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This page was generated on 2021-11-24 15:04:57 -0500 (Wed, 24 Nov 2021).

CHECK results for ClassifyR on nebbiolo2

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: 2021-11-23 04:15:06 -0500 (Tue, 23 Nov 2021)
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 20.04.3 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ClassifyR_2.14.0.tar.gz
StartedAt: 2021-11-23 08:35:59 -0500 (Tue, 23 Nov 2021)
EndedAt: 2021-11-23 08:40:17 -0500 (Tue, 23 Nov 2021)
EllapsedTime: 257.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ClassifyR_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ClassifyR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.14.0’
* 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   57.293  2.758  21.495
runTests               24.854  8.807  11.556
elasticNetFeatures     24.141  2.006   9.249
DLDAinterface          19.058  0.992   0.108
elasticNetGLMinterface 14.046  1.376   9.655
distribution           13.185  2.024   6.287
previousTrained         6.017  3.529   4.876
samplesMetricMap        6.406  1.303   3.845
DMDselection            6.031  0.200   6.232
randomForestInterface   4.007  1.978   1.609
ROCplot                 5.090  0.084   5.175
previousSelection       3.307  1.758   4.502
* 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-3.14-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.



Installation output

ClassifyR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ClassifyR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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-class57.293 2.75821.495
DLDAinterface19.058 0.992 0.108
DMDselection6.0310.2006.232
EasyHardClassifier-class0.0130.0000.013
FeatureSetCollection-class0.0050.0000.005
FeatureSetCollectionOrNULL-class0.0020.0000.002
KolmogorovSmirnovSelection1.6980.0561.754
KullbackLeiblerSelection1.5790.0161.595
MixModelsListsSet-class0.2680.0040.278
NSCpredictInterface0.1080.0040.112
NSCselectionInterface0.0760.0000.076
NSCtrainInterface0.0550.0000.055
PredictParams-class0.0020.0000.002
ROCplot5.0900.0845.175
ResubstituteParams-class0.0020.0000.002
SVMinterface0.1590.0040.163
SelectParams-class0.0080.0000.008
SelectResult-class0.0000.0000.001
TrainParams-class0.0000.0000.001
TransformParams-class0.0010.0000.001
bartlettSelection2.0210.0322.052
calcPerformance0.0030.0000.003
characterOrDataFrame-class0.0100.0000.011
classifyInterface0.6510.0240.676
differentMeansSelection1.7710.0161.788
distribution13.185 2.024 6.287
easyHardClassifier0.4170.0360.453
easyHardFeatures0.3370.0120.349
edgeRselection3.2220.1123.335
edgesToHubNetworks0.0020.0000.002
elasticNetFeatures24.141 2.006 9.249
elasticNetGLMinterface14.046 1.376 9.655
featureSetSummary0.0040.0020.005
fisherDiscriminant0.1080.0240.133
forestFeatures0.1430.0320.175
functionOrList-class0.0090.0000.009
functionOrNULL-class0.0040.0000.004
getLocationsAndScales0.0370.0000.037
integerOrNumeric-class0.0150.0040.019
interactorDifferences0.0360.0040.040
kTSPclassifier0.0810.0120.093
knnInterface0.0430.0000.042
leveneSelection0.8640.0120.876
likelihoodRatioSelection3.8680.0483.917
limmaSelection0.3120.0000.312
listOrCharacterOrNULL-class0.0030.0000.003
listOrNULL-class0.0030.0000.003
mixmodels0.2180.0040.222
naiveBayesKernel0.2980.0080.305
networkCorrelationsSelection0.1660.0040.171
pairsDifferencesSelection0.2660.0080.275
performancePlot0.3110.0000.312
plotFeatureClasses1.850.021.87
previousSelection3.3071.7584.502
previousTrained6.0173.5294.876
randomForestInterface4.0071.9781.609
rankingPlot1.1110.4001.319
runTest4.4680.1324.601
runTests24.854 8.80711.556
samplesMetricMap6.4061.3033.845
selectionPlot1.8480.4282.031
subtractFromLocation0.0010.0000.001