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CHECK report for Rmagpie on celaya2

This page was generated on 2020-01-16 13:31:59 -0500 (Thu, 16 Jan 2020).

Package 1440/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rmagpie 1.43.0
Camille Maumet
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/Rmagpie
Branch: master
Last Commit: 35e1709
Last Changed Date: 2019-10-29 13:34:58 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Rmagpie
Version: 1.43.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rmagpie.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rmagpie_1.43.0.tar.gz
StartedAt: 2020-01-16 08:15:14 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 08:17:43 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 148.9 seconds
RetCode: 0
Status:  OK 
CheckDir: Rmagpie.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rmagpie.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rmagpie_1.43.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Rmagpie.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rmagpie/DESCRIPTION’ ... OK
* this is package ‘Rmagpie’ version ‘1.43.0’
* 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 ‘Rmagpie’ 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:
  ‘Biobase’
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
twoLayerExtCV: warning in performAValidation(data = eset, trainIndices
  = extInds[[i]], noGenes = upToBestSelectedFeature, classes = classes,
  classifierName = classifierName, verbose = verbose, kernel = kernel,
  featureSelectionFun = featureSelectionFun, trainTestFun =
  trainTestFun): partial argument match of 'data' to 'dataset'
getFeatureSelectionOptions<-,assessment: no visible global function
  definition for ‘getNoOfOptions<-’
getFeatureSelectionOptions<-,assessment: no visible global function
  definition for ‘getNoModels<-’
Undefined global functions or variables:
  getNoModels<- getNoOfOptions<-
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
runTwoLayerExtCV-methods         11.163  0.169  11.342
plotErrorsFoldTwoLayerCV-methods  5.890  0.047   5.938
getResults-methods                4.856  0.287   5.143
* 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-3.11-bioc/meat/Rmagpie.Rcheck/00check.log’
for details.



Installation output

Rmagpie.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rmagpie
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Rmagpie’ ...
** using staged installation
** R
** data
** demo
** 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 (Rmagpie)

Tests output


Example timings

Rmagpie.Rcheck/Rmagpie-Ex.timings

nameusersystemelapsed
classifyNewSamples-methods1.9400.2012.142
experiment-class0.1400.0280.168
finalClassifier-class0.0930.0110.104
findFinalClassifier-methods0.1620.0100.172
geneSubsets-class0.0080.0010.009
getDataset-methods0.0100.0020.012
getFeatureSelectionOptions-methods0.0090.0040.013
getFinalClassifier0.1400.0190.160
getResults-methods4.8560.2875.143
plotErrorsFoldTwoLayerCV-methods5.8900.0475.938
plotErrorsRepeatedOneLayerCV1.2900.0161.307
plotErrorsSummaryOneLayerCV-methods1.1790.0151.196
rankedGenesImg-methods0.0000.0000.001
runOneLayerExtCV-methods1.0860.0291.115
runTwoLayerExtCV-methods11.163 0.16911.342
setDataset-methods0.0010.0000.001
setFeatureSelectionOptions-methods0.0120.0030.015
thresholds-class0.0020.0010.003
vV70genes0.0040.0020.007