Package: Rmagpie

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rmagpie_1.13.0.tar.gz

StartedAt: 2012-06-21 03:14:36 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 03:17:02 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 146.1 seconds

RetCode: 0

Status:  OK

CheckDir: Rmagpie.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/Rmagpie.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Rmagpie/DESCRIPTION' ... OK
* this is package 'Rmagpie' version '1.13.0'
* 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 whether package 'Rmagpie' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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'
* 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 sizes of PDF files under 'inst/doc' ... 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
* 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
  '/Users/biocbuild/bbs-2.11-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	3.053	0.193	3.540
experiment-class	0.185	0.015	0.204
finalClassifier-class	0.130	0.010	0.141
findFinalClassifier-methods	0.271	0.034	0.317
geneSubsets-class	0.017	0.000	0.018
getDataset-methods	0.019	0.001	0.021
getFeatureSelectionOptions-methods	0.014	0.002	0.016
getFinalClassifier	0.380	0.120	0.561
getResults-methods	8.996	0.327	9.494
plotErrorsFoldTwoLayerCV-methods	9.252	0.049	9.623
plotErrorsRepeatedOneLayerCV	1.767	0.012	1.789
plotErrorsSummaryOneLayerCV-methods	1.628	0.014	1.694
rankedGenesImg-methods	0.000	0.001	0.000
runOneLayerExtCV-methods	1.427	0.011	1.592
runTwoLayerExtCV-methods	17.306	0.075	17.663
setDataset-methods	0.000	0.000	0.001
setFeatureSelectionOptions-methods	0.021	0.002	0.022
thresholds-class	0.002	0.000	0.003
vV70genes	0.007	0.001	0.009