Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-17 15:06:02 -0400 (Fri, 17 Sep 2021).

CHECK results for debrowser on tokay2

To the developers/maintainers of the debrowser package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/debrowser.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 453/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.20.1  (landing page)
Alper Kucukural
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: RELEASE_3_13
git_last_commit: 3379462
git_last_commit_date: 2021-08-11 22:11:22 -0400 (Wed, 11 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: debrowser
Version: 1.20.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:debrowser.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings debrowser_1.20.1.tar.gz
StartedAt: 2021-09-16 22:00:15 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 22:09:31 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 556.0 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:debrowser.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings debrowser_1.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/debrowser.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'debrowser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'debrowser' version '1.20.1'
* 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 'debrowser' 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 ... NOTE
checkCountData : <anonymous>: no visible binding for global variable
  'err'
debrowserdataload: no visible binding for global variable 'demodata'
debrowserhistogram: no visible global function definition for 'config'
getBarMainPlot: no visible global function definition for 'config'
getBoxMainPlot: no visible global function definition for 'config'
getDensityPlot: no visible binding for global variable 'samples'
getDensityPlot: no visible global function definition for 'config'
getGOPlots: no visible global function definition for 'facet_grid'
getIQRPlot: no visible global function definition for 'config'
mainScatterNew: no visible global function definition for 'config'
plot_pca: no visible binding for global variable 'x'
plot_pca: no visible binding for global variable 'y'
plot_pca: no visible binding for global variable 'samples'
plot_pca: no visible global function definition for 'config'
runHeatmap: no visible global function definition for 'config'
Undefined global functions or variables:
  config demodata err facet_grid samples x y
* 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 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 'test-demo.R'
  Running 'test-deseq.R'
  Running 'test-null.R'
  Running 'test-ui.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-demo.R'
  Running 'test-deseq.R'
  Running 'test-null.R'
  Running 'test-ui.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-3.13-bioc/meat/debrowser.Rcheck/00check.log'
for details.



Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/debrowser_1.20.1.tar.gz && rm -rf debrowser.buildbin-libdir && mkdir debrowser.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=debrowser.buildbin-libdir debrowser_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL debrowser_1.20.1.zip && rm debrowser_1.20.1.tar.gz debrowser_1.20.1.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
 16 2472k   16  409k    0     0  1072k      0  0:00:02 --:--:--  0:00:02 1073k
100 2472k  100 2472k    0     0  2624k      0 --:--:-- --:--:-- --:--:-- 2624k

install for i386

* installing *source* package 'debrowser' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'debrowser'
    finding HTML links ... done
    BoxMainPlotControlsUI                   html  
    IQRPlotControlsUI                       html  
    actionButtonDE                          html  
    addDataCols                             html  
    addID                                   html  
    all2all                                 html  
    all2allControlsUI                       html  
    applyFilters                            html  
    applyFiltersNew                         html  
    applyFiltersToMergedComparison          html  
    barMainPlotControlsUI                   html  
    batchEffectUI                           html  
    batchMethod                             html  
    changeClusterOrder                      html  
    checkCountData                          html  
    checkMetaData                           html  
    clustFunParamsUI                        html  
    clusterData                             html  
    compareClust                            html  
    condSelectUI                            html  
    correctCombat                           html  
    correctHarman                           html  
    customColorsUI                          html  
    cutOffSelectionUI                       html  
    dataLCFUI                               html  
    dataLoadUI                              html  
    deServer                                html  
    deUI                                    html  
    debrowserIQRplot                        html  
    debrowserall2all                        html  
    debrowserbarmainplot                    html  
    debrowserbatcheffect                    html  
    debrowserboxmainplot                    html  
    debrowsercondselect                     html  
    debrowserdataload                       html  
    debrowserdeanalysis                     html  
    debrowserdensityplot                    html  
    debrowserheatmap                        html  
    debrowserhistogram                      html  
    debrowserlowcountfilter                 html  
    debrowsermainplot                       html  
    debrowserpcaplot                        html  
    dendControlsUI                          html  
    densityPlotControlsUI                   html  
    distFunParamsUI                         html  
    drawKEGG                                html  
    drawPCAExplained                        html  
    fileTypes                               html  
    fileUploadBox                           html  
    generateTestData                        html  
    getAfterLoadMsg                         html  
    getAll2AllPlotUI                        html  
    getBSTableUI                            html  
    getBarMainPlot                          html  
    getBarMainPlotUI                        html  
    getBoxMainPlot                          html  
    getBoxMainPlotUI                        html  
    getColorShapeSelection                  html  
    getColors                               html  
    getCompSelection                        html  
    getCondMsg                              html  
    getConditionSelector                    html  
    getConditionSelectorFromMeta            html  
    getCutOffSelection                      html  
    getDEAnalysisText                       html  
    getDEResultsUI                          html  
    getDataAssesmentText                    html  
    getDataForTables                        html  
    getDataPreparationText                  html  
    getDensityPlot                          html  
    getDensityPlotUI                        html  
    getDomains                              html  
    getDown                                 html  
    getDownloadSection                      html  
    getEnrichDO                             html  
    getEnrichGO                             html  
    getEnrichKEGG                           html  
    getEntrezIds                            html  
    getEntrezTable                          html  
    getGOLeftMenu                           html  
    getGOPlots                              html  
    getGSEA                                 html  
    getGeneList                             html  
    getGeneSetData                          html  
    getGoPanel                              html  
    getHeatmapUI                            html  
    getHelpButton                           html  
    getHideLegendOnOff                      html  
    getHistogramUI                          html  
    getIQRPlot                              html  
    getIQRPlotUI                            html  
    getIntroText                            html  
    getJSLine                               html  
    getKEGGModal                            html  
    getLeftMenu                             html  
    getLegendColors                         html  
    getLegendRadio                          html  
    getLegendSelect                         html  
    getLevelOrder                           html  
    getLoadingMsg                           html  
    getLogo                                 html  
    getMainPanel                            html  
    getMainPlotUI                           html  
    getMainPlotsLeftMenu                    html  
    getMean                                 html  
    getMergedComparison                     html  
    getMetaSelector                         html  
    getMethodDetails                        html  
    getMostVariedList                       html  
    getNormalizedMatrix                     html  
    getOrganism                             html  
    getOrganismBox                          html  
    getOrganismPathway                      html  
    getPCAPlotUI                            html  
    getPCAcontolUpdatesJS                   html  
    getPCAexplained                         html  
    getPCselection                          html  
    getPlotArea                             html  
    getProgramTitle                         html  
    getQAText                               html  
    getQCLeftMenu                           html  
    getQCPanel                              html  
    getSampleDetails                        html  
    getSampleNames                          html  
    getSamples                              html  
    getSearchData                           html  
    getSelHeat                              html  
    getSelectInputBox                       html  
    getSelectedCols                         html  
    getSelectedDatasetInput                 html  
    getShapeColor                           html  
    getStartPlotsMsg                        html  
    getStartupMsg                           html  
    getTabUpdateJS                          html  
    getTableDetails                         html  
    getTableModal                           html  
    getTableStyle                           html  
    getTextOnOff                            html  
    getUp                                   html  
    getUpDown                               html  
    getVariationData                        html  
    get_conditions_given_selection          html  
    heatmapControlsUI                       html  
    heatmapJScode                           html  
    heatmapServer                           html  
    heatmapUI                               html  
    hideObj                                 html  
    histogramControlsUI                     html  
    installpack                             html  
    kmeansControlsUI                        html  
    lcfMetRadio                             html  
    loadpack                                html  
    mainPlotControlsUI                      html  
    mainScatterNew                          html  
    niceKmeans                              html  
    normalizationMethods                    html  
    palUI                                   html  
    panel.cor                               html  
    panel.hist                              html  
    pcaPlotControlsUI                       html  
    plotData                                html  
    plotMarginsUI                           html  
    plotSizeMarginsUI                       html  
    plotSizeUI                              html  
    plotTypeUI                              html  
    plot_pca                                html  
    prepDEOutput                            html  
    prepDataContainer                       html  
    prepGroup                               html  
    prepHeatData                            html  
    prepPCADat                              html  
    push                                    html  
    removeCols                              html  
    removeExtraCols                         html  
    round_vals                              html  
    runDE                                   html  
    runDESeq2                               html  
    runEdgeR                                html  
    runHeatmap                              html  
    runHeatmap2                             html  
    runLimma                                html  
    run_pca                                 html  
    selectConditions                        html  
    selectGroupInfo                         html  
    selectedInput                           html  
    sepRadio                                html  
    setBatch                                html  
    showObj                                 html  
    startDEBrowser                          html  
    startHeatmap                            html  
    textareaInput                           html  
    togglePanels                            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 'debrowser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'debrowser' as debrowser_1.20.1.zip
* DONE (debrowser)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'debrowser' successfully unpacked and MD5 sums checked

Tests output

debrowser.Rcheck/tests_i386/test-demo.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> require(shiny)
Loading required package: shiny
> library(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.20.1  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("demo data can be loaded", {
+     load(system.file("extdata", "demo", "demodata.Rda",
+         package = "debrowser"))
+     expect_true(is.data.frame(demodata))
+     expect_equal(demodata[29311, 2], 2)
+     expect_equal(demodata[29311, 5], 7.1)
+     expect_equal(demodata[29311, 6], 6)
+     expect_null(demodata[1, 7])
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
  12.32    1.28   13.61 

debrowser.Rcheck/tests_x64/test-demo.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> require(shiny)
Loading required package: shiny
> library(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.20.1  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("demo data can be loaded", {
+     load(system.file("extdata", "demo", "demodata.Rda",
+         package = "debrowser"))
+     expect_true(is.data.frame(demodata))
+     expect_equal(demodata[29311, 2], 2)
+     expect_equal(demodata[29311, 5], 7.1)
+     expect_equal(demodata[29311, 6], 6)
+     expect_null(demodata[1, 7])
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
  13.04    0.68   13.71 

debrowser.Rcheck/tests_i386/test-deseq.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.20.1  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> load(system.file("extdata", "demo", "demodata.Rda",
+     package = "debrowser"))
> columns <- c("exper_rep1", "exper_rep2", "exper_rep3",
+     "control_rep1", "control_rep2", "control_rep3")
> conds <- factor( c("Control", "Control", "Control",
+     "Treat", "Treat", "Treat") )
> data <- data.frame(demodata[, columns])
> 
> #Run DESeq2 with the following parameters
> params <- c("DESeq2", "parametric", F, "Wald", "None") 
> non_expressed_cutoff <- 10
> data <- subset(data, rowSums(data) > 10)
> test_that("Able to run DESeq2", {
+     deseqrun <- runDE(data, columns, conds, params)
+     expect_true(exists("deseqrun"))
+ })
Test passed 
> 
> ##################################################
> deseqrun <- runDE(data, columns, conds, params)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> 
> de_res <- data.frame(deseqrun)
> norm_data <- getNormalizedMatrix(data[, columns])
> rdata <- cbind(rownames(de_res), norm_data[rownames(de_res), columns],
+                 log10(rowMeans(norm_data[rownames(de_res),
+                 paste(c("exper_rep1", "exper_rep2", "exper_rep3"))])
+                 + 0.1), log10( rowMeans( norm_data[ rownames( de_res ),
+                 paste(c("control_rep1", "control_rep2", "control_rep3"))])
+                 + 0.1), de_res[rownames(de_res),
+                 c("padj", "log2FoldChange")], 2 ^ de_res[rownames(de_res),
+                 "log2FoldChange"], -1 *
+                 log10(de_res[rownames(de_res), "padj"]))
> colnames(rdata) <- c("ID", columns, "Cond1", "Cond2", "padj",
+                 "log2FoldChange", "foldChange", "log10padj")
> rdata <- as.data.frame(rdata)
> rdata$padj[is.na(rdata$padj)] <- 1
> 
> padj_cutoff <- 0.01
> foldChange_cutoff <- 2
> 
> rdata$Legend <- character(nrow(rdata))
> rdata$Legend[rdata$log2FoldChange > log2(foldChange_cutoff) &
+         rdata$padj < padj_cutoff] <- "Up"
> rdata$Legend[rdata$log2FoldChange < log2(1 / foldChange_cutoff) &
+         rdata$padj < padj_cutoff] <- "Down"
> rdata$Legend[abs(rdata$log2FoldChange) <= 
+         log2(foldChange_cutoff)] <- "NS"
> rdata$Legend[is.null(rdata$log10padj)] <- "NA"
> rdata$Size <- character(nrow(rdata))
> rdata[, "Size"] <- "40"
> 
> dat <- rdata
> dat$M <- rdata$Cond1 - rdata$Cond2
> dat$A <- (rdata$Cond1 + rdata$Cond2) / 2
> 
> updown <- rdata[rdata$Legend=="Up" | rdata$Legend=="Down",columns]
> ##################################################
> 
> test_that("Check the QC plots", {
+     expect_silent( all2all(data) )
+ })
Test passed 
> 
> 
> proc.time()
   user  system elapsed 
  35.84    2.31   38.14 

debrowser.Rcheck/tests_x64/test-deseq.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.20.1  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> load(system.file("extdata", "demo", "demodata.Rda",
+     package = "debrowser"))
> columns <- c("exper_rep1", "exper_rep2", "exper_rep3",
+     "control_rep1", "control_rep2", "control_rep3")
> conds <- factor( c("Control", "Control", "Control",
+     "Treat", "Treat", "Treat") )
> data <- data.frame(demodata[, columns])
> 
> #Run DESeq2 with the following parameters
> params <- c("DESeq2", "parametric", F, "Wald", "None") 
> non_expressed_cutoff <- 10
> data <- subset(data, rowSums(data) > 10)
> test_that("Able to run DESeq2", {
+     deseqrun <- runDE(data, columns, conds, params)
+     expect_true(exists("deseqrun"))
+ })
Test passed 
> 
> ##################################################
> deseqrun <- runDE(data, columns, conds, params)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> 
> de_res <- data.frame(deseqrun)
> norm_data <- getNormalizedMatrix(data[, columns])
> rdata <- cbind(rownames(de_res), norm_data[rownames(de_res), columns],
+                 log10(rowMeans(norm_data[rownames(de_res),
+                 paste(c("exper_rep1", "exper_rep2", "exper_rep3"))])
+                 + 0.1), log10( rowMeans( norm_data[ rownames( de_res ),
+                 paste(c("control_rep1", "control_rep2", "control_rep3"))])
+                 + 0.1), de_res[rownames(de_res),
+                 c("padj", "log2FoldChange")], 2 ^ de_res[rownames(de_res),
+                 "log2FoldChange"], -1 *
+                 log10(de_res[rownames(de_res), "padj"]))
> colnames(rdata) <- c("ID", columns, "Cond1", "Cond2", "padj",
+                 "log2FoldChange", "foldChange", "log10padj")
> rdata <- as.data.frame(rdata)
> rdata$padj[is.na(rdata$padj)] <- 1
> 
> padj_cutoff <- 0.01
> foldChange_cutoff <- 2
> 
> rdata$Legend <- character(nrow(rdata))
> rdata$Legend[rdata$log2FoldChange > log2(foldChange_cutoff) &
+         rdata$padj < padj_cutoff] <- "Up"
> rdata$Legend[rdata$log2FoldChange < log2(1 / foldChange_cutoff) &
+         rdata$padj < padj_cutoff] <- "Down"
> rdata$Legend[abs(rdata$log2FoldChange) <= 
+         log2(foldChange_cutoff)] <- "NS"
> rdata$Legend[is.null(rdata$log10padj)] <- "NA"
> rdata$Size <- character(nrow(rdata))
> rdata[, "Size"] <- "40"
> 
> dat <- rdata
> dat$M <- rdata$Cond1 - rdata$Cond2
> dat$A <- (rdata$Cond1 + rdata$Cond2) / 2
> 
> updown <- rdata[rdata$Legend=="Up" | rdata$Legend=="Down",columns]
> ##################################################
> 
> test_that("Check the QC plots", {
+     expect_silent( all2all(data) )
+ })
Test passed 
> 
> 
> proc.time()
   user  system elapsed 
  41.03    0.85   41.89 

debrowser.Rcheck/tests_i386/test-null.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> require(shiny)
Loading required package: shiny
> library(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.20.1  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("passing no data returns NULL", {
+     expect_null(compareClust() )
+     expect_null(getGOPlots(NULL, NULL))
+     null_deseq <- runDE(NULL)
+     expect_null(null_deseq)
+     expect_null(plot_pca(NULL))
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
  11.37    1.26   12.62 

debrowser.Rcheck/tests_x64/test-null.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> require(shiny)
Loading required package: shiny
> library(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.20.1  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("passing no data returns NULL", {
+     expect_null(compareClust() )
+     expect_null(getGOPlots(NULL, NULL))
+     null_deseq <- runDE(NULL)
+     expect_null(null_deseq)
+     expect_null(plot_pca(NULL))
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
  13.37    0.65   14.01 

debrowser.Rcheck/tests_i386/test-ui.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> require(shiny)
Loading required package: shiny
> library(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.20.1  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("able to create panel UI", {
+     expect_silent( QCPanel <- getQCPanel() )
+     expect_true(exists("QCPanel"))
+     expect_equal(QCPanel[[1]][[1]], "div")
+ 
+     expect_silent( downloads <- getDownloadSection() )
+     expect_true(exists("downloads"))
+     expect_equal(downloads[[1]][[1]], "div")
+ 
+     expect_silent( getMain <- getMainPanel() )
+     expect_true(exists("getMain"))
+     expect_equal(getMain[[1]][[1]], "div")
+ 
+     expect_silent( getStart <- getStartupMsg() )
+     expect_true(exists("getStart"))
+     expect_equal(getStart[[1]][[1]], "div")
+ 
+     expect_silent( getAfter <- getAfterLoadMsg() )
+     expect_true(exists("getAfter"))
+     expect_equal(getAfter[[1]][[1]], "div")
+ 
+     expect_silent(getGO <- getGoPanel() )
+     expect_true(exists("getGO"))
+     expect_equal(getGO[[1]][[1]], "div")
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
  11.70    1.57   13.25 

debrowser.Rcheck/tests_x64/test-ui.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> require(shiny)
Loading required package: shiny
> library(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.20.1  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("able to create panel UI", {
+     expect_silent( QCPanel <- getQCPanel() )
+     expect_true(exists("QCPanel"))
+     expect_equal(QCPanel[[1]][[1]], "div")
+ 
+     expect_silent( downloads <- getDownloadSection() )
+     expect_true(exists("downloads"))
+     expect_equal(downloads[[1]][[1]], "div")
+ 
+     expect_silent( getMain <- getMainPanel() )
+     expect_true(exists("getMain"))
+     expect_equal(getMain[[1]][[1]], "div")
+ 
+     expect_silent( getStart <- getStartupMsg() )
+     expect_true(exists("getStart"))
+     expect_equal(getStart[[1]][[1]], "div")
+ 
+     expect_silent( getAfter <- getAfterLoadMsg() )
+     expect_true(exists("getAfter"))
+     expect_equal(getAfter[[1]][[1]], "div")
+ 
+     expect_silent(getGO <- getGoPanel() )
+     expect_true(exists("getGO"))
+     expect_equal(getGO[[1]][[1]], "div")
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
  13.15    0.82   14.00 

Example timings

debrowser.Rcheck/examples_i386/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI000
IQRPlotControlsUI000
actionButtonDE000
addDataCols000
addID000
all2all0.160.000.15
all2allControlsUI0.040.000.03
applyFilters0.000.010.02
applyFiltersNew000
applyFiltersToMergedComparison000
barMainPlotControlsUI000
batchEffectUI0.010.050.06
batchMethod000
changeClusterOrder000
checkCountData000
checkMetaData000
clustFunParamsUI000
clusterData000
compareClust0.020.000.02
condSelectUI000
correctCombat000
correctHarman000
customColorsUI0.010.000.09
cutOffSelectionUI000
dataLCFUI0.030.030.06
dataLoadUI0.020.020.03
deServer0.020.000.02
deUI0.20.00.2
debrowserIQRplot000
debrowserall2all000
debrowserbarmainplot000
debrowserbatcheffect000
debrowserboxmainplot000
debrowsercondselect000
debrowserdataload000
debrowserdeanalysis000
debrowserdensityplot000
debrowserheatmap000
debrowserhistogram000
debrowserlowcountfilter000
debrowsermainplot000
debrowserpcaplot000
dendControlsUI0.010.000.01
densityPlotControlsUI000
distFunParamsUI000
drawKEGG000
drawPCAExplained000
fileTypes000
fileUploadBox000
generateTestData000
getAfterLoadMsg000
getAll2AllPlotUI000
getBSTableUI000
getBarMainPlot0.020.000.02
getBarMainPlotUI000
getBoxMainPlot000
getBoxMainPlotUI000
getColorShapeSelection000
getColors000
getCompSelection000
getCondMsg000
getConditionSelector000
getConditionSelectorFromMeta000
getCutOffSelection000
getDEAnalysisText000
getDEResultsUI000
getDataAssesmentText000
getDataForTables000
getDataPreparationText000
getDensityPlot000
getDensityPlotUI000
getDomains000
getDown000
getDownloadSection0.020.000.02
getEnrichDO000
getEnrichGO000
getEnrichKEGG000
getEntrezIds000
getEntrezTable000
getGOLeftMenu000
getGOPlots000
getGSEA000
getGeneList0.600.301.01
getGeneSetData000
getGoPanel0.030.000.03
getHeatmapUI000
getHelpButton000
getHideLegendOnOff000
getHistogramUI000
getIQRPlot000
getIQRPlotUI000
getIntroText000
getJSLine000
getKEGGModal0.020.000.01
getLeftMenu000
getLegendColors000
getLegendRadio000
getLegendSelect000
getLevelOrder000
getLoadingMsg000
getLogo000
getMainPanel000
getMainPlotUI000
getMainPlotsLeftMenu0.070.000.06
getMean000
getMergedComparison000
getMetaSelector000
getMethodDetails000
getMostVariedList000
getNormalizedMatrix0.010.000.02
getOrganism000
getOrganismBox000
getOrganismPathway000
getPCAPlotUI000
getPCAcontolUpdatesJS000
getPCAexplained2.970.173.22
getPCselection0.020.000.01
getPlotArea000
getProgramTitle000
getQAText000
getQCLeftMenu000
getQCPanel000
getSampleDetails000
getSampleNames000
getSamples000
getSearchData000
getSelHeat000
getSelectInputBox000
getSelectedCols000
getSelectedDatasetInput000
getShapeColor000
getStartPlotsMsg000
getStartupMsg000
getTabUpdateJS000
getTableDetails000
getTableModal0.010.000.02
getTableStyle000
getTextOnOff000
getUp000
getUpDown000
getVariationData000
get_conditions_given_selection000
heatmapControlsUI0.030.020.05
heatmapJScode000
heatmapServer000
heatmapUI0.080.000.07
hideObj000
histogramControlsUI000
installpack000
kmeansControlsUI000
lcfMetRadio000
loadpack0.040.140.19
mainPlotControlsUI000
mainScatterNew000
niceKmeans000
normalizationMethods000
palUI000
panel.cor000
panel.hist000
pcaPlotControlsUI0.010.000.02
plotData000
plotMarginsUI000
plotSizeMarginsUI0.020.000.01
plotSizeUI000
plotTypeUI000
plot_pca1.060.061.13
prepDEOutput000
prepDataContainer000
prepGroup000
prepHeatData000
prepPCADat000
push000
removeCols000
removeExtraCols000
round_vals000
runDE000
runDESeq2000
runEdgeR0.000.020.02
runHeatmap000
runHeatmap2000
runLimma000
run_pca1.440.011.45
selectConditions000
selectGroupInfo000
selectedInput000
sepRadio0.020.000.01
setBatch000
showObj000
startDEBrowser000
startHeatmap000
textareaInput000
togglePanels000

debrowser.Rcheck/examples_x64/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.020.000.01
IQRPlotControlsUI000
actionButtonDE0.010.000.02
addDataCols000
addID000
all2all0.170.000.17
all2allControlsUI0.050.000.05
applyFilters000
applyFiltersNew000
applyFiltersToMergedComparison000
barMainPlotControlsUI000
batchEffectUI0.060.000.06
batchMethod000
changeClusterOrder000
checkCountData000
checkMetaData000
clustFunParamsUI000
clusterData000
compareClust000
condSelectUI0.000.010.02
correctCombat000
correctHarman000
customColorsUI0.000.020.01
cutOffSelectionUI000
dataLCFUI0.040.010.05
dataLoadUI0.030.000.03
deServer0.010.000.02
deUI0.190.020.20
debrowserIQRplot000
debrowserall2all000
debrowserbarmainplot000
debrowserbatcheffect000
debrowserboxmainplot000
debrowsercondselect000
debrowserdataload000
debrowserdeanalysis000
debrowserdensityplot000
debrowserheatmap000
debrowserhistogram000
debrowserlowcountfilter000
debrowsermainplot000
debrowserpcaplot000
dendControlsUI0.010.000.02
densityPlotControlsUI000
distFunParamsUI000
drawKEGG000
drawPCAExplained000
fileTypes000
fileUploadBox000
generateTestData000
getAfterLoadMsg0.020.000.02
getAll2AllPlotUI000
getBSTableUI000
getBarMainPlot000
getBarMainPlotUI000
getBoxMainPlot000
getBoxMainPlotUI000
getColorShapeSelection000
getColors000
getCompSelection000
getCondMsg000
getConditionSelector000
getConditionSelectorFromMeta0.010.000.01
getCutOffSelection000
getDEAnalysisText000
getDEResultsUI000
getDataAssesmentText000
getDataForTables000
getDataPreparationText0.020.000.02
getDensityPlot000
getDensityPlotUI000
getDomains000
getDown000
getDownloadSection000
getEnrichDO000
getEnrichGO000
getEnrichKEGG000
getEntrezIds000
getEntrezTable000
getGOLeftMenu000
getGOPlots000
getGSEA000
getGeneList0.780.291.08
getGeneSetData000
getGoPanel0.050.000.04
getHeatmapUI0.000.020.02
getHelpButton000
getHideLegendOnOff000
getHistogramUI000
getIQRPlot000
getIQRPlotUI000
getIntroText000
getJSLine0.020.000.01
getKEGGModal000
getLeftMenu000
getLegendColors000
getLegendRadio0.010.000.02
getLegendSelect000
getLevelOrder000
getLoadingMsg000
getLogo000
getMainPanel0.000.010.02
getMainPlotUI000
getMainPlotsLeftMenu0.100.020.10
getMean000
getMergedComparison000
getMetaSelector000
getMethodDetails000
getMostVariedList000
getNormalizedMatrix0.010.000.02
getOrganism000
getOrganismBox000
getOrganismPathway000
getPCAPlotUI000
getPCAcontolUpdatesJS000
getPCAexplained2.420.112.53
getPCselection000
getPlotArea000
getProgramTitle000
getQAText000
getQCLeftMenu000
getQCPanel000
getSampleDetails000
getSampleNames000
getSamples000
getSearchData000
getSelHeat000
getSelectInputBox000
getSelectedCols000
getSelectedDatasetInput000
getShapeColor000
getStartPlotsMsg0.020.000.01
getStartupMsg000
getTabUpdateJS000
getTableDetails000
getTableModal0.010.000.02
getTableStyle000
getTextOnOff000
getUp000
getUpDown000
getVariationData000
get_conditions_given_selection000
heatmapControlsUI0.030.000.03
heatmapJScode000
heatmapServer000
heatmapUI0.110.000.11
hideObj000
histogramControlsUI000
installpack000
kmeansControlsUI000
lcfMetRadio000
loadpack0.090.140.23
mainPlotControlsUI000
mainScatterNew000
niceKmeans000
normalizationMethods0.020.000.01
palUI000
panel.cor000
panel.hist000
pcaPlotControlsUI0.010.000.02
plotData000
plotMarginsUI0.020.000.01
plotSizeMarginsUI0.010.000.02
plotSizeUI000
plotTypeUI000
plot_pca1.600.031.62
prepDEOutput000
prepDataContainer000
prepGroup000
prepHeatData000
prepPCADat000
push000
removeCols000
removeExtraCols000
round_vals000
runDE000
runDESeq2000
runEdgeR000
runHeatmap000
runHeatmap2000
runLimma000
run_pca1.600.011.61
selectConditions000
selectGroupInfo000
selectedInput000
sepRadio000
setBatch000
showObj000
startDEBrowser000
startHeatmap000
textareaInput000
togglePanels000