Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:07:25 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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? 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 324/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.14.0  (landing page)
Dario Strbenac
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 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 -0500 (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: 2022-01-23 11:22:00 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 11:29:26 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 445.1 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 4.1.2 (2021-11-01)
* 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     120.616  5.178  43.451
runTests                  41.569 15.988  18.210
elasticNetGLMinterface    44.374  3.796  18.302
elasticNetFeatures        43.694  3.911  17.799
DLDAinterface             40.350  1.780   0.170
distribution              24.269  3.746  11.502
previousTrained            8.919  6.421   7.540
DMDselection              10.497  0.403  10.908
previousSelection          5.721  3.314   7.506
likelihoodRatioSelection   7.814  0.166   7.990
ROCplot                    5.759  0.089   5.852
runTest                    5.376  0.286   5.668
samplesMetricMap           5.264  0.383   5.657
edgeRselection             4.877  0.163   5.050
* 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-class120.616 5.178 43.451
DLDAinterface40.35 1.78 0.17
DMDselection10.497 0.40310.908
EasyHardClassifier-class0.0200.0010.020
FeatureSetCollection-class0.0090.0030.012
FeatureSetCollectionOrNULL-class0.0040.0010.005
KolmogorovSmirnovSelection3.2560.0893.351
KullbackLeiblerSelection2.1700.0272.197
MixModelsListsSet-class0.5650.0120.583
NSCpredictInterface0.1730.0100.186
NSCselectionInterface0.1160.0040.121
NSCtrainInterface0.1200.0060.126
PredictParams-class0.0030.0010.004
ROCplot5.7590.0895.852
ResubstituteParams-class0.0040.0020.005
SVMinterface0.1740.0160.191
SelectParams-class0.0130.0040.018
SelectResult-class0.0010.0010.001
TrainParams-class0.0010.0000.001
TransformParams-class0.0010.0010.002
bartlettSelection3.2760.0453.323
calcPerformance0.0050.0010.005
characterOrDataFrame-class0.0160.0000.015
classifyInterface1.1190.1221.242
differentMeansSelection3.0530.0523.107
distribution24.269 3.74611.502
easyHardClassifier0.5800.0630.644
easyHardFeatures0.7110.0600.772
edgeRselection4.8770.1635.050
edgesToHubNetworks0.0030.0010.004
elasticNetFeatures43.694 3.91117.799
elasticNetGLMinterface44.374 3.79618.302
featureSetSummary0.0050.0050.010
fisherDiscriminant0.1370.0290.166
forestFeatures0.1640.0220.186
functionOrList-class0.0090.0040.013
functionOrNULL-class0.0060.0020.007
getLocationsAndScales0.0540.0070.060
integerOrNumeric-class0.0210.0040.024
interactorDifferences0.0660.0100.076
kTSPclassifier0.1360.0170.152
knnInterface0.0590.0070.068
leveneSelection1.7820.0751.858
likelihoodRatioSelection7.8140.1667.990
limmaSelection0.5560.0060.562
listOrCharacterOrNULL-class0.0050.0010.006
listOrNULL-class0.0050.0000.005
mixmodels0.4920.0110.504
naiveBayesKernel0.6160.0190.636
networkCorrelationsSelection0.2130.0030.216
pairsDifferencesSelection0.4480.0100.459
performancePlot0.5920.0090.602
plotFeatureClasses3.5960.0293.628
previousSelection5.7213.3147.506
previousTrained8.9196.4217.540
randomForestInterface3.0031.8541.785
rankingPlot2.2360.5562.615
runTest5.3760.2865.668
runTests41.56915.98818.210
samplesMetricMap5.2640.3835.657
selectionPlot2.6630.7563.150
subtractFromLocation0.0020.0010.003