Package: ClassifyR

Version: 2.3.6

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_2.3.6.tar.gz

StartedAt: 2019-04-08 23:55:22 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-09 00:01:04 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 342.5 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_2.3.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ClassifyR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘2.3.6’
* 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’
kTSPclassifier,DataFrame : <anonymous>: no visible global function
  definition for ‘Pairs’
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’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘key’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘value’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable ‘ID’
rankingPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for ‘first’
rankingPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for ‘second’
rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘first’
rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘second’
runTest,DataFrame: no visible binding for global variable ‘setsNodes’
runTests,DataFrame: no visible binding for global variable ‘setsNodes’
samplesMetricMap,list: no visible binding for global variable ‘Class’
samplesMetricMap,list: no visible binding for global variable ‘Group’
samplesMetricMap,list: no visible binding for global variable
  ‘measurements’
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’
samplesMetricMap,matrix: no visible binding for global variable ‘Class’
samplesMetricMap,matrix: no visible binding for global variable ‘Group’
samplesMetricMap,matrix: no visible binding for global variable
  ‘measurements’
samplesMetricMap,matrix: no visible binding for global variable ‘name’
samplesMetricMap,matrix: no visible binding for global variable ‘type’
samplesMetricMap,matrix: no visible binding for global variable
  ‘Metric’
selectionPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for ‘first’
selectionPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for ‘second’
selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for ‘first’
selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for ‘second’
selectionPlot,list: no visible binding for global variable ‘Freq’
Undefined global functions or variables:
  ..density.. Class Freq Group ID Metric Pairs dmvnorm first key
  legends grouping measurement measurements name second setsNodes type
  value
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     116.139  6.175  32.923
elasticNetFeatures        45.949  3.911  19.084
elasticNetGLMinterface    45.276  3.667  18.904
distribution              19.397  6.206   9.357
samplesMetricMap          13.697  2.400   5.942
likelihoodRatioSelection   9.602  0.350  10.088
DMDselection               7.917  0.250   8.266
edgeRselection             6.121  0.320   6.499
previousTrained            3.709  2.041   2.856
previousSelection          3.412  1.724   2.861
runTests                   0.450  0.245   6.978
* 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-3.9-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/3.6/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	116.139	6.175	32.923
DLDAinterface	0.061	0.002	0.063
DMDselection	7.917	0.250	8.266
FeatureSetCollection-class	0.008	0.001	0.009
FeatureSetCollectionOrNULL-class	0.003	0.001	0.003
KolmogorovSmirnovSelection	2.619	0.032	2.696
KullbackLeiblerSelection	1.396	0.008	1.425
NSCpredictInterface	0.116	0.007	0.124
NSCselectionInterface	0.078	0.002	0.080
NSCtrainInterface	0.087	0.003	0.091
PredictParams-class	0.003	0.000	0.003
ROCplot	1.496	0.026	1.544
ResubstituteParams-class	0.002	0.000	0.002
SVMinterface	0.059	0.002	0.062
SelectParams-class	0.009	0.001	0.011
SelectResult-class	0.001	0.000	0.001
TrainParams-class	0.001	0.000	0.001
TransformParams-class	0.001	0.000	0.002
bartlettSelection	1.830	0.019	1.870
calcPerformance	0.005	0.000	0.006
characterOrDataFrame-class	0.011	0.000	0.011
classifyInterface	0.701	0.117	0.824
differentMeansSelection	1.678	0.023	1.713
distribution	19.397	6.206	9.357
edgeRselection	6.121	0.320	6.499
edgesToHubNetworks	0.004	0.000	0.005
elasticNetFeatures	45.949	3.911	19.084
elasticNetGLMinterface	45.276	3.667	18.904
featureSetSummary	0.004	0.002	0.005
fisherDiscriminant	0.136	0.029	0.168
forestFeatures	0.123	0.022	0.146
functionOrList-class	0.011	0.002	0.014
functionOrNULL-class	0.004	0.000	0.004
getLocationsAndScales	0.050	0.005	0.056
integerOrNumeric-class	0.019	0.003	0.022
interactorDifferences	0.060	0.007	0.070
kTSPclassifier	0.114	0.016	0.130
knnInterface	0.041	0.003	0.045
leveneSelection	1.959	0.153	2.140
likelihoodRatioSelection	9.602	0.350	10.088
limmaSelection	0.628	0.026	0.659
mixmodels	0.779	0.031	0.829
naiveBayesKernel	0.563	0.015	0.595
networkCorrelationsSelection	0.205	0.004	0.211
pairsDifferencesSelection	0.313	0.001	0.322
performancePlot	0.276	0.002	0.280
plotFeatureClasses	3.546	0.012	3.589
previousSelection	3.412	1.724	2.861
previousTrained	3.709	2.041	2.856
randomForestInterface	0.285	0.059	0.346
rankingPlot	2.949	0.835	3.434
runTest	0.840	0.042	0.886
runTests	0.450	0.245	6.978
samplesMetricMap	13.697	2.400	5.942
selectionPlot	3.283	0.431	3.641
subtractFromLocation	0.002	0.001	0.003