BioC 2.12: CHECK report for Rmagpie on george2

Package: Rmagpie

Version: 1.16.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Rmagpie_1.16.0.tar.gz

StartedAt: 2013-10-09 04:36:36 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:39:25 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 169.2 seconds

RetCode: 0

Status:  OK

CheckDir: Rmagpie.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Rmagpie.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [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 ... [52s/62s] OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
runTwoLayerExtCV-methods         16.109  0.012  16.141
plotErrorsFoldTwoLayerCV-methods 10.480  0.016  12.472
getResults-methods               10.221  0.088  15.991
* 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
  ‘/home/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	3.340	0.016	3.357
experiment-class	0.140	0.008	0.150
finalClassifier-class	0.160	0.024	0.181
findFinalClassifier-methods	0.308	0.016	0.325
geneSubsets-class	0.056	0.004	0.056
getDataset-methods	0.036	0.008	0.045
getFeatureSelectionOptions-methods	0.080	0.004	0.085
getFinalClassifier	0.392	0.080	0.479
getResults-methods	10.221	0.088	15.991
plotErrorsFoldTwoLayerCV-methods	10.480	0.016	12.472
plotErrorsRepeatedOneLayerCV	2.140	0.008	2.947
plotErrorsSummaryOneLayerCV-methods	1.640	0.020	2.422
rankedGenesImg-methods	0.016	0.012	0.026
runOneLayerExtCV-methods	1.380	0.008	1.401
runTwoLayerExtCV-methods	16.109	0.012	16.141
setDataset-methods	0.028	0.004	0.030
setFeatureSelectionOptions-methods	0.104	0.008	0.112
thresholds-class	0.280	0.000	0.282
vV70genes	0.024	0.000	0.023