BioC 3.1: CHECK report for Rmagpie on petty

Package: Rmagpie

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rmagpie_1.24.0.tar.gz

StartedAt: 2015-10-09 01:38:37 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:40:41 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 123.8 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 Rmagpie_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Rmagpie.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.24.0’
* 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 ... [8s/8s] 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 ... [37s/37s] OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
runTwoLayerExtCV-methods         13.103  0.056  13.165
plotErrorsFoldTwoLayerCV-methods  7.654  0.015   7.679
getResults-methods                6.493  0.073   6.570
* 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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	2.073	0.042	2.115
experiment-class	0.071	0.003	0.074
finalClassifier-class	0.094	0.002	0.096
findFinalClassifier-methods	0.189	0.003	0.191
geneSubsets-class	0.009	0.000	0.010
getDataset-methods	0.011	0.000	0.012
getFeatureSelectionOptions-methods	0.014	0.001	0.015
getFinalClassifier	0.401	0.083	0.485
getResults-methods	6.493	0.073	6.570
plotErrorsFoldTwoLayerCV-methods	7.654	0.015	7.679
plotErrorsRepeatedOneLayerCV	1.013	0.006	1.020
plotErrorsSummaryOneLayerCV-methods	1.182	0.006	1.188
rankedGenesImg-methods	0.002	0.000	0.002
runOneLayerExtCV-methods	1.195	0.008	1.204
runTwoLayerExtCV-methods	13.103	0.056	13.165
setDataset-methods	0.003	0.000	0.002
setFeatureSelectionOptions-methods	0.020	0.001	0.022
thresholds-class	0.004	0.001	0.005
vV70genes	0.007	0.001	0.007