BioC 2.14: CHECK report for Rmagpie on petty

Package: Rmagpie

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rmagpie_1.20.0.tar.gz

StartedAt: 2014-10-07 23:51:50 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:55:03 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 192.6 seconds

RetCode: 0

Status:  OK

CheckDir: Rmagpie.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rmagpie_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Rmagpie.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rmagpie/DESCRIPTION’ ... OK
* this is package ‘Rmagpie’ version ‘1.20.0’
* 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 ... [12s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
runTwoLayerExtCV-methods         19.796  0.070  20.008
plotErrorsFoldTwoLayerCV-methods 10.872  0.026  10.943
getResults-methods               10.136  0.094  10.282
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	3.269	0.043	3.353
experiment-class	0.099	0.003	0.103
finalClassifier-class	0.138	0.003	0.141
findFinalClassifier-methods	0.288	0.005	0.293
geneSubsets-class	0.021	0.001	0.023
getDataset-methods	0.023	0.001	0.025
getFeatureSelectionOptions-methods	0.020	0.001	0.022
getFinalClassifier	0.506	0.098	0.615
getResults-methods	10.136	0.094	10.282
plotErrorsFoldTwoLayerCV-methods	10.872	0.026	10.943
plotErrorsRepeatedOneLayerCV	1.937	0.011	2.052
plotErrorsSummaryOneLayerCV-methods	1.980	0.009	1.993
rankedGenesImg-methods	0.002	0.001	0.002
runOneLayerExtCV-methods	1.688	0.009	1.702
runTwoLayerExtCV-methods	19.796	0.070	20.008
setDataset-methods	0.002	0.001	0.003
setFeatureSelectionOptions-methods	0.027	0.002	0.031
thresholds-class	0.005	0.001	0.006
vV70genes	0.009	0.001	0.011