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CHECK report for NormalyzerDE on tokay1

This page was generated on 2020-04-15 12:31:06 -0400 (Wed, 15 Apr 2020).

Package 1158/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormalyzerDE 1.4.0
Jakob Willforss
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/NormalyzerDE
Branch: RELEASE_3_10
Last Commit: 96750a1
Last Changed Date: 2019-10-29 13:11:21 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NormalyzerDE
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NormalyzerDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings NormalyzerDE_1.4.0.tar.gz
StartedAt: 2020-04-15 05:08:53 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:15:50 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 416.4 seconds
RetCode: 0
Status:  OK  
CheckDir: NormalyzerDE.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NormalyzerDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings NormalyzerDE_1.4.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/NormalyzerDE.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NormalyzerDE/DESCRIPTION' ... OK
* this is package 'NormalyzerDE' version '1.4.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'NormalyzerDE' 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
Missing or unexported object: 'SummarizedExperiment::metadata'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
generatePlots               13.80   0.78   14.58
NormalyzerEvaluationResults  4.91   0.39    5.30
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
generatePlots               15.36   0.64   16.01
NormalyzerEvaluationResults  5.19   0.05    5.26
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/NormalyzerDE.Rcheck/00check.log'
for details.



Installation output

NormalyzerDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/NormalyzerDE_1.4.0.tar.gz && rm -rf NormalyzerDE.buildbin-libdir && mkdir NormalyzerDE.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NormalyzerDE.buildbin-libdir NormalyzerDE_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL NormalyzerDE_1.4.0.zip && rm NormalyzerDE_1.4.0.tar.gz NormalyzerDE_1.4.0.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  905k  100  905k    0     0  3667k      0 --:--:-- --:--:-- --:--:-- 3725k

install for i386

* installing *source* package 'NormalyzerDE' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NormalyzerDE'
    finding HTML links ... done
    NormalyzerDataset                       html  
    NormalyzerEvaluationResults             html  
    NormalyzerResults                       html  
    NormalyzerStatistics                    html  
    analyzeNormalizations                   html  
    calculateANOVAPValues                   html  
    calculateAvgMadMem                      html  
    calculateAvgReplicateVariation          html  
    calculateContrasts                      html  
    calculateCorrSum                        html  
    calculateFeatureCV                      html  
    calculatePercentageAvgDiffInMat         html  
    calculateReplicateCV                    html  
    calculateSummarizedCorrelationVector    html  
    createDirectory                         html  
    detectSingleReplicate                   html  
    detectSingletonSample                   html  
    elapsedSecondsBetweenSystimes           html  
    example_data                            html  
    example_data_only_values                html  
    example_design                          html  
    example_stat_data                       html  
    example_stat_summarized_experiment      html  
    example_summarized_experiment           html  
    example_wide_data                       html  
    example_wide_design                     html  
    filterLowRep                            html  
    findLowlyVariableFeaturesCVs            html  
    generateAnnotatedMatrix                 html  
    generatePlots                           html  
    generateStatsReport                     html  
    getCombinedMatrix                       html  
    getIndexList                            html  
    getLowCountSampleFiltered               html  
    getRTNormalizedMatrix                   html  
    getReplicateSortedData                  html  
    getRowNAFilterContrast                  html  
    getSmoothedRTNormalizedMatrix           html  
    getVerifiedNormalyzerObject             html  
    getWidenedRTRange                       html  
    globalIntensityNormalization            html  
    loadData                                html  
    loadDesign                              html  
    loadRawDataFromFile                     html  
    meanNormalization                       html  
    medianNormalization                     html  
    normMethods                             html  
    normalyzer                              html  
    normalyzerDE                            html  
    performCyclicLoessNormalization         html  
    performGlobalRLRNormalization           html  
    performNoNormalization                  html  
    performNormalizations                   html  
    performQuantileNormalization            html  
    performSMADNormalization                html  
    performVSNNormalization                 html  
    plotBoxPlot                             html  
    plotCVvsIntensity                       html  
    plotComparisonVenns                     html  
    plotContrastPCA                         html  
    plotContrastPHists                      html  
    plotCorrelation                         html  
    plotDendrograms                         html  
    plotDensity                             html  
    plotFrontPage                           html  
    plotMA                                  html  
    plotMDS                                 html  
    plotMeanSD                              html  
    plotPHist                               html  
    plotQQ                                  html  
    plotRLE                                 html  
    plotReplicateVarAndStableVariables      html  
    plotReplicateVariance                   html  
    plotSampleOutlierSummary                html  
    plotScatter                             html  
    plotSigScatter                          html  
    preprocessData                          html  
    printMeta                               html  
    printPlots                              html  
    reduceTechnicalReplicates               html  
    setupJobDir                             html  
    setupPlotting                           html  
    setupRawContrastObject                  html  
    setupRawDataObject                      html  
    setupTestData                           html  
    validateSampleReplication               html  
    verifyContrasts                         html  
    verifyDesignMatrix                      html  
    verifyMultipleSamplesPresent            html  
    verifySummarizedExperiment              html  
    verifyValidNumbers                      html  
    writeNormalizedDatasets                 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 'NormalyzerDE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NormalyzerDE' as NormalyzerDE_1.4.0.zip
* DONE (NormalyzerDE)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'NormalyzerDE' successfully unpacked and MD5 sums checked

Tests output

NormalyzerDE.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(NormalyzerDE)
> test_check("NormalyzerDE")
== testthat results  ===========================================================
[ OK: 85 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  24.95    1.07   26.26 

NormalyzerDE.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(NormalyzerDE)
> test_check("NormalyzerDE")
== testthat results  ===========================================================
[ OK: 85 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  31.28    0.51   31.79 

Example timings

NormalyzerDE.Rcheck/examples_i386/NormalyzerDE-Ex.timings

nameusersystemelapsed
NormalyzerEvaluationResults4.910.395.30
NormalyzerResults0.060.000.07
NormalyzerStatistics0.040.000.03
analyzeNormalizations3.900.033.94
calculateContrasts0.10.00.1
generateAnnotatedMatrix0.040.000.04
generatePlots13.80 0.7814.58
generateStatsReport2.050.052.09
getRTNormalizedMatrix1.840.091.94
getSmoothedRTNormalizedMatrix4.050.024.06
getVerifiedNormalyzerObject0.030.010.05
globalIntensityNormalization000
loadData000
loadDesign000
meanNormalization000
medianNormalization000
normMethods1.790.011.81
normalyzer000
normalyzerDE1.630.021.66
performCyclicLoessNormalization0.020.000.01
performGlobalRLRNormalization0.010.000.02
performQuantileNormalization000
performSMADNormalization000
performVSNNormalization0.020.000.02
reduceTechnicalReplicates0.010.000.01
setupJobDir000
setupRawContrastObject0.020.000.02
setupRawDataObject000
setupTestData000
writeNormalizedDatasets4.500.004.58

NormalyzerDE.Rcheck/examples_x64/NormalyzerDE-Ex.timings

nameusersystemelapsed
NormalyzerEvaluationResults5.190.055.26
NormalyzerResults0.080.000.08
NormalyzerStatistics0.030.000.03
analyzeNormalizations4.380.004.37
calculateContrasts0.110.000.11
generateAnnotatedMatrix0.050.000.05
generatePlots15.36 0.6416.01
generateStatsReport2.920.022.94
getRTNormalizedMatrix1.730.001.74
getSmoothedRTNormalizedMatrix3.860.013.87
getVerifiedNormalyzerObject0.050.000.05
globalIntensityNormalization000
loadData000
loadDesign000
meanNormalization000
medianNormalization000
normMethods2.590.002.60
normalyzer000
normalyzerDE1.170.021.19
performCyclicLoessNormalization0.020.000.02
performGlobalRLRNormalization0.030.000.03
performQuantileNormalization000
performSMADNormalization0.000.020.01
performVSNNormalization0.030.000.03
reduceTechnicalReplicates0.030.000.03
setupJobDir000
setupRawContrastObject0.030.000.04
setupRawDataObject0.020.000.01
setupTestData0.020.000.02
writeNormalizedDatasets4.530.034.56