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This page was generated on 2022-04-13 12:07:14 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for Rmagpie on tokay2


To the developers/maintainers of the Rmagpie package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rmagpie.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1620/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rmagpie 1.50.0  (landing page)
Camille Maumet
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/Rmagpie
git_branch: RELEASE_3_14
git_last_commit: e8a3cac
git_last_commit_date: 2021-10-26 11:53:55 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: Rmagpie
Version: 1.50.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rmagpie.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rmagpie_1.50.0.tar.gz
StartedAt: 2022-04-13 01:47:22 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:49:36 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 133.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Rmagpie.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rmagpie.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rmagpie_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Rmagpie.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rmagpie/DESCRIPTION' ... OK
* this is package 'Rmagpie' version '1.50.0'
* 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 'Rmagpie' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
twoLayerExtCV: warning in performAValidation(data = eset, trainIndices
  = extInds[[i]], noGenes = upToBestSelectedFeature, classes = classes,
  classifierName = classifierName, verbose = verbose, kernel = kernel,
  featureSelectionFun = featureSelectionFun, trainTestFun =
  trainTestFun): partial argument match of 'data' to 'dataset'
getFeatureSelectionOptions<-,assessment: no visible global function
  definition for 'getNoOfOptions<-'
getFeatureSelectionOptions<-,assessment: no visible global function
  definition for 'getNoModels<-'
Undefined global functions or variables:
  getNoModels<- getNoOfOptions<-
* checking Rd files ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
runTwoLayerExtCV-methods 5.99   0.02       6
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
runTwoLayerExtCV-methods 6.79      0     6.8
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/Rmagpie.Rcheck/00check.log'
for details.



Installation output

Rmagpie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Rmagpie_1.50.0.tar.gz && rm -rf Rmagpie.buildbin-libdir && mkdir Rmagpie.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rmagpie.buildbin-libdir Rmagpie_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Rmagpie_1.50.0.zip && rm Rmagpie_1.50.0.tar.gz Rmagpie_1.50.0.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  140k  100  140k    0     0   530k      0 --:--:-- --:--:-- --:--:--  532k

install for i386

* installing *source* package 'Rmagpie' ...
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rmagpie'
    finding HTML links ... done
    classifyNewSamples-methods              html  
    experiment-class                        html  
    featureSelectionOptions-class           html  
    finalClassifier-class                   html  
    findFinalClassifier-methods             html  
    geneSubsets-class                       html  
    getDataset-methods                      html  
    getFeatureSelectionOptions-methods      html  
    getFinalClassifier                      html  
    getResults-methods                      html  
    initialize-methods                      html  
    plotErrorsFoldTwoLayerCV-methods        html  
    plotErrorsRepeatedOneLayerCV            html  
    plotErrorsSummaryOneLayerCV-methods     html  
    rankedGenesImg-methods                  html  
    runOneLayerExtCV-methods                html  
    runTwoLayerExtCV-methods                html  
    setDataset-methods                      html  
    setFeatureSelectionOptions-methods      html  
    show-methods                            html  
    thresholds-class                        html  
    vV70genes                               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 'Rmagpie' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rmagpie' as Rmagpie_1.50.0.zip
* DONE (Rmagpie)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Rmagpie' successfully unpacked and MD5 sums checked

Tests output


Example timings

Rmagpie.Rcheck/examples_i386/Rmagpie-Ex.timings

nameusersystemelapsed
classifyNewSamples-methods1.300.121.42
experiment-class0.060.000.06
finalClassifier-class0.090.010.11
findFinalClassifier-methods0.140.000.14
geneSubsets-class0.020.000.02
getDataset-methods0.010.000.01
getFeatureSelectionOptions-methods0.020.000.02
getFinalClassifier0.110.020.13
getResults-methods3.470.003.46
plotErrorsFoldTwoLayerCV-methods3.710.003.72
plotErrorsRepeatedOneLayerCV0.720.000.72
plotErrorsSummaryOneLayerCV-methods0.630.000.63
rankedGenesImg-methods000
runOneLayerExtCV-methods0.500.010.51
runTwoLayerExtCV-methods5.990.026.00
setDataset-methods000
setFeatureSelectionOptions-methods0.010.000.01
thresholds-class000
vV70genes000

Rmagpie.Rcheck/examples_x64/Rmagpie-Ex.timings

nameusersystemelapsed
classifyNewSamples-methods1.120.031.16
experiment-class0.060.000.07
finalClassifier-class0.050.000.05
findFinalClassifier-methods0.090.000.09
geneSubsets-class000
getDataset-methods000
getFeatureSelectionOptions-methods000
getFinalClassifier0.080.020.10
getResults-methods3.630.003.62
plotErrorsFoldTwoLayerCV-methods3.790.013.81
plotErrorsRepeatedOneLayerCV0.600.020.61
plotErrorsSummaryOneLayerCV-methods0.580.000.58
rankedGenesImg-methods000
runOneLayerExtCV-methods0.50.00.5
runTwoLayerExtCV-methods6.790.006.80
setDataset-methods000
setFeatureSelectionOptions-methods000
thresholds-class000
vV70genes0.000.020.01