| Back to Rapid builds (Linux only) of a subset of BioC 3.23 Report updated every 6 hours |
This page was generated on 2025-11-14 10:17 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences" | 917 |
| 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 146/230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| MLInterfaces 1.91.0 (landing page) Vincent Carey
| teran2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
|
To the developers/maintainers of the MLInterfaces package: - 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: 1.91.0 |
| Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:MLInterfaces.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings MLInterfaces_1.91.0.tar.gz |
| StartedAt: 2025-11-14 09:05:05 -0500 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 09:08:48 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 223.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MLInterfaces.Rcheck |
| Warnings: 1 |
##############################################################################
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### Running command:
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### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:MLInterfaces.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings MLInterfaces_1.91.0.tar.gz
###
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##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/MLInterfaces.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MLInterfaces/DESCRIPTION’ ... OK
* this is package ‘MLInterfaces’ version ‘1.91.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Vincent Carey <stvjc@channing.harvard.edu>’
Unknown, possibly misspelled, fields in DESCRIPTION:
‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’
The Title field should be in title case. Current version is:
‘Uniform interfaces to R machine learning procedures for data in Bioconductor containers’
In title case that is:
‘Uniform Interfaces to R Machine Learning Procedures for Data in Bioconductor Containers’
The Description field should not start with the package name,
'This package' or similar.
Found the following URLs which should use \doi (with the DOI name only):
File ‘brennan_2013_tabS7exc.Rd’:
https://doi.org/10.1016/j.cell.2013.09.034
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘ggvis’ ‘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’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MLearn-new 6.948 0.224 7.300
varImpStruct-class 6.367 0.161 6.648
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 6 NOTEs
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/MLInterfaces.Rcheck/00check.log’
for details.
MLInterfaces.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL MLInterfaces ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’ * installing *source* package ‘MLInterfaces’ ... ** this is package ‘MLInterfaces’ version ‘1.91.0’ ** 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 Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
6.485 0.466 6.936
MLInterfaces.Rcheck/MLInterfaces-Ex.timings
| name | user | system | elapsed | |
| MLearn-new | 6.948 | 0.224 | 7.300 | |
| RAB | 0.066 | 0.001 | 0.068 | |
| balKfold.xvspec | 0.014 | 0.000 | 0.014 | |
| brennan_2013_tabS7exc | 0.004 | 0.001 | 0.004 | |
| classifierOutput-class | 1.189 | 0.006 | 1.195 | |
| clusteringOutput-class | 0.001 | 0.000 | 0.000 | |
| confuMat-methods | 0.143 | 0.011 | 0.156 | |
| confuTab | 0.003 | 0.000 | 0.003 | |
| fs.absT | 0.018 | 0.002 | 0.020 | |
| fsHistory | 0.027 | 0.001 | 0.029 | |
| hclustWidget | 0 | 0 | 0 | |
| learnerSchema-class | 0 | 0 | 0 | |
| performance-analytics | 0.001 | 0.000 | 0.002 | |
| planarPlot-methods | 1.809 | 0.082 | 1.891 | |
| plspinHcube | 0 | 0 | 0 | |
| predict.classifierOutput | 0 | 0 | 0 | |
| projectLearnerToGrid | 2.746 | 0.077 | 2.832 | |
| projectedLearner-class | 0.000 | 0.000 | 0.001 | |
| raboostCont-class | 0.000 | 0.001 | 0.001 | |
| varImpStruct-class | 6.367 | 0.161 | 6.648 | |
| xvalLoop | 0 | 0 | 0 | |
| xvalSpec | 0.077 | 0.005 | 0.083 | |