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CHECK report for DAPAR on tokay1

This page was generated on 2018-04-12 13:26:54 -0400 (Thu, 12 Apr 2018).

Package 330/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.10.4
Samuel Wieczorek
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/DAPAR
Branch: RELEASE_3_6
Last Commit: 6e078f3
Last Changed Date: 2018-03-26 03:03:38 -0400 (Mon, 26 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DAPAR
Version: 1.10.4
Command: rm -rf DAPAR.buildbin-libdir DAPAR.Rcheck && mkdir DAPAR.buildbin-libdir DAPAR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DAPAR.buildbin-libdir DAPAR_1.10.4.tar.gz >DAPAR.Rcheck\00install.out 2>&1 && cp DAPAR.Rcheck\00install.out DAPAR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DAPAR.buildbin-libdir --install="check:DAPAR-install.out" --force-multiarch --no-vignettes --timings DAPAR_1.10.4.tar.gz
StartedAt: 2018-04-11 23:21:00 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:33:23 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 743.6 seconds
RetCode: 0
Status:  OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DAPAR.buildbin-libdir DAPAR.Rcheck && mkdir DAPAR.buildbin-libdir DAPAR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DAPAR.buildbin-libdir DAPAR_1.10.4.tar.gz >DAPAR.Rcheck\00install.out 2>&1 && cp DAPAR.Rcheck\00install.out DAPAR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DAPAR.buildbin-libdir --install="check:DAPAR-install.out" --force-multiarch --no-vignettes --timings DAPAR_1.10.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DAPAR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DAPAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DAPAR' version '1.10.4'
* 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 'DAPAR' 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
compareNormalizationD_HC         25.18   0.03   25.21
wrapper.compareNormalizationD_HC 23.32   0.03   23.59
wrapper.dapar.impute.mi          17.91   0.01   17.92
enrich_GO                        13.66   0.85   14.78
group_GO                          9.16   0.25    9.42
BuildColumnToProteinDataset_par   0.72   0.00   11.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
wrapper.dapar.impute.mi          47.28   0.04   47.31
wrapper.compareNormalizationD_HC 38.69   0.04   38.74
compareNormalizationD_HC         30.91   0.09   31.00
enrich_GO                        13.59   0.58   14.17
group_GO                         11.11   0.63   11.74
mvImage                           5.50   0.03    5.53
BuildColumnToProteinDataset_par   0.70   0.05   12.79
* 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

DAPAR.Rcheck/00install.out


install for i386

* installing *source* package 'DAPAR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DAPAR'
    finding HTML links ... done
    BuildAdjacencyMatrix                    html  
    BuildColumnToProteinDataset             html  
    BuildColumnToProteinDataset_par         html  
    CVDistD                                 html  
    CVDistD_HC                              html  
    CountPep                                html  
    GOAnalysisSave                          html  
    finding level-2 HTML links ... done

    GraphPepProt                            html  
    LH0                                     html  
    LH1                                     html  
    MeanPeptides                            html  
    StringBasedFiltering                    html  
    SumPeptides                             html  
    TopnPeptides                            html  
    barplotEnrichGO_HC                      html  
    barplotGroupGO_HC                       html  
    boxPlotD                                html  
    boxPlotD_HC                             html  
    compareNormalizationD                   html  
    compareNormalizationD_HC                html  
    corrMatrixD                             html  
    corrMatrixD_HC                          html  
    createMSnset                            html  
    deleteLinesFromIndices                  html  
    densityPlotD                            html  
    densityPlotD_HC                         html  
    diffAna                                 html  
    diffAnaComputeFDR                       html  
    diffAnaGetSignificant                   html  
    diffAnaLimma                            html  
    diffAnaSave                             html  
    diffAnaVolcanoplot_rCharts              html  
    diffAnaWelch                            html  
    enrich_GO                               html  
    fudge2LRT                               html  
    getIndicesConditions                    html  
    getIndicesOfLinesToRemove               html  
    getNumberOf                             html  
    getNumberOfEmptyLines                   html  
    getPaletteForLabels                     html  
    getPaletteForLabels_HC                  html  
    getPaletteForReplicates                 html  
    getPaletteForReplicates_HC              html  
    getPourcentageOfMV                      html  
    getProcessingInfo                       html  
    getProteinsStats                        html  
    getQuantile4Imp                         html  
    group_GO                                html  
    heatmap.DAPAR                           html  
    heatmapD                                html  
    impute.detQuant                         html  
    impute.pa2                              html  
    limmaCompleteTest                       html  
    listSheets                              html  
    mvFilter                                html  
    mvFilterFromIndices                     html  
    mvFilterGetIndices                      html  
    mvHisto                                 html  
    mvHisto_HC                              html  
    mvImage                                 html  
    mvImputation                            html  
    mvPerLinesHisto                         html  
    mvPerLinesHistoPerCondition             html  
    mvPerLinesHistoPerCondition_HC          html  
    mvPerLinesHisto_HC                      html  
    mvTypePlot                              html  
    my_hc_ExportMenu                        html  
    my_hc_chart                             html  
    nonzero                                 html  
    normalizeD                              html  
    normalizeD2                             html  
    pepAgregate                             html  
    pepa.test                               html  
    proportionConRev_HC                     html  
    readExcel                               html  
    removeLines                             html  
    samLRT                                  html  
    scatterplotEnrichGO_HC                  html  
    translatedRandomBeta                    html  
    univ_AnnotDbPkg                         html  
    violinPlotD                             html  
    wrapper.CVDistD                         html  
    wrapper.CVDistD_HC                      html  
    wrapper.boxPlotD                        html  
    wrapper.boxPlotD_HC                     html  
    wrapper.compareNormalizationD           html  
    wrapper.compareNormalizationD_HC        html  
    wrapper.corrMatrixD                     html  
    wrapper.corrMatrixD_HC                  html  
    wrapper.dapar.impute.mi                 html  
    wrapper.densityPlotD                    html  
    wrapper.densityPlotD_HC                 html  
    wrapper.diffAnaLimma                    html  
    wrapper.diffAnaWelch                    html  
    wrapper.heatmapD                        html  
    wrapper.impute.detQuant                 html  
    wrapper.impute.pa                       html  
    wrapper.impute.pa2                      html  
    wrapper.mvHisto                         html  
    wrapper.mvHisto_HC                      html  
    wrapper.mvImage                         html  
    wrapper.mvImputation                    html  
    wrapper.mvPerLinesHisto                 html  
    wrapper.mvPerLinesHistoPerCondition     html  
    wrapper.mvPerLinesHistoPerCondition_HC
                                            html  
    wrapper.mvPerLinesHisto_HC              html  
    wrapper.mvTypePlot                      html  
    wrapper.normalizeD                      html  
    wrapper.normalizeD2                     html  
    wrapper.violinPlotD                     html  
    wrapperCalibrationPlot                  html  
    writeMSnsetToExcel                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DAPAR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DAPAR' as DAPAR_1.10.4.zip
* DONE (DAPAR)
In R CMD INSTALL
In R CMD INSTALL

Tests output

DAPAR.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(DAPAR)

> 
> test_check("DAPAR")
Procedure of Benjamini-Hochberg is used. pi0 is fixed to 1.
1 2 3 4 5   
5 2 2 4 1 0 
1 2 3 4 5   
5 2 2 4 1 0 
1 2 3 4 5   
5 2 2 4 1 0 
== testthat results  ===========================================================
OK: 125 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  15.35    0.67   16.54

DAPAR.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(DAPAR)

> 
> test_check("DAPAR")
Procedure of Benjamini-Hochberg is used. pi0 is fixed to 1.
1 2 3 4 5   
5 2 2 4 1 0 
1 2 3 4 5   
5 2 2 4 1 0 
1 2 3 4 5   
5 2 2 4 1 0 
== testthat results  ===========================================================
OK: 125 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  20.56    0.43   21.12

Example timings

DAPAR.Rcheck/examples_i386/DAPAR-Ex.timings

nameusersystemelapsed
BuildAdjacencyMatrix1.050.041.15
BuildColumnToProteinDataset1.260.011.28
BuildColumnToProteinDataset_par 0.72 0.0011.89
CVDistD2.520.002.51
CVDistD_HC2.030.054.97
CountPep0.480.030.52
GraphPepProt0.630.020.64
MeanPeptides0.310.000.31
StringBasedFiltering0.770.000.77
SumPeptides0.280.010.29
TopnPeptides2.150.032.19
boxPlotD0.740.020.75
boxPlotD_HC1.370.031.41
compareNormalizationD0.490.050.53
compareNormalizationD_HC25.18 0.0325.21
corrMatrixD101
corrMatrixD_HC0.330.030.36
createMSnset0.80.01.5
deleteLinesFromIndices0.320.020.34
densityPlotD0.290.050.33
densityPlotD_HC1.530.011.56
diffAna0.420.000.42
diffAnaComputeFDR0.860.000.86
diffAnaGetSignificant0.250.000.25
diffAnaLimma0.260.000.27
diffAnaSave0.260.000.27
diffAnaVolcanoplot_rCharts0.750.020.80
diffAnaWelch0.250.010.26
enrich_GO13.66 0.8514.78
getIndicesConditions0.230.000.23
getIndicesOfLinesToRemove0.220.000.22
getNumberOf0.220.000.22
getNumberOfEmptyLines0.260.010.28
getPaletteForLabels0.240.000.24
getPaletteForLabels_HC0.230.000.23
getPaletteForReplicates0.220.000.22
getPaletteForReplicates_HC0.240.000.23
getPourcentageOfMV0.250.000.25
getProcessingInfo0.210.000.22
getProteinsStats0.270.000.27
getQuantile4Imp0.230.000.23
group_GO9.160.259.42
heatmap.DAPAR0.560.000.56
heatmapD0.870.000.88
impute.detQuant0.500.110.61
impute.pa20.300.020.31
limmaCompleteTest0.280.010.30
mvFilter0.300.000.29
mvFilterFromIndices0.230.020.25
mvFilterGetIndices0.280.010.30
mvHisto0.30.00.3
mvHisto_HC0.270.040.29
mvImage2.670.002.68
mvImputation0.220.000.21
mvPerLinesHisto0.280.030.32
mvPerLinesHistoPerCondition0.240.010.25
mvPerLinesHistoPerCondition_HC0.300.030.33
mvPerLinesHisto_HC0.250.070.31
mvTypePlot1.420.001.42
my_hc_ExportMenu0.140.040.19
my_hc_chart0.200.030.24
nonzero0.060.000.06
normalizeD0.290.000.28
normalizeD20.280.000.28
pepAgregate0.310.000.31
proportionConRev_HC0.010.040.49
removeLines0.220.010.23
translatedRandomBeta000
violinPlotD1.750.031.95
wrapper.CVDistD2.440.002.44
wrapper.CVDistD_HC1.780.031.81
wrapper.boxPlotD0.260.000.27
wrapper.boxPlotD_HC1.000.081.08
wrapper.compareNormalizationD0.500.020.51
wrapper.compareNormalizationD_HC23.32 0.0323.59
wrapper.corrMatrixD1.390.001.40
wrapper.corrMatrixD_HC0.40.00.4
wrapper.dapar.impute.mi17.91 0.0117.92
wrapper.densityPlotD0.310.000.32
wrapper.densityPlotD_HC1.300.041.32
wrapper.diffAnaLimma0.230.010.25
wrapper.diffAnaWelch0.280.020.30
wrapper.heatmapD1.190.011.20
wrapper.impute.detQuant0.30.00.3
wrapper.impute.pa0.330.000.33
wrapper.impute.pa20.280.000.28
wrapper.mvHisto0.280.000.28
wrapper.mvHisto_HC0.260.000.27
wrapper.mvImage2.800.022.81
wrapper.mvImputation0.270.000.27
wrapper.mvPerLinesHisto0.330.010.34
wrapper.mvPerLinesHistoPerCondition0.290.000.30
wrapper.mvPerLinesHistoPerCondition_HC0.250.020.26
wrapper.mvPerLinesHisto_HC0.240.020.25
wrapper.mvTypePlot1.340.011.36
wrapper.normalizeD0.230.000.23
wrapper.normalizeD20.310.000.31
wrapper.violinPlotD1.390.001.39
wrapperCalibrationPlot0.280.000.29
writeMSnsetToExcel0.020.000.01

DAPAR.Rcheck/examples_x64/DAPAR-Ex.timings

nameusersystemelapsed
BuildAdjacencyMatrix0.920.000.92
BuildColumnToProteinDataset1.410.051.45
BuildColumnToProteinDataset_par 0.70 0.0512.79
CVDistD3.430.013.44
CVDistD_HC2.290.032.33
CountPep0.530.020.54
GraphPepProt0.730.060.80
MeanPeptides0.30.00.3
StringBasedFiltering0.970.031.00
SumPeptides0.280.020.29
TopnPeptides2.090.012.11
boxPlotD0.880.000.88
boxPlotD_HC1.640.031.67
compareNormalizationD0.420.040.45
compareNormalizationD_HC30.91 0.0931.00
corrMatrixD1.730.051.78
corrMatrixD_HC0.280.030.32
createMSnset0.820.020.83
deleteLinesFromIndices0.250.000.25
densityPlotD0.250.010.27
densityPlotD_HC1.480.001.53
diffAna0.470.000.47
diffAnaComputeFDR1.160.001.15
diffAnaGetSignificant0.230.000.24
diffAnaLimma0.230.020.25
diffAnaSave0.250.000.25
diffAnaVolcanoplot_rCharts0.830.020.85
diffAnaWelch0.220.010.24
enrich_GO13.59 0.5814.17
getIndicesConditions0.20.00.2
getIndicesOfLinesToRemove0.190.010.21
getNumberOf0.190.020.20
getNumberOfEmptyLines0.210.000.22
getPaletteForLabels0.210.000.20
getPaletteForLabels_HC0.250.000.25
getPaletteForReplicates0.190.020.20
getPaletteForReplicates_HC0.180.010.21
getPourcentageOfMV0.210.020.22
getProcessingInfo0.180.010.20
getProteinsStats0.270.030.30
getQuantile4Imp0.220.000.21
group_GO11.11 0.6311.74
heatmap.DAPAR0.530.000.53
heatmapD1.030.031.06
impute.detQuant0.450.090.55
impute.pa20.310.000.32
limmaCompleteTest0.290.000.30
mvFilter0.360.000.36
mvFilterFromIndices0.250.000.25
mvFilterGetIndices0.280.020.30
mvHisto0.220.030.25
mvHisto_HC0.300.050.40
mvImage5.500.035.53
mvImputation0.200.000.21
mvPerLinesHisto0.280.000.28
mvPerLinesHistoPerCondition0.240.000.23
mvPerLinesHistoPerCondition_HC0.260.030.30
mvPerLinesHisto_HC0.250.050.30
mvTypePlot1.440.011.45
my_hc_ExportMenu0.130.100.22
my_hc_chart0.150.040.20
nonzero0.130.000.13
normalizeD0.230.020.25
normalizeD20.260.000.27
pepAgregate0.280.010.29
proportionConRev_HC0.050.040.08
removeLines0.200.000.21
translatedRandomBeta000
violinPlotD2.070.012.07
wrapper.CVDistD3.690.023.70
wrapper.CVDistD_HC2.160.042.21
wrapper.boxPlotD0.220.020.23
wrapper.boxPlotD_HC1.230.021.52
wrapper.compareNormalizationD0.470.000.46
wrapper.compareNormalizationD_HC38.69 0.0438.74
wrapper.corrMatrixD2.610.032.64
wrapper.corrMatrixD_HC0.540.030.58
wrapper.dapar.impute.mi47.28 0.0447.31
wrapper.densityPlotD0.250.000.25
wrapper.densityPlotD_HC1.940.041.98
wrapper.diffAnaLimma0.360.000.36
wrapper.diffAnaWelch0.340.020.36
wrapper.heatmapD1.870.011.89
wrapper.impute.detQuant0.230.020.25
wrapper.impute.pa0.30.00.3
wrapper.impute.pa20.410.000.41
wrapper.mvHisto0.440.000.44
wrapper.mvHisto_HC0.340.000.34
wrapper.mvImage3.680.033.71
wrapper.mvImputation0.230.000.23
wrapper.mvPerLinesHisto0.50.00.5
wrapper.mvPerLinesHistoPerCondition0.440.020.46
wrapper.mvPerLinesHistoPerCondition_HC0.260.000.26
wrapper.mvPerLinesHisto_HC0.340.000.34
wrapper.mvTypePlot1.640.001.64
wrapper.normalizeD0.220.010.24
wrapper.normalizeD20.270.000.26
wrapper.violinPlotD1.680.001.67
wrapperCalibrationPlot0.250.020.26
writeMSnsetToExcel000