BioC 3.3: CHECK report for ClassifyR on morelia

Package: ClassifyR

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.5.1.tar.gz

StartedAt: 2015-10-22 04:32:35 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 04:35:02 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 146.9 seconds

RetCode: 0

Status:  OK

CheckDir: ClassifyR.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 ClassifyR_1.5.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ClassifyR.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.1’
* 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 ... [4s/4s] 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: no visible binding for global variable ‘FPR’
ROCplot,list: no visible binding for global variable ‘TPR’
ROCplot,list: no visible binding for global variable ‘validation’
ROCplot,list: no visible binding for global variable ‘selection’
ROCplot,list: no visible binding for global variable ‘dataset’
ROCplot,list: no visible binding for global variable ‘analysis’
TrainParams,ANY: no visible binding for global variable ‘dlda’
distribution,ClassifyResult: no visible binding for global variable
  ‘..density..’
errorMap,list: no visible binding for global variable ‘Class’
errorMap,list: no visible binding for global variable ‘name’
errorMap,list: no visible binding for global variable ‘type’
errorMap,list: no visible binding for global variable ‘Error’
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous>: no
  visible binding for global variable ‘classes’
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
  <anonymous> : <anonymous>: no visible binding for global variable
  ‘largerClass’
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
  <anonymous> : <anonymous>: no visible binding for global variable
  ‘classes’
naiveBayesKernel,ExpressionSet: no visible binding for global variable
  ‘featureValues’
performancePlot,list: no visible binding for global variable ‘Freq’
performancePlot,list: no visible binding for global variable
  ‘validation’
performancePlot,list: no visible binding for global variable ‘dataset’
performancePlot,list: no visible binding for global variable ‘analysis’
performancePlot,list: no visible binding for global variable
  ‘selection’
plotFeatureClasses,ExpressionSet : <anonymous>: no visible binding for
  global variable ‘expr’
plotFeatureClasses,ExpressionSet : <anonymous>: no visible binding for
  global variable ‘..density..’
rankingPlot,list: no visible binding for global variable ‘top’
rankingPlot,list: no visible binding for global variable ‘overlap’
rankingPlot,list: no visible binding for global variable ‘validation’
rankingPlot,list: no visible binding for global variable ‘dataset’
rankingPlot,list: no visible binding for global variable ‘analysis’
rankingPlot,list: no visible binding for global variable ‘selection’
selectionPlot,list: no visible binding for global variable ‘validation’
selectionPlot,list: no visible binding for global variable ‘dataset’
selectionPlot,list: no visible binding for global variable ‘analysis’
selectionPlot,list: no visible binding for global variable ‘overlap’
selectionPlot,list: no visible binding for global variable ‘size’
selectionPlot,list: no visible binding for global variable ‘Freq’
Undefined global functions or variables:
  ..density.. Class Error FPR Freq TPR analysis classes dataset dlda
  expr featureValues largerClass name overlap selection size top type
  validation
* 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 ... [114s/103s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
distribution               12.654  0.800  11.597
ClassifyResult-class       11.903  0.523  11.179
DMDselection                9.531  0.189   9.724
runTest                     9.071  0.171   9.254
runTests                    8.113  0.130  10.822
KullbackLeiblerSelection    7.124  0.086   7.211
KolmogorovSmirnovSelection  6.392  0.102   6.494
likelihoodRatioSelection    6.336  0.073   6.410
edgeRselection              5.911  0.236   6.196
selectionPlot               4.285  1.559   2.166
previousSelection           3.978  1.052   3.997
mixmodels                   4.846  0.042   5.064
* 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
  ‘/Users/biocbuild/bbs-3.3-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	11.903	0.523	11.179
DMDselection	9.531	0.189	9.724
KolmogorovSmirnovSelection	6.392	0.102	6.494
KullbackLeiblerSelection	7.124	0.086	7.211
PredictParams-class	0.003	0.000	0.004
ROCplot	0.693	0.010	0.703
ResubstituteParams-class	0.002	0.001	0.002
SelectParams-class	0.004	0.000	0.005
SelectResult-class	0.001	0.000	0.001
TrainParams-class	0.007	0.000	0.007
TransformParams-class	0.002	0.000	0.001
bartlettSelection	0.757	0.002	0.759
calcPerformance	0.008	0.001	0.008
classifyInterface	0.685	0.048	0.755
distribution	12.654	0.800	11.597
edgeRselection	5.911	0.236	6.196
errorMap	0.006	0.000	0.006
fisherDiscriminant	0.048	0.001	0.048
functionOrList-class	0.007	0.000	0.008
getLocationsAndScales	0.045	0.001	0.046
leveneSelection	2.654	0.061	2.901
likelihoodRatioSelection	6.336	0.073	6.410
limmaSelection	0.471	0.002	0.473
mixmodels	4.846	0.042	5.064
naiveBayesKernel	0.512	0.011	0.524
nearestShrunkenCentroidPredictInterface	0.490	0.007	0.527
nearestShrunkenCentroidSelectionInterface	0.151	0.002	0.152
nearestShrunkenCentroidTrainInterface	0.094	0.002	0.096
pamrtrained-class	0.075	0.001	0.076
performancePlot	0.379	0.002	0.414
plotFeatureClasses	2.217	0.006	2.225
previousSelection	3.978	1.052	3.997
rankingPlot	3.119	1.555	2.197
runTest	9.071	0.171	9.254
runTests	8.113	0.130	10.822
selectionPlot	4.285	1.559	2.166
subtractFromLocation	0.029	0.000	0.030