Back to Build/check report for BioC 3.17:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-02-27 02:34:32 -0000 (Mon, 27 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4259
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 kunpeng1


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 478/2169HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.27.1  (landing page)
Alper Kucukural
Snapshot Date: 2023-02-23 09:40:21 -0000 (Thu, 23 Feb 2023)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: master
git_last_commit: dc27555
git_last_commit_date: 2023-02-20 19:24:20 -0000 (Mon, 20 Feb 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: debrowser
Version: 1.27.1
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings debrowser_1.27.1.tar.gz
StartedAt: 2023-02-24 09:53:32 -0000 (Fri, 24 Feb 2023)
EndedAt: 2023-02-24 10:08:51 -0000 (Fri, 24 Feb 2023)
EllapsedTime: 918.5 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings debrowser_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/debrowser.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.27.1’
* 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 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’
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 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
getPCAexplained 3.56  0.992   5.427
* 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-3.17-bioc/meat/debrowser.Rcheck/00check.log’
for details.

Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL debrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 v1.27.1  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 
 15.835   0.674  16.839

debrowser.Rcheck/tests/test-deseq.Rout


R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 v1.27.1  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"))
> 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 
 41.027   1.118  42.134

debrowser.Rcheck/tests/test-null.Rout


R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 v1.27.1  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 
 15.983   0.898  17.288

debrowser.Rcheck/tests/test-ui.Rout


R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 v1.27.1  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 
 15.891   0.768  16.767

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0300.0000.036
IQRPlotControlsUI0.0020.0000.002
actionButtonDE0.0050.0000.004
addDataCols0.0000.0000.001
addID000
all2all0.1720.0080.182
all2allControlsUI0.0410.0000.065
applyFilters0.0010.0000.000
applyFiltersNew000
applyFiltersToMergedComparison000
barMainPlotControlsUI0.0010.0000.002
batchEffectUI0.0500.0000.061
batchMethod0.0020.0000.002
changeClusterOrder000
checkCountData0.0010.0000.000
checkMetaData000
clustFunParamsUI000
clusterData0.0000.0000.001
compareClust0.0000.0010.001
condSelectUI0.0060.0000.006
correctCombat0.0010.0000.000
correctHarman000
customColorsUI0.0040.0040.010
cutOffSelectionUI0.0050.0000.005
dataLCFUI0.0140.0000.014
dataLoadUI0.0100.0040.015
deServer0.0380.0040.041
deUI0.1190.0040.124
debrowserIQRplot000
debrowserall2all0.0010.0000.000
debrowserbarmainplot0.0010.0000.000
debrowserbatcheffect0.0010.0000.000
debrowserboxmainplot0.0010.0000.000
debrowsercondselect000
debrowserdataload0.0010.0000.000
debrowserdeanalysis0.0010.0000.000
debrowserdensityplot0.0010.0000.000
debrowserheatmap0.0010.0000.000
debrowserhistogram0.0010.0000.000
debrowserlowcountfilter0.0010.0000.000
debrowsermainplot0.0010.0000.000
debrowserpcaplot0.0010.0000.000
dendControlsUI0.0080.0000.007
densityPlotControlsUI0.0020.0000.002
distFunParamsUI000
drawKEGG0.0010.0000.000
drawPCAExplained0.0010.0000.000
fileTypes000
fileUploadBox0.0030.0000.004
generateTestData0.0010.0000.000
getAfterLoadMsg0.0010.0000.000
getAll2AllPlotUI0.0010.0000.000
getBSTableUI0.0010.0000.000
getBarMainPlot0.0010.0000.000
getBarMainPlotUI0.0010.0000.000
getBoxMainPlot0.0010.0000.000
getBoxMainPlotUI0.0010.0000.000
getColorShapeSelection000
getColors000
getCompSelection0.0020.0000.003
getCondMsg0.0000.0000.001
getConditionSelector000
getConditionSelectorFromMeta000
getCovariateDetails000
getCutOffSelection0.0030.0000.002
getDEAnalysisText0.0030.0000.002
getDEResultsUI0.0020.0000.001
getDataAssesmentText0.0010.0000.002
getDataForTables0.0010.0000.000
getDataPreparationText0.0010.0000.001
getDensityPlot0.0010.0000.000
getDensityPlotUI0.0010.0000.000
getDomains000
getDown0.0000.0000.001
getDownloadSection0.0090.0000.009
getEnrichDO000
getEnrichGO0.0010.0000.000
getEnrichKEGG0.0010.0000.000
getEntrezIds0.0010.0000.000
getEntrezTable0.0010.0000.000
getGOLeftMenu0.0130.0000.012
getGOPlots0.0010.0000.000
getGSEA0.0010.0000.000
getGeneList0.4580.0790.572
getGeneSetData0.0000.0000.001
getGoPanel0.0130.0010.013
getGroupSelector0.0010.0000.000
getHeatmapUI0.0010.0000.000
getHelpButton000
getHideLegendOnOff0.0020.0000.002
getHistogramUI0.0000.0000.001
getIQRPlot0.0000.0000.001
getIQRPlotUI0.0000.0000.001
getIntroText0.0010.0000.002
getJSLine0.0020.0000.003
getKEGGModal0.0030.0000.003
getLeftMenu000
getLegendColors0.0010.0000.001
getLegendRadio0.0040.0000.003
getLegendSelect0.0020.0000.002
getLevelOrder0.0000.0000.001
getLoadingMsg0.0000.0010.002
getLogo0.0010.0010.001
getMainPanel0.0030.0000.002
getMainPlotUI000
getMainPlotsLeftMenu0.2150.0040.219
getMean000
getMergedComparison000
getMetaSelector000
getMethodDetails0.0010.0000.000
getMostVariedList000
getNormalizedMatrix0.0180.0000.019
getOrganism0.0000.0000.001
getOrganismBox0.0020.0000.003
getOrganismPathway000
getPCAPlotUI000
getPCAcontolUpdatesJS0.0010.0000.000
getPCAexplained3.5600.9925.427
getPCselection0.0010.0000.001
getPlotArea000
getProgramTitle0.0000.0010.000
getQAText0.0000.0020.002
getQCLeftMenu000
getQCPanel0.0050.0000.004
getSampleDetails0.0000.0000.001
getSampleNames0.0000.0010.001
getSamples000
getSearchData000
getSelHeat000
getSelectInputBox000
getSelectedCols0.0000.0000.001
getSelectedDatasetInput000
getShapeColor000
getStartPlotsMsg0.0000.0030.003
getStartupMsg0.0030.0000.003
getTabUpdateJS0.0000.0000.001
getTableDetails0.0010.0000.001
getTableModal0.0010.0040.007
getTableStyle000
getUp000
getUpDown000
getVariationData000
get_conditions_given_selection000
heatmapControlsUI0.0490.0030.060
heatmapJScode000
heatmapServer0.0010.0010.001
heatmapUI0.0840.0080.097
hideObj000
histogramControlsUI0.0000.0000.001
installpack000
kmeansControlsUI0.0090.0000.008
lcfMetRadio0.0030.0000.003
loadpack0.0170.3553.385
mainPlotControlsUI0.0090.0000.009
mainScatterNew0.0010.0000.001
niceKmeans000
normalizationMethods0.0020.0000.003
palUI0.0030.0000.002
panel.cor0.0020.0010.004
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0060.0000.007
plotData0.0010.0000.001
plotMarginsUI0.0060.0000.007
plotSizeMarginsUI0.0080.0030.012
plotSizeUI0.0040.0000.004
plotTypeUI0.0000.0010.001
plot_pca1.2270.0431.332
prepDEOutput0.0000.0010.001
prepDataContainer0.0000.0000.001
prepGroup0.0000.0010.000
prepHeatData0.0000.0010.000
prepPCADat000
push000
removeCols0.0000.0000.001
removeExtraCols0.0020.0000.002
round_vals0.0010.0000.001
runDE0.0000.0000.001
runDESeq20.0000.0000.001
runEdgeR0.0000.0000.001
runHeatmap0.0010.0000.000
runHeatmap2000
runLimma0.0010.0000.001
run_pca1.0620.0271.091
selectConditions0.0000.0000.001
selectGroupInfo0.0000.0010.000
selectedInput000
sepRadio0.0010.0020.002
setBatch0.0010.0000.000
showObj000
startDEBrowser000
startHeatmap0.0010.0000.000
textareaInput0.0010.0000.001
togglePanels0.0010.0000.001