080.0000.008
FeatureSetCollectionOrNULL-class0.0040.0000.004
KolmogorovSmirnovSelection2.4960.0002.499
KullbackLeiblerSelection1.6600.0001.663
MixModelsListsSet-class0.6600.0040.732
NSCpredictInterface0.1720.0000.211
NSCselectionInterface0.120.000.12
NSCtrainInterface0.1040.0040.109
PredictParams-class0.0040.0000.004
ROCplot0.8920.0040.897
ResubstituteParams-class0.0040.0000.003
SVMinterface0.2080.0040.215
SelectParams-class0.0120.0040.017
SelectResult-class0.0000.0000.001
TrainParams-class0.0000.0000.001
TransformParams-class0.0000.0000.002
bartlettSelection2.1040.0042.109
calcPerformance0.0040.0000.003
characterOrDataFrame-class0.0080.0000.009
classifyInterface0.6360.0880.765
differentMeansSelection1.0840.0081.092
distribution16.188 1.808 7.423
easyHardClassifier0.6000.0360.635
easyHardFeatures0.6400.0200.663
edgeRselection4.4960.1004.636
edgesToHubNetworks0.0040.0000.002
elasticNetFeatures40.304 1.54416.490
elasticNetGLMinterface22.800 1.07214.083
featureSetSummary0.0000.0040.005
fisherDiscriminant13.788 0.440 0.265
forestFeatures0.1680.0080.192
functionOrList-class0.0120.0000.010
functionOrNULL-class0.0040.0000.006
getLocationsAndScales0.0440.0000.046
integerOrNumeric-class0.0160.0000.015
interactorDifferences0.0480.0000.050
kTSPclassifier0.0800.0040.085
knnInterface0.0320.0000.045
leveneSelection1.6720.0361.706
likelihoodRatioSelection6.9200.0406.977
limmaSelection0.5880.0000.587
listOrCharacterOrNULL-class0.0040.0000.004
listOrNULL-class0.0040.0000.006
mixmodels0.3960.0000.397
naiveBayesKernel0.620.000.62
networkCorrelationsSelection0.3160.0000.315
pairsDifferencesSelection0.4080.0040.414
performancePlot0.7440.0040.749
plotFeatureClasses2.8120.0042.827
previousSelection2.9880.8562.135
previousTrained3.3520.8962.258
randomForestInterface0.6880.1040.457
rankingPlot1.6920.2201.690
runTest6.3480.1606.521
runTests29.884 6.33213.051
samplesMetricMap3.1320.0003.144
selectionPlot1.7160.3481.880
subtractFromLocation0.0000.0000.001