Back to Multiple platform build/check report for BioC 3.11
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

CHECK report for debrowser on celaya2

This page was generated on 2020-01-16 13:44:45 -0500 (Thu, 16 Jan 2020).

Package 415/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.15.2
Alper Kucukural
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/debrowser
Branch: master
Last Commit: 3aa063f
Last Changed Date: 2019-12-23 16:08:34 -0500 (Mon, 23 Dec 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: debrowser
Version: 1.15.2
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_1.15.2.tar.gz
StartedAt: 2020-01-16 03:33:15 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 03:43:54 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 639.3 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_1.15.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/debrowser.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.15.2’
* 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’
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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 v1.15.2  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])
+ })
> 
> proc.time()
   user  system elapsed 
 23.142   2.299  25.399

debrowser.Rcheck/tests/test-deseq.Rout


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 v1.15.2  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])
> params <-
+         #Run DESeq2 with the following parameters
+         c("DESeq2", "parametric", F, "Wald") 
> 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"))
+ })
> 
> ##################################################
> 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) )
+ })
> 
> 
> proc.time()
   user  system elapsed 
 68.766   3.392  74.965

debrowser.Rcheck/tests/test-null.Rout


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 v1.15.2  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))
+ })
> 
> proc.time()
   user  system elapsed 
 22.448   2.320  24.724

debrowser.Rcheck/tests/test-ui.Rout


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 v1.15.2  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")
+ })
> 
> proc.time()
   user  system elapsed 
 23.080   2.418  25.451

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0170.0040.020
IQRPlotControlsUI0.0030.0010.003
actionButtonDE0.0050.0010.006
addDataCols0.0000.0000.001
addID0.0010.0000.001
all2all0.3490.0050.355
all2allControlsUI0.0030.0000.003
applyFilters0.0010.0010.001
applyFiltersNew0.0000.0000.001
applyFiltersToMergedComparison000
barMainPlotControlsUI0.0020.0010.003
batchEffectUI0.1170.0100.126
batchMethod0.0050.0010.006
changeClusterOrder0.0010.0010.001
checkCountData0.0010.0010.001
checkMetaData0.0010.0010.001
clustFunParamsUI0.0000.0010.001
clusterData0.0000.0000.001
compareClust0.0000.0000.001
condSelectUI0.0090.0000.010
correctCombat0.0000.0000.001
correctHarman0.0000.0000.001
customColorsUI0.0130.0030.018
cutOffSelectionUI0.0060.0000.007
dataLCFUI0.0430.0040.048
dataLoadUI0.0380.0030.041
deServer0.0180.0040.022
deUI1.3660.2071.677
debrowserIQRplot0.0010.0000.000
debrowserall2all0.0010.0010.001
debrowserbarmainplot0.0010.0000.001
debrowserbatcheffect0.0010.0000.001
debrowserboxmainplot0.0000.0000.001
debrowsercondselect0.0000.0010.001
debrowserdataload0.0010.0000.002
debrowserdeanalysis0.0010.0000.001
debrowserdensityplot0.0010.0000.001
debrowserheatmap0.0010.0000.002
debrowserhistogram0.0000.0010.001
debrowserlowcountfilter0.0010.0000.001
debrowsermainplot0.0010.0000.001
debrowserpcaplot0.0010.0000.001
dendControlsUI0.0150.0000.014
densityPlotControlsUI0.0030.0000.003
distFunParamsUI0.0000.0000.001
drawKEGG0.0000.0000.001
drawPCAExplained0.0000.0000.001
fileTypes0.0010.0010.001
fileUploadBox0.0070.0000.007
generateTestData0.0010.0000.001
getAfterLoadMsg0.0010.0000.001
getAll2AllPlotUI0.0010.0010.001
getBSTableUI0.0010.0000.001
getBarMainPlot0.0010.0000.001
getBarMainPlotUI0.0010.0000.001
getBoxMainPlot0.0010.0010.001
getBoxMainPlotUI0.0010.0010.001
getColorShapeSelection0.0010.0000.001
getColors0.0010.0000.001
getCompSelection0.0040.0010.004
getCondMsg0.0000.0000.001
getConditionSelector0.0000.0000.001
getConditionSelectorFromMeta0.0050.0000.005
getCutOffSelection0.0030.0000.004
getDEAnalysisText0.0040.0000.005
getDEResultsUI0.0040.0000.005
getDataAssesmentText0.0040.0000.004
getDataForTables0.0010.0000.001
getDataPreparationText0.0030.0000.003
getDensityPlot0.0000.0010.001
getDensityPlotUI0.0000.0000.001
getDomains0.0000.0000.001
getDown0.0010.0000.000
getDownloadSection0.0150.0010.015
getEnrichDO000
getEnrichGO0.0010.0000.001
getEnrichKEGG0.0010.0000.001
getEntrezIds0.0000.0010.000
getEntrezTable0.0010.0000.001
getGOLeftMenu0.0140.0000.013
getGOPlots000
getGeneList1.0830.1181.202
getGeneSetData0.0000.0000.001
getGoPanel0.0290.0040.032
getHeatmapUI0.0010.0000.001
getHelpButton0.0000.0000.001
getHideLegendOnOff0.0040.0010.004
getHistogramUI0.0000.0000.001
getIQRPlot0.0010.0000.001
getIQRPlotUI0.0010.0000.000
getIntroText0.0030.0000.003
getJSLine0.0120.0020.014
getKEGGModal0.0050.0000.006
getLeftMenu0.0010.0010.000
getLegendColors000
getLegendRadio0.0040.0000.005
getLegendSelect0.0030.0000.003
getLevelOrder0.0010.0000.001
getLoadingMsg0.0030.0000.004
getLogo0.0020.0000.003
getMainPanel0.0030.0000.003
getMainPlotUI0.0010.0000.000
getMainPlotsLeftMenu0.1260.0030.129
getMean0.0010.0000.001
getMergedComparison0.0010.0000.001
getMetaSelector0.0010.0000.001
getMethodDetails0.0000.0010.001
getMostVariedList0.0000.0000.001
getNormalizedMatrix0.0250.0010.026
getOrganism0.0010.0000.001
getOrganismBox0.0050.0000.005
getOrganismPathway0.0000.0010.001
getPCAPlotUI0.0010.0000.001
getPCAcontolUpdatesJS0.0000.0000.001
getPCAexplained3.2220.2513.476
getPCselection0.0020.0000.001
getPlotArea0.0010.0010.001
getProgramTitle0.0000.0000.001
getQAText0.0010.0010.002
getQCLeftMenu0.0000.0000.001
getQCPanel0.0070.0010.007
getSampleDetails0.0010.0000.001
getSampleNames0.0000.0000.001
getSamples0.0010.0000.000
getSearchData0.0010.0010.001
getSelHeat000
getSelectInputBox0.0010.0000.001
getSelectedCols0.0000.0010.001
getSelectedDatasetInput000
getShapeColor0.0000.0000.001
getStartPlotsMsg0.0040.0010.004
getStartupMsg0.0050.0000.005
getTabUpdateJS0.0010.0000.001
getTableDetails0.0010.0000.000
getTableModal0.0200.0030.023
getTableStyle0.0010.0010.001
getTextOnOff0.0050.0000.005
getUp0.0000.0000.001
getUpDown000
getVariationData0.0010.0000.001
get_conditions_given_selection0.0000.0000.001
heatmapControlsUI0.0680.0030.071
heatmapJScode0.0010.0000.000
heatmapServer0.0020.0010.003
heatmapUI0.1110.0060.117
hideObj0.0010.0000.001
histogramControlsUI0.0010.0000.001
installpack0.0000.0010.001
kmeansControlsUI0.010.000.01
lcfMetRadio0.0050.0000.005
loadpack0.0260.0410.066
mainPlotControlsUI0.0090.0000.010
mainScatterNew0.0000.0000.001
niceKmeans0.0000.0000.001
normalizationMethods0.0030.0000.003
palUI0.0030.0000.003
panel.cor0.0010.0000.001
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0090.0000.009
plotData0.0010.0010.001
plotMarginsUI0.0070.0000.007
plotSizeMarginsUI0.0080.0000.008
plotSizeUI0.0030.0010.003
plotTypeUI000
plot_pca1.7380.1471.890
prepDEOutput0.0000.0000.001
prepDataContainer0.0010.0010.001
prepGroup0.0010.0000.001
prepHeatData0.0000.0000.001
prepPCADat0.0010.0000.001
push000
removeCols0.0010.0010.001
removeExtraCols0.0020.0000.003
round_vals0.0010.0000.000
runDE0.0000.0010.001
runDESeq20.0000.0000.001
runEdgeR0.0000.0000.001
runHeatmap0.0010.0010.002
runHeatmap20.0010.0000.001
runLimma0.0010.0000.001
run_pca1.3590.1211.482
selectConditions0.0010.0000.001
selectGroupInfo0.0000.0010.000
selectedInput0.0010.0010.001
sepRadio0.0050.0000.005
setBatch0.0000.0000.001
showObj0.0000.0000.001
startDEBrowser0.0010.0010.000
startHeatmap0.0010.0010.001
textareaInput0.0010.0000.002
togglePanels0.0000.0000.001