BioC 3.2: CHECK report for ClassifyR on zin1

Package: ClassifyR

Version: 1.3.13

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.3.13.tar.gz

StartedAt: 2015-08-23 22:35:19 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:37:21 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 121.9 seconds

RetCode: 0

Status:  OK

CheckDir: ClassifyR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.3.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ClassifyR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClassifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClassifyR’ version ‘1.3.13’
* 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 ‘ClassifyR’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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
ROCplot,list : .local: no visible binding for global variable ‘FPR’
ROCplot,list : .local: no visible binding for global variable ‘TPR’
ROCplot,list : .local: no visible binding for global variable
  ‘validation’
ROCplot,list : .local: no visible binding for global variable
  ‘selection’
ROCplot,list : .local: no visible binding for global variable ‘dataset’
ROCplot,list : .local: no visible binding for global variable
  ‘analysis’
TrainParams,ANY : .local: no visible binding for global variable ‘dlda’
distribution,ClassifyResult : .local: no visible binding for global
  variable ‘..density..’
errorMap,list : .local: no visible binding for global variable ‘Class’
errorMap,list : .local: no visible binding for global variable ‘name’
errorMap,list : .local: no visible binding for global variable ‘type’
errorMap,list : .local: no visible binding for global variable ‘Error’
mixModelsTest,list-ExpressionSet : .local : <anonymous> : <anonymous>:
  no visible binding for global variable ‘classesSizes’
mixModelsTest,list-ExpressionSet : .local : <anonymous> : <anonymous>:
  no visible binding for global variable ‘classes’
performancePlot,list : .local: no visible binding for global variable
  ‘Freq’
performancePlot,list : .local: no visible binding for global variable
  ‘validation’
performancePlot,list : .local: no visible binding for global variable
  ‘dataset’
performancePlot,list : .local: no visible binding for global variable
  ‘analysis’
performancePlot,list : .local: no visible binding for global variable
  ‘selection’
plotFeatureClasses,ExpressionSet : .local : <anonymous>: no visible
  binding for global variable ‘expr’
plotFeatureClasses,ExpressionSet : .local : <anonymous>: no visible
  binding for global variable ‘..density..’
rankingPlot,list : .local: no visible binding for global variable ‘top’
rankingPlot,list : .local: no visible binding for global variable
  ‘overlap’
rankingPlot,list : .local: no visible binding for global variable
  ‘validation’
rankingPlot,list : .local: no visible binding for global variable
  ‘dataset’
rankingPlot,list : .local: no visible binding for global variable
  ‘analysis’
rankingPlot,list : .local: no visible binding for global variable
  ‘selection’
selectionPlot,list : .local: no visible binding for global variable
  ‘validation’
selectionPlot,list : .local: no visible binding for global variable
  ‘dataset’
selectionPlot,list : .local: no visible binding for global variable
  ‘analysis’
selectionPlot,list : .local: no visible binding for global variable
  ‘overlap’
selectionPlot,list : .local: no visible binding for global variable
  ‘size’
selectionPlot,list : .local: no visible binding for global variable
  ‘Freq’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [86s/85s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ClassifyResult-class 12.150  0.124  12.451
distribution         11.673  0.111  11.797
runTests             10.213  0.052  10.274
runTest               8.824  0.116   8.945
edgeRselection        8.063  0.100   8.221
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.

* installing *source* package ‘ClassifyR’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘performance’ in package ‘ClassifyR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ClassifyR)

name	user	system	elapsed
ClassifyResult-class	12.150	0.124	12.451
DMDselection	2.158	0.000	2.157
KolmogorovSmirnovSelection	2.359	0.000	2.385
KullbackLeiblerSelection	2.183	0.007	2.193
PredictParams-class	0.002	0.000	0.003
ROCplot	0.646	0.000	0.646
ResubstituteParams-class	0.002	0.000	0.003
SelectParams-class	0.005	0.000	0.005
SelectResult-class	0.002	0.000	0.001
TrainParams-class	0.012	0.000	0.012
TransformParams-class	0.002	0.000	0.002
bartlettSelection	0.922	0.000	0.922
calcPerformance	0.006	0.000	0.007
classifyInterface	0.809	0.003	0.829
distribution	11.673	0.111	11.797
edgeRselection	8.063	0.100	8.221
errorMap	0.004	0.000	0.004
fisherDiscriminant	0.039	0.000	0.039
functionOrList-class	0.006	0.000	0.006
getLocationsAndScales	0.033	0.004	0.037
leveneSelection	3.177	0.016	3.191
likelihoodRatioSelection	2.511	0.012	2.570
limmaSelection	0.682	0.000	0.682
mixmodels	3.659	0.012	3.728
naiveBayesKernel	0.261	0.016	0.277
nearestShrunkenCentroidPredictInterface	0.199	0.000	0.200
nearestShrunkenCentroidSelectionInterface	0.167	0.000	0.167
nearestShrunkenCentroidTrainInterface	0.132	0.000	0.133
pamrtrained-class	0.075	0.000	0.076
performancePlot	0.415	0.004	0.432
plotFeatureClasses	2.372	0.000	2.396
previousSelection	2.707	0.000	2.718
rankingPlot	3.267	0.700	3.014
runTest	8.824	0.116	8.945
runTests	10.213	0.052	10.274
selectionPlot	2.927	0.713	2.709
subtractFromLocation	0.037	0.000	0.039