Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-03-29 11:05:02 -0400 (Wed, 29 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4482
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4278
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4306
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for debrowser on nebbiolo2


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? 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 486/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.26.3  (landing page)
Alper Kucukural
Snapshot Date: 2023-03-27 14:00:04 -0400 (Mon, 27 Mar 2023)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: RELEASE_3_16
git_last_commit: 4fb9588
git_last_commit_date: 2023-03-12 18:21:05 -0400 (Sun, 12 Mar 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: debrowser
Version: 1.26.3
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings debrowser_1.26.3.tar.gz
StartedAt: 2023-03-27 20:12:45 -0400 (Mon, 27 Mar 2023)
EndedAt: 2023-03-27 20:19:07 -0400 (Mon, 27 Mar 2023)
EllapsedTime: 382.5 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings debrowser_1.26.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/debrowser.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.26.3’
* 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 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 loading without being on the library search path ... 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’
generateTestData: no visible binding for global variable ‘metadata’
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’
getGSEA: no visible global function definition for ‘is’
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 ‘textName’
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 is metadata samples textName x y
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ...
  ‘DEBrowser.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/debrowser.Rcheck/00check.log’
for details.



Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL debrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 v1.26.3  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 
 13.296   1.465  14.748 

debrowser.Rcheck/tests/test-deseq.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 v1.26.3  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"))
> metadata <- metadatatable 
> 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", "NoCovariate", "parametric", F, "Wald", "None") 
> non_expressed_cutoff <- 10
> data <- subset(data, rowSums(data) > 10)
> test_that("Able to run DESeq2", {
+     deseqrun <- runDE(data, metadata, columns, conds, params)
+     expect_true(exists("deseqrun"))
+ })
Test passed 🥇
> 
> ##################################################
> deseqrun <- runDE(data, metadata, 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]
> ##################################################
> 
> 
> 
> proc.time()
   user  system elapsed 
 28.936   1.133  30.056 

debrowser.Rcheck/tests/test-null.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 v1.26.3  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 
 12.711   1.344  14.042 

debrowser.Rcheck/tests/test-ui.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 v1.26.3  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 
 13.313   0.823  14.124 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0500.0240.074
IQRPlotControlsUI0.0010.0000.001
actionButtonDE0.0040.0000.004
addDataCols000
addID0.0000.0000.001
all2all0.1370.0040.141
all2allControlsUI0.0300.0000.031
applyFilters0.0010.0000.001
applyFiltersNew0.0010.0000.001
applyFiltersToMergedComparison000
barMainPlotControlsUI0.0010.0000.001
batchEffectUI0.0340.0040.038
batchMethod0.0010.0000.002
changeClusterOrder0.0010.0000.001
checkCountData000
checkMetaData000
clustFunParamsUI000
clusterData000
compareClust0.0010.0000.001
condSelectUI0.0040.0000.004
correctCombat000
correctHarman000
customColorsUI0.0020.0040.006
cutOffSelectionUI0.0000.0040.004
dataLCFUI0.0110.0000.012
dataLoadUI0.0110.0000.011
deServer0.0060.0000.006
deUI0.0920.0040.096
debrowserIQRplot000
debrowserall2all000
debrowserbarmainplot0.0000.0000.001
debrowserbatcheffect0.0000.0000.001
debrowserboxmainplot000
debrowsercondselect000
debrowserdataload0.0000.0010.001
debrowserdeanalysis0.0000.0000.001
debrowserdensityplot0.0000.0010.000
debrowserheatmap0.0000.0010.000
debrowserhistogram0.0000.0000.001
debrowserlowcountfilter0.0000.0000.001
debrowsermainplot0.0000.0000.001
debrowserpcaplot000
dendControlsUI0.0050.0000.006
densityPlotControlsUI0.0010.0000.001
distFunParamsUI000
drawKEGG000
drawPCAExplained000
fileTypes000
fileUploadBox0.0030.0000.003
generateTestData0.0000.0000.001
getAfterLoadMsg0.0000.0000.001
getAll2AllPlotUI000
getBSTableUI0.0000.0010.000
getBarMainPlot0.0000.0000.001
getBarMainPlotUI000
getBoxMainPlot0.0000.0010.000
getBoxMainPlotUI0.0010.0000.000
getColorShapeSelection000
getColors000
getCompSelection0.0020.0000.002
getCondMsg0.0010.0000.000
getConditionSelector000
getConditionSelectorFromMeta000
getCovariateDetails0.0000.0000.001
getCutOffSelection0.0020.0000.002
getDEAnalysisText0.0020.0000.002
getDEResultsUI0.0010.0000.002
getDataAssesmentText0.0010.0000.001
getDataForTables000
getDataPreparationText0.0010.0000.001
getDensityPlot000
getDensityPlotUI0.0010.0000.000
getDomains000
getDown0.0010.0000.000
getDownloadSection0.0070.0000.007
getEnrichDO000
getEnrichGO000
getEnrichKEGG000
getEntrezIds0.0010.0000.000
getEntrezTable0.0000.0000.001
getGOLeftMenu0.0090.0000.010
getGOPlots0.0000.0000.001
getGSEA000
getGeneList0.5440.0640.607
getGeneSetData0.0010.0000.000
getGoPanel0.0110.0000.010
getGroupSelector000
getHeatmapUI0.0010.0000.000
getHelpButton000
getHideLegendOnOff0.0010.0000.002
getHistogramUI000
getIQRPlot0.0010.0000.000
getIQRPlotUI0.0000.0000.001
getIntroText0.0010.0000.001
getJSLine0.0020.0000.002
getKEGGModal0.0000.0020.003
getLeftMenu000
getLegendColors0.0010.0000.001
getLegendRadio0.0020.0000.002
getLegendSelect0.0020.0000.002
getLevelOrder0.0000.0000.001
getLoadingMsg0.0010.0000.001
getLogo0.0000.0000.001
getMainPanel0.0010.0000.001
getMainPlotUI0.0000.0000.001
getMainPlotsLeftMenu0.0570.0040.061
getMean000
getMergedComparison0.0010.0000.001
getMetaSelector000
getMethodDetails000
getMostVariedList0.0010.0000.000
getNormalizedMatrix0.0130.0040.017
getOrganism0.0010.0000.000
getOrganismBox0.0030.0000.003
getOrganismPathway0.0010.0000.000
getPCAPlotUI0.0000.0000.001
getPCAcontolUpdatesJS000
getPCAexplained2.930.283.21
getPCselection000
getPlotArea000
getProgramTitle0.0000.0010.000
getQAText0.0000.0010.001
getQCLeftMenu0.0000.0000.001
getQCPanel0.0040.0000.003
getSampleDetails000
getSampleNames000
getSearchData000
getSelHeat0.0000.0000.001
getSelectInputBox000
getSelectedCols000
getSelectedDatasetInput0.0010.0000.000
getShapeColor000
getStartPlotsMsg0.0020.0000.002
getStartupMsg0.0020.0000.002
getTabUpdateJS0.0010.0000.000
getTableDetails000
getTableModal0.0030.0000.003
getTableStyle000
getUp000
getUpDown000
getVariationData000
get_conditions_given_selection000
heatmapControlsUI0.0300.0040.035
heatmapJScode000
heatmapServer0.0010.0000.000
heatmapUI0.0550.0120.067
hideObj000
histogramControlsUI0.0000.0000.001
installpack000
kmeansControlsUI0.0030.0020.005
lcfMetRadio0.0020.0000.002
loadpack0.0050.0200.025
mainPlotControlsUI0.0060.0000.005
mainScatterNew0.0010.0000.000
niceKmeans000
normalizationMethods0.0000.0010.002
palUI0.0000.0020.001
panel.cor0.0010.0000.001
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0040.0000.004
plotData000
plotMarginsUI0.0040.0000.005
plotSizeMarginsUI0.0030.0040.008
plotSizeUI0.0020.0000.002
plotTypeUI0.0000.0000.001
plot_pca0.7430.0720.814
prepDataContainer0.0010.0000.001
prepGroup0.0010.0000.000
prepHeatData000
prepPCADat000
push000
removeCols0.0010.0000.000
removeExtraCols0.0010.0000.001
round_vals0.0000.0000.001
runDE000
runDESeq20.0000.0000.001
runEdgeR0.0000.0000.001
runHeatmap0.0000.0000.001
runHeatmap20.0010.0000.000
runLimma0.0010.0000.000
run_pca0.6480.0120.660
selectConditions0.0000.0000.001
selectGroupInfo0.0000.0000.001
selectedInput000
sepRadio0.0020.0000.002
setBatch000
showObj0.0010.0000.000
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