Package: ClassifyR

Version: 2.0.10

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ClassifyR_2.0.10.tar.gz

StartedAt: 2018-10-15 23:15:43 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 23:18:59 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 195.7 seconds

RetCode: 0

Status:  OK

CheckDir: ClassifyR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ClassifyR_2.0.10.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ClassifyR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.0.10’
* 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 ... 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 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
.posterior_probs : <anonymous>: no visible global function definition
  for ‘dmvnorm’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘measurement’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘..density..’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘legends grouping’
samplesMetricMap,list: no visible binding for global variable ‘Class’
samplesMetricMap,list: no visible binding for global variable ‘name’
samplesMetricMap,list: no visible binding for global variable ‘type’
samplesMetricMap,list: no visible binding for global variable ‘Metric’
selectionPlot,list: no visible binding for global variable ‘Freq’
Undefined global functions or variables:
  ..density.. Class Freq Metric dmvnorm legends grouping measurement
  name type
Consider adding
  importFrom("base", "grouping")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
distribution             26.656  1.560  11.034
DLDAinterface            24.516  1.620   0.066
samplesMetricMap         23.828  1.376   1.077
likelihoodRatioSelection  5.936  0.004   5.943
DMDselection              5.772  0.124   5.904
edgeRselection            5.072  0.124   5.257
ClassifyResult-class      0.920  0.156  10.140
runTests                  0.348  0.104   9.173
* 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-3.7-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ClassifyR
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘ClassifyR’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ClassifyR)

name	user	system	elapsed
ClassifyResult-class	0.920	0.156	10.140
DLDAinterface	24.516	1.620	0.066
DMDselection	5.772	0.124	5.904
KolmogorovSmirnovSelection	2.340	0.016	2.361
KullbackLeiblerSelection	1.692	0.000	1.690
NSCpredictInterface	0.120	0.004	0.137
NSCselectionInterface	0.068	0.000	0.069
NSCtrainInterface	0.056	0.000	0.055
PredictParams-class	0.004	0.000	0.002
ROCplot	0.564	0.004	0.569
ResubstituteParams-class	0.004	0.000	0.001
SVMinterface	0.052	0.000	0.052
SelectParams-class	0.012	0.000	0.008
SelectResult-class	0.000	0.000	0.001
TrainParams-class	0	0	0
TransformParams-class	0.000	0.000	0.002
bartlettSelection	2.464	0.000	2.464
calcPerformance	0.004	0.000	0.003
characterOrDataFrame-class	0.008	0.000	0.009
classifyInterface	1.292	0.024	1.345
distribution	26.656	1.560	11.034
edgeRselection	5.072	0.124	5.257
elasticNetGLMinterface	1.456	0.284	3.082
fisherDiscriminant	2.784	0.264	0.287
forestFeatures	0.040	0.008	0.086
functionOrList-class	0.008	0.000	0.006
functionOrNULL-class	0.004	0.000	0.003
getLocationsAndScales	0.024	0.000	0.024
leveneSelection	2.108	0.008	2.116
likelihoodRatioSelection	5.936	0.004	5.943
limmaSelection	0.772	0.000	0.772
logisticRegressionInterface	0.740	0.040	0.797
mixmodels	0.804	0.008	0.859
naiveBayesKernel	0.420	0.012	0.433
performancePlot	0.204	0.000	0.202
plotFeatureClasses	4.048	0.004	4.055
previousSelection	3.152	0.436	2.139
randomForestInterface	0.376	0.184	0.080
rankingPlot	1.368	0.156	1.502
runTest	0.928	0.008	0.937
runTests	0.348	0.104	9.173
samplesMetricMap	23.828	1.376	1.077
selectionPlot	1.852	0.124	1.951
subtractFromLocation	0.004	0.000	0.001