Back to Multiple platform build/check report for BioC 3.6
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

CHECK report for Rmagpie on tokay1

This page was generated on 2018-04-12 13:19:42 -0400 (Thu, 12 Apr 2018).

Package 1187/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rmagpie 1.34.0
Camille Maumet
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/Rmagpie
Branch: RELEASE_3_6
Last Commit: 1c28243
Last Changed Date: 2017-10-30 12:39:26 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rmagpie
Version: 1.34.0
Command: rm -rf Rmagpie.buildbin-libdir Rmagpie.Rcheck && mkdir Rmagpie.buildbin-libdir Rmagpie.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rmagpie.buildbin-libdir Rmagpie_1.34.0.tar.gz >Rmagpie.Rcheck\00install.out 2>&1 && cp Rmagpie.Rcheck\00install.out Rmagpie-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Rmagpie.buildbin-libdir --install="check:Rmagpie-install.out" --force-multiarch --no-vignettes --timings Rmagpie_1.34.0.tar.gz
StartedAt: 2018-04-12 02:43:54 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:46:08 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 134.5 seconds
RetCode: 0
Status:  OK  
CheckDir: Rmagpie.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rmagpie.buildbin-libdir Rmagpie.Rcheck && mkdir Rmagpie.buildbin-libdir Rmagpie.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rmagpie.buildbin-libdir Rmagpie_1.34.0.tar.gz >Rmagpie.Rcheck\00install.out 2>&1 && cp Rmagpie.Rcheck\00install.out Rmagpie-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Rmagpie.buildbin-libdir --install="check:Rmagpie-install.out" --force-multiarch --no-vignettes --timings Rmagpie_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Rmagpie.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rmagpie/DESCRIPTION' ... OK
* this is package 'Rmagpie' version '1.34.0'
* 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 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
runTwoLayerExtCV-methods 5.17   0.01    5.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
runTwoLayerExtCV-methods 8.61      0    8.61
* 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Rmagpie.Rcheck/00check.log'
for details.



Installation output

Rmagpie.Rcheck/00install.out


install for i386

* installing *source* package 'Rmagpie' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Rmagpie'
    finding HTML links ... done
    classifyNewSamples-methods              html  
    experiment-class                        html  
    featureSelectionOptions-class           html  
    finalClassifier-class                   html  
    findFinalClassifier-methods             html  
    geneSubsets-class                       html  
    getDataset-methods                      html  
    getFeatureSelectionOptions-methods      html  
    getFinalClassifier                      html  
    getResults-methods                      html  
    initialize-methods                      html  
    plotErrorsFoldTwoLayerCV-methods        html  
    plotErrorsRepeatedOneLayerCV            html  
    plotErrorsSummaryOneLayerCV-methods     html  
    rankedGenesImg-methods                  html  
    runOneLayerExtCV-methods                html  
    runTwoLayerExtCV-methods                html  
    setDataset-methods                      html  
    setFeatureSelectionOptions-methods      html  
    show-methods                            html  
    thresholds-class                        html  
    vV70genes                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Rmagpie' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rmagpie' as Rmagpie_1.34.0.zip
* DONE (Rmagpie)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

Rmagpie.Rcheck/examples_i386/Rmagpie-Ex.timings

nameusersystemelapsed
classifyNewSamples-methods1.450.061.52
experiment-class0.160.000.15
finalClassifier-class0.070.000.06
findFinalClassifier-methods0.180.010.20
geneSubsets-class000
getDataset-methods0.020.020.03
getFeatureSelectionOptions-methods000
getFinalClassifier0.170.010.19
getResults-methods2.880.002.87
plotErrorsFoldTwoLayerCV-methods2.670.002.67
plotErrorsRepeatedOneLayerCV0.480.000.49
plotErrorsSummaryOneLayerCV-methods0.520.000.51
rankedGenesImg-methods000
runOneLayerExtCV-methods0.420.020.44
runTwoLayerExtCV-methods5.170.015.19
setDataset-methods000
setFeatureSelectionOptions-methods0.020.000.01
thresholds-class000
vV70genes0.030.000.04

Rmagpie.Rcheck/examples_x64/Rmagpie-Ex.timings

nameusersystemelapsed
classifyNewSamples-methods1.780.031.81
experiment-class0.20.00.2
finalClassifier-class0.080.000.07
findFinalClassifier-methods0.260.000.27
geneSubsets-class0.020.000.02
getDataset-methods0.030.000.03
getFeatureSelectionOptions-methods0.010.000.01
getFinalClassifier0.180.020.19
getResults-methods3.900.003.91
plotErrorsFoldTwoLayerCV-methods4.190.004.20
plotErrorsRepeatedOneLayerCV1.100.011.10
plotErrorsSummaryOneLayerCV-methods1.110.001.11
rankedGenesImg-methods000
runOneLayerExtCV-methods1.080.021.11
runTwoLayerExtCV-methods8.610.008.61
setDataset-methods000
setFeatureSelectionOptions-methods0.000.020.01
thresholds-class0.010.000.02
vV70genes0.060.000.06