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CHECK report for ClassifyR on malbec2

This page was generated on 2021-01-18 12:46:59 -0500 (Mon, 18 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: 2021-01-17 14:40:31 -0500 (Sun, 17 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: /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_2.11.0.tar.gz
StartedAt: 2021-01-18 00:09:51 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 00:15:32 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 340.7 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_2.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘2.11.0’
* 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     110.557  3.146  37.801
elasticNetFeatures        43.589  1.782  19.862
elasticNetGLMinterface    43.518  1.614  17.731
runTests                  18.085  3.212   8.998
distribution              17.707  2.284   8.247
DMDselection               7.087  0.168   7.255
runTest                    6.515  0.236   6.752
likelihoodRatioSelection   6.225  0.016   6.240
previousTrained            4.107  1.117   2.170
* 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
  ‘/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
###
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* 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-class110.557 3.146 37.801
DLDAinterface0.0990.0000.099
DMDselection7.0870.1687.255
EasyHardClassifier-class0.0190.0000.020
FeatureSetCollection-class0.0080.0000.009
FeatureSetCollectionOrNULL-class0.0040.0000.003
KolmogorovSmirnovSelection3.3010.0143.314
KullbackLeiblerSelection1.6690.0001.669
MixModelsListsSet-class0.7180.0030.801
NSCpredictInterface0.1860.0120.215
NSCselectionInterface0.1360.0000.136
NSCtrainInterface0.1210.0000.121
PredictParams-class0.0040.0000.004
ROCplot0.9600.0040.964
ResubstituteParams-class0.0030.0000.003
SVMinterface0.2180.0000.218
SelectParams-class0.0150.0000.015
SelectResult-class0.0000.0000.001
TrainParams-class0.0010.0000.001
TransformParams-class0.0020.0000.002
bartlettSelection2.3170.0042.321
calcPerformance0.0030.0000.003
characterOrDataFrame-class0.0090.0000.009
classifyInterface0.5280.0320.560
differentMeansSelection1.1630.0001.163
distribution17.707 2.284 8.247
easyHardClassifier1.0270.0641.093
easyHardFeatures0.3390.0120.350
edgeRselection3.7190.0803.839
edgesToHubNetworks0.0020.0000.003
elasticNetFeatures43.589 1.78219.862
elasticNetGLMinterface43.518 1.61417.731
featureSetSummary0.0060.0000.006
fisherDiscriminant0.1260.0000.125
forestFeatures0.1790.0130.206
functionOrList-class0.0060.0040.010
functionOrNULL-class0.0050.0000.005
getLocationsAndScales0.0450.0000.045
integerOrNumeric-class0.0210.0000.022
interactorDifferences0.0470.0070.055
kTSPclassifier0.1270.0150.142
knnInterface0.0440.0040.063
leveneSelection2.4560.0442.508
likelihoodRatioSelection6.2250.0166.240
limmaSelection0.3610.0010.361
listOrCharacterOrNULL-class0.0030.0000.004
listOrNULL-class0.0030.0000.003
mixmodels0.3700.0080.395
naiveBayesKernel0.4150.0000.415
networkCorrelationsSelection0.3520.0080.360
pairsDifferencesSelection0.2450.0000.245
performancePlot0.5690.0110.581
plotFeatureClasses3.1780.0083.187
previousSelection3.5180.6782.798
previousTrained4.1071.1172.170
randomForestInterface0.4140.0990.201
rankingPlot1.6940.2251.687
runTest6.5150.2366.752
runTests18.085 3.212 8.998
samplesMetricMap3.5020.1563.658
selectionPlot2.1570.2912.168
subtractFromLocation0.0000.0020.002