Vincent Carey
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/MLInterfaces |
| git_branch: RELEASE_3_21 |
| git_last_commit: 4cddc2c |
| git_last_commit_date: 2025-05-08 12:28:54 -0400 (Thu, 08 May 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1317/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MLInterfaces 1.88.1 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.88.1 |
| 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_1.88.1.tar.gz |
| StartedAt: 2025-10-14 06:42:54 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 06:50:11 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 436.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MLInterfaces.Rcheck |
| Warnings: 1 |
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### Running command:
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### /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_1.88.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MLInterfaces.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* 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 ‘1.88.1’
* 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MLearn-new 17.760 0.613 19.859
projectLearnerToGrid 6.861 0.376 7.866
* 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-3.21-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/4.5-x86_64/Resources/library’ * installing *source* package ‘MLInterfaces’ ... ** this is package ‘MLInterfaces’ version ‘1.88.1’ ** 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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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
17.668 0.924 19.129
MLInterfaces.Rcheck/MLInterfaces-Ex.timings
| name | user | system | elapsed | |
| MLearn-new | 17.760 | 0.613 | 19.859 | |
| RAB | 0.206 | 0.015 | 0.240 | |
| balKfold.xvspec | 0.035 | 0.006 | 0.046 | |
| brennan_2013_tabS7exc | 0.014 | 0.012 | 0.027 | |
| classifierOutput-class | 2.809 | 0.048 | 3.054 | |
| clusteringOutput-class | 0.001 | 0.001 | 0.001 | |
| confuMat-methods | 0.309 | 0.023 | 0.353 | |
| confuTab | 0.006 | 0.001 | 0.008 | |
| fs.absT | 0.046 | 0.006 | 0.053 | |
| fsHistory | 0.090 | 0.005 | 0.100 | |
| hclustWidget | 0.001 | 0.001 | 0.002 | |
| learnerSchema-class | 0.000 | 0.001 | 0.001 | |
| performance-analytics | 0.004 | 0.002 | 0.005 | |
| planarPlot-methods | 3.376 | 0.339 | 3.997 | |
| plspinHcube | 0.000 | 0.001 | 0.001 | |
| predict.classifierOutput | 0.001 | 0.001 | 0.002 | |
| projectLearnerToGrid | 6.861 | 0.376 | 7.866 | |
| projectedLearner-class | 0.002 | 0.002 | 0.003 | |
| raboostCont-class | 0.002 | 0.000 | 0.003 | |
| varImpStruct-class | 2.230 | 0.059 | 2.439 | |
| xvalLoop | 0.001 | 0.002 | 0.003 | |
| xvalSpec | 0.219 | 0.010 | 0.244 | |