Multiple platform build/check report for BioC 3.22 - CHECK results for MLInterfaces on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4898
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4688
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4634
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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*

CHECK results for MLInterfaces on kjohnson3

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.

raw results

Summary

Package: MLInterfaces

Version: 1.89.2

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_1.89.2.tar.gz

StartedAt: 2025-10-23 20:53:24 -0400 (Thu, 23 Oct 2025)

EndedAt: 2025-10-23 20:54:54 -0400 (Thu, 23 Oct 2025)

EllapsedTime: 90.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: MLInterfaces.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.89.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MLInterfaces.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLInterfaces/DESCRIPTION’ ... OK
* this is package ‘MLInterfaces’ version ‘1.89.2’
* 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’ ‘ggvis’ ‘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 ‘plotlyOutput’
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
  ‘renderPlotly’
hclustWidget : <anonymous>: no visible global function definition for
  ‘ggplot’
hclustWidget : <anonymous>: no visible global function definition for
  ‘aes’
hclustWidget : <anonymous>: no visible binding for global variable
  ‘PC1’
hclustWidget : <anonymous>: no visible binding for global variable
  ‘PC2’
hclustWidget : <anonymous>: no visible binding for global variable
  ‘assigned’
hclustWidget : <anonymous>: no visible global function definition for
  ‘geom_point’
hclustWidget : <anonymous>: no visible global function definition for
  ‘ggplotly’
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:
  PC1 PC2 abstract actionButton aes annotation assigned br column div
  em exprs featureNames fluidPage fluidRow gbm geom_point ggplot
  ggplotly h1 htmlOutput isolate lookUp mainPanel mlbench.hypercube
  numericInput observe p pData plotOutput plotcp plotlyOutput points3d
  predict.gbm reactive renderPlot renderPlotly 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hclustWidget.Rd: ExpressionSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/MLInterfaces.Rcheck/00check.log’
for details.

Installation output

MLInterfaces.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MLInterfaces
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘MLInterfaces’ ...
** this is package ‘MLInterfaces’ version ‘1.89.2’
** 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)

Tests output

MLInterfaces.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 
  3.293   0.125   3.415

Example timings

MLInterfaces.Rcheck/MLInterfaces-Ex.timings

name	user	system	elapsed
MLearn-new	3.417	0.096	3.527
RAB	0.036	0.003	0.048
balKfold.xvspec	0.007	0.001	0.009
brennan_2013_tabS7exc	0.002	0.001	0.003
classifierOutput-class	1.013	0.005	1.032
clusteringOutput-class	0	0	0
confuMat-methods	0.092	0.002	0.095
confuTab	0.001	0.000	0.002
fs.absT	0.009	0.001	0.010
fsHistory	0.011	0.001	0.012
hclustWidget	0	0	0
learnerSchema-class	0	0	0
performance-analytics	0	0	0
planarPlot-methods	1.062	0.059	1.123
plspinHcube	0	0	0
predict.classifierOutput	0.000	0.001	0.000
projectLearnerToGrid	2.290	0.048	2.347
projectedLearner-class	0	0	0
raboostCont-class	0	0	0
varImpStruct-class	3.523	0.044	3.589
xvalLoop	0.000	0.001	0.000
xvalSpec	0.037	0.003	0.039