Back to Build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-03-27 05:50:32 -0000 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6083
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 495/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.27.3  (landing page)
Alper Kucukural
Snapshot Date: 2023-03-24 01:40:07 -0000 (Fri, 24 Mar 2023)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: devel
git_last_commit: 0c2f380
git_last_commit_date: 2023-03-12 22:23:20 -0000 (Sun, 12 Mar 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: debrowser
Version: 1.27.3
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/site-library --timings debrowser_1.27.3.tar.gz
StartedAt: 2023-03-25 00:41:35 -0000 (Sat, 25 Mar 2023)
EndedAt: 2023-03-25 00:54:23 -0000 (Sat, 25 Mar 2023)
EllapsedTime: 767.7 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/site-library --timings debrowser_1.27.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/debrowser.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.27.3’
* 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 startup messages can be suppressed ... 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-3.17-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-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "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 v1.27.3  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 
 15.658   0.788  17.091

debrowser.Rcheck/tests/test-deseq.Rout


R Under development (unstable) (2023-03-12 r83975) -- "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 v1.27.3  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 
 39.435   1.332  40.772

debrowser.Rcheck/tests/test-null.Rout


R Under development (unstable) (2023-03-12 r83975) -- "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 v1.27.3  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 
 15.984   3.269  22.940

debrowser.Rcheck/tests/test-ui.Rout


R Under development (unstable) (2023-03-12 r83975) -- "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 v1.27.3  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 
 15.570   1.031  17.015

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0630.0040.074
IQRPlotControlsUI0.0020.0000.002
actionButtonDE0.0040.0000.004
addDataCols0.0010.0000.000
addID000
all2all0.1700.0080.179
all2allControlsUI0.0290.0040.035
applyFilters000
applyFiltersNew000
applyFiltersToMergedComparison000
barMainPlotControlsUI0.0010.0000.001
batchEffectUI0.0480.0000.051
batchMethod0.0020.0000.002
changeClusterOrder000
checkCountData0.0000.0000.001
checkMetaData0.0000.0000.001
clustFunParamsUI0.0000.0000.001
clusterData0.0000.0000.001
compareClust0.0010.0000.000
condSelectUI0.0060.0000.006
correctCombat000
correctHarman000
customColorsUI0.0070.0000.009
cutOffSelectionUI0.0050.0000.005
dataLCFUI0.0140.0000.013
dataLoadUI0.0130.0000.013
deServer0.0080.0000.008
deUI0.1060.0040.111
debrowserIQRplot000
debrowserall2all000
debrowserbarmainplot000
debrowserbatcheffect0.0010.0000.000
debrowserboxmainplot0.0010.0000.000
debrowsercondselect0.0010.0000.000
debrowserdataload0.0010.0000.001
debrowserdeanalysis0.0010.0000.000
debrowserdensityplot0.0010.0000.000
debrowserheatmap0.0010.0000.001
debrowserhistogram0.0010.0000.001
debrowserlowcountfilter0.0010.0000.001
debrowsermainplot0.0010.0000.000
debrowserpcaplot0.0010.0000.000
dendControlsUI0.0080.0000.007
densityPlotControlsUI0.0020.0000.002
distFunParamsUI0.0010.0000.000
drawKEGG0.0000.0000.001
drawPCAExplained000
fileTypes000
fileUploadBox0.0040.0000.003
generateTestData000
getAfterLoadMsg000
getAll2AllPlotUI000
getBSTableUI000
getBarMainPlot000
getBarMainPlotUI000
getBoxMainPlot000
getBoxMainPlotUI0.0010.0000.000
getColorShapeSelection0.0010.0000.000
getColors0.0010.0000.001
getCompSelection0.0020.0000.002
getCondMsg000
getConditionSelector000
getConditionSelectorFromMeta0.0010.0000.000
getCovariateDetails0.0010.0000.000
getCutOffSelection0.0020.0000.002
getDEAnalysisText0.0020.0000.002
getDEResultsUI0.0010.0000.001
getDataAssesmentText0.0020.0000.002
getDataForTables0.0010.0000.000
getDataPreparationText0.0020.0000.002
getDensityPlot0.0010.0000.001
getDensityPlotUI0.0000.0000.001
getDomains000
getDown000
getDownloadSection0.0080.0000.008
getEnrichDO000
getEnrichGO0.0010.0000.000
getEnrichKEGG0.0010.0000.001
getEntrezIds0.0000.0000.001
getEntrezTable000
getGOLeftMenu0.0120.0000.012
getGOPlots0.0010.0000.000
getGSEA0.0010.0000.000
getGeneList0.6890.1751.058
getGeneSetData000
getGoPanel0.0040.0080.012
getGroupSelector000
getHeatmapUI000
getHelpButton0.0000.0010.001
getHideLegendOnOff0.0010.0010.002
getHistogramUI000
getIQRPlot000
getIQRPlotUI000
getIntroText0.0010.0000.001
getJSLine0.0020.0000.002
getKEGGModal0.0020.0000.003
getLeftMenu000
getLegendColors0.0010.0000.001
getLegendRadio0.0020.0000.003
getLegendSelect0.0020.0000.002
getLevelOrder0.0000.0000.001
getLoadingMsg0.0020.0000.002
getLogo0.0000.0010.001
getMainPanel0.0000.0020.002
getMainPlotUI0.0000.0000.001
getMainPlotsLeftMenu0.0780.0030.082
getMean0.0000.0010.001
getMergedComparison0.0010.0000.001
getMetaSelector0.0010.0000.000
getMethodDetails0.0010.0000.001
getMostVariedList0.0010.0000.000
getNormalizedMatrix0.9490.0000.950
getOrganism000
getOrganismBox0.0030.0000.004
getOrganismPathway000
getPCAPlotUI0.0010.0000.000
getPCAcontolUpdatesJS000
getPCAexplained2.3870.0842.472
getPCselection0.0010.0000.000
getPlotArea000
getProgramTitle000
getQAText0.0000.0010.001
getQCLeftMenu000
getQCPanel0.0010.0040.006
getSampleDetails0.0010.0000.001
getSampleNames0.0010.0000.000
getSearchData000
getSelHeat000
getSelectInputBox000
getSelectedCols000
getSelectedDatasetInput0.0000.0000.001
getShapeColor0.0010.0000.001
getStartPlotsMsg0.0030.0000.003
getStartupMsg0.0040.0000.004
getTabUpdateJS0.0010.0000.000
getTableDetails0.0010.0000.001
getTableModal0.0040.0000.004
getTableStyle0.0010.0000.001
getUp0.0000.0000.001
getUpDown000
getVariationData000
get_conditions_given_selection000
heatmapControlsUI0.0380.0080.047
heatmapJScode0.0000.0000.001
heatmapServer0.0010.0000.001
heatmapUI0.0780.0040.084
hideObj0.0000.0000.001
histogramControlsUI0.0010.0000.001
installpack0.0000.0000.001
kmeansControlsUI0.0040.0030.007
lcfMetRadio0.0030.0000.002
loadpack0.0200.2001.938
mainPlotControlsUI0.0030.0040.007
mainScatterNew0.0010.0010.004
niceKmeans0.0000.0000.001
normalizationMethods0.0030.0000.004
palUI0.0030.0000.002
panel.cor0.0010.0000.001
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0050.0000.005
plotData000
plotMarginsUI0.0060.0000.006
plotSizeMarginsUI0.0110.0000.011
plotSizeUI0.0040.0000.004
plotTypeUI0.0010.0000.001
plot_pca1.1540.0471.265
prepDataContainer0.0000.0000.001
prepGroup000
prepHeatData000
prepPCADat000
push0.0000.0000.001
removeCols000
removeExtraCols0.0010.0000.002
round_vals0.0000.0000.001
runDE000
runDESeq20.0000.0000.001
runEdgeR0.0000.0000.001
runHeatmap0.0010.0000.001
runHeatmap20.0010.0000.000
runLimma0.0010.0000.000
run_pca1.0540.0001.054
selectConditions0.0010.0000.002
selectGroupInfo000
selectedInput0.0000.0000.001
sepRadio0.0030.0000.003
setBatch0.0010.0000.001
showObj000
startDEBrowser0.0000.0000.001
startHeatmap0.0000.0010.001
textareaInput0.0000.0000.001
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