Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-21 11:39 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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

Package 526/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.36.0  (landing page)
Alper Kucukural
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: RELEASE_3_21
git_last_commit: 9804323
git_last_commit_date: 2025-04-15 10:59:48 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for debrowser on merida1

To the developers/maintainers of the debrowser package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: debrowser
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:debrowser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings debrowser_1.36.0.tar.gz
StartedAt: 2025-08-19 03:20:17 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 03:34:59 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 881.7 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:debrowser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings debrowser_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/debrowser.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.36.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 code 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 whether 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 ... 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-3.21-bioc/meat/debrowser.Rcheck/00check.log’
for details.


Installation output

debrowser.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘debrowser’ ...
** this is package ‘debrowser’ version ‘1.36.0’
** 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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 v1.36.0  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 
 28.702   2.056  37.377 

debrowser.Rcheck/tests/test-deseq.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 v1.36.0  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 
 69.242   2.639  91.603 

debrowser.Rcheck/tests/test-null.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 v1.36.0  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 
 28.034   1.943  36.248 

debrowser.Rcheck/tests/test-ui.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 v1.36.0  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 
 28.161   1.801  33.752 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0310.0050.040
IQRPlotControlsUI0.0030.0010.005
actionButtonDE0.0060.0010.008
addDataCols0.0000.0000.001
addID0.0010.0000.001
all2all0.2970.0120.347
all2allControlsUI0.0600.0110.093
applyFilters0.0010.0010.001
applyFiltersNew0.0000.0000.001
applyFiltersToMergedComparison0.0010.0000.001
barMainPlotControlsUI0.0030.0000.005
batchEffectUI0.0860.0110.113
batchMethod0.0030.0010.004
changeClusterOrder0.0010.0000.001
checkCountData0.0000.0000.001
checkMetaData0.0010.0010.000
clustFunParamsUI0.0000.0010.001
clusterData0.0010.0010.001
compareClust0.0000.0000.001
condSelectUI0.0090.0000.011
correctCombat0.0010.0010.001
correctHarman0.0000.0010.001
customColorsUI0.0090.0020.011
cutOffSelectionUI0.0080.0010.009
dataLCFUI0.0240.0010.032
dataLoadUI0.0250.0020.034
deServer0.0120.0080.025
deUI0.2100.0100.245
debrowserIQRplot0.0000.0010.001
debrowserall2all0.0010.0000.001
debrowserbarmainplot0.0010.0000.001
debrowserbatcheffect0.0000.0000.004
debrowserboxmainplot0.0010.0010.001
debrowsercondselect0.0000.0010.001
debrowserdataload0.0010.0010.002
debrowserdeanalysis0.0010.0000.000
debrowserdensityplot0.0000.0010.001
debrowserheatmap0.0010.0010.001
debrowserhistogram0.0000.0000.001
debrowserlowcountfilter0.0010.0000.001
debrowsermainplot0.0010.0010.001
debrowserpcaplot0.0010.0010.001
dendControlsUI0.0130.0000.013
densityPlotControlsUI0.0030.0000.004
distFunParamsUI0.0000.0000.001
drawKEGG0.0010.0010.001
drawPCAExplained0.0000.0010.000
fileTypes0.0000.0010.001
fileUploadBox0.0070.0010.010
generateTestData0.0010.0000.002
getAfterLoadMsg0.0010.0000.001
getAll2AllPlotUI0.0000.0000.001
getBSTableUI0.0010.0010.001
getBarMainPlot0.0000.0010.001
getBarMainPlotUI0.0010.0010.001
getBoxMainPlot0.0000.0010.001
getBoxMainPlotUI0.0010.0010.001
getColorShapeSelection0.0000.0010.001
getColors0.0010.0000.001
getCompSelection0.0030.0000.005
getCondMsg0.0010.0000.003
getConditionSelector0.0000.0010.001
getConditionSelectorFromMeta0.0010.0010.001
getCovariateDetails0.0000.0010.001
getCutOffSelection0.0040.0000.005
getDEAnalysisText0.0050.0000.006
getDEResultsUI0.0030.0010.004
getDataAssesmentText0.0030.0010.007
getDataForTables0.0010.0010.000
getDataPreparationText0.0020.0010.004
getDensityPlot0.0010.0000.001
getDensityPlotUI0.0000.0000.001
getDomains0.0010.0000.001
getDown0.0010.0000.001
getDownloadSection0.0150.0010.018
getEnrichDO0.0000.0010.000
getEnrichGO0.0010.0000.000
getEnrichKEGG0.0000.0000.001
getEntrezIds0.0000.0000.001
getEntrezTable0.0010.0000.001
getGOLeftMenu0.0210.0010.027
getGOPlots0.0010.0000.001
getGSEA0.0000.0000.001
getGeneList1.4200.2141.936
getGeneSetData0.0010.0010.001
getGoPanel0.0220.0020.028
getGroupSelector0.0000.0010.001
getHeatmapUI0.0010.0010.001
getHelpButton000
getHideLegendOnOff0.0030.0000.004
getHistogramUI0.0000.0010.004
getIQRPlot0.0010.0000.001
getIQRPlotUI0.0000.0000.001
getIntroText0.0030.0000.004
getJSLine0.0040.0010.004
getKEGGModal0.0050.0000.006
getLeftMenu000
getLegendColors0.0000.0010.000
getLegendRadio0.0050.0000.005
getLegendSelect0.0030.0000.004
getLevelOrder000
getLoadingMsg0.0030.0010.004
getLogo0.0030.0020.003
getMainPanel0.0020.0010.003
getMainPlotUI0.0010.0000.001
getMainPlotsLeftMenu0.1430.0020.169
getMean0.0010.0000.000
getMergedComparison0.0010.0000.001
getMetaSelector0.0000.0000.001
getMethodDetails0.0010.0000.001
getMostVariedList0.0000.0000.001
getNormalizedMatrix0.0240.0030.029
getOrganism0.0010.0010.001
getOrganismBox0.0040.0000.005
getOrganismPathway000
getPCAPlotUI0.0010.0010.003
getPCAcontolUpdatesJS0.0000.0010.001
getPCAexplained3.2930.1093.992
getPCselection0.0020.0000.002
getPlotArea0.0000.0000.001
getProgramTitle0.0000.0000.001
getQAText0.0030.0010.004
getQCLeftMenu0.0010.0010.001
getQCPanel0.0060.0000.009
getSampleDetails0.0000.0000.001
getSampleNames0.0010.0000.001
getSearchData0.0010.0000.001
getSelHeat0.0010.0000.001
getSelectInputBox0.0000.0000.001
getSelectedCols0.0000.0010.001
getSelectedDatasetInput0.0010.0010.001
getShapeColor0.0010.0010.000
getStartPlotsMsg0.0040.0010.008
getStartupMsg0.0040.0000.008
getTabUpdateJS0.0010.0000.001
getTableDetails0.0000.0010.001
getTableModal0.0070.0010.007
getTableStyle0.0000.0000.001
getUp0.0010.0010.001
getUpDown0.0000.0010.001
getVariationData0.0000.0000.001
get_conditions_given_selection0.0010.0000.001
heatmapControlsUI0.0770.0030.091
heatmapJScode000
heatmapServer0.0010.0010.003
heatmapUI0.1350.0060.170
hideObj0.0000.0000.001
histogramControlsUI0.0010.0000.001
installpack0.0010.0010.004
kmeansControlsUI0.0110.0010.014
lcfMetRadio0.0040.0000.004
loadpack0.0230.0560.088
mainPlotControlsUI0.0110.0000.016
mainScatterNew0.0010.0010.002
niceKmeans0.0000.0010.001
normalizationMethods0.0040.0000.007
palUI0.0050.0010.006
panel.cor0.0010.0010.002
panel.hist0.0010.0000.002
pcaPlotControlsUI0.0090.0010.010
plotData0.0010.0010.001
plotMarginsUI0.0100.0010.011
plotSizeMarginsUI0.0180.0000.023
plotSizeUI0.0050.0010.007
plotTypeUI0.0020.0000.002
plot_pca1.7150.0432.068
prepDataContainer0.0010.0000.003
prepGroup0.0010.0000.001
prepHeatData0.0000.0000.001
prepPCADat0.0000.0000.001
push0.0000.0010.001
removeCols0.0010.0010.001
removeExtraCols0.0020.0000.002
round_vals0.0000.0000.001
runDE000
runDESeq20.0010.0000.001
runEdgeR0.0010.0000.001
runHeatmap0.0010.0010.001
runHeatmap20.0000.0010.001
runLimma0.0010.0010.001
run_pca1.4490.0271.734
selectConditions0.0010.0000.001
selectGroupInfo0.0010.0000.001
selectedInput0.0000.0000.001
sepRadio0.0040.0000.005
setBatch0.0000.0010.001
showObj0.0000.0010.001
startDEBrowser0.0010.0000.001
startHeatmap000
textareaInput0.0010.0000.002
togglePanels0.0000.0000.001