Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:47 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ClassifyR on machv2


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? 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 324/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.14.0  (landing page)
Dario Strbenac
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/ClassifyR
git_branch: RELEASE_3_14
git_last_commit: 133d20a
git_last_commit_date: 2021-10-26 12:15:09 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 2.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClassifyR_2.14.0.tar.gz
StartedAt: 2022-04-12 11:35:13 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 11:42:31 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 438.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClassifyR_2.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ClassifyR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘2.14.0’
* 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘MultiAssayExperiment’
A package should be listed in only one of these fields.
* 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 global function definition for ‘mcols’
runTests,DataFrame: no visible binding for global variable ‘setsNodes’
runTests,DataFrame: no visible binding for global variable ‘dataset’
runTests,DataFrame : <anonymous>: no visible global function definition
  for ‘mcols’
runTests,DataFrame : <anonymous>: no visible global function definition
  for ‘mcols<-’
runTests,DataFrame: no visible global function definition for ‘mcols<-’
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 dataset
  dmvnorm first key legends grouping mcols mcols<- 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     119.392  5.146  43.323
elasticNetGLMinterface    45.007  3.864  18.473
elasticNetFeatures        44.172  4.015  17.890
runTests                  34.915  9.023  14.612
DLDAinterface             40.036  1.727   0.204
distribution              24.116  3.797  11.298
previousTrained            8.902  6.472   7.596
DMDselection              10.016  0.373  10.397
previousSelection          5.568  3.267   7.485
likelihoodRatioSelection   8.116  0.127   8.278
randomForestInterface      3.492  3.255   0.418
ROCplot                    5.331  0.045   5.380
edgeRselection             5.145  0.179   5.329
runTest                    4.829  0.264   5.101
* 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-3.14-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.



Installation output

ClassifyR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ClassifyR
###
##############################################################################
##############################################################################


* 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-class119.392 5.146 43.323
DLDAinterface40.036 1.727 0.204
DMDselection10.016 0.37310.397
EasyHardClassifier-class0.0250.0010.025
FeatureSetCollection-class0.0070.0010.008
FeatureSetCollectionOrNULL-class0.0040.0010.005
KolmogorovSmirnovSelection3.2850.1093.398
KullbackLeiblerSelection2.0320.0302.062
MixModelsListsSet-class0.5920.0130.613
NSCpredictInterface0.1790.0140.195
NSCselectionInterface0.1120.0050.116
NSCtrainInterface0.120.010.13
PredictParams-class0.0020.0000.002
ROCplot5.3310.0455.380
ResubstituteParams-class0.0030.0000.003
SVMinterface0.2500.0130.263
SelectParams-class0.0160.0050.020
SelectResult-class0.0010.0010.002
TrainParams-class0.0010.0000.001
TransformParams-class0.0020.0010.002
bartlettSelection3.3110.0533.367
calcPerformance0.0050.0000.006
characterOrDataFrame-class0.0160.0000.017
classifyInterface1.0900.1141.205
differentMeansSelection2.4500.0342.485
distribution24.116 3.79711.298
easyHardClassifier0.5270.0570.585
easyHardFeatures0.6020.0490.651
edgeRselection5.1450.1795.329
edgesToHubNetworks0.0030.0000.004
elasticNetFeatures44.172 4.01517.890
elasticNetGLMinterface45.007 3.86418.473
featureSetSummary0.0040.0020.007
fisherDiscriminant0.1240.0280.152
forestFeatures0.1860.0280.213
functionOrList-class0.0090.0040.014
functionOrNULL-class0.0040.0010.005
getLocationsAndScales0.0550.0070.062
integerOrNumeric-class0.0210.0040.025
interactorDifferences0.0530.0070.060
kTSPclassifier0.1510.0190.171
knnInterface0.0560.0060.062
leveneSelection1.7450.0741.822
likelihoodRatioSelection8.1160.1278.278
limmaSelection0.6180.0090.630
listOrCharacterOrNULL-class0.0050.0000.005
listOrNULL-class0.0040.0000.005
mixmodels0.3460.0080.355
naiveBayesKernel0.6780.0190.697
networkCorrelationsSelection0.3110.0040.315
pairsDifferencesSelection0.4880.0100.499
performancePlot0.5760.0140.594
plotFeatureClasses3.5800.0333.618
previousSelection5.5683.2677.485
previousTrained8.9026.4727.596
randomForestInterface3.4923.2550.418
rankingPlot3.3600.8344.021
runTest4.8290.2645.101
runTests34.915 9.02314.612
samplesMetricMap4.5930.1984.792
selectionPlot2.8661.2243.549
subtractFromLocation0.0030.0020.005