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CHECK report for DAPAR on tokay2

This page was generated on 2020-10-17 11:56:24 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DAPAR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 421/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.20.3
Samuel Wieczorek
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DAPAR
Branch: RELEASE_3_11
Last Commit: 567c24a
Last Changed Date: 2020-10-06 09:59:30 -0400 (Tue, 06 Oct 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DAPAR
Version: 1.20.3
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DAPAR_1.20.3.tar.gz
StartedAt: 2020-10-17 03:09:11 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:19:47 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 635.6 seconds
RetCode: 0
Status:  OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DAPAR_1.20.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DAPAR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.20.3'
* 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 ... NOTE
Namespace in Imports field not imported from: 'tidyverse'
  All declared Imports should be used.
Package in Depends field not imported from: 'igraph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
boxPlotD: warning in axis(side = 1, at = 1:ncol(qData), label =
  legend): partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(1, 1:nc, label = labCol, las = 2, line =
  -0.5 + offsetCol, tick = 0, cex.axis = cexCol, hadj = NA, padj = 0):
  partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(1, 1:nc, label = rep("", nc), las = 2,
  tick = 0): partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(4, iy, label = labRow, las = 5, line =
  -0.5 + offsetRow, tick = 0, cex.axis = cexRow, hadj = 0, padj = NA):
  partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(4, iy, label = rep("", nr), las = 2,
  line = -0.5, tick = 0): partial argument match of 'label' to 'labels'
violinPlotD: warning in axis(side = 1, at = 1:ncol(qData), label = if
  (is.vector(legend)) {: partial argument match of 'label' to 'labels'
violinPlotD: warning in legend: partial argument match of 'label' to
  'labels'
violinPlotD: warning in } else {: partial argument match of 'label' to
  'labels'
violinPlotD: warning in legend[, i]: partial argument match of 'label'
  to 'labels'
violinPlotD: warning in }, line = 2 * i - 1): partial argument match of
  'label' to 'labels'
aggregateIterParallel: no visible binding for global variable 'cond'
diffAnaVolcanoplot_rCharts: no visible binding for global variable 'x'
diffAnaVolcanoplot_rCharts: no visible binding for global variable 'y'
diffAnaVolcanoplot_rCharts: no visible binding for global variable 'g'
display.CC.visNet: no visible binding for global variable
  'layout_nicely'
getTextForGOAnalysis: no visible binding for global variable
  'textGOParams'
getTextForGOAnalysis: no visible binding for global variable 'input'
Undefined global functions or variables:
  cond g input layout_nicely textGOParams x y
* checking Rd files ... NOTE
prepare_Rd: plotJitter_rCharts.Rd:20-23: Dropping empty section \examples
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
compareNormalizationD_HC 2.24   0.08    5.75
CVDistD_HC               1.76   0.13   10.81
createMSnset             1.33   0.02    6.42
aggregateIterParallel    0.67   0.07   21.70
corrMatrixD_HC           0.37   0.01    6.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
aggregateIterParallel 0.74   0.03   16.08
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/DAPAR.Rcheck/00check.log'
for details.



Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DAPAR_1.20.3.tar.gz && rm -rf DAPAR.buildbin-libdir && mkdir DAPAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DAPAR.buildbin-libdir DAPAR_1.20.3.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DAPAR_1.20.3.zip && rm DAPAR_1.20.3.tar.gz DAPAR_1.20.3.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 3953k  100 3953k    0     0  22.3M      0 --:--:-- --:--:-- --:--:-- 23.2M

install for i386

* installing *source* package 'DAPAR' ...
** using staged installation
** R
** inst
** byte-compile and prepare 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

    GetDetailedNbPeptides                   html  
    GetDetailedNbPeptidesUsed               html  
    GetNbPeptidesUsed                       html  
    Get_AllComparisons                      html  
    GraphPepProt                            html  
    LH0                                     html  
    LH0.lm                                  html  
    LH1                                     html  
    LH1.lm                                  html  
    NumericalFiltering                      html  
    NumericalgetIndicesOfLinesToRemove      html  
    StringBasedFiltering                    html  
    StringBasedFiltering2                   html  
    addOriginOfValue                        html  
    aggregateIter                           html  
    aggregateIterParallel                   html  
    aggregateMean                           html  
    aggregateSum                            html  
    aggregateTopn                           html  
    barplotEnrichGO_HC                      html  
    barplotGroupGO_HC                       html  
    boxPlotD                                html  
    boxPlotD_HC                             html  
    buildGraph                              html  
    check.conditions                        html  
    check.design                            html  
    compareNormalizationD                   html  
    compareNormalizationD_HC                html  
    compute.t.tests                         html  
    corrMatrixD                             html  
    corrMatrixD_HC                          html  
    createMSnset                            html  
    deleteLinesFromIndices                  html  
    densityPlotD                            html  
    densityPlotD_HC                         html  
    diffAnaComputeFDR                       html  
    diffAnaGetSignificant                   html  
    diffAnaSave                             html  
    diffAnaVolcanoplot                      html  
    diffAnaVolcanoplot_rCharts              html  
    display.CC.visNet                       html  
    enrich_GO                               html  
    finalizeAggregation                     html  
    findMECBlock                            html  
    formatLimmaResult                       html  
    fudge2LRT                               html  
    get.pep.prot.cc                         html  
    getIndicesConditions                    html  
    getIndicesOfLinesToRemove               html  
    getListNbValuesInLines                  html  
    getNumberOf                             html  
    getNumberOfEmptyLines                   html  
    getPourcentageOfMV                      html  
    getProcessingInfo                       html  
    getProteinsStats                        html  
    getQuantile4Imp                         html  
    getTextForAggregation                   html  
    getTextForAnaDiff                       html  
    getTextForFiltering                     html  
    getTextForGOAnalysis                    html  
    getTextForHypothesisTest                html  
    getTextForNewDataset                    html  
    getTextForNormalization                 html  
    getTextForpeptideImputation             html  
    getTextForproteinImputation             html  
    group_GO                                html  
    hc_logFC_DensityPlot                    html  
    hc_mvTypePlot2                          html  
    heatmap.DAPAR                           html  
    heatmapD                                html  
    histPValue_HC                           html  
    impute.detQuant                         html  
    impute.pa2                              html  
    inner.aggregate.iter                    html  
    inner.aggregate.topn                    html  
    inner.mean                              html  
    inner.sum                               html  
    is.MV                                   html  
    is.OfType                               html  
    limmaCompleteTest                       html  
    listSheets                              html  
    make.contrast                           html  
    make.design.1                           html  
    make.design.2                           html  
    make.design.3                           html  
    make.design                             html  
    mvFilter                                html  
    mvFilterFromIndices                     html  
    mvFilterGetIndices                      html  
    mvHisto                                 html  
    mvHisto_HC                              html  
    mvImage                                 html  
    mvPerLinesHisto                         html  
    mvPerLinesHistoPerCondition             html  
    mvPerLinesHistoPerCondition_HC          html  
    mvPerLinesHisto_HC                      html  
    my_hc_ExportMenu                        html  
    my_hc_chart                             html  
    nonzero                                 html  
    pepa.test                               html  
    plotJitter                              html  
    plotJitter_rCharts                      html  
    plotPCA_Eigen                           html  
    plotPCA_Eigen_hc                        html  
    plotPCA_Ind                             html  
    plotPCA_Var                             html  
    proportionConRev_HC                     html  
    rbindMSnset                             html  
    reIntroduceMEC                          html  
    readExcel                               html  
    removeLines                             html  
    samLRT                                  html  
    saveParameters                          html  
    scatterplotEnrichGO_HC                  html  
    setMEC                                  html  
    splitAdjacencyMat                       html  
    test.design                             html  
    translatedRandomBeta                    html  
    univ_AnnotDbPkg                         html  
    violinPlotD                             html  
    wrapper.CVDistD                         html  
    wrapper.CVDistD_HC                      html  
    wrapper.compareNormalizationD           html  
    wrapper.compareNormalizationD_HC        html  
    wrapper.corrMatrixD                     html  
    wrapper.corrMatrixD_HC                  html  
    wrapper.dapar.impute.mi                 html  
    wrapper.hc_mvTypePlot2                  html  
    wrapper.heatmapD                        html  
    wrapper.impute.KNN                      html  
    wrapper.impute.detQuant                 html  
    wrapper.impute.fixedValue               html  
    wrapper.impute.mle                      html  
    wrapper.impute.pa                       html  
    wrapper.impute.pa2                      html  
    wrapper.impute.slsa                     html  
    wrapper.mvHisto                         html  
    wrapper.mvHisto_HC                      html  
    wrapper.mvImage                         html  
    wrapper.mvPerLinesHisto                 html  
    wrapper.mvPerLinesHistoPerCondition     html  
    wrapper.mvPerLinesHistoPerCondition_HC
                                            html  
    wrapper.mvPerLinesHisto_HC              html  
    wrapper.normalizeD                      html  
    wrapper.pca                             html  
    wrapper.t_test_Complete                 html  
    wrapperCalibrationPlot                  html  
    writeMSnsetToCSV                        html  
    writeMSnsetToExcel                      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 'DAPAR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DAPAR' as DAPAR_1.20.3.zip
* DONE (DAPAR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DAPAR' successfully unpacked and MD5 sums checked

Tests output

DAPAR.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(DAPAR)
Loading required package: foreach
Loading required package: parallel
Loading required package: doParallel
Loading required package: iterators
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


> 
> test_check("DAPAR")
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.64    1.06   13.00 

DAPAR.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(DAPAR)
Loading required package: foreach
Loading required package: parallel
Loading required package: doParallel
Loading required package: iterators
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


> 
> test_check("DAPAR")
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.40    0.75   12.15 

Example timings

DAPAR.Rcheck/examples_i386/DAPAR-Ex.timings

nameusersystemelapsed
BuildAdjacencyMatrix0.750.074.15
BuildColumnToProteinDataset4.180.684.88
BuildColumnToProteinDataset_par000
CVDistD000
CVDistD_HC 1.76 0.1310.81
CountPep0.690.090.78
GetDetailedNbPeptides0.560.060.62
Get_AllComparisons0.660.020.68
GraphPepProt0.520.050.70
NumericalFiltering0.500.060.56
NumericalgetIndicesOfLinesToRemove0.470.000.47
StringBasedFiltering0.430.050.48
StringBasedFiltering20.320.010.33
addOriginOfValue0.230.000.24
aggregateIter2.470.372.85
aggregateIterParallel 0.67 0.0721.70
aggregateMean0.440.040.48
aggregateSum0.480.030.52
aggregateTopn2.110.112.22
boxPlotD0.330.020.35
boxPlotD_HC000
buildGraph000
check.conditions0.320.000.33
check.design0.430.000.42
compareNormalizationD2.260.062.33
compareNormalizationD_HC2.240.085.75
compute.t.tests1.260.011.28
corrMatrixD2.220.072.28
corrMatrixD_HC0.370.016.33
createMSnset1.330.026.42
deleteLinesFromIndices0.450.000.46
densityPlotD0.430.000.44
densityPlotD_HC1.600.062.09
diffAnaComputeFDR0.510.000.74
diffAnaGetSignificant0.580.000.58
diffAnaSave0.920.000.93
diffAnaVolcanoplot0.520.000.52
diffAnaVolcanoplot_rCharts000
display.CC.visNet000
enrich_GO000
findMECBlock0.480.000.48
formatLimmaResult0.390.000.39
get.pep.prot.cc1.400.031.43
getIndicesConditions0.310.000.31
getIndicesOfLinesToRemove0.230.000.23
getListNbValuesInLines0.250.000.25
getNumberOf0.220.020.24
getNumberOfEmptyLines0.440.000.44
getPourcentageOfMV0.40.00.4
getProcessingInfo0.400.000.39
getProteinsStats0.400.000.41
getQuantile4Imp0.240.000.23
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset000
getTextForNormalization000
getTextForpeptideImputation000
getTextForproteinImputation0.010.000.02
group_GO000
hc_logFC_DensityPlot0.490.040.53
hc_mvTypePlot22.040.082.12
heatmap.DAPAR0.990.021.00
heatmapD000
histPValue_HC0.680.030.88
impute.detQuant0.910.060.97
impute.pa20.30.00.3
is.MV0.700.130.82
is.OfType0.840.181.03
limmaCompleteTest0.550.020.57
make.contrast0.420.020.43
make.design.10.430.010.44
make.design.2000
make.design.30.400.000.41
make.design0.390.020.40
mvFilter0.510.000.52
mvFilterFromIndices0.440.000.43
mvFilterGetIndices0.450.030.49
mvHisto0.380.000.37
mvHisto_HC0.440.060.50
mvImage3.200.023.22
mvPerLinesHisto0.420.010.44
mvPerLinesHistoPerCondition0.420.020.44
mvPerLinesHistoPerCondition_HC0.410.061.17
mvPerLinesHisto_HC0.440.020.76
my_hc_ExportMenu0.140.170.38
my_hc_chart0.110.090.20
nonzero0.010.000.02
plotJitter1.030.001.03
plotPCA_Eigen0.280.000.29
plotPCA_Eigen_hc0.220.000.21
plotPCA_Ind0.230.000.24
plotPCA_Var0.290.000.28
proportionConRev_HC0.060.030.91
rbindMSnset0.530.000.53
reIntroduceMEC0.610.020.62
removeLines0.400.010.42
saveParameters0.440.000.44
setMEC0.420.020.44
test.design0.360.020.37
translatedRandomBeta000
violinPlotD0.860.000.86
wrapper.CVDistD000
wrapper.CVDistD_HC2.220.012.64
wrapper.compareNormalizationD1.900.021.92
wrapper.compareNormalizationD_HC000
wrapper.corrMatrixD2.220.012.24
wrapper.corrMatrixD_HC0.520.030.54
wrapper.dapar.impute.mi000
wrapper.hc_mvTypePlot21.420.111.53
wrapper.heatmapD000
wrapper.impute.KNN0.470.000.47
wrapper.impute.detQuant0.440.000.44
wrapper.impute.fixedValue0.450.000.45
wrapper.impute.mle0.490.020.61
wrapper.impute.pa0.420.000.42
wrapper.impute.pa20.490.000.49
wrapper.impute.slsa2.400.052.45
wrapper.mvHisto0.450.000.45
wrapper.mvHisto_HC0.500.040.55
wrapper.mvImage0.790.000.78
wrapper.mvPerLinesHisto0.370.000.37
wrapper.mvPerLinesHistoPerCondition0.490.000.49
wrapper.mvPerLinesHistoPerCondition_HC0.430.020.45
wrapper.mvPerLinesHisto_HC0.250.000.25
wrapper.normalizeD0.270.000.27
wrapper.pca0.340.010.36
wrapper.t_test_Complete0.280.000.28
wrapperCalibrationPlot0.360.000.36
writeMSnsetToCSV000
writeMSnsetToExcel000

DAPAR.Rcheck/examples_x64/DAPAR-Ex.timings

nameusersystemelapsed
BuildAdjacencyMatrix1.110.031.14
BuildColumnToProteinDataset3.140.954.10
BuildColumnToProteinDataset_par000
CVDistD000
CVDistD_HC1.480.091.58
CountPep0.390.080.47
GetDetailedNbPeptides0.450.000.46
Get_AllComparisons0.580.000.57
GraphPepProt0.310.000.32
NumericalFiltering0.410.000.40
NumericalgetIndicesOfLinesToRemove0.370.000.38
StringBasedFiltering0.600.000.59
StringBasedFiltering20.280.000.28
addOriginOfValue0.280.000.28
aggregateIter3.760.444.21
aggregateIterParallel 0.74 0.0316.08
aggregateMean1.470.031.50
aggregateSum0.560.020.57
aggregateTopn2.970.012.99
boxPlotD0.420.030.45
boxPlotD_HC000
buildGraph000
check.conditions0.370.000.38
check.design0.220.020.23
compareNormalizationD1.690.061.75
compareNormalizationD_HC2.740.032.77
compute.t.tests0.930.000.93
corrMatrixD2.360.032.39
corrMatrixD_HC0.560.050.61
createMSnset1.460.001.46
deleteLinesFromIndices0.470.000.47
densityPlotD0.360.000.36
densityPlotD_HC1.820.031.87
diffAnaComputeFDR0.360.000.36
diffAnaGetSignificant0.460.000.45
diffAnaSave0.480.000.49
diffAnaVolcanoplot0.310.000.31
diffAnaVolcanoplot_rCharts000
display.CC.visNet000
enrich_GO000
findMECBlock0.430.000.42
formatLimmaResult0.560.000.56
get.pep.prot.cc2.260.002.27
getIndicesConditions0.360.000.36
getIndicesOfLinesToRemove0.360.000.36
getListNbValuesInLines0.410.000.40
getNumberOf0.340.000.35
getNumberOfEmptyLines0.350.020.36
getPourcentageOfMV0.320.000.33
getProcessingInfo0.350.010.36
getProteinsStats0.470.000.46
getQuantile4Imp0.370.000.38
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset000
getTextForNormalization000
getTextForpeptideImputation000
getTextForproteinImputation000
group_GO000
hc_logFC_DensityPlot0.750.040.79
hc_mvTypePlot22.120.032.15
heatmap.DAPAR0.500.010.52
heatmapD000
histPValue_HC0.410.060.50
impute.detQuant0.560.210.76
impute.pa20.330.000.33
is.MV0.410.170.58
is.OfType0.430.230.67
limmaCompleteTest0.440.000.44
make.contrast0.280.020.30
make.design.10.350.000.34
make.design.2000
make.design.30.210.000.22
make.design0.350.000.34
mvFilter0.560.000.56
mvFilterFromIndices0.250.000.25
mvFilterGetIndices0.270.050.32
mvHisto0.210.010.23
mvHisto_HC0.460.030.49
mvImage3.420.003.42
mvPerLinesHisto0.370.020.39
mvPerLinesHistoPerCondition0.240.000.23
mvPerLinesHistoPerCondition_HC0.260.030.30
mvPerLinesHisto_HC0.290.030.31
my_hc_ExportMenu0.090.130.28
my_hc_chart0.120.150.28
nonzero0.020.000.02
plotJitter1.150.001.15
plotPCA_Eigen0.360.000.36
plotPCA_Eigen_hc0.190.000.19
plotPCA_Ind0.20.00.2
plotPCA_Var0.210.000.21
proportionConRev_HC0.040.030.07
rbindMSnset0.270.000.27
reIntroduceMEC0.310.000.32
removeLines0.20.00.2
saveParameters0.210.000.20
setMEC0.310.000.32
test.design0.190.000.18
translatedRandomBeta0.010.000.02
violinPlotD0.740.000.73
wrapper.CVDistD000
wrapper.CVDistD_HC1.540.061.94
wrapper.compareNormalizationD1.520.061.58
wrapper.compareNormalizationD_HC000
wrapper.corrMatrixD2.560.052.61
wrapper.corrMatrixD_HC0.310.050.47
wrapper.dapar.impute.mi000
wrapper.hc_mvTypePlot22.380.062.50
wrapper.heatmapD000
wrapper.impute.KNN0.310.000.31
wrapper.impute.detQuant0.20.00.2
wrapper.impute.fixedValue0.220.020.24
wrapper.impute.mle0.250.000.62
wrapper.impute.pa0.550.000.55
wrapper.impute.pa20.330.010.34
wrapper.impute.slsa1.900.001.91
wrapper.mvHisto0.380.000.37
wrapper.mvHisto_HC0.470.050.52
wrapper.mvImage0.800.010.81
wrapper.mvPerLinesHisto0.390.000.39
wrapper.mvPerLinesHistoPerCondition0.440.000.44
wrapper.mvPerLinesHistoPerCondition_HC0.340.040.37
wrapper.mvPerLinesHisto_HC0.220.000.22
wrapper.normalizeD0.240.000.23
wrapper.pca0.280.010.30
wrapper.t_test_Complete0.290.000.30
wrapperCalibrationPlot0.390.000.39
writeMSnsetToCSV000
writeMSnsetToExcel000