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This page was generated on 2024-02-22 11:36:59 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 1285/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLInterfaces 1.82.0  (landing page)
Vincent Carey
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/MLInterfaces
git_branch: RELEASE_3_18
git_last_commit: 597f246
git_last_commit_date: 2023-10-24 09:33:54 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for MLInterfaces on palomino4


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: 1.82.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MLInterfaces.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings MLInterfaces_1.82.0.tar.gz
StartedAt: 2024-02-22 03:53:17 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 03:56:45 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 208.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MLInterfaces.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MLInterfaces.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings MLInterfaces_1.82.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/MLInterfaces.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MLInterfaces/DESCRIPTION' ... OK
* this is package 'MLInterfaces' version '1.82.0'
* 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 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
* 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 8.57   0.47    9.37
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 1 WARNING, 3 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/MLInterfaces.Rcheck/00check.log'
for details.



Installation output

MLInterfaces.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL MLInterfaces
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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)

Tests output

MLInterfaces.Rcheck/tests/testthat.Rout


R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 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

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, 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:utils':

    findMatches

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

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 
   8.56    0.56    9.06 

Example timings

MLInterfaces.Rcheck/MLInterfaces-Ex.timings

nameusersystemelapsed
MLearn-new8.570.479.37
RAB0.140.030.18
balKfold.xvspec0.030.020.05
brennan_2013_tabS7exc0.020.000.01
classifierOutput-class1.780.041.83
clusteringOutput-class000
confuMat-methods0.170.040.20
confuTab000
fs.absT0.000.020.02
fsHistory0.780.000.78
hclustWidget000
learnerSchema-class000
performance-analytics000
planarPlot-methods2.710.082.78
plspinHcube000
predict.classifierOutput000
projectLearnerToGrid3.560.063.67
projectedLearner-class000
raboostCont-class000
varImpStruct-class1.390.031.47
xvalLoop000
xvalSpec0.140.000.14