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This page was generated on 2021-09-22 15:05:39 -0400 (Wed, 22 Sep 2021).

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 317/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.12.0  (landing page)
Dario Strbenac
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/ClassifyR
git_branch: RELEASE_3_13
git_last_commit: ede130d
git_last_commit_date: 2021-05-19 12:06:37 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 2.12.0
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_2.12.0.tar.gz
StartedAt: 2021-09-21 17:29:21 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 17:35:41 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 379.5 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_2.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.12.0’
* 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     130.078  7.020  40.989
elasticNetFeatures        40.919  5.271  16.221
elasticNetGLMinterface    40.731  5.011  16.486
runTests                  29.742  8.640  14.731
distribution              18.264  4.177   8.386
selectionPlot              5.682  3.219   6.074
DMDselection               7.940  0.342   8.286
runTest                    6.697  0.288   6.989
likelihoodRatioSelection   5.977  0.140   6.117
previousSelection          3.785  2.158   3.136
previousTrained            3.711  2.106   3.061
edgeRselection             4.854  0.180   5.037
* 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
###
##############################################################################
##############################################################################


* 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-class130.078 7.020 40.989
DLDAinterface0.3930.0090.402
DMDselection7.9400.3428.286
EasyHardClassifier-class0.0150.0000.014
FeatureSetCollection-class0.0070.0010.008
FeatureSetCollectionOrNULL-class0.0030.0010.003
KolmogorovSmirnovSelection2.8020.0482.854
KullbackLeiblerSelection1.3890.0081.398
MixModelsListsSet-class0.4570.0100.472
NSCpredictInterface0.1420.0090.179
NSCselectionInterface0.1270.0040.130
NSCtrainInterface0.0820.0050.088
PredictParams-class0.0040.0000.003
ROCplot0.9660.0060.974
ResubstituteParams-class0.0020.0000.003
SVMinterface0.1080.0050.114
SelectParams-class0.0120.0030.016
SelectResult-class0.0000.0010.001
TrainParams-class0.0010.0000.001
TransformParams-class0.0020.0010.002
bartlettSelection1.9150.0101.925
calcPerformance0.0030.0000.004
characterOrDataFrame-class0.0090.0000.009
classifyInterface0.5990.0770.676
differentMeansSelection2.2270.0412.268
distribution18.264 4.177 8.386
easyHardClassifier0.7600.0910.852
easyHardFeatures0.4690.0450.514
edgeRselection4.8540.1805.037
edgesToHubNetworks0.0030.0000.003
elasticNetFeatures40.919 5.27116.221
elasticNetGLMinterface40.731 5.01116.486
featureSetSummary0.0060.0080.012
fisherDiscriminant0.2400.0440.285
forestFeatures0.1720.0250.198
functionOrList-class0.0090.0040.013
functionOrNULL-class0.0060.0010.007
getLocationsAndScales0.0540.0070.061
integerOrNumeric-class0.0190.0040.022
interactorDifferences0.0440.0070.051
kTSPclassifier0.1090.0120.122
knnInterface0.0310.0030.034
leveneSelection1.9040.1132.017
likelihoodRatioSelection5.9770.1406.117
limmaSelection0.6070.0060.613
listOrCharacterOrNULL-class0.0060.0000.006
listOrNULL-class0.0050.0000.006
mixmodels0.3320.0040.338
naiveBayesKernel0.4300.0130.443
networkCorrelationsSelection0.3420.0210.363
pairsDifferencesSelection0.4150.0030.418
performancePlot0.5420.0040.547
plotFeatureClasses3.1510.0153.170
previousSelection3.7852.1583.136
previousTrained3.7112.1063.061
randomForestInterface0.2650.0460.311
rankingPlot2.2270.6032.492
runTest6.6970.2886.989
runTests29.742 8.64014.731
samplesMetricMap3.5440.1403.686
selectionPlot5.6823.2196.074
subtractFromLocation0.0020.0010.003