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This page was generated on 2021-09-17 15:05:37 -0400 (Fri, 17 Sep 2021).

CHECK results for ClassifyR on nebbiolo1

To the developers/maintainers of the ClassifyR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ClassifyR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 317/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.12.0  (landing page)
Dario Strbenac
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/ClassifyR
git_branch: RELEASE_3_13
git_last_commit: ede130d
git_last_commit_date: 2021-05-19 12:06:37 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ClassifyR
Version: 2.12.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ClassifyR_2.12.0.tar.gz
StartedAt: 2021-09-16 09:14:52 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 09:19:14 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 262.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ClassifyR_2.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.12.0’
* 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   81.332  4.382  28.766
elasticNetGLMinterface 24.006  2.907   9.207
runTests               16.766  5.849   7.945
elasticNetFeatures     15.818  2.865  10.365
distribution           10.527  2.888   5.070
fisherDiscriminant      8.487  0.624   0.065
samplesMetricMap        5.357  1.004   3.121
runTest                 5.537  0.616   6.154
DMDselection            4.874  0.156   5.031
* 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-3.13-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.



Installation output

ClassifyR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ClassifyR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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-class81.332 4.38228.766
DLDAinterface0.0660.0120.079
DMDselection4.8740.1565.031
EasyHardClassifier-class0.0110.0040.014
FeatureSetCollection-class0.0060.0000.006
FeatureSetCollectionOrNULL-class0.0000.0020.002
KolmogorovSmirnovSelection1.6250.0171.641
KullbackLeiblerSelection0.7680.0120.780
MixModelsListsSet-class0.3310.0080.345
NSCpredictInterface0.1230.0040.127
NSCselectionInterface0.0890.0000.088
NSCtrainInterface0.0810.0000.080
PredictParams-class0.0020.0000.003
ROCplot0.540.000.54
ResubstituteParams-class0.0070.0160.023
SVMinterface0.0730.0040.077
SelectParams-class0.0100.0000.011
SelectResult-class0.0010.0000.001
TrainParams-class000
TransformParams-class0.0010.0000.001
bartlettSelection1.6400.0241.664
calcPerformance0.0030.0000.003
characterOrDataFrame-class0.0090.0000.009
classifyInterface0.4360.0520.488
differentMeansSelection1.4980.0201.518
distribution10.527 2.888 5.070
easyHardClassifier0.4580.0480.506
easyHardFeatures0.3550.0600.414
edgeRselection3.9270.7804.711
edgesToHubNetworks0.0030.0000.003
elasticNetFeatures15.818 2.86510.365
elasticNetGLMinterface24.006 2.907 9.207
featureSetSummary0.0030.0000.003
fisherDiscriminant8.4870.6240.065
forestFeatures0.0870.0240.110
functionOrList-class0.0050.0040.009
functionOrNULL-class0.0040.0000.003
getLocationsAndScales0.0160.0080.025
integerOrNumeric-class0.0070.0080.015
interactorDifferences0.0310.0080.038
kTSPclassifier0.0840.0080.092
knnInterface0.0300.0040.034
leveneSelection1.4660.1511.618
likelihoodRatioSelection3.8720.1003.972
limmaSelection0.3220.0030.326
listOrCharacterOrNULL-class0.0030.0010.003
listOrNULL-class0.0020.0000.002
mixmodels0.1550.0190.176
naiveBayesKernel0.3450.0000.346
networkCorrelationsSelection0.1630.0000.164
pairsDifferencesSelection0.2200.0040.223
performancePlot0.3990.0080.406
plotFeatureClasses1.9510.0311.984
previousSelection1.7051.0831.583
previousTrained1.7781.1911.517
randomForestInterface0.3580.1550.242
rankingPlot1.2140.2061.264
runTest5.5370.6166.154
runTests16.766 5.849 7.945
samplesMetricMap5.3571.0043.121
selectionPlot1.2080.2541.305
subtractFromLocation0.0000.0010.002