Back to Multiple platform build/check report for BioC 3.10
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ClassifyR on malbec1

This page was generated on 2020-04-15 12:08:58 -0400 (Wed, 15 Apr 2020).

Package 295/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.6.1
Dario Strbenac
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: RELEASE_3_10
Last Commit: 1faa6ba
Last Changed Date: 2020-01-22 20:31:42 -0400 (Wed, 22 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ClassifyR
Version: 2.6.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ClassifyR_2.6.1.tar.gz
StartedAt: 2020-04-15 02:23:20 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:28:47 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 327.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ClassifyR_2.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ClassifyR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.6.1’
* 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 ... 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 or elapsed time > 5s
                            user system elapsed
ClassifyResult-class     113.452  3.252  37.572
elasticNetGLMinterface    34.080  2.180  14.915
elasticNetFeatures        19.336  1.520  15.282
runTests                  16.236  3.736   7.750
distribution              14.896  1.428   7.080
fisherDiscriminant        13.104  0.608   0.102
DMDselection               7.712  0.092   7.817
likelihoodRatioSelection   7.456  0.012   7.566
edgeRselection             6.232  0.176   6.493
runTest                    5.576  0.164   5.755
samplesMetricMap           4.972  0.116   5.105
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.



Installation output

ClassifyR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ClassifyR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-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-class113.452 3.252 37.572
DLDAinterface0.0680.0000.070
DMDselection7.7120.0927.817
EasyHardClassifier-class0.0200.0000.018
FeatureSetCollection-class0.0080.0000.008
FeatureSetCollectionOrNULL-class0.0040.0000.003
KolmogorovSmirnovSelection2.8440.0162.871
KullbackLeiblerSelection1.5640.0001.566
MixModelsListsSet-class0.6440.0000.785
NSCpredictInterface0.180.000.24
NSCselectionInterface0.1120.0040.120
NSCtrainInterface0.0880.0040.095
PredictParams-class0.0000.0000.002
ROCplot0.7640.0040.770
ResubstituteParams-class0.0040.0000.002
SVMinterface0.0520.0000.053
SelectParams-class0.0120.0000.010
SelectResult-class0.0000.0000.001
TrainParams-class0.0000.0000.001
TransformParams-class0.0040.0000.001
bartlettSelection1.8000.0041.808
calcPerformance0.0040.0000.003
characterOrDataFrame-class0.0080.0000.008
classifyInterface0.8800.0520.969
differentMeansSelection1.6920.0041.707
distribution14.896 1.428 7.080
easyHardClassifier0.7720.0320.804
easyHardFeatures0.5280.0080.538
edgeRselection6.2320.1766.493
edgesToHubNetworks0.0040.0000.003
elasticNetFeatures19.336 1.52015.282
elasticNetGLMinterface34.080 2.18014.915
featureSetSummary0.0040.0000.006
fisherDiscriminant13.104 0.608 0.102
forestFeatures0.1560.0040.337
functionOrList-class0.0080.0000.014
functionOrNULL-class0.0040.0000.008
getLocationsAndScales0.0320.0120.069
integerOrNumeric-class0.0160.0000.024
interactorDifferences0.0440.0080.068
kTSPclassifier0.0960.0000.099
knnInterface0.0400.0000.086
leveneSelection1.3520.0961.580
likelihoodRatioSelection7.4560.0127.566
limmaSelection0.3760.0040.381
listOrCharacterOrNULL-class0.0040.0000.004
listOrNULL-class0.0080.0000.004
mixmodels0.3480.0000.350
naiveBayesKernel0.4120.0000.411
networkCorrelationsSelection0.2560.0000.254
pairsDifferencesSelection0.3560.0000.356
performancePlot0.3320.0040.337
plotFeatureClasses3.7800.0003.786
previousSelection2.1760.7801.647
previousTrained2.1440.8001.509
randomForestInterface0.3440.0600.266
rankingPlot2.5320.2242.678
runTest5.5760.1645.755
runTests16.236 3.736 7.750
samplesMetricMap4.9720.1165.105
selectionPlot2.8760.2843.111
subtractFromLocation0.0000.0000.002