Package: ClassifyR

Version: 2.4.4

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ClassifyR_2.4.4.tar.gz

StartedAt: 2019-10-16 00:33:52 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:38:43 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 290.6 seconds

RetCode: 0

Status:  OK

CheckDir: ClassifyR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ClassifyR_2.4.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ClassifyR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.4.4’
* 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 : : no visible global function definition
  for ‘dmvnorm’
kTSPclassifier,DataFrame : : no visible global function
  definition for ‘Pairs’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘measurement’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘..density..’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘legends grouping’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘key’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘value’
plotFeatureClasses,DataFrame : : no visible binding for
  global variable ‘ID’
rankingPlot,list :  : : no visible global
  function definition for ‘first’
rankingPlot,list :  : : no visible global
  function definition for ‘second’
rankingPlot,list :  :  : : no visible
  global function definition for ‘first’
rankingPlot,list :  :  : : 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 :  : : no visible global
  function definition for ‘first’
selectionPlot,list :  : : no visible global
  function definition for ‘second’
selectionPlot,list :  :  : : no
  visible global function definition for ‘first’
selectionPlot,list :  :  : : 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     99.954  2.861  28.061
fisherDiscriminant       32.544  1.397   0.106
elasticNetGLMinterface   32.040  1.512  14.469
distribution             14.983  1.912   8.115
samplesMetricMap         14.243  1.203   4.369
DMDselection              6.098  0.188   6.288
likelihoodRatioSelection  5.055  0.016   5.082
runTests                  1.283  0.267   5.951
elasticNetFeatures        0.999  0.172  12.671
* 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-3.9-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ClassifyR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ClassifyR’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ClassifyR)

name	user	system	elapsed
ClassifyResult-class	99.954	2.861	28.061
DLDAinterface	0.090	0.004	0.094
DMDselection	6.098	0.188	6.288
FeatureSetCollection-class	0.005	0.000	0.005
FeatureSetCollectionOrNULL-class	0.002	0.000	0.002
KolmogorovSmirnovSelection	1.807	0.103	1.909
KullbackLeiblerSelection	1.456	0.012	1.482
MixModelsListsSet-class	0.309	0.008	0.364
NSCpredictInterface	0.124	0.004	0.144
NSCselectionInterface	0.110	0.004	0.114
NSCtrainInterface	0.097	0.000	0.097
PredictParams-class	0.004	0.000	0.003
ROCplot	1.048	0.000	1.048
ResubstituteParams-class	0.000	0.003	0.003
SVMinterface	0.082	0.000	0.083
SelectParams-class	0.011	0.004	0.014
SelectResult-class	0.001	0.000	0.001
TrainParams-class	0.001	0.000	0.001
TransformParams-class	0.000	0.002	0.002
bartlettSelection	1.887	0.012	1.900
calcPerformance	0.005	0.000	0.004
characterOrDataFrame-class	0.012	0.000	0.012
classifyInterface	0.994	0.036	1.326
differentMeansSelection	1.540	0.016	1.556
distribution	14.983	1.912	8.115
edgeRselection	4.093	0.080	4.210
edgesToHubNetworks	0.003	0.000	0.002
elasticNetFeatures	0.999	0.172	12.671
elasticNetGLMinterface	32.040	1.512	14.469
featureSetSummary	0.006	0.000	0.006
fisherDiscriminant	32.544	1.397	0.106
forestFeatures	0.152	0.019	0.171
functionOrList-class	0.007	0.002	0.009
functionOrNULL-class	0.001	0.004	0.004
getLocationsAndScales	0.040	0.004	0.044
integerOrNumeric-class	0.017	0.000	0.018
interactorDifferences	0.053	0.000	0.053
kTSPclassifier	0.115	0.004	0.119
knnInterface	0.040	0.004	0.044
leveneSelection	1.179	0.024	1.203
likelihoodRatioSelection	5.055	0.016	5.082
limmaSelection	0.486	0.004	0.490
mixmodels	0.227	0.000	0.239
naiveBayesKernel	0.479	0.000	0.482
networkCorrelationsSelection	0.267	0.000	0.267
pairsDifferencesSelection	0.343	0.004	0.346
performancePlot	0.328	0.000	0.328
plotFeatureClasses	3.379	0.000	3.379
previousSelection	3.579	0.762	3.347
previousTrained	3.593	1.027	3.214
randomForestInterface	0.428	0.127	0.264
rankingPlot	2.907	0.312	3.102
runTest	0.725	0.004	0.735
runTests	1.283	0.267	5.951
samplesMetricMap	14.243	1.203	4.369
selectionPlot	3.359	0.293	3.520
subtractFromLocation	0.002	0.000	0.002