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

* 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.

* 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)

name	user	system	elapsed
classifyNewSamples-methods	2.496	0.012	2.514
experiment-class	0.112	0.004	0.116
finalClassifier-class	0.124	0.008	0.134
findFinalClassifier-methods	0.352	0.000	0.353
geneSubsets-class	0.040	0.004	0.045
getDataset-methods	0.028	0.004	0.031
getFeatureSelectionOptions-methods	0.052	0.000	0.053
getFinalClassifier	0.280	0.044	0.323
getResults-methods	7.364	0.052	7.421
plotErrorsFoldTwoLayerCV-methods	7.189	0.020	7.208
plotErrorsRepeatedOneLayerCV	1.26	0.00	1.26
plotErrorsSummaryOneLayerCV-methods	1.284	0.016	1.302
rankedGenesImg-methods	0.020	0.000	0.018
runOneLayerExtCV-methods	1.136	0.012	1.145
runTwoLayerExtCV-methods	13.673	0.008	13.689
setDataset-methods	0.028	0.008	0.038
setFeatureSelectionOptions-methods	0.064	0.032	0.096
thresholds-class	0.016	0.012	0.027
vV70genes	0.016	0.000	0.017