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Package 521/631HostnameOS / ArchBUILDCHECKBUILD BIN
Rmagpie 1.15.1
Camille Maumet
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rmagpie
Last Changed Rev: 72298 / Revision: 72575
Last Changed Date: 2013-01-04 13:18:09 -0800 (Fri, 04 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: Rmagpie
Version: 1.15.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Rmagpie_1.15.1.tar.gz
StartedAt: 2013-01-16 05:57:55 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 05:59:51 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 116.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Rmagpie.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Rmagpie.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rmagpie/DESCRIPTION’ ... OK
* this is package ‘Rmagpie’ version ‘1.15.1’
* 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 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 for unstated 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’ ... NOTE
The following files should probably not be installed:
  ‘fancyvrb.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
runTwoLayerExtCV-methods         13.673  0.008  13.689
getResults-methods                7.364  0.052   7.421
plotErrorsFoldTwoLayerCV-methods  7.189  0.020   7.208
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Rmagpie.Rcheck/00check.log’
for details.

Rmagpie.Rcheck/00install.out:

* installing *source* package ‘Rmagpie’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Magpie_examples.Rnw’ using ‘latin1’ 
** testing if installed package can be loaded

* DONE (Rmagpie)

Rmagpie.Rcheck/Rmagpie-Ex.timings:

nameusersystemelapsed
classifyNewSamples-methods2.4960.0122.514
experiment-class0.1120.0040.116
finalClassifier-class0.1240.0080.134
findFinalClassifier-methods0.3520.0000.353
geneSubsets-class0.0400.0040.045
getDataset-methods0.0280.0040.031
getFeatureSelectionOptions-methods0.0520.0000.053
getFinalClassifier0.2800.0440.323
getResults-methods7.3640.0527.421
plotErrorsFoldTwoLayerCV-methods7.1890.0207.208
plotErrorsRepeatedOneLayerCV1.260.001.26
plotErrorsSummaryOneLayerCV-methods1.2840.0161.302
rankedGenesImg-methods0.0200.0000.018
runOneLayerExtCV-methods1.1360.0121.145
runTwoLayerExtCV-methods13.673 0.00813.689
setDataset-methods0.0280.0080.038
setFeatureSelectionOptions-methods0.0640.0320.096
thresholds-class0.0160.0120.027
vV70genes0.0160.0000.017