Package: Rmagpie

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings Rmagpie_1.4.0.tar.gz

StartedAt: 2010-10-04 18:30:56 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:33:16 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 140.1 seconds

RetCode: 0

Status:  OK

CheckDir: Rmagpie.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/Rmagpie.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rmagpie/DESCRIPTION' ... OK
* this is package 'Rmagpie' version '1.4.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Rmagpie' can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package ‘Rmagpie’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Rmagpie)

name	user	system	elapsed
classifyNewSamples-methods	3.893	0.195	4.253
experiment-class	0.119	0.014	0.137
finalClassifier-class	0.182	0.013	0.195
findFinalClassifier-methods	0.405	0.034	0.442
geneSubsets-class	0.020	0.001	0.021
getDataset-methods	0.027	0.001	0.029
getFeatureSelectionOptions-methods	0.030	0.002	0.032
getFinalClassifier	0.612	0.126	0.743
getResults-methods	12.734	0.370	13.172
plotErrorsFoldTwoLayerCV-methods	13.366	0.044	13.564
plotErrorsRepeatedOneLayerCV	2.285	0.010	2.310
plotErrorsSummaryOneLayerCV-methods	2.345	0.011	2.379
rankedGenesImg-methods	0.000	0.001	0.000
runOneLayerExtCV-methods	1.771	0.007	1.788
runTwoLayerExtCV-methods	23.097	0.098	23.896
setDataset-methods	0.000	0.000	0.001
setFeatureSelectionOptions-methods	0.034	0.002	0.037
thresholds-class	0.004	0.001	0.005
vV70genes	0.009	0.001	0.011