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CHECK report for Rmagpie on tokay2

This page was generated on 2018-10-17 08:34:16 -0400 (Wed, 17 Oct 2018).

Package 1251/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rmagpie 1.36.0
Camille Maumet
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Rmagpie
Branch: RELEASE_3_7
Last Commit: 957c795
Last Changed Date: 2018-04-30 10:35:11 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rmagpie
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rmagpie.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Rmagpie_1.36.0.tar.gz
StartedAt: 2018-10-17 04:27:50 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:30:07 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 137.0 seconds
RetCode: 0
Status:  OK  
CheckDir: Rmagpie.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rmagpie.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Rmagpie_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Rmagpie.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.36.0'
* 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 or elapsed time > 5s
                         user system elapsed
runTwoLayerExtCV-methods 5.94      0    5.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
runTwoLayerExtCV-methods         8.21   0.00    8.20
getResults-methods               5.64   0.01    5.66
plotErrorsFoldTwoLayerCV-methods 5.44   0.02    5.45
* 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-3.7-bioc/meat/Rmagpie.Rcheck/00check.log'
for details.



Installation output

Rmagpie.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Rmagpie_1.36.0.tar.gz && rm -rf Rmagpie.buildbin-libdir && mkdir Rmagpie.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rmagpie.buildbin-libdir Rmagpie_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Rmagpie_1.36.0.zip && rm Rmagpie_1.36.0.tar.gz Rmagpie_1.36.0.zip
###
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  % 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  141k  100  141k    0     0  2771k      0 --:--:-- --:--:-- --:--:-- 3223k

install for i386

* installing *source* package 'Rmagpie' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'Rmagpie' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rmagpie' as Rmagpie_1.36.0.zip
* DONE (Rmagpie)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Rmagpie' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

Rmagpie.Rcheck/examples_i386/Rmagpie-Ex.timings

nameusersystemelapsed
classifyNewSamples-methods1.220.101.31
experiment-class0.070.000.06
finalClassifier-class0.040.010.07
findFinalClassifier-methods0.100.000.09
geneSubsets-class0.010.000.01
getDataset-methods000
getFeatureSelectionOptions-methods0.020.000.02
getFinalClassifier0.160.030.19
getResults-methods3.590.023.61
plotErrorsFoldTwoLayerCV-methods3.560.003.58
plotErrorsRepeatedOneLayerCV0.720.000.71
plotErrorsSummaryOneLayerCV-methods0.560.010.58
rankedGenesImg-methods000
runOneLayerExtCV-methods0.500.020.52
runTwoLayerExtCV-methods5.940.005.94
setDataset-methods000
setFeatureSelectionOptions-methods0.020.000.01
thresholds-class000
vV70genes0.010.000.02

Rmagpie.Rcheck/examples_x64/Rmagpie-Ex.timings

nameusersystemelapsed
classifyNewSamples-methods1.640.011.66
experiment-class0.110.020.12
finalClassifier-class0.110.000.11
findFinalClassifier-methods0.120.010.14
geneSubsets-class000
getDataset-methods000
getFeatureSelectionOptions-methods0.000.020.02
getFinalClassifier0.140.050.18
getResults-methods5.640.015.66
plotErrorsFoldTwoLayerCV-methods5.440.025.45
plotErrorsRepeatedOneLayerCV1.080.011.10
plotErrorsSummaryOneLayerCV-methods1.070.001.08
rankedGenesImg-methods000
runOneLayerExtCV-methods0.980.000.99
runTwoLayerExtCV-methods8.210.008.20
setDataset-methods000
setFeatureSelectionOptions-methods0.010.000.01
thresholds-class000
vV70genes0.020.000.02