BioC 3.4: CHECK report for Rmagpie on zin1

Package: Rmagpie

Version: 1.29.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rmagpie_1.29.0.tar.gz

StartedAt: 2016-09-20 11:52:16 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:53:30 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 74.3 seconds

RetCode: 0

Status:  OK

CheckDir: Rmagpie.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rmagpie_1.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Rmagpie.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rmagpie/DESCRIPTION’ ... OK
* this is package ‘Rmagpie’ version ‘1.29.0’
* 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 ... 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<-’
Undefined global functions or variables:
  getNoModels<- getNoOfOptions<-
* 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
runTwoLayerExtCV-methods 6.38  0.004   6.384
* 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
  ‘/home/biocbuild/bbs-3.4-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	1.076	0.000	1.078
experiment-class	0.036	0.004	0.040
finalClassifier-class	0.048	0.000	0.049
findFinalClassifier-methods	0.104	0.000	0.101
geneSubsets-class	0.004	0.000	0.005
getDataset-methods	0.008	0.000	0.008
getFeatureSelectionOptions-methods	0.004	0.000	0.006
getFinalClassifier	0.164	0.020	0.185
getResults-methods	3.212	0.028	3.240
plotErrorsFoldTwoLayerCV-methods	3.288	0.008	3.293
plotErrorsRepeatedOneLayerCV	0.616	0.000	0.618
plotErrorsSummaryOneLayerCV-methods	0.612	0.000	0.614
rankedGenesImg-methods	0.004	0.000	0.001
runOneLayerExtCV-methods	0.528	0.000	0.530
runTwoLayerExtCV-methods	6.380	0.004	6.384
setDataset-methods	0.000	0.000	0.001
setFeatureSelectionOptions-methods	0.008	0.000	0.007
thresholds-class	0.000	0.004	0.002
vV70genes	0.004	0.000	0.003