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BioC 3.0: CHECK report for Rmagpie on moscato1

This page was generated on 2015-04-10 09:45:47 -0700 (Fri, 10 Apr 2015).

Package 755/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rmagpie 1.22.0
Camille Maumet
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Rmagpie
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: Rmagpie
Version: 1.22.0
Command: rm -rf Rmagpie.buildbin-libdir Rmagpie.Rcheck && mkdir Rmagpie.buildbin-libdir Rmagpie.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rmagpie.buildbin-libdir Rmagpie_1.22.0.tar.gz >Rmagpie.Rcheck\00install.out 2>&1 && cp Rmagpie.Rcheck\00install.out Rmagpie-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Rmagpie.buildbin-libdir --install="check:Rmagpie-install.out" --force-multiarch --no-vignettes --timings Rmagpie_1.22.0.tar.gz
StartedAt: 2015-04-10 05:04:34 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:07:21 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 166.5 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-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rmagpie.buildbin-libdir Rmagpie_1.22.0.tar.gz >Rmagpie.Rcheck\00install.out 2>&1 && cp Rmagpie.Rcheck\00install.out Rmagpie-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Rmagpie.buildbin-libdir --install="check:Rmagpie-install.out" --force-multiarch --no-vignettes --timings Rmagpie_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/Rmagpie.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rmagpie/DESCRIPTION' ... OK
* this is package 'Rmagpie' version '1.22.0'
* 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<-'
* 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' ... [27s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
runTwoLayerExtCV-methods 9.97   0.00    9.98
getResults-methods       5.02   0.01    5.04
** running examples for arch 'x64' ... [38s] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
runTwoLayerExtCV-methods         11.33   0.00   11.32
plotErrorsFoldTwoLayerCV-methods  7.41   0.01    7.43
getResults-methods                6.86   0.00    6.86
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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_1.22.0.zip
* DONE (Rmagpie)

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

nameusersystemelapsed
classifyNewSamples-methods1.610.001.61
experiment-class0.050.000.04
finalClassifier-class0.060.000.06
findFinalClassifier-methods0.140.000.14
geneSubsets-class0.010.000.02
getDataset-methods0.020.000.01
getFeatureSelectionOptions-methods0.020.000.02
getFinalClassifier0.340.020.36
getResults-methods5.020.015.04
plotErrorsFoldTwoLayerCV-methods4.680.004.68
plotErrorsRepeatedOneLayerCV0.910.000.90
plotErrorsSummaryOneLayerCV-methods0.870.000.87
rankedGenesImg-methods000
runOneLayerExtCV-methods0.750.020.77
runTwoLayerExtCV-methods9.970.009.98
setDataset-methods000
setFeatureSelectionOptions-methods0.010.000.02
thresholds-class000
vV70genes000

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

nameusersystemelapsed
classifyNewSamples-methods2.690.002.68
experiment-class0.090.000.09
finalClassifier-class0.120.000.13
findFinalClassifier-methods0.220.020.23
geneSubsets-class0.020.000.02
getDataset-methods0.030.000.03
getFeatureSelectionOptions-methods0.010.000.02
getFinalClassifier0.240.030.26
getResults-methods6.860.006.86
plotErrorsFoldTwoLayerCV-methods7.410.017.43
plotErrorsRepeatedOneLayerCV1.050.001.05
plotErrorsSummaryOneLayerCV-methods1.140.001.13
rankedGenesImg-methods000
runOneLayerExtCV-methods0.860.000.86
runTwoLayerExtCV-methods11.33 0.0011.32
setDataset-methods000
setFeatureSelectionOptions-methods0.000.020.02
thresholds-class000
vV70genes0.010.000.01