BioC 2.12: CHECK report for Rmagpie on petty

Package: Rmagpie

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rmagpie_1.16.0.tar.gz

StartedAt: 2013-10-08 23:43:07 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:46:10 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 183.1 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 3.0.1 (2013-05-16)
* 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 '1.16.0'
* 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 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 ... [11s/12s] 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 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 ... [58s/59s] OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
runTwoLayerExtCV-methods         20.657  0.089  21.090
plotErrorsFoldTwoLayerCV-methods 11.240  0.033  11.480
getResults-methods               10.377  0.152  10.669
* 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
** testing if installed package can be loaded
* DONE (Rmagpie)

name	user	system	elapsed
classifyNewSamples-methods	3.522	0.074	3.614
experiment-class	0.135	0.006	0.141
finalClassifier-class	0.164	0.003	0.168
findFinalClassifier-methods	0.306	0.013	0.321
geneSubsets-class	0.163	0.004	0.167
getDataset-methods	0.032	0.004	0.035
getFeatureSelectionOptions-methods	0.050	0.003	0.054
getFinalClassifier	0.350	0.106	0.459
getResults-methods	10.377	0.152	10.669
plotErrorsFoldTwoLayerCV-methods	11.240	0.033	11.480
plotErrorsRepeatedOneLayerCV	2.081	0.010	2.102
plotErrorsSummaryOneLayerCV-methods	2.094	0.015	2.143
rankedGenesImg-methods	0.016	0.001	0.016
runOneLayerExtCV-methods	1.789	0.009	1.812
runTwoLayerExtCV-methods	20.657	0.089	21.090
setDataset-methods	0.031	0.002	0.036
setFeatureSelectionOptions-methods	0.061	0.003	0.065
thresholds-class	0.022	0.002	0.025
vV70genes	0.016	0.002	0.025