BioC 3.2: CHECK report for Rmagpie on oaxaca

Package: Rmagpie

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rmagpie_1.26.0.tar.gz

StartedAt: 2016-04-23 03:51:30 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:53:30 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 119.9 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_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rmagpie.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rmagpie/DESCRIPTION’ ... OK
* this is package ‘Rmagpie’ version ‘1.26.0’
* 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 ... [9s/9s] 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 ... [30s/31s] OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
runTwoLayerExtCV-methods         10.040  0.041  10.105
plotErrorsFoldTwoLayerCV-methods  5.655  0.027   5.691
getResults-methods                5.075  0.059   5.165
* 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-3.2-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	1.611	0.035	1.668
experiment-class	0.057	0.003	0.060
finalClassifier-class	0.086	0.002	0.088
findFinalClassifier-methods	0.295	0.005	0.299
geneSubsets-class	0.008	0.001	0.009
getDataset-methods	0.011	0.001	0.012
getFeatureSelectionOptions-methods	0.012	0.001	0.013
getFinalClassifier	0.248	0.058	0.307
getResults-methods	5.075	0.059	5.165
plotErrorsFoldTwoLayerCV-methods	5.655	0.027	5.691
plotErrorsRepeatedOneLayerCV	0.930	0.004	0.938
plotErrorsSummaryOneLayerCV-methods	1.035	0.004	1.040
rankedGenesImg-methods	0.001	0.000	0.001
runOneLayerExtCV-methods	0.981	0.006	0.987
runTwoLayerExtCV-methods	10.040	0.041	10.105
setDataset-methods	0.001	0.000	0.001
setFeatureSelectionOptions-methods	0.008	0.001	0.010
thresholds-class	0.002	0.000	0.003
vV70genes	0.005	0.001	0.006