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CHECK report for MLInterfaces on tokay2

This page was generated on 2020-10-17 11:57:10 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MLInterfaces PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1106/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLInterfaces 1.68.0
V. Carey
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MLInterfaces
Branch: RELEASE_3_11
Last Commit: 4f3493e
Last Changed Date: 2020-04-27 14:10:11 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MLInterfaces
Version: 1.68.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLInterfaces.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MLInterfaces_1.68.0.tar.gz
StartedAt: 2020-10-17 06:09:54 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:13:26 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 212.0 seconds
RetCode: 0
Status:  OK  
CheckDir: MLInterfaces.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLInterfaces.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MLInterfaces_1.68.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MLInterfaces.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MLInterfaces/DESCRIPTION' ... OK
* this is package 'MLInterfaces' version '1.68.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'rda'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'fpc' 'gbm' 'ggvis' 'hwriter' '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 predict.rdaML
  predict.rdacvML print.rdaML print.rdacvML
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: no visible global function definition for 'ggvisOutput'
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
  'clusterboot'
hclustWidget : <anonymous>: no visible binding for global variable
  'hclustCBI'
hclustWidget : <anonymous>: no visible global function definition for
  'reactive'
hclustWidget : <anonymous>: no visible global function definition for
  '%>%'
hclustWidget : <anonymous>: no visible global function definition for
  'ggvis'
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
  'layer_points'
hclustWidget : <anonymous>: no visible global function definition for
  'add_tooltip'
hclustWidget : <anonymous>: no visible global function definition for
  'bind_shiny'
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> : totext: no visible global function
  definition for 'hwrite'
mlearnWidget : <anonymous> : tize: no visible global function
  definition for 'hwrite'
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 'brewer.pal'
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
  'brewer.pal'
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 '%>%'
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
  'brewer.pal'
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
  '%>%'
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 add_tooltip annotation bind_shiny br
  brewer.pal clusterboot column div em exprs featureNames fluidPage
  fluidRow gbm ggvis ggvisOutput h1 hclustCBI htmlOutput hwrite isolate
  key layer_points 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
MLearn-new           14.35   0.75   16.49
projectLearnerToGrid  6.95   0.14    8.64
planarPlot-methods    5.96   0.22    6.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
MLearn-new           9.87   0.33   10.42
projectLearnerToGrid 5.45   0.11    6.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/MLInterfaces.Rcheck/00check.log'
for details.



Installation output

MLInterfaces.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MLInterfaces_1.68.0.tar.gz && rm -rf MLInterfaces.buildbin-libdir && mkdir MLInterfaces.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MLInterfaces.buildbin-libdir MLInterfaces_1.68.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MLInterfaces_1.68.0.zip && rm MLInterfaces_1.68.0.tar.gz MLInterfaces_1.68.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  206k  100  206k    0     0  1137k      0 --:--:-- --:--:-- --:--:-- 1175k

install for i386

* installing *source* package 'MLInterfaces' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MLInterfaces'
    finding HTML links ... done
    MLIntInternals                          html  
    MLearn-new                              html  
    RAB                                     html  
    balKfold.xvspec                         html  
    classifierOutput-class                  html  
    clusteringOutput-class                  html  
    confuMat-methods                        html  
    confuTab                                html  
    fs.absT                                 html  
    fsHistory                               html  
    hclustWidget                            html  
    finding level-2 HTML links ... done

    learnerSchema-class                     html  
    performance-analytics                   html  
    planarPlot-methods                      html  
    plspinHcube                             html  
    predict.classifierOutput                html  
    projectLearnerToGrid                    html  
    projectedLearner-class                  html  
    raboostCont-class                       html  
    varImpStruct-class                      html  
    xvalLoop                                html  
    xvalSpec                                html  
** 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

install for x64

* installing *source* package 'MLInterfaces' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MLInterfaces' as MLInterfaces_1.68.0.zip
* DONE (MLInterfaces)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MLInterfaces' successfully unpacked and MD5 sums checked

Tests output

MLInterfaces.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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:base':

    expand.grid


Attaching package: 'IRanges'

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

    windows

Loading required package: XML
Loading required package: cluster
> 
> test_check("MLInterfaces")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   4.67    0.39    5.04 

MLInterfaces.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
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, 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:base':

    expand.grid


Attaching package: 'IRanges'

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

    windows

Loading required package: XML
Loading required package: cluster
> 
> test_check("MLInterfaces")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   5.04    0.40    5.59 

Example timings

MLInterfaces.Rcheck/examples_i386/MLInterfaces-Ex.timings

nameusersystemelapsed
MLearn-new14.35 0.7516.49
RAB0.160.030.19
balKfold.xvspec0.050.000.04
classifierOutput-class3.160.013.17
clusteringOutput-class0.010.000.02
confuMat-methods0.420.000.50
confuTab0.020.000.02
fs.absT0.050.000.04
fsHistory0.070.000.08
hclustWidget000
learnerSchema-class000
performance-analytics000
planarPlot-methods5.960.226.59
plspinHcube000
predict.classifierOutput000
projectLearnerToGrid6.950.148.64
projectedLearner-class000
raboostCont-class000
varImpStruct-class2.250.052.30
xvalLoop000
xvalSpec0.230.000.23

MLInterfaces.Rcheck/examples_x64/MLInterfaces-Ex.timings

nameusersystemelapsed
MLearn-new 9.87 0.3310.42
RAB0.100.010.11
balKfold.xvspec0.020.000.01
classifierOutput-class2.020.022.03
clusteringOutput-class000
confuMat-methods0.200.010.22
confuTab000
fs.absT0.030.000.03
fsHistory0.050.000.04
hclustWidget000
learnerSchema-class000
performance-analytics000
planarPlot-methods4.130.054.17
plspinHcube000
predict.classifierOutput000
projectLearnerToGrid5.450.116.11
projectedLearner-class000
raboostCont-class000
varImpStruct-class1.610.011.63
xvalLoop000
xvalSpec0.270.000.26