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This page was generated on 2021-05-06 12:32:18 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the MLInterfaces package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1123/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MLInterfaces 1.70.0 (landing page) V. Carey
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MLInterfaces |
Version: 1.70.0 |
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLInterfaces.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MLInterfaces_1.70.0.tar.gz |
StartedAt: 2021-05-06 04:44:15 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 04:47:27 -0400 (Thu, 06 May 2021) |
EllapsedTime: 191.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MLInterfaces.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLInterfaces.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MLInterfaces_1.70.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MLInterfaces.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'MLInterfaces/DESCRIPTION' ... OK * this is package 'MLInterfaces' version '1.70.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: 'rda' * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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: 'fpc' 'gbm' 'ggvis' 'hwriter' '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 ... NOTE Found the following apparent S3 methods exported but not registered: predict.RAB predict.classifierOutput predict.dlda2 predict.gbm2 predict.knn.cv2 predict.knn2 predict.lvq predict.rdaML predict.rdacvML print.rdaML print.rdacvML See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * 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 'ggvisOutput' 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 'clusterboot' hclustWidget : <anonymous>: no visible binding for global variable 'hclustCBI' hclustWidget : <anonymous>: no visible global function definition for 'reactive' hclustWidget : <anonymous>: no visible global function definition for '%>%' hclustWidget : <anonymous>: no visible global function definition for 'ggvis' 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 'layer_points' hclustWidget : <anonymous>: no visible global function definition for 'add_tooltip' hclustWidget : <anonymous>: no visible global function definition for 'bind_shiny' 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> : totext: no visible global function definition for 'hwrite' mlearnWidget : <anonymous> : tize: no visible global function definition for 'hwrite' 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 'brewer.pal' 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 'brewer.pal' 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 '%>%' 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 'brewer.pal' 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 '%>%' 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 add_tooltip annotation bind_shiny br brewer.pal clusterboot column div em exprs featureNames fluidPage fluidRow gbm ggvis ggvisOutput h1 hclustCBI htmlOutput hwrite isolate key layer_points 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 ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MLearn-new 9.70 0.41 14.06 projectLearnerToGrid 6.41 0.18 8.42 planarPlot-methods 5.10 0.14 5.25 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MLearn-new 12.32 0.27 12.87 projectLearnerToGrid 6.77 0.18 7.09 planarPlot-methods 5.72 0.33 6.05 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * 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: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MLInterfaces.Rcheck/00check.log' for details.
MLInterfaces.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MLInterfaces_1.70.0.tar.gz && rm -rf MLInterfaces.buildbin-libdir && mkdir MLInterfaces.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MLInterfaces.buildbin-libdir MLInterfaces_1.70.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MLInterfaces_1.70.0.zip && rm MLInterfaces_1.70.0.tar.gz MLInterfaces_1.70.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 206k 100 206k 0 0 11.2M 0 --:--:-- --:--:-- --:--:-- 11.8M install for i386 * installing *source* package 'MLInterfaces' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MLInterfaces' finding HTML links ... done MLIntInternals html MLearn-new html RAB html balKfold.xvspec html classifierOutput-class html clusteringOutput-class html confuMat-methods html confuTab html fs.absT html fsHistory html hclustWidget html finding level-2 HTML links ... done learnerSchema-class html performance-analytics html planarPlot-methods html plspinHcube html predict.classifierOutput html projectLearnerToGrid html projectedLearner-class html raboostCont-class html varImpStruct-class html xvalLoop html xvalSpec html ** 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 install for x64 * installing *source* package 'MLInterfaces' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'MLInterfaces' as MLInterfaces_1.70.0.zip * DONE (MLInterfaces) * installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library' package 'MLInterfaces' successfully unpacked and MD5 sums checked
MLInterfaces.Rcheck/tests_i386/testthat.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("testthat") > library("MLInterfaces") Loading required package: Rcpp Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XML Loading required package: cluster > > test_check("MLInterfaces") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 3.76 0.29 4.04 |
MLInterfaces.Rcheck/tests_x64/testthat.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("testthat") > library("MLInterfaces") Loading required package: Rcpp Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XML Loading required package: cluster > > test_check("MLInterfaces") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 3.82 0.23 4.06 |
MLInterfaces.Rcheck/examples_i386/MLInterfaces-Ex.timings
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MLInterfaces.Rcheck/examples_x64/MLInterfaces-Ex.timings
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