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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 505/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.33.0  (landing page)
Alper Kucukural
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: devel
git_last_commit: ec057cc
git_last_commit_date: 2024-04-30 10:49:26 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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: 1.33.0
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_1.33.0.tar.gz
StartedAt: 2024-06-10 02:20:42 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 02:36:17 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 935.7 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_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/debrowser.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.33.0’
* 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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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 v1.33.0  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 
 29.019   1.898  37.317 

debrowser.Rcheck/tests/test-deseq.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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 v1.33.0  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 
 71.078   2.547  85.418 

debrowser.Rcheck/tests/test-null.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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 v1.33.0  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 
 28.534   1.909  36.101 

debrowser.Rcheck/tests/test-ui.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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 v1.33.0  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 
 29.008   1.939  37.157 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0340.0060.053
IQRPlotControlsUI0.0030.0000.005
actionButtonDE0.0070.0000.012
addDataCols0.0010.0010.001
addID0.0000.0010.001
all2all0.3180.0150.401
all2allControlsUI0.0640.0090.098
applyFilters0.0010.0000.002
applyFiltersNew0.0000.0000.001
applyFiltersToMergedComparison0.0010.0000.001
barMainPlotControlsUI0.0030.0010.004
batchEffectUI0.0870.0130.159
batchMethod0.0040.0010.004
changeClusterOrder000
checkCountData0.0010.0000.001
checkMetaData0.0000.0010.001
clustFunParamsUI0.0010.0000.001
clusterData0.0000.0010.004
compareClust0.0010.0010.001
condSelectUI0.0100.0010.012
correctCombat0.0010.0010.001
correctHarman0.0000.0000.001
customColorsUI0.0100.0010.011
cutOffSelectionUI0.0100.0010.018
dataLCFUI0.0270.0020.044
dataLoadUI0.0250.0020.033
deServer0.0140.0080.032
deUI0.2330.0260.321
debrowserIQRplot0.0000.0010.001
debrowserall2all0.0010.0000.000
debrowserbarmainplot0.0000.0000.001
debrowserbatcheffect0.0010.0000.001
debrowserboxmainplot0.0010.0010.006
debrowsercondselect0.0000.0000.001
debrowserdataload0.0010.0010.001
debrowserdeanalysis0.0010.0010.001
debrowserdensityplot0.0000.0000.001
debrowserheatmap0.0000.0010.002
debrowserhistogram0.0010.0010.002
debrowserlowcountfilter0.0010.0000.001
debrowsermainplot0.0010.0010.002
debrowserpcaplot0.0010.0000.001
dendControlsUI0.0140.0020.021
densityPlotControlsUI0.0040.0010.006
distFunParamsUI0.0000.0010.000
drawKEGG0.0000.0000.001
drawPCAExplained0.0010.0000.001
fileTypes000
fileUploadBox0.0070.0020.008
generateTestData0.0010.0000.003
getAfterLoadMsg0.0010.0000.002
getAll2AllPlotUI0.0010.0010.001
getBSTableUI0.0000.0010.001
getBarMainPlot0.0000.0010.001
getBarMainPlotUI0.0010.0000.004
getBoxMainPlot0.0010.0010.002
getBoxMainPlotUI0.0010.0000.001
getColorShapeSelection0.0000.0000.001
getColors0.0000.0000.001
getCompSelection0.0040.0010.007
getCondMsg0.0000.0010.001
getConditionSelector0.0010.0000.001
getConditionSelectorFromMeta0.0000.0010.001
getCovariateDetails0.0000.0010.001
getCutOffSelection0.0040.0010.008
getDEAnalysisText0.0050.0010.015
getDEResultsUI0.0030.0010.004
getDataAssesmentText0.0050.0010.010
getDataForTables0.0000.0000.001
getDataPreparationText0.0030.0010.006
getDensityPlot0.0010.0000.001
getDensityPlotUI0.0010.0010.002
getDomains0.0000.0010.001
getDown000
getDownloadSection0.0170.0030.021
getEnrichDO0.0010.0010.003
getEnrichGO0.0000.0000.001
getEnrichKEGG0.0000.0010.001
getEntrezIds0.0010.0010.001
getEntrezTable0.0000.0000.001
getGOLeftMenu0.0260.0040.037
getGOPlots0.0010.0000.001
getGSEA0.0000.0000.001
getGeneList1.4630.2482.167
getGeneSetData0.0010.0010.001
getGoPanel0.0260.0020.035
getGroupSelector0.0010.0010.001
getHeatmapUI0.0010.0010.003
getHelpButton0.0000.0010.001
getHideLegendOnOff0.0040.0000.004
getHistogramUI0.0000.0000.001
getIQRPlot0.0010.0000.001
getIQRPlotUI0.0000.0000.001
getIntroText0.0030.0000.005
getJSLine0.0040.0010.005
getKEGGModal0.0060.0000.007
getLeftMenu0.0010.0010.001
getLegendColors0.0000.0010.001
getLegendRadio0.0050.0000.006
getLegendSelect0.0030.0000.004
getLevelOrder000
getLoadingMsg0.0030.0020.006
getLogo0.0030.0010.005
getMainPanel0.0030.0010.003
getMainPlotUI0.0000.0010.001
getMainPlotsLeftMenu0.1630.0030.203
getMean0.0000.0010.001
getMergedComparison0.0010.0010.001
getMetaSelector0.0000.0000.001
getMethodDetails0.0010.0000.001
getMostVariedList0.0000.0000.001
getNormalizedMatrix0.0270.0020.036
getOrganism0.0000.0010.001
getOrganismBox0.0050.0010.010
getOrganismPathway0.0010.0000.001
getPCAPlotUI000
getPCAcontolUpdatesJS0.0010.0000.001
getPCAexplained3.3670.1734.397
getPCselection0.0010.0000.002
getPlotArea0.0010.0000.001
getProgramTitle0.0000.0010.000
getQAText0.0030.0000.006
getQCLeftMenu0.0010.0010.001
getQCPanel0.0070.0020.011
getSampleDetails0.0010.0010.000
getSampleNames0.0010.0000.001
getSearchData000
getSelHeat0.0000.0000.001
getSelectInputBox0.0010.0000.001
getSelectedCols0.0000.0010.001
getSelectedDatasetInput0.0000.0010.001
getShapeColor0.0010.0000.005
getStartPlotsMsg0.0040.0010.006
getStartupMsg0.0040.0010.006
getTabUpdateJS0.0010.0000.001
getTableDetails0.0010.0010.001
getTableModal0.0060.0010.012
getTableStyle0.0000.0010.001
getUp0.0000.0010.001
getUpDown0.0010.0000.000
getVariationData0.0000.0000.001
get_conditions_given_selection0.0010.0000.001
heatmapControlsUI0.0810.0110.109
heatmapJScode000
heatmapServer0.0010.0010.002
heatmapUI0.1510.0210.215
hideObj0.0000.0000.001
histogramControlsUI0.0010.0010.002
installpack0.0010.0000.001
kmeansControlsUI0.0120.0020.019
lcfMetRadio0.0050.0010.005
loadpack0.0220.0540.093
mainPlotControlsUI0.0120.0020.018
mainScatterNew0.0010.0010.004
niceKmeans0.0010.0010.001
normalizationMethods0.0040.0010.006
palUI0.0050.0010.006
panel.cor0.0020.0000.003
panel.hist0.0010.0010.002
pcaPlotControlsUI0.0110.0010.019
plotData0.0000.0010.002
plotMarginsUI0.0130.0010.019
plotSizeMarginsUI0.0220.0030.030
plotSizeUI0.0060.0010.011
plotTypeUI0.0010.0000.004
plot_pca1.7840.0522.288
prepDataContainer0.0010.0010.003
prepGroup0.0010.0000.001
prepHeatData0.0000.0000.001
prepPCADat000
push0.0010.0000.003
removeCols0.0000.0010.001
removeExtraCols0.0030.0010.003
round_vals0.0000.0000.004
runDE0.0010.0000.001
runDESeq20.0010.0000.001
runEdgeR0.0010.0000.003
runHeatmap0.0010.0010.001
runHeatmap20.0010.0000.001
runLimma0.0010.0010.003
run_pca1.4310.0311.858
selectConditions0.0020.0010.006
selectGroupInfo000
selectedInput0.0000.0000.001
sepRadio0.0050.0000.007
setBatch0.0000.0010.002
showObj0.0000.0010.000
startDEBrowser0.0010.0010.003
startHeatmap000
textareaInput0.0010.0000.001
togglePanels0.0000.0000.001