############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MLInterfaces.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MLInterfaces_1.86.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MLInterfaces.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MLInterfaces/DESCRIPTION’ ... OK * this is package ‘MLInterfaces’ version ‘1.86.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘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 : : no visible global function definition for ‘renderText’ hclustWidget : : no visible global function definition for ‘renderPlot’ hclustWidget : : no visible global function definition for ‘reactive’ hclustWidget : : no visible global function definition for ‘:=’ hclustWidget : : no visible binding for global variable ‘key’ hclustWidget : : no visible global function definition for ‘observe’ hclustWidget : : no visible global function definition for ‘isolate’ hclustWidget : : 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 : : no visible global function definition for ‘reactive’ mlearnWidget : : no visible global function definition for ‘renderText’ mlearnWidget : : no visible global function definition for ‘renderTable’ mlearnWidget : : no visible global function definition for ‘renderPlot’ mlearnWidget : : no visible global function definition for ‘annotation’ mlearnWidget : : no visible global function definition for ‘plotcp’ mlearnWidget : : no visible global function definition for ‘abstract’ mlearnWidget : : no visible global function definition for ‘featureNames’ mlearnWidget : : no visible global function definition for ‘observe’ mlearnWidget : : no visible global function definition for ‘isolate’ mlearnWidget : : 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 : : no visible global function definition for ‘reactive’ plspinDF : : no visible global function definition for ‘renderText’ plspinDF : : no visible global function definition for ‘scatterplot3js’ plspinDF : : no visible global function definition for ‘renderScatterplotThree’ plspinDF : : 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 : : no visible global function definition for ‘reactive’ plspinHcube : : no visible global function definition for ‘mlbench.hypercube’ plspinHcube : : no visible global function definition for ‘renderText’ plspinHcube : : no visible global function definition for ‘scatterplot3js’ plspinHcube : : no visible global function definition for ‘renderScatterplotThree’ plspinHcube : : 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 7.655 0.267 7.992 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/MLInterfaces.Rcheck/00check.log’ for details.