Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1289/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MLInterfaces 1.86.0 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the MLInterfaces package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MLInterfaces.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: MLInterfaces |
Version: 1.86.0 |
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 |
StartedAt: 2024-12-21 01:41:19 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 01:45:25 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 246.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MLInterfaces.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * 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 ... 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 : <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 10.597 0.288 10.939 projectLearnerToGrid 7.055 0.157 7.231 * 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.
MLInterfaces.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MLInterfaces ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘MLInterfaces’ ... ** 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 (MLInterfaces)
MLInterfaces.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 Attaching package: 'BiocGenerics' 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, aperm, 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, saveRDS, setdiff, 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:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: XML Loading required package: cluster > > test_check("MLInterfaces") [1] "k" [1] "k" [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 10.120 0.471 10.581
MLInterfaces.Rcheck/MLInterfaces-Ex.timings
name | user | system | elapsed | |
MLearn-new | 10.597 | 0.288 | 10.939 | |
RAB | 0.117 | 0.010 | 0.127 | |
balKfold.xvspec | 0.020 | 0.004 | 0.025 | |
brennan_2013_tabS7exc | 0.007 | 0.003 | 0.011 | |
classifierOutput-class | 2.346 | 0.020 | 2.371 | |
clusteringOutput-class | 0.000 | 0.001 | 0.000 | |
confuMat-methods | 0.301 | 0.011 | 0.314 | |
confuTab | 0.004 | 0.001 | 0.004 | |
fs.absT | 0.023 | 0.004 | 0.028 | |
fsHistory | 0.041 | 0.003 | 0.044 | |
hclustWidget | 0.000 | 0.000 | 0.001 | |
learnerSchema-class | 0.000 | 0.001 | 0.000 | |
performance-analytics | 0.002 | 0.001 | 0.002 | |
planarPlot-methods | 3.533 | 0.152 | 3.708 | |
plspinHcube | 0.000 | 0.000 | 0.001 | |
predict.classifierOutput | 0.001 | 0.000 | 0.000 | |
projectLearnerToGrid | 7.055 | 0.157 | 7.231 | |
projectedLearner-class | 0.001 | 0.000 | 0.001 | |
raboostCont-class | 0.001 | 0.000 | 0.001 | |
varImpStruct-class | 2.183 | 0.027 | 2.211 | |
xvalLoop | 0 | 0 | 0 | |
xvalSpec | 0.112 | 0.005 | 0.118 | |