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CHECK report for ClassifyR on malbec2

This page was generated on 2019-10-16 12:05:00 -0400 (Wed, 16 Oct 2019).

Package 280/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.4.4
Dario Strbenac
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: RELEASE_3_9
Last Commit: a2993e1
Last Changed Date: 2019-06-14 02:44:32 -0400 (Fri, 14 Jun 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

Summary

Package: ClassifyR
Version: 2.4.4
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ClassifyR_2.4.4.tar.gz
StartedAt: 2019-10-16 00:33:52 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:38:43 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 290.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ClassifyR_2.4.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ClassifyR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.4.4’
* 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 : : no visible global function definition
  for ‘dmvnorm’
kTSPclassifier,DataFrame : : no visible global function
  definition for ‘Pairs’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘measurement’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘..density..’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘legends grouping’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘key’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘value’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘ID’
rankingPlot,list :  : : no visible global
  function definition for ‘first’
rankingPlot,list :  : : no visible global
  function definition for ‘second’
rankingPlot,list :  :  : : no visible
  global function definition for ‘first’
rankingPlot,list :  :  : : 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 :  : : no visible global
  function definition for ‘first’
selectionPlot,list :  : : no visible global
  function definition for ‘second’
selectionPlot,list :  :  : : no
  visible global function definition for ‘first’
selectionPlot,list :  :  : : 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     99.954  2.861  28.061
fisherDiscriminant       32.544  1.397   0.106
elasticNetGLMinterface   32.040  1.512  14.469
distribution             14.983  1.912   8.115
samplesMetricMap         14.243  1.203   4.369
DMDselection              6.098  0.188   6.288
likelihoodRatioSelection  5.055  0.016   5.082
runTests                  1.283  0.267   5.951
elasticNetFeatures        0.999  0.172  12.671
* 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-3.9-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.



Installation output

ClassifyR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ClassifyR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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-class99.954 2.86128.061
DLDAinterface0.0900.0040.094
DMDselection6.0980.1886.288
FeatureSetCollection-class0.0050.0000.005
FeatureSetCollectionOrNULL-class0.0020.0000.002
KolmogorovSmirnovSelection1.8070.1031.909
KullbackLeiblerSelection1.4560.0121.482
MixModelsListsSet-class0.3090.0080.364
NSCpredictInterface0.1240.0040.144
NSCselectionInterface0.1100.0040.114
NSCtrainInterface0.0970.0000.097
PredictParams-class0.0040.0000.003
ROCplot1.0480.0001.048
ResubstituteParams-class0.0000.0030.003
SVMinterface0.0820.0000.083
SelectParams-class0.0110.0040.014
SelectResult-class0.0010.0000.001
TrainParams-class0.0010.0000.001
TransformParams-class0.0000.0020.002
bartlettSelection1.8870.0121.900
calcPerformance0.0050.0000.004
characterOrDataFrame-class0.0120.0000.012
classifyInterface0.9940.0361.326
differentMeansSelection1.5400.0161.556
distribution14.983 1.912 8.115
edgeRselection4.0930.0804.210
edgesToHubNetworks0.0030.0000.002
elasticNetFeatures 0.999 0.17212.671
elasticNetGLMinterface32.040 1.51214.469
featureSetSummary0.0060.0000.006
fisherDiscriminant32.544 1.397 0.106
forestFeatures0.1520.0190.171
functionOrList-class0.0070.0020.009
functionOrNULL-class0.0010.0040.004
getLocationsAndScales0.0400.0040.044
integerOrNumeric-class0.0170.0000.018
interactorDifferences0.0530.0000.053
kTSPclassifier0.1150.0040.119
knnInterface0.0400.0040.044
leveneSelection1.1790.0241.203
likelihoodRatioSelection5.0550.0165.082
limmaSelection0.4860.0040.490
mixmodels0.2270.0000.239
naiveBayesKernel0.4790.0000.482
networkCorrelationsSelection0.2670.0000.267
pairsDifferencesSelection0.3430.0040.346
performancePlot0.3280.0000.328
plotFeatureClasses3.3790.0003.379
previousSelection3.5790.7623.347
previousTrained3.5931.0273.214
randomForestInterface0.4280.1270.264
rankingPlot2.9070.3123.102
runTest0.7250.0040.735
runTests1.2830.2675.951
samplesMetricMap14.243 1.203 4.369
selectionPlot3.3590.2933.520
subtractFromLocation0.0020.0000.002