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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 515/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.34.0  (landing page)
Alper Kucukural
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: RELEASE_3_20
git_last_commit: e323fef
git_last_commit_date: 2024-10-29 10:08:44 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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    ERROR  skippedskipped


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: 1.34.0
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_1.34.0.tar.gz
StartedAt: 2024-12-20 02:10:49 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 02:25:22 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 872.8 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_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/debrowser.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.34.0’
* 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 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-3.20-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/4.4-x86_64/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 v1.34.0  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 
 28.036   1.861  33.695 

debrowser.Rcheck/tests/test-deseq.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 v1.34.0  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 
 71.157   2.522  85.624 

debrowser.Rcheck/tests/test-null.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 v1.34.0  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 
 28.288   1.975  36.104 

debrowser.Rcheck/tests/test-ui.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 v1.34.0  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 
 28.689   2.065  35.628 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0320.0060.043
IQRPlotControlsUI0.0030.0000.003
actionButtonDE0.0070.0010.008
addDataCols0.0000.0010.001
addID0.0000.0010.001
all2all0.3160.0140.357
all2allControlsUI0.0600.0130.115
applyFilters0.0010.0000.002
applyFiltersNew0.0010.0010.001
applyFiltersToMergedComparison0.0010.0010.001
barMainPlotControlsUI0.0030.0000.003
batchEffectUI0.0860.0120.107
batchMethod0.0040.0010.004
changeClusterOrder0.0000.0000.001
checkCountData000
checkMetaData0.0000.0000.002
clustFunParamsUI0.0010.0010.001
clusterData0.0000.0010.001
compareClust0.0010.0010.001
condSelectUI0.0090.0010.011
correctCombat0.0010.0010.001
correctHarman000
customColorsUI0.0100.0010.014
cutOffSelectionUI0.0080.0010.013
dataLCFUI0.0250.0010.028
dataLoadUI0.0240.0020.028
deServer0.0130.0070.022
deUI0.2340.0280.316
debrowserIQRplot0.0000.0010.001
debrowserall2all0.0010.0000.001
debrowserbarmainplot0.0000.0000.001
debrowserbatcheffect0.0010.0010.001
debrowserboxmainplot0.0010.0000.001
debrowsercondselect0.0000.0000.001
debrowserdataload0.0010.0010.002
debrowserdeanalysis0.0010.0000.001
debrowserdensityplot0.0000.0000.001
debrowserheatmap0.0010.0010.001
debrowserhistogram0.0010.0000.001
debrowserlowcountfilter0.0000.0000.001
debrowsermainplot0.0000.0010.002
debrowserpcaplot0.0010.0000.001
dendControlsUI0.0130.0020.016
densityPlotControlsUI0.0030.0010.005
distFunParamsUI0.0010.0000.000
drawKEGG0.0000.0000.001
drawPCAExplained0.0000.0010.000
fileTypes0.0000.0010.000
fileUploadBox0.0070.0020.008
generateTestData0.0010.0000.001
getAfterLoadMsg0.0010.0010.002
getAll2AllPlotUI0.0000.0010.001
getBSTableUI0.0000.0010.001
getBarMainPlot0.0010.0000.001
getBarMainPlotUI0.0000.0000.002
getBoxMainPlot0.0010.0010.001
getBoxMainPlotUI0.0010.0000.001
getColorShapeSelection0.0000.0010.001
getColors0.0000.0000.001
getCompSelection0.0040.0010.004
getCondMsg0.0000.0010.001
getConditionSelector0.0010.0000.001
getConditionSelectorFromMeta0.0000.0000.001
getCovariateDetails0.0000.0010.001
getCutOffSelection0.0040.0010.010
getDEAnalysisText0.0050.0020.006
getDEResultsUI0.0030.0010.004
getDataAssesmentText0.0050.0010.005
getDataForTables0.0000.0010.001
getDataPreparationText0.0030.0010.004
getDensityPlot0.0010.0000.001
getDensityPlotUI0.0000.0010.001
getDomains0.0010.0000.001
getDown0.0000.0000.001
getDownloadSection0.0170.0030.021
getEnrichDO0.0010.0000.001
getEnrichGO0.0000.0010.001
getEnrichKEGG0.0010.0000.001
getEntrezIds0.0000.0000.001
getEntrezTable0.0010.0010.001
getGOLeftMenu0.0230.0030.027
getGOPlots0.0010.0000.001
getGSEA0.0010.0010.001
getGeneList1.4270.2491.755
getGeneSetData0.0010.0010.001
getGoPanel0.0220.0020.024
getGroupSelector0.0010.0000.001
getHeatmapUI0.0000.0000.001
getHelpButton000
getHideLegendOnOff0.0040.0000.003
getHistogramUI0.0000.0000.001
getIQRPlot0.0010.0000.001
getIQRPlotUI0.0000.0010.001
getIntroText0.0030.0010.003
getJSLine0.0040.0010.005
getKEGGModal0.0050.0000.006
getLeftMenu0.0010.0010.001
getLegendColors0.0000.0010.001
getLegendRadio0.0060.0000.007
getLegendSelect0.0030.0000.005
getLevelOrder0.0000.0010.000
getLoadingMsg0.0040.0010.004
getLogo0.0020.0010.004
getMainPanel0.0020.0000.003
getMainPlotUI0.0010.0000.000
getMainPlotsLeftMenu0.1450.0030.158
getMean0.0000.0010.001
getMergedComparison0.0010.0000.001
getMetaSelector0.0000.0000.001
getMethodDetails0.0010.0000.001
getMostVariedList0.0000.0010.002
getNormalizedMatrix0.0250.0020.029
getOrganism0.0000.0010.001
getOrganismBox0.0040.0010.005
getOrganismPathway0.0010.0000.001
getPCAPlotUI0.0000.0000.001
getPCAcontolUpdatesJS0.0010.0000.001
getPCAexplained3.2800.1583.623
getPCselection0.0020.0010.001
getPlotArea000
getProgramTitle0.0010.0010.001
getQAText0.0030.0000.005
getQCLeftMenu0.0010.0010.001
getQCPanel0.0070.0020.009
getSampleDetails0.0000.0000.002
getSampleNames0.0010.0000.000
getSearchData0.0000.0010.001
getSelHeat0.0000.0000.001
getSelectInputBox0.0010.0010.001
getSelectedCols0.0000.0010.001
getSelectedDatasetInput0.0010.0000.001
getShapeColor0.0000.0010.001
getStartPlotsMsg0.0040.0010.005
getStartupMsg0.0050.0010.006
getTabUpdateJS0.0010.0010.001
getTableDetails0.0010.0010.002
getTableModal0.0060.0010.009
getTableStyle0.0010.0010.001
getUp0.0000.0010.001
getUpDown0.0000.0000.001
getVariationData0.0010.0000.001
get_conditions_given_selection0.0000.0010.001
heatmapControlsUI0.0810.0110.099
heatmapJScode000
heatmapServer0.0010.0010.003
heatmapUI0.1420.0190.167
hideObj0.0010.0010.001
histogramControlsUI0.0010.0010.002
installpack000
kmeansControlsUI0.0120.0010.014
lcfMetRadio0.0050.0010.006
loadpack0.0230.0560.081
mainPlotControlsUI0.0110.0010.013
mainScatterNew0.0010.0010.001
niceKmeans0.0010.0000.001
normalizationMethods0.0040.0010.005
palUI0.0040.0010.006
panel.cor0.0020.0010.002
panel.hist0.0010.0010.002
pcaPlotControlsUI0.0100.0010.011
plotData0.0010.0010.002
plotMarginsUI0.0110.0010.014
plotSizeMarginsUI0.0210.0030.024
plotSizeUI0.0070.0010.009
plotTypeUI0.0010.0010.004
plot_pca1.7840.0491.971
prepDataContainer0.0010.0010.003
prepGroup0.0010.0000.001
prepHeatData0.0000.0010.001
prepPCADat0.0000.0010.001
push0.0010.0000.000
removeCols0.0000.0000.001
removeExtraCols0.0030.0000.003
round_vals0.0000.0000.001
runDE0.0000.0010.000
runDESeq20.0010.0010.001
runEdgeR0.0010.0010.001
runHeatmap0.0010.0000.001
runHeatmap20.0010.0000.001
runLimma0.0010.0000.001
run_pca1.4420.0271.587
selectConditions0.0010.0010.001
selectGroupInfo0.0010.0010.001
selectedInput0.0000.0010.001
sepRadio0.0040.0000.005
setBatch0.0010.0000.001
showObj0.0000.0010.001
startDEBrowser0.0000.0010.001
startHeatmap0.0010.0000.001
textareaInput0.0000.0000.001
togglePanels0.0010.0000.000