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BioC 3.4: CHECK report for Rmagpie on moscato1

This page was generated on 2016-09-21 03:42:46 -0700 (Wed, 21 Sep 2016).

Package 1027/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rmagpie 1.29.0
Camille Maumet
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rmagpie
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rmagpie
Version: 1.29.0
Command: rm -rf Rmagpie.buildbin-libdir Rmagpie.Rcheck && mkdir Rmagpie.buildbin-libdir Rmagpie.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rmagpie.buildbin-libdir Rmagpie_1.29.0.tar.gz >Rmagpie.Rcheck\00install.out 2>&1 && cp Rmagpie.Rcheck\00install.out Rmagpie-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Rmagpie.buildbin-libdir --install="check:Rmagpie-install.out" --force-multiarch --no-vignettes --timings Rmagpie_1.29.0.tar.gz
StartedAt: 2016-09-20 15:33:41 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:36:27 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 165.5 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rmagpie.buildbin-libdir Rmagpie_1.29.0.tar.gz >Rmagpie.Rcheck\00install.out 2>&1 && cp Rmagpie.Rcheck\00install.out Rmagpie-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Rmagpie.buildbin-libdir --install="check:Rmagpie-install.out" --force-multiarch --no-vignettes --timings Rmagpie_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Rmagpie.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.29.0'
* 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 7.62      0    7.63
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
runTwoLayerExtCV-methods 8.27      0    8.27
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/Rmagpie.Rcheck/00check.log'
for details.


Rmagpie.Rcheck/00install.out:


install for i386

* installing *source* package 'Rmagpie' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Rmagpie' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rmagpie' as Rmagpie_1.29.0.zip
* DONE (Rmagpie)

Rmagpie.Rcheck/examples_i386/Rmagpie-Ex.timings:

nameusersystemelapsed
classifyNewSamples-methods1.250.001.25
experiment-class0.140.000.14
finalClassifier-class0.040.000.04
findFinalClassifier-methods0.120.000.12
geneSubsets-class000
getDataset-methods0.000.020.02
getFeatureSelectionOptions-methods0.020.000.01
getFinalClassifier0.190.010.21
getResults-methods4.330.024.35
plotErrorsFoldTwoLayerCV-methods3.900.023.92
plotErrorsRepeatedOneLayerCV0.710.000.70
plotErrorsSummaryOneLayerCV-methods0.700.010.72
rankedGenesImg-methods000
runOneLayerExtCV-methods0.840.000.84
runTwoLayerExtCV-methods7.620.007.63
setDataset-methods0.020.000.01
setFeatureSelectionOptions-methods000
thresholds-class0.020.000.02
vV70genes000

Rmagpie.Rcheck/examples_x64/Rmagpie-Ex.timings:

nameusersystemelapsed
classifyNewSamples-methods1.470.001.47
experiment-class0.050.000.05
finalClassifier-class0.060.000.06
findFinalClassifier-methods0.120.000.12
geneSubsets-class0.020.000.02
getDataset-methods0.010.000.01
getFeatureSelectionOptions-methods000
getFinalClassifier0.170.040.20
getResults-methods4.240.014.26
plotErrorsFoldTwoLayerCV-methods4.10.04.1
plotErrorsRepeatedOneLayerCV0.760.000.76
plotErrorsSummaryOneLayerCV-methods0.800.000.79
rankedGenesImg-methods000
runOneLayerExtCV-methods0.700.020.72
runTwoLayerExtCV-methods8.270.008.27
setDataset-methods000
setFeatureSelectionOptions-methods0.020.000.01
thresholds-class000
vV70genes000