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CHECK report for ClassifyR on machv2

This page was generated on 2021-01-14 13:03:29 -0500 (Thu, 14 Jan 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 306/1931HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.11.0
Dario Strbenac
Snapshot Date: 2021-01-13 14:40:33 -0500 (Wed, 13 Jan 2021)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: master
Last Commit: e4a0740
Last Changed Date: 2020-10-27 10:58:03 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 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
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ClassifyR
Version: 2.11.0
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_2.11.0.tar.gz
StartedAt: 2021-01-13 23:18:24 -0500 (Wed, 13 Jan 2021)
EndedAt: 2021-01-13 23:24:57 -0500 (Wed, 13 Jan 2021)
EllapsedTime: 393.7 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_2.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck’
* using R Under development (unstable) (2021-01-06 r79800)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.11.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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     132.959  6.970  42.620
elasticNetFeatures        41.696  4.384  17.401
runTests                  26.832  7.483  11.418
elasticNetGLMinterface    26.065  3.198  17.569
distribution              21.269  4.890   9.557
DMDselection               7.356  0.246   7.612
likelihoodRatioSelection   7.275  0.173   7.465
runTest                    6.060  0.338   6.403
edgeRselection             5.792  0.252   6.056
previousTrained            4.039  1.992   3.049
previousSelection          3.841  1.948   2.959
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-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/4.1/Resources/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-class132.959 6.970 42.620
DLDAinterface0.1040.0030.109
DMDselection7.3560.2467.612
EasyHardClassifier-class0.0150.0000.016
FeatureSetCollection-class0.0080.0010.010
FeatureSetCollectionOrNULL-class0.0030.0010.004
KolmogorovSmirnovSelection2.9170.0612.998
KullbackLeiblerSelection1.3030.0081.314
MixModelsListsSet-class0.5200.0120.539
NSCpredictInterface0.2990.0120.315
NSCselectionInterface0.1240.0030.127
NSCtrainInterface0.1080.0060.113
PredictParams-class0.0030.0000.004
ROCplot0.8120.0030.819
ResubstituteParams-class0.0030.0000.003
SVMinterface0.0970.0050.103
SelectParams-class0.0130.0030.016
SelectResult-class0.0000.0000.001
TrainParams-class0.0010.0000.001
TransformParams-class0.0030.0000.002
bartlettSelection2.8530.0132.878
calcPerformance0.0030.0000.004
characterOrDataFrame-class0.0140.0010.014
classifyInterface0.8650.0600.929
differentMeansSelection1.9250.0361.962
distribution21.269 4.890 9.557
easyHardClassifier0.6160.0700.686
easyHardFeatures0.8280.0980.925
edgeRselection5.7920.2526.056
edgesToHubNetworks0.0040.0000.004
elasticNetFeatures41.696 4.38417.401
elasticNetGLMinterface26.065 3.19817.569
featureSetSummary0.0060.0030.009
fisherDiscriminant0.1380.0290.168
forestFeatures0.2700.0430.313
functionOrList-class0.0090.0030.013
functionOrNULL-class0.0040.0010.005
getLocationsAndScales0.0480.0050.053
integerOrNumeric-class0.0160.0030.019
interactorDifferences0.0510.0080.060
kTSPclassifier0.1270.0140.141
knnInterface0.0460.0040.051
leveneSelection1.8730.1362.009
likelihoodRatioSelection7.2750.1737.465
limmaSelection0.6150.0060.622
listOrCharacterOrNULL-class0.0040.0000.005
listOrNULL-class0.0040.0000.005
mixmodels0.3580.0050.363
naiveBayesKernel0.6210.0300.652
networkCorrelationsSelection0.3090.0290.339
pairsDifferencesSelection0.2480.0030.250
performancePlot0.5250.0060.532
plotFeatureClasses3.0980.0253.126
previousSelection3.8411.9482.959
previousTrained4.0391.9923.049
randomForestInterface0.2880.0470.335
rankingPlot2.3570.5802.558
runTest6.0600.3386.403
runTests26.832 7.48311.418
samplesMetricMap3.8120.2374.053
selectionPlot2.6270.8413.173
subtractFromLocation0.0020.0020.004