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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MLInterfaces.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MLInterfaces_1.84.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/MLInterfaces.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MLInterfaces/DESCRIPTION' ... OK
* this is package 'MLInterfaces' version '1.84.0'
* 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 whether package 'MLInterfaces' 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 code 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 ... NOTE
Namespaces in Imports field not imported from:
  'gbm' 'mlbench' 'pls' 'shiny' 'stats4' 'threejs' 'tools'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'Biobase' 'BiocGenerics' 'Rcpp' 'annotate' 'cluster'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'MASS:::predict.lda' 'ada:::predict.ada' 'e1071:::predict.svm'
  'rpart:::predict.rpart' 'stats:::plot.hclust'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DAB: no visible global function definition for 'rpart'
RAB: no visible global function definition for 'rpart'
RAB4es: no visible global function definition for 'exprs'
es2df: no visible global function definition for 'exprs'
es2df: no visible global function definition for 'pData'
gbm2: no visible global function definition for 'gbm'
hclustWidget: no visible global function definition for 'shinyApp'
hclustWidget: no visible global function definition for 'fluidPage'
hclustWidget: no visible global function definition for 'fluidRow'
hclustWidget: no visible global function definition for 'column'
hclustWidget: no visible global function definition for 'textOutput'
hclustWidget: no visible binding for global variable 'h1'
hclustWidget: no visible global function definition for 'actionButton'
hclustWidget: no visible global function definition for 'numericInput'
hclustWidget: no visible global function definition for 'selectInput'
hclustWidget: no visible global function definition for 'plotOutput'
hclustWidget : <anonymous>: no visible global function definition for
  'renderText'
hclustWidget : <anonymous>: no visible global function definition for
  'renderPlot'
hclustWidget : <anonymous>: no visible global function definition for
  'reactive'
hclustWidget : <anonymous>: no visible global function definition for
  ':='
hclustWidget : <anonymous>: no visible binding for global variable
  'key'
hclustWidget : <anonymous>: no visible global function definition for
  'observe'
hclustWidget : <anonymous>: no visible global function definition for
  'isolate'
hclustWidget : <anonymous>: no visible global function definition for
  'stopApp'
mapPSvec: no visible global function definition for 'lookUp'
mlearnWidget: no visible global function definition for 'shinyApp'
mlearnWidget: no visible global function definition for 'fluidPage'
mlearnWidget: no visible global function definition for 'fluidRow'
mlearnWidget: no visible global function definition for 'column'
mlearnWidget: no visible global function definition for 'textOutput'
mlearnWidget: no visible binding for global variable 'h1'
mlearnWidget: no visible global function definition for 'actionButton'
mlearnWidget: no visible global function definition for 'selectInput'
mlearnWidget: no visible global function definition for 'numericInput'
mlearnWidget: no visible global function definition for 'htmlOutput'
mlearnWidget: no visible global function definition for 'tableOutput'
mlearnWidget: no visible global function definition for 'plotOutput'
mlearnWidget : <anonymous>: no visible global function definition for
  'reactive'
mlearnWidget : <anonymous>: no visible global function definition for
  'renderText'
mlearnWidget : <anonymous>: no visible global function definition for
  'renderTable'
mlearnWidget : <anonymous>: no visible global function definition for
  'renderPlot'
mlearnWidget : <anonymous>: no visible global function definition for
  'annotation'
mlearnWidget : <anonymous>: no visible global function definition for
  'plotcp'
mlearnWidget : <anonymous>: no visible global function definition for
  'abstract'
mlearnWidget : <anonymous>: no visible global function definition for
  'featureNames'
mlearnWidget : <anonymous>: no visible global function definition for
  'observe'
mlearnWidget : <anonymous>: no visible global function definition for
  'isolate'
mlearnWidget : <anonymous>: no visible global function definition for
  'stopApp'
planarPlot2: no visible global function definition for 'exprs'
plspinDF: no visible global function definition for 'shinyApp'
plspinDF: no visible global function definition for 'fluidPage'
plspinDF: no visible global function definition for 'fluidRow'
plspinDF: no visible global function definition for 'column'
plspinDF: no visible global function definition for 'textOutput'
plspinDF: no visible binding for global variable 'h1'
plspinDF: no visible global function definition for 'sidebarLayout'
plspinDF: no visible global function definition for 'sidebarPanel'
plspinDF: no visible global function definition for 'p'
plspinDF: no visible global function definition for 'strong'
plspinDF: no visible global function definition for 'div'
plspinDF: no visible global function definition for 'numericInput'
plspinDF: no visible global function definition for 'selectInput'
plspinDF: no visible global function definition for 'em'
plspinDF: no visible global function definition for 'br'
plspinDF: no visible global function definition for 'mainPanel'
plspinDF: no visible global function definition for
  'scatterplotThreeOutput'
plspinDF : <anonymous>: no visible global function definition for
  'reactive'
plspinDF : <anonymous>: no visible global function definition for
  'renderText'
plspinDF : <anonymous>: no visible global function definition for
  'scatterplot3js'
plspinDF : <anonymous>: no visible global function definition for
  'renderScatterplotThree'
plspinDF : <anonymous>: no visible global function definition for
  'points3d'
plspinHcube: no visible global function definition for 'shinyApp'
plspinHcube: no visible global function definition for 'fluidPage'
plspinHcube: no visible global function definition for 'fluidRow'
plspinHcube: no visible global function definition for 'column'
plspinHcube: no visible global function definition for 'textOutput'
plspinHcube: no visible binding for global variable 'h1'
plspinHcube: no visible global function definition for 'sidebarLayout'
plspinHcube: no visible global function definition for 'sidebarPanel'
plspinHcube: no visible global function definition for 'p'
plspinHcube: no visible global function definition for 'strong'
plspinHcube: no visible global function definition for 'div'
plspinHcube: no visible global function definition for 'numericInput'
plspinHcube: no visible global function definition for 'selectInput'
plspinHcube: no visible global function definition for 'em'
plspinHcube: no visible global function definition for 'br'
plspinHcube: no visible global function definition for 'mainPanel'
plspinHcube: no visible global function definition for
  'scatterplotThreeOutput'
plspinHcube : <anonymous>: no visible global function definition for
  'reactive'
plspinHcube : <anonymous>: no visible global function definition for
  'mlbench.hypercube'
plspinHcube : <anonymous>: no visible global function definition for
  'renderText'
plspinHcube : <anonymous>: no visible global function definition for
  'scatterplot3js'
plspinHcube : <anonymous>: no visible global function definition for
  'renderScatterplotThree'
plspinHcube : <anonymous>: no visible global function definition for
  'points3d'
predict.classifierOutput: no visible global function definition for
  'exprs'
predict.gbm2: no visible global function definition for 'predict.gbm'
rab: no visible global function definition for 'rpart'
getGrid,ExpressionSet: no visible global function definition for
  'exprs'
planarPlot,classifierOutput-ExpressionSet-character: no visible global
  function definition for 'exprs'
predScore,classifierOutput: no visible global function definition for
  'rowMax'
Undefined global functions or variables:
  := abstract actionButton annotation br column div em exprs
  featureNames fluidPage fluidRow gbm h1 htmlOutput isolate key lookUp
  mainPanel mlbench.hypercube numericInput observe p pData plotOutput
  plotcp points3d predict.gbm reactive renderPlot
  renderScatterplotThree renderTable renderText rowMax rpart
  scatterplot3js scatterplotThreeOutput selectInput shinyApp
  sidebarLayout sidebarPanel stopApp strong tableOutput textOutput
* checking Rd files ... NOTE
prepare_Rd: plspinHcube.Rd:17-19: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  'NULL_OR_list'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
MLearn-new           10.78   0.45   11.62
projectLearnerToGrid  5.21   0.20    5.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/MLInterfaces.Rcheck/00check.log'
for details.