Package: Rmagpie

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rmagpie_1.12.0.tar.gz

StartedAt: 2012-09-24 01:34:08 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:36:20 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 131.9 seconds

RetCode: 0

Status:  OK

CheckDir: Rmagpie.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/Rmagpie.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.12.0'
* 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-2.10-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	2.236	0.113	2.354
experiment-class	0.110	0.013	0.123
finalClassifier-class	0.146	0.010	0.156
findFinalClassifier-methods	0.377	0.032	0.408
geneSubsets-class	0.020	0.001	0.021
getDataset-methods	0.022	0.001	0.023
getFeatureSelectionOptions-methods	0.016	0.002	0.018
getFinalClassifier	0.350	0.128	0.478
getResults-methods	8.388	0.246	8.642
plotErrorsFoldTwoLayerCV-methods	9.646	0.037	9.684
plotErrorsRepeatedOneLayerCV	1.895	0.012	1.908
plotErrorsSummaryOneLayerCV-methods	1.983	0.011	1.995
rankedGenesImg-methods	0.000	0.001	0.000
runOneLayerExtCV-methods	1.565	0.006	1.571
runTwoLayerExtCV-methods	17.102	0.098	17.202
setDataset-methods	0	0	0
setFeatureSelectionOptions-methods	0.015	0.001	0.017
thresholds-class	0.002	0.000	0.002
vV70genes	0.006	0.001	0.007