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This page was generated on 2022-04-13 12:07:00 -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 NormalyzerDE on tokay2


To the developers/maintainers of the NormalyzerDE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NormalyzerDE.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 1301/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormalyzerDE 1.12.0  (landing page)
Jakob Willforss
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/NormalyzerDE
git_branch: RELEASE_3_14
git_last_commit: bc472c8
git_last_commit_date: 2021-10-26 12:46:39 -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: NormalyzerDE
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NormalyzerDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NormalyzerDE_1.12.0.tar.gz
StartedAt: 2022-04-12 23:49:02 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:58:29 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 567.7 seconds
RetCode: 0
Status:   OK  
CheckDir: NormalyzerDE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NormalyzerDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NormalyzerDE_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/NormalyzerDE.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 'NormalyzerDE/DESCRIPTION' ... OK
* this is package 'NormalyzerDE' version '1.12.0'
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
generatePlots                 21.06   1.31   22.37
NormalyzerEvaluationResults    6.33   0.52    6.84
analyzeNormalizations          6.45   0.03    6.50
writeNormalizedDatasets        5.72   0.00    5.72
getSmoothedRTNormalizedMatrix  5.00   0.01    5.01
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
generatePlots               17.14   1.00   18.14
writeNormalizedDatasets      6.39   0.03    6.43
NormalyzerEvaluationResults  5.76   0.11    5.88
analyzeNormalizations        5.30   0.01    5.31
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/NormalyzerDE.Rcheck/00check.log'
for details.



Installation output

NormalyzerDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/NormalyzerDE_1.12.0.tar.gz && rm -rf NormalyzerDE.buildbin-libdir && mkdir NormalyzerDE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NormalyzerDE.buildbin-libdir NormalyzerDE_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL NormalyzerDE_1.12.0.zip && rm NormalyzerDE_1.12.0.tar.gz NormalyzerDE_1.12.0.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
 85  893k   85  767k    0     0  1581k      0 --:--:-- --:--:-- --:--:-- 1581k
100  893k  100  893k    0     0  1704k      0 --:--:-- --:--:-- --:--:-- 1704k

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  
    plotSampleMappingPage                   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_1.12.0.zip
* DONE (NormalyzerDE)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'NormalyzerDE' successfully unpacked and MD5 sums checked

Tests output

NormalyzerDE.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 85 ]
> 
> proc.time()
   user  system elapsed 
  29.25    1.37   30.82 

NormalyzerDE.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 85 ]
> 
> proc.time()
   user  system elapsed 
  36.39    0.59   36.95 

Example timings

NormalyzerDE.Rcheck/examples_i386/NormalyzerDE-Ex.timings

nameusersystemelapsed
NormalyzerEvaluationResults6.330.526.84
NormalyzerResults0.190.000.19
NormalyzerStatistics0.050.000.05
analyzeNormalizations6.450.036.50
calculateContrasts0.140.010.16
generateAnnotatedMatrix0.100.020.11
generatePlots21.06 1.3122.37
generateStatsReport2.930.022.95
getRTNormalizedMatrix2.720.172.90
getSmoothedRTNormalizedMatrix5.000.015.01
getVerifiedNormalyzerObject0.060.020.08
globalIntensityNormalization000
loadData000
loadDesign000
meanNormalization000
medianNormalization000
normMethods2.370.032.41
normalyzer000
normalyzerDE1.170.001.17
performCyclicLoessNormalization000
performGlobalRLRNormalization0.020.010.03
performQuantileNormalization0.010.000.02
performSMADNormalization000
performVSNNormalization0.020.000.01
reduceTechnicalReplicates0.050.000.04
setupJobDir000
setupRawContrastObject0.020.000.02
setupRawDataObject0.030.000.03
setupTestData000
writeNormalizedDatasets5.720.005.72

NormalyzerDE.Rcheck/examples_x64/NormalyzerDE-Ex.timings

nameusersystemelapsed
NormalyzerEvaluationResults5.760.115.88
NormalyzerResults0.110.000.11
NormalyzerStatistics0.030.000.03
analyzeNormalizations5.300.015.31
calculateContrasts0.110.000.11
generateAnnotatedMatrix0.050.020.06
generatePlots17.14 1.0018.14
generateStatsReport2.110.032.15
getRTNormalizedMatrix2.100.032.14
getSmoothedRTNormalizedMatrix3.930.003.92
getVerifiedNormalyzerObject0.090.000.09
globalIntensityNormalization0.020.000.02
loadData000
loadDesign000
meanNormalization000
medianNormalization0.010.000.01
normMethods2.50.02.5
normalyzer000
normalyzerDE1.10.01.1
performCyclicLoessNormalization000
performGlobalRLRNormalization0.030.000.03
performQuantileNormalization000
performSMADNormalization000
performVSNNormalization0.030.000.03
reduceTechnicalReplicates0.040.000.05
setupJobDir0.000.000.02
setupRawContrastObject0.020.000.01
setupRawDataObject0.030.000.03
setupTestData000
writeNormalizedDatasets6.390.036.43