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CHECK report for ClassifyR on malbec1

This page was generated on 2019-04-16 11:50:44 -0400 (Tue, 16 Apr 2019).

Package 266/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.2.6
Dario Strbenac
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: RELEASE_3_8
Last Commit: f4f1b0a
Last Changed Date: 2019-02-14 20:45:02 -0400 (Thu, 14 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ClassifyR
Version: 2.2.6
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ClassifyR_2.2.6.tar.gz
StartedAt: 2019-04-15 22:56:36 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:01:27 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 290.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ClassifyR_2.2.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ClassifyR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.2.6’
* 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     108.168  2.972  31.315
elasticNetGLMinterface    54.704  2.076  16.428
samplesMetricMap          19.644  3.004   4.371
distribution              16.596  2.268   7.343
fisherDiscriminant        15.672  0.308   0.136
elasticNetFeatures         8.192  0.396  15.983
likelihoodRatioSelection   8.296  0.080   8.384
edgeRselection             5.864  0.172   6.074
DMDselection               5.960  0.040   6.005
runTests                   0.424  0.136   6.812
* 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-3.8-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.



Installation output

ClassifyR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ClassifyR
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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-class108.168 2.972 31.315
DLDAinterface0.6000.0760.680
DMDselection5.9600.0406.005
FeatureSetCollection-class0.0040.0000.005
FeatureSetCollectionOrNULL-class0.0040.0000.002
KolmogorovSmirnovSelection2.2680.0122.292
KullbackLeiblerSelection1.3840.0041.392
NSCpredictInterface0.1480.0080.156
NSCselectionInterface0.1160.0000.117
NSCtrainInterface0.0840.0080.092
PredictParams-class0.0040.0000.002
ROCplot0.6440.0000.645
ResubstituteParams-class0.0000.0000.002
SVMinterface0.0480.0040.054
SelectParams-class0.0080.0000.007
SelectResult-class000
TrainParams-class0.0040.0000.000
TransformParams-class0.0000.0000.001
bartlettSelection2.1200.0002.121
calcPerformance0.0040.0000.004
characterOrDataFrame-class0.0160.0000.014
classifyInterface0.9560.0321.046
differentMeansSelection1.6880.0041.694
distribution16.596 2.268 7.343
edgeRselection5.8640.1726.074
edgesToHubNetworks0.0040.0000.003
elasticNetFeatures 8.192 0.39615.983
elasticNetGLMinterface54.704 2.07616.428
featureSetSummary0.0040.0000.005
fisherDiscriminant15.672 0.308 0.136
forestFeatures0.2640.0200.297
functionOrList-class0.0080.0000.008
functionOrNULL-class0.0040.0000.006
getLocationsAndScales0.0400.0040.043
integerOrNumeric-class0.0120.0040.017
interactorDifferences0.0440.0080.051
kTSPclassifier0.1120.0000.114
knnInterface0.0400.0000.043
leveneSelection1.7200.0641.807
likelihoodRatioSelection8.2960.0808.384
limmaSelection0.5080.0040.512
mixmodels0.5240.0040.641
naiveBayesKernel0.5200.0040.525
networkCorrelationsSelection0.1920.0000.192
pairsDifferencesSelection0.2320.0000.232
performancePlot0.3600.0040.364
plotFeatureClasses3.5240.0123.539
previousSelection2.6880.8362.083
previousTrained2.7721.0001.995
randomForestInterface0.4360.1480.274
rankingPlot2.0640.2402.272
runTest0.6480.0080.655
runTests0.4240.1366.812
samplesMetricMap19.644 3.004 4.371
selectionPlot2.4600.2762.688
subtractFromLocation0.0000.0000.002