Package: ClassifyR

Version: 2.0.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClassifyR_2.0.10.tar.gz

StartedAt: 2018-10-16 20:29:58 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:34:51 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 293.4 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 --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClassifyR_2.0.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ClassifyR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘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
ClassifyResult-class     40.957  5.276  17.451
samplesMetricMap         40.567  4.208   2.094
distribution             34.721  3.537  15.019
elasticNetGLMinterface   10.209  2.576   4.636
likelihoodRatioSelection  9.592  0.156   9.880
DMDselection              8.826  0.387   9.290
previousSelection         6.268  1.288   4.513
edgeRselection            6.492  0.350   6.922
plotFeatureClasses        6.212  0.018   6.287
runTests                  0.474  0.177  16.709
* 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-3.7-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ClassifyR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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	40.957	5.276	17.451
DLDAinterface	0.098	0.019	0.118
DMDselection	8.826	0.387	9.290
KolmogorovSmirnovSelection	3.627	0.065	3.725
KullbackLeiblerSelection	2.742	0.015	2.784
NSCpredictInterface	0.098	0.005	0.104
NSCselectionInterface	0.107	0.002	0.110
NSCtrainInterface	0.101	0.003	0.104
PredictParams-class	0.005	0.001	0.005
ROCplot	0.899	0.003	0.912
ResubstituteParams-class	0.003	0.001	0.004
SVMinterface	0.087	0.003	0.092
SelectParams-class	0.013	0.002	0.016
SelectResult-class	0.002	0.000	0.002
TrainParams-class	0.002	0.000	0.002
TransformParams-class	0.003	0.001	0.004
bartlettSelection	3.492	0.007	3.538
calcPerformance	0.004	0.000	0.005
characterOrDataFrame-class	0.010	0.001	0.011
classifyInterface	1.082	0.095	1.190
distribution	34.721	3.537	15.019
edgeRselection	6.492	0.350	6.922
elasticNetGLMinterface	10.209	2.576	4.636
fisherDiscriminant	0.494	0.076	0.573
forestFeatures	0.092	0.013	0.106
functionOrList-class	0.010	0.002	0.012
functionOrNULL-class	0.004	0.001	0.006
getLocationsAndScales	0.038	0.004	0.041
leveneSelection	3.441	0.042	3.526
likelihoodRatioSelection	9.592	0.156	9.880
limmaSelection	1.157	0.004	1.170
logisticRegressionInterface	0.898	0.127	1.032
mixmodels	1.404	0.014	1.430
naiveBayesKernel	0.624	0.024	0.652
performancePlot	0.341	0.002	0.345
plotFeatureClasses	6.212	0.018	6.287
previousSelection	6.268	1.288	4.513
randomForestInterface	0.843	0.658	0.165
rankingPlot	2.532	0.247	2.745
runTest	1.741	0.039	1.800
runTests	0.474	0.177	16.709
samplesMetricMap	40.567	4.208	2.094
selectionPlot	3.264	0.245	3.509
subtractFromLocation	0.002	0.001	0.003