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CHECK report for geneClassifiers on riesling1

This page was generated on 2021-01-25 12:39:22 -0500 (Mon, 25 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE geneClassifiers PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 675/1938HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneClassifiers 1.15.0
R Kuiper
Snapshot Date: 2021-01-24 14:40:26 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/geneClassifiers
Branch: master
Last Commit: 2b79514
Last Changed Date: 2020-10-27 11:21:25 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 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
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geneClassifiers
Version: 1.15.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneClassifiers.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings geneClassifiers_1.15.0.tar.gz
StartedAt: 2021-01-24 20:30:45 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 20:31:32 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 47.2 seconds
RetCode: 0
Status:  OK  
CheckDir: geneClassifiers.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneClassifiers.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings geneClassifiers_1.15.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-bioc/meat/geneClassifiers.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneClassifiers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geneClassifiers' version '1.15.0'
* package encoding: UTF-8
* 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 'geneClassifiers' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: OK


Installation output

geneClassifiers.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/bioc/src/contrib/geneClassifiers_1.15.0.tar.gz && rm -rf geneClassifiers.buildbin-libdir && mkdir geneClassifiers.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneClassifiers.buildbin-libdir geneClassifiers_1.15.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL geneClassifiers_1.15.0.zip && rm geneClassifiers_1.15.0.tar.gz geneClassifiers_1.15.0.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 1281k  100 1281k    0     0  44.6M      0 --:--:-- --:--:-- --:--:-- 44.6M

install for i386

* installing *source* package 'geneClassifiers' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geneClassifiers'
    finding HTML links ... done
    ClassifierParameters                    html  
REDIRECT:topic	 ClassifierParameters -> ClassifierParameters.html [ SUCCESS ]
    ClassifierResults                       html  
REDIRECT:topic	 ClassifierResults -> ClassifierResults.html [ SUCCESS ]
    FixedExpressionData                     html  
REDIRECT:topic	 FixedExpressionData -> FixedExpressionData.html [ SUCCESS ]
    bracket-methods                         html  
REDIRECT:topic	 [,FixedExpressionData,ANY,ANY-method -> bracket-methods.html [ SUCCESS ]
REDIRECT:topic	 [,FixedExpressionData,ANY,missing-method -> bracket-methods.html [ SUCCESS ]
REDIRECT:topic	 bracket,FixedExpressionData-method -> bracket-methods.html [ SUCCESS ]
REDIRECT:topic	 [,FixedExpressionData,missing,ANY-method -> bracket-methods.html [ SUCCESS ]
REDIRECT:topic	 [[,FixedExpressionData,ANY,missing-method -> bracket-methods.html [ SUCCESS ]
REDIRECT:topic	 [[,FixedExpressionData,missing,ANY-method -> bracket-methods.html [ SUCCESS ]
REDIRECT:topic	 [[,FixedExpressionData,ANY,ANY-method -> bracket-methods.html [ SUCCESS ]
REDIRECT:file	 bracket-methods.html -> bracket-methods.html [ SUCCESS ]
    dim-methods                             html  
REDIRECT:topic	 dim,FixedExpressionData-method -> dim-methods.html [ SUCCESS ]
REDIRECT:file	 dim-methods.html -> dim-methods.html [ SUCCESS ]
    exampleMAS5                             html  
REDIRECT:topic	 exampleMAS5 -> exampleMAS5.html [ SUCCESS ]
    finding level-2 HTML links ... done

    geneClassifiers-package                 html  
REDIRECT:topic	 geneClassifiers -> geneClassifiers-package.html [ SUCCESS ]
REDIRECT:topic	 geneClassifiers-package -> geneClassifiers-package.html [ SUCCESS ]
    getBatchCorrection-methods              html  
REDIRECT:topic	 getBatchCorrection -> getBatchCorrection-methods.html [ SUCCESS ]
REDIRECT:topic	 getBatchCorrection,ClassifierResults-method -> getBatchCorrection-methods.html [ SUCCESS ]
REDIRECT:file	 getBatchCorrection-methods.html -> getBatchCorrection-methods.html [ SUCCESS ]
    getCitations-methods                    html  
REDIRECT:topic	 getCitations -> getCitations-methods.html [ SUCCESS ]
REDIRECT:topic	 getCitations,ClassifierParameters-method -> getCitations-methods.html [ SUCCESS ]
REDIRECT:file	 getCitations-methods.html -> getCitations-methods.html [ SUCCESS ]
    getClassifications-methods              html  
REDIRECT:topic	 getClassifications -> getClassifications-methods.html [ SUCCESS ]
REDIRECT:topic	 getClassifications,ClassifierResults-method -> getClassifications-methods.html [ SUCCESS ]
REDIRECT:file	 getClassifications-methods.html -> getClassifications-methods.html [ SUCCESS ]
    getClassifier-methods                   html  
REDIRECT:topic	 getClassifier -> getClassifier-methods.html [ SUCCESS ]
REDIRECT:topic	 getClassifier,ClassifierResults-method -> getClassifier-methods.html [ SUCCESS ]
REDIRECT:topic	 getClassifier,character-method -> getClassifier-methods.html [ SUCCESS ]
REDIRECT:file	 getClassifier-methods.html -> getClassifier-methods.html [ SUCCESS ]
    getDecisionBoundaries-methods           html  
REDIRECT:topic	 getDecisionBoundaries -> getDecisionBoundaries-methods.html [ SUCCESS ]
REDIRECT:topic	 getDecisionBoundaries,ClassifierParameters-method -> getDecisionBoundaries-methods.html [ SUCCESS ]
REDIRECT:file	 getDecisionBoundaries-methods.html -> getDecisionBoundaries-methods.html [ SUCCESS ]
    getDescription-methods                  html  
REDIRECT:topic	 getDescription -> getDescription-methods.html [ SUCCESS ]
REDIRECT:topic	 getDescription,ClassifierParameters-method -> getDescription-methods.html [ SUCCESS ]
REDIRECT:file	 getDescription-methods.html -> getDescription-methods.html [ SUCCESS ]
    getEventChain-methods                   html  
REDIRECT:topic	 getEventChain -> getEventChain-methods.html [ SUCCESS ]
REDIRECT:topic	 getEventChain,ClassifierParameters-method -> getEventChain-methods.html [ SUCCESS ]
REDIRECT:file	 getEventChain-methods.html -> getEventChain-methods.html [ SUCCESS ]
    getIntercept-methods                    html  
REDIRECT:topic	 getIntercept -> getIntercept-methods.html [ SUCCESS ]
REDIRECT:topic	 getIntercept,ClassifierParameters-method -> getIntercept-methods.html [ SUCCESS ]
REDIRECT:file	 getIntercept-methods.html -> getIntercept-methods.html [ SUCCESS ]
    getMeans-methods                        html  
REDIRECT:topic	 getMeans -> getMeans-methods.html [ SUCCESS ]
REDIRECT:topic	 getMeans,ClassifierParameters-method -> getMeans-methods.html [ SUCCESS ]
REDIRECT:file	 getMeans-methods.html -> getMeans-methods.html [ SUCCESS ]
    getName-methods                         html  
REDIRECT:topic	 getName -> getName-methods.html [ SUCCESS ]
REDIRECT:topic	 getName,TransformationProcess-method -> getName-methods.html [ SUCCESS ]
REDIRECT:topic	 getName,ClassifierParameters-method -> getName-methods.html [ SUCCESS ]
REDIRECT:topic	 getName,ClassifierResults-method -> getName-methods.html [ SUCCESS ]
REDIRECT:file	 getName-methods.html -> getName-methods.html [ SUCCESS ]
    getNormalizationMethod-methods          html  
REDIRECT:topic	 getNormalizationMethod -> getNormalizationMethod-methods.html [ SUCCESS ]
REDIRECT:topic	 getNormalizationMethods -> getNormalizationMethod-methods.html [ SUCCESS ]
REDIRECT:topic	 getNormalizationMethod,FixedExpressionData-method -> getNormalizationMethod-methods.html [ SUCCESS ]
REDIRECT:topic	 getNormalizationMethod,ClassifierParameters-method -> getNormalizationMethod-methods.html [ SUCCESS ]
REDIRECT:file	 getNormalizationMethod-methods.html -> getNormalizationMethod-methods.html [ SUCCESS ]
    getProbeNames-methods                   html  
REDIRECT:topic	 getProbeNames -> getProbeNames-methods.html [ SUCCESS ]
REDIRECT:topic	 getProbeNames,ClassifierParameters-method -> getProbeNames-methods.html [ SUCCESS ]
REDIRECT:file	 getProbeNames-methods.html -> getProbeNames-methods.html [ SUCCESS ]
    getScores-methods                       html  
REDIRECT:topic	 getScores -> getScores-methods.html [ SUCCESS ]
REDIRECT:topic	 getScores,ClassifierResults-method -> getScores-methods.html [ SUCCESS ]
REDIRECT:file	 getScores-methods.html -> getScores-methods.html [ SUCCESS ]
    getSds-methods                          html  
REDIRECT:topic	 getSds -> getSds-methods.html [ SUCCESS ]
REDIRECT:topic	 getSds,ClassifierParameters-method -> getSds-methods.html [ SUCCESS ]
REDIRECT:file	 getSds-methods.html -> getSds-methods.html [ SUCCESS ]
    getTargetValue-methods                  html  
REDIRECT:topic	 getTargetValue -> getTargetValue-methods.html [ SUCCESS ]
REDIRECT:topic	 getTargetValue,FixedExpressionData-method -> getTargetValue-methods.html [ SUCCESS ]
REDIRECT:file	 getTargetValue-methods.html -> getTargetValue-methods.html [ SUCCESS ]
    getTrainingData-methods                 html  
REDIRECT:topic	 getTrainingData -> getTrainingData-methods.html [ SUCCESS ]
REDIRECT:topic	 getTrainingData,ClassifierParameters-method -> getTrainingData-methods.html [ SUCCESS ]
REDIRECT:file	 getTrainingData-methods.html -> getTrainingData-methods.html [ SUCCESS ]
    getWeightingType-methods                html  
REDIRECT:topic	 getWeightingType -> getWeightingType-methods.html [ SUCCESS ]
REDIRECT:topic	 getWeightingTypes -> getWeightingType-methods.html [ SUCCESS ]
REDIRECT:topic	 getWeightingType,ClassifierResults-method -> getWeightingType-methods.html [ SUCCESS ]
REDIRECT:file	 getWeightingType-methods.html -> getWeightingType-methods.html [ SUCCESS ]
    getWeights-methods                      html  
REDIRECT:topic	 getWeights -> getWeights-methods.html [ SUCCESS ]
REDIRECT:topic	 getWeights,ClassifierParameters-method -> getWeights-methods.html [ SUCCESS ]
REDIRECT:file	 getWeights-methods.html -> getWeights-methods.html [ SUCCESS ]
    runClassifier-methods                   html  
REDIRECT:topic	 runClassifier -> runClassifier-methods.html [ SUCCESS ]
REDIRECT:topic	 runClassifier,character,FixedExpressionData-method -> runClassifier-methods.html [ SUCCESS ]
REDIRECT:topic	 runClassifier,ClassifierParameters,FixedExpressionData-method -> runClassifier-methods.html [ SUCCESS ]
REDIRECT:topic	 runClassifier,ClassifierResults,FixedExpressionData-method -> runClassifier-methods.html [ SUCCESS ]
REDIRECT:file	 runClassifier-methods.html -> runClassifier-methods.html [ SUCCESS ]
    setNormalizationMethod-methods          html  
REDIRECT:topic	 setNormalizationMethod -> setNormalizationMethod-methods.html [ SUCCESS ]
REDIRECT:file	 setNormalizationMethod-methods.html -> setNormalizationMethod-methods.html [ SUCCESS ]
    showClassifierList-methods              html  
REDIRECT:topic	 showClassifierList -> showClassifierList-methods.html [ SUCCESS ]
REDIRECT:file	 showClassifierList-methods.html -> showClassifierList-methods.html [ SUCCESS ]
** 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 'geneClassifiers' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geneClassifiers' as geneClassifiers_1.15.0.zip
* DONE (geneClassifiers)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'geneClassifiers' successfully unpacked and MD5 sums checked

Tests output

geneClassifiers.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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(geneClassifiers)
> 
> test_check("geneClassifiers")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 191 ]
> 
> proc.time()
   user  system elapsed 
   2.04    0.18    2.18 

geneClassifiers.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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(geneClassifiers)
> 
> test_check("geneClassifiers")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 191 ]
> 
> proc.time()
   user  system elapsed 
   2.37    0.07    2.40 

Example timings

geneClassifiers.Rcheck/examples_i386/geneClassifiers-Ex.timings

nameusersystemelapsed
bracket-methods0.010.000.02
dim-methods000
getBatchCorrection-methods0.160.000.15
getCitations-methods000
getClassifications-methods000
getClassifier-methods000
getDecisionBoundaries-methods000
getDescription-methods000
getEventChain-methods000
getIntercept-methods0.010.000.02
getMeans-methods000
getName-methods000
getNormalizationMethod-methods0.030.000.03
getProbeNames-methods000
getScores-methods0.020.000.01
getSds-methods000
getTargetValue-methods000
getTrainingData-methods0.030.000.03
getWeightingType-methods0.020.000.01
getWeights-methods000
runClassifier-methods0.020.000.01
setNormalizationMethod-methods0.030.000.03
showClassifierList-methods0.010.000.02

geneClassifiers.Rcheck/examples_x64/geneClassifiers-Ex.timings

nameusersystemelapsed
bracket-methods0.030.020.05
dim-methods0.010.000.01
getBatchCorrection-methods0.270.000.26
getCitations-methods000
getClassifications-methods0.030.000.03
getClassifier-methods000
getDecisionBoundaries-methods0.010.000.02
getDescription-methods000
getEventChain-methods000
getIntercept-methods000
getMeans-methods000
getName-methods0.020.000.02
getNormalizationMethod-methods0.030.000.03
getProbeNames-methods000
getScores-methods0.010.010.03
getSds-methods000
getTargetValue-methods0.020.000.02
getTrainingData-methods0.050.000.04
getWeightingType-methods0.010.000.02
getWeights-methods000
runClassifier-methods0.030.000.04
setNormalizationMethod-methods0.040.000.03
showClassifierList-methods0.030.000.03