Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:06:43 -0400 (Fri, 15 Oct 2021).

CHECK results for MLInterfaces on machv2

To the developers/maintainers of the MLInterfaces package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1162/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLInterfaces 1.72.0  (landing page)
V. Carey
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MLInterfaces
git_branch: RELEASE_3_13
git_last_commit: a48dad8
git_last_commit_date: 2021-05-19 11:34:43 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MLInterfaces
Version: 1.72.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MLInterfaces.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MLInterfaces_1.72.0.tar.gz
StartedAt: 2021-10-14 21:16:21 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 21:19:19 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 177.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MLInterfaces.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MLInterfaces.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MLInterfaces_1.72.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MLInterfaces.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLInterfaces/DESCRIPTION’ ... OK
* this is package ‘MLInterfaces’ version ‘1.72.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  predict.RAB predict.classifierOutput predict.dlda2 predict.gbm2
  predict.knn.cv2 predict.knn2 predict.lvq
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 14.979  1.673  15.342
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/MLInterfaces.Rcheck/00check.log’
for details.



Installation output

MLInterfaces.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘MLInterfaces’ ...
** using staged installation
** R
** 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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: XML
Loading required package: cluster
> 
> test_check("MLInterfaces")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  6.379   0.372   6.735 

Example timings

MLInterfaces.Rcheck/MLInterfaces-Ex.timings

nameusersystemelapsed
MLearn-new14.979 1.67315.342
RAB0.1840.0170.203
balKfold.xvspec0.0230.0040.026
classifierOutput-class2.6740.4301.963
clusteringOutput-class0.0010.0010.001
confuMat-methods0.3480.0300.379
confuTab0.0040.0010.006
fs.absT0.0460.0080.053
fsHistory0.1130.0950.140
hclustWidget0.0000.0020.002
learnerSchema-class0.0010.0010.001
performance-analytics0.0030.0040.007
planarPlot-methods3.7650.3564.125
plspinHcube0.0010.0000.000
predict.classifierOutput0.0000.0000.001
projectLearnerToGrid4.6310.2514.897
projectedLearner-class0.0010.0010.002
raboostCont-class0.0010.0010.001
varImpStruct-class1.7470.0361.790
xvalLoop0.0000.0010.001
xvalSpec0.3150.2820.360