Back to Multiple platform build/check report for BioC 3.7
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ClassifyR on merida2

This page was generated on 2018-10-17 08:53:21 -0400 (Wed, 17 Oct 2018).

Package 250/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.0.10
Dario Strbenac
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: RELEASE_3_7
Last Commit: e553f79
Last Changed Date: 2018-09-03 21:30:01 -0400 (Mon, 03 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ClassifyR
Version: 2.0.10
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_2.0.10.tar.gz
StartedAt: 2018-10-16 20:29:58 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:34:51 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 293.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.0.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ClassifyR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.0.10’
* 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’
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’
samplesMetricMap,list: no visible binding for global variable ‘Class’
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’
selectionPlot,list: no visible binding for global variable ‘Freq’
Undefined global functions or variables:
  ..density.. Class Freq Metric dmvnorm legends grouping measurement
  name type
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     40.957  5.276  17.451
samplesMetricMap         40.567  4.208   2.094
distribution             34.721  3.537  15.019
elasticNetGLMinterface   10.209  2.576   4.636
likelihoodRatioSelection  9.592  0.156   9.880
DMDselection              8.826  0.387   9.290
previousSelection         6.268  1.288   4.513
edgeRselection            6.492  0.350   6.922
plotFeatureClasses        6.212  0.018   6.287
runTests                  0.474  0.177  16.709
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.



Installation output

ClassifyR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ClassifyR’ ...
** 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
* DONE (ClassifyR)

Tests output


Example timings

ClassifyR.Rcheck/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class40.957 5.27617.451
DLDAinterface0.0980.0190.118
DMDselection8.8260.3879.290
KolmogorovSmirnovSelection3.6270.0653.725
KullbackLeiblerSelection2.7420.0152.784
NSCpredictInterface0.0980.0050.104
NSCselectionInterface0.1070.0020.110
NSCtrainInterface0.1010.0030.104
PredictParams-class0.0050.0010.005
ROCplot0.8990.0030.912
ResubstituteParams-class0.0030.0010.004
SVMinterface0.0870.0030.092
SelectParams-class0.0130.0020.016
SelectResult-class0.0020.0000.002
TrainParams-class0.0020.0000.002
TransformParams-class0.0030.0010.004
bartlettSelection3.4920.0073.538
calcPerformance0.0040.0000.005
characterOrDataFrame-class0.0100.0010.011
classifyInterface1.0820.0951.190
distribution34.721 3.53715.019
edgeRselection6.4920.3506.922
elasticNetGLMinterface10.209 2.576 4.636
fisherDiscriminant0.4940.0760.573
forestFeatures0.0920.0130.106
functionOrList-class0.0100.0020.012
functionOrNULL-class0.0040.0010.006
getLocationsAndScales0.0380.0040.041
leveneSelection3.4410.0423.526
likelihoodRatioSelection9.5920.1569.880
limmaSelection1.1570.0041.170
logisticRegressionInterface0.8980.1271.032
mixmodels1.4040.0141.430
naiveBayesKernel0.6240.0240.652
performancePlot0.3410.0020.345
plotFeatureClasses6.2120.0186.287
previousSelection6.2681.2884.513
randomForestInterface0.8430.6580.165
rankingPlot2.5320.2472.745
runTest1.7410.0391.800
runTests 0.474 0.17716.709
samplesMetricMap40.567 4.208 2.094
selectionPlot3.2640.2453.509
subtractFromLocation0.0020.0010.003