Package: Rmagpie

Version: 1.15.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rmagpie_1.15.1.tar.gz

StartedAt: 2013-03-24 09:45:56 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:48:28 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 151.9 seconds

RetCode: 0

Status:  OK

CheckDir: Rmagpie.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Rmagpie.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [10s/10s] 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 ... [49s/49s] OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
runTwoLayerExtCV-methods         16.926  0.109  17.498
getResults-methods                9.132  0.177   9.360
plotErrorsFoldTwoLayerCV-methods  8.945  0.031   9.017
* 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-2.12-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	2.970	0.075	3.100
experiment-class	0.138	0.007	0.146
finalClassifier-class	0.154	0.005	0.160
findFinalClassifier-methods	0.433	0.009	0.444
geneSubsets-class	0.046	0.002	0.049
getDataset-methods	0.033	0.004	0.038
getFeatureSelectionOptions-methods	0.044	0.006	0.051
getFinalClassifier	0.321	0.115	0.441
getResults-methods	9.132	0.177	9.360
plotErrorsFoldTwoLayerCV-methods	8.945	0.031	9.017
plotErrorsRepeatedOneLayerCV	1.674	0.017	1.710
plotErrorsSummaryOneLayerCV-methods	1.622	0.015	1.658
rankedGenesImg-methods	0.167	0.004	0.177
runOneLayerExtCV-methods	1.279	0.018	1.314
runTwoLayerExtCV-methods	16.926	0.109	17.498
setDataset-methods	0.037	0.002	0.041
setFeatureSelectionOptions-methods	0.057	0.006	0.064
thresholds-class	0.023	0.003	0.026
vV70genes	0.014	0.001	0.016