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This page was generated on 2023-05-10 10:04:29 -0000 (Wed, 10 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6211
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CHECK results for debrowser on kunpeng1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 494/2194HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.29.0  (landing page)
Alper Kucukural
Snapshot Date: 2023-05-08 19:11:19 -0000 (Mon, 08 May 2023)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: devel
git_last_commit: 574dbf2
git_last_commit_date: 2023-04-25 14:45:24 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: debrowser
Version: 1.29.0
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_1.29.0.tar.gz
StartedAt: 2023-05-09 13:43:10 -0000 (Tue, 09 May 2023)
EndedAt: 2023-05-09 13:56:25 -0000 (Tue, 09 May 2023)
EllapsedTime: 794.1 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_1.29.0.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 ‘1.29.0’
* 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 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 v1.29.0  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 
 17.276   0.798  18.055

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 v1.29.0  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 
 40.171   0.835  40.989

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 v1.29.0  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 
 17.072   0.934  17.987

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 v1.29.0  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 
 17.033   1.576  18.590

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0270.0000.026
IQRPlotControlsUI0.0020.0000.001
actionButtonDE0.0050.0000.004
addDataCols000
addID000
all2all0.1630.0040.168
all2allControlsUI0.0320.0000.033
applyFilters0.0010.0000.001
applyFiltersNew000
applyFiltersToMergedComparison0.0000.0000.001
barMainPlotControlsUI0.0010.0000.002
batchEffectUI0.0430.0000.043
batchMethod0.0020.0000.002
changeClusterOrder000
checkCountData0.0000.0000.001
checkMetaData0.0000.0000.001
clustFunParamsUI000
clusterData0.0000.0010.000
compareClust0.0000.0010.000
condSelectUI0.0050.0010.005
correctCombat000
correctHarman000
customColorsUI0.0070.0000.007
cutOffSelectionUI0.0040.0000.005
dataLCFUI0.0080.0040.013
dataLoadUI0.0120.0000.013
deServer0.0030.0040.006
deUI0.1020.0040.106
debrowserIQRplot000
debrowserall2all000
debrowserbarmainplot0.0010.0000.000
debrowserbatcheffect0.0010.0000.000
debrowserboxmainplot0.0010.0000.000
debrowsercondselect000
debrowserdataload0.0010.0000.001
debrowserdeanalysis0.0010.0000.000
debrowserdensityplot000
debrowserheatmap0.0010.0000.000
debrowserhistogram0.0010.0000.000
debrowserlowcountfilter0.0010.0000.000
debrowsermainplot0.0000.0010.000
debrowserpcaplot0.0000.0010.000
dendControlsUI0.0060.0020.007
densityPlotControlsUI0.0020.0000.001
distFunParamsUI000
drawKEGG0.0000.0000.001
drawPCAExplained0.0000.0000.001
fileTypes000
fileUploadBox0.0040.0000.003
generateTestData0.0010.0000.000
getAfterLoadMsg0.0000.0000.001
getAll2AllPlotUI0.0000.0000.001
getBSTableUI000
getBarMainPlot000
getBarMainPlotUI000
getBoxMainPlot000
getBoxMainPlotUI0.0010.0000.000
getColorShapeSelection0.0010.0000.000
getColors0.0010.0000.000
getCompSelection0.0020.0000.002
getCondMsg0.0000.0000.001
getConditionSelector000
getConditionSelectorFromMeta0.0010.0000.000
getCovariateDetails0.0010.0000.000
getCutOffSelection0.0020.0000.002
getDEAnalysisText0.0020.0000.003
getDEResultsUI0.0010.0000.002
getDataAssesmentText0.0020.0000.002
getDataForTables0.0010.0000.000
getDataPreparationText0.0020.0000.001
getDensityPlot0.0010.0000.000
getDensityPlotUI0.0010.0000.000
getDomains0.0010.0000.000
getDown000
getDownloadSection0.0050.0040.009
getEnrichDO0.0010.0000.000
getEnrichGO0.0010.0000.000
getEnrichKEGG000
getEntrezIds000
getEntrezTable0.0000.0000.001
getGOLeftMenu0.0040.0080.013
getGOPlots0.0000.0000.001
getGSEA0.0420.0000.042
getGeneList0.5870.0320.619
getGeneSetData000
getGoPanel0.0120.0000.012
getGroupSelector0.0000.0000.001
getHeatmapUI0.0000.0000.001
getHelpButton000
getHideLegendOnOff0.0020.0000.002
getHistogramUI0.0000.0000.001
getIQRPlot0.0000.0000.001
getIQRPlotUI0.0000.0000.001
getIntroText0.0010.0000.002
getJSLine0.0020.0000.002
getKEGGModal0.0030.0000.003
getLeftMenu0.0000.0000.001
getLegendColors0.0000.0010.001
getLegendRadio0.0000.0030.003
getLegendSelect0.0020.0000.002
getLevelOrder0.0010.0000.000
getLoadingMsg0.0020.0000.002
getLogo0.0010.0000.002
getMainPanel0.0010.0000.002
getMainPlotUI0.0000.0000.001
getMainPlotsLeftMenu0.0800.0000.081
getMean000
getMergedComparison0.0000.0000.001
getMetaSelector0.0000.0000.001
getMethodDetails0.0000.0000.001
getMostVariedList0.0000.0000.001
getNormalizedMatrix0.0150.0020.017
getOrganism0.0010.0000.000
getOrganismBox0.0030.0000.002
getOrganismPathway000
getPCAPlotUI000
getPCAcontolUpdatesJS0.0000.0000.001
getPCAexplained2.6760.0162.694
getPCselection0.0010.0000.000
getPlotArea000
getProgramTitle0.0010.0000.000
getQAText0.0020.0000.001
getQCLeftMenu000
getQCPanel0.0040.0000.004
getSampleDetails0.0010.0000.000
getSampleNames000
getSearchData0.0000.0000.001
getSelHeat000
getSelectInputBox000
getSelectedCols0.0010.0000.000
getSelectedDatasetInput000
getShapeColor0.0000.0000.001
getStartPlotsMsg0.0020.0000.002
getStartupMsg0.0020.0000.002
getTabUpdateJS0.0010.0000.000
getTableDetails0.0010.0000.000
getTableModal0.0040.0000.003
getTableStyle000
getUp0.0000.0000.001
getUpDown000
getVariationData0.0010.0000.000
get_conditions_given_selection0.0010.0000.000
heatmapControlsUI0.0410.0000.040
heatmapJScode000
heatmapServer0.0010.0000.001
heatmapUI0.0710.0000.071
hideObj000
histogramControlsUI0.0000.0000.001
installpack000
kmeansControlsUI0.0060.0000.006
lcfMetRadio0.0020.0000.002
loadpack0.0100.0120.022
mainPlotControlsUI0.0060.0000.006
mainScatterNew0.0010.0000.000
niceKmeans0.0010.0000.000
normalizationMethods0.0020.0000.002
palUI0.0020.0000.002
panel.cor0.0000.0000.001
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0050.0000.005
plotData0.0000.0000.001
plotMarginsUI0.0030.0030.006
plotSizeMarginsUI0.0100.0000.009
plotSizeUI0.0030.0000.003
plotTypeUI0.0000.0000.001
plot_pca1.2240.0081.232
prepDataContainer0.0000.0000.001
prepGroup0.0000.0000.001
prepHeatData0.0000.0000.001
prepPCADat000
push000
removeCols0.0000.0000.001
removeExtraCols0.0010.0000.002
round_vals0.0000.0000.001
runDE0.0000.0000.001
runDESeq20.0000.0000.001
runEdgeR0.0000.0000.001
runHeatmap0.0000.0010.001
runHeatmap20.0000.0010.000
runLimma0.0000.0010.000
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