Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:05:41 -0400 (Wed, 22 Sep 2021).

CHECK results for debrowser on machv2

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: 2021-09-21 04:50:12 -0400 (Tue, 21 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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:debrowser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings debrowser_1.20.1.tar.gz
StartedAt: 2021-09-21 18:11:29 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 18:19:07 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 457.8 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:debrowser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings debrowser_1.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/debrowser.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/debrowser.Rcheck/00check.log’
for details.



Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL debrowser
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘debrowser’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (debrowser)

Tests output

debrowser.Rcheck/tests/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-apple-darwin17.0 (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 
 17.263   0.880  18.134 

debrowser.Rcheck/tests/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-apple-darwin17.0 (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 
 53.270   1.269  54.565 

debrowser.Rcheck/tests/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-apple-darwin17.0 (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 
 16.217   0.840  17.043 

debrowser.Rcheck/tests/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-apple-darwin17.0 (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 
 16.614   0.872  17.471 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0050.0010.005
IQRPlotControlsUI0.0020.0000.002
actionButtonDE0.0050.0010.005
addDataCols0.0000.0000.001
addID0.0010.0000.000
all2all0.2100.0240.234
all2allControlsUI0.0390.0060.046
applyFilters0.0010.0000.001
applyFiltersNew0.0010.0000.000
applyFiltersToMergedComparison0.0000.0000.001
barMainPlotControlsUI0.0020.0000.002
batchEffectUI0.0670.0100.078
batchMethod0.0030.0010.004
changeClusterOrder0.0000.0010.000
checkCountData0.0010.0000.001
checkMetaData0.0010.0000.000
clustFunParamsUI000
clusterData0.0000.0000.001
compareClust000
condSelectUI0.0080.0010.009
correctCombat0.0000.0000.001
correctHarman0.0000.0010.001
customColorsUI0.0100.0030.013
cutOffSelectionUI0.0040.0010.005
dataLCFUI0.0280.0050.033
dataLoadUI0.0220.0030.026
deServer0.0100.0050.015
deUI0.1610.0250.187
debrowserIQRplot0.0010.0000.000
debrowserall2all0.0000.0000.001
debrowserbarmainplot000
debrowserbatcheffect0.0000.0000.001
debrowserboxmainplot000
debrowsercondselect0.0010.0010.000
debrowserdataload0.0010.0000.001
debrowserdeanalysis0.0010.0000.001
debrowserdensityplot0.0010.0000.001
debrowserheatmap0.0010.0000.002
debrowserhistogram0.0010.0000.001
debrowserlowcountfilter0.0000.0000.002
debrowsermainplot0.0010.0000.001
debrowserpcaplot0.0000.0000.001
dendControlsUI0.0060.0010.007
densityPlotControlsUI0.0020.0010.002
distFunParamsUI0.0000.0000.001
drawKEGG000
drawPCAExplained000
fileTypes000
fileUploadBox0.0040.0010.004
generateTestData0.0010.0000.001
getAfterLoadMsg0.0010.0000.001
getAll2AllPlotUI0.0010.0000.000
getBSTableUI000
getBarMainPlot0.0000.0010.001
getBarMainPlotUI000
getBoxMainPlot0.0000.0000.001
getBoxMainPlotUI000
getColorShapeSelection0.0000.0000.001
getColors0.0000.0010.000
getCompSelection0.0040.0010.004
getCondMsg0.0000.0000.001
getConditionSelector0.0000.0000.001
getConditionSelectorFromMeta0.0030.0000.003
getCutOffSelection0.0030.0000.004
getDEAnalysisText0.0020.0000.003
getDEResultsUI0.0020.0000.002
getDataAssesmentText0.0030.0000.004
getDataForTables0.0010.0000.001
getDataPreparationText0.0010.0010.002
getDensityPlot0.0010.0000.001
getDensityPlotUI0.0000.0000.001
getDomains0.0000.0000.001
getDown0.0010.0000.000
getDownloadSection0.0090.0010.009
getEnrichDO000
getEnrichGO000
getEnrichKEGG0.0010.0000.001
getEntrezIds0.0000.0010.000
getEntrezTable000
getGOLeftMenu0.0130.0020.015
getGOPlots0.0000.0000.001
getGSEA0.0010.0000.001
getGeneList0.4920.0750.569
getGeneSetData0.0000.0000.001
getGoPanel0.0290.0030.033
getHeatmapUI0.0000.0000.001
getHelpButton000
getHideLegendOnOff0.0010.0010.002
getHistogramUI000
getIQRPlot0.0000.0010.000
getIQRPlotUI0.0010.0000.001
getIntroText0.0030.0010.002
getJSLine0.0020.0000.003
getKEGGModal0.0030.0000.002
getLeftMenu0.0010.0000.001
getLegendColors0.0010.0000.001
getLegendRadio0.0030.0000.004
getLegendSelect0.0020.0000.002
getLevelOrder000
getLoadingMsg0.0020.0010.003
getLogo0.0010.0010.002
getMainPanel0.0020.0000.002
getMainPlotUI000
getMainPlotsLeftMenu0.0800.0020.083
getMean0.0010.0010.000
getMergedComparison0.0000.0000.001
getMetaSelector000
getMethodDetails0.0000.0000.001
getMostVariedList0.0000.0000.001
getNormalizedMatrix0.0180.0010.020
getOrganism000
getOrganismBox0.0010.0000.002
getOrganismPathway0.0000.0000.001
getPCAPlotUI0.0010.0000.001
getPCAcontolUpdatesJS0.0000.0010.001
getPCAexplained2.6300.1222.754
getPCselection0.0010.0000.002
getPlotArea0.0000.0000.001
getProgramTitle0.0000.0000.001
getQAText0.0030.0010.003
getQCLeftMenu0.0010.0000.001
getQCPanel0.0040.0010.004
getSampleDetails0.0010.0010.000
getSampleNames0.0000.0010.000
getSamples000
getSearchData0.0000.0000.001
getSelHeat0.0010.0000.001
getSelectInputBox0.0000.0000.001
getSelectedCols0.0000.0000.001
getSelectedDatasetInput0.0000.0010.001
getShapeColor0.0000.0000.001
getStartPlotsMsg0.0040.0010.005
getStartupMsg0.0040.0000.004
getTabUpdateJS0.0000.0010.001
getTableDetails0.0010.0010.001
getTableModal0.0100.0020.012
getTableStyle0.0000.0000.001
getTextOnOff0.0030.0000.003
getUp0.0000.0000.001
getUpDown0.0000.0010.001
getVariationData0.0000.0010.001
get_conditions_given_selection0.0010.0000.001
heatmapControlsUI0.0400.0010.041
heatmapJScode000
heatmapServer0.0010.0010.001
heatmapUI0.0920.0050.097
hideObj0.0000.0010.001
histogramControlsUI0.0010.0000.001
installpack000
kmeansControlsUI0.0070.0010.007
lcfMetRadio0.0030.0000.003
loadpack0.0160.0310.047
mainPlotControlsUI0.0060.0000.007
mainScatterNew0.0000.0000.001
niceKmeans000
normalizationMethods0.0020.0000.002
palUI0.0020.0010.002
panel.cor0.0010.0000.001
panel.hist0.0000.0010.000
pcaPlotControlsUI0.0080.0000.009
plotData0.0010.0000.001
plotMarginsUI0.0050.0010.006
plotSizeMarginsUI0.0090.0000.009
plotSizeUI0.0020.0000.003
plotTypeUI0.0010.0000.001
plot_pca1.9290.0381.973
prepDEOutput0.0010.0000.000
prepDataContainer0.0000.0000.001
prepGroup0.0000.0000.001
prepHeatData000
prepPCADat0.0000.0000.001
push0.0010.0000.000
removeCols000
removeExtraCols0.0020.0000.003
round_vals0.0010.0000.001
runDE0.0010.0010.001
runDESeq20.0010.0000.001
runEdgeR0.0000.0000.001
runHeatmap0.0010.0000.001
runHeatmap20.0010.0010.001
runLimma0.0010.0000.001
run_pca1.0230.0351.058
selectConditions0.0010.0000.001
selectGroupInfo000
selectedInput000
sepRadio0.0030.0000.002
setBatch0.0000.0000.001
showObj0.0000.0000.001
startDEBrowser000
startHeatmap0.0010.0000.000
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