Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:10 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for debrowser on nebbiolo1


To the developers/maintainers of the debrowser package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/debrowser.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 479/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.24.1  (landing page)
Alper Kucukural
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: RELEASE_3_15
git_last_commit: c03e0a0
git_last_commit_date: 2022-08-01 13:53:14 -0400 (Mon, 01 Aug 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: debrowser
Version: 1.24.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings debrowser_1.24.1.tar.gz
StartedAt: 2022-10-18 19:19:16 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:24:23 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 306.9 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings debrowser_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/debrowser.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.24.1’
* 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 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’
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’
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 samples textName x y
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/debrowser.Rcheck/00check.log’
for details.

Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL debrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 v1.24.1  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 
 12.320   1.464  13.769

debrowser.Rcheck/tests/test-deseq.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 v1.24.1  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 
 27.431   1.172  28.583

debrowser.Rcheck/tests/test-null.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 v1.24.1  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 
 11.152   0.756  11.897

debrowser.Rcheck/tests/test-ui.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 v1.24.1  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 
 11.753   0.720  12.457

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0210.0090.029
IQRPlotControlsUI0.0020.0000.001
actionButtonDE0.0050.0000.004
addDataCols0.0010.0000.000
addID0.0010.0000.000
all2all0.1270.0110.139
all2allControlsUI0.0300.0010.030
applyFilters0.0010.0000.000
applyFiltersNew000
applyFiltersToMergedComparison0.0010.0000.000
barMainPlotControlsUI0.0000.0010.001
batchEffectUI0.0440.0020.045
batchMethod0.0020.0010.001
changeClusterOrder000
checkCountData000
checkMetaData000
clustFunParamsUI000
clusterData0.0000.0010.000
compareClust0.0000.0010.000
condSelectUI0.0030.0020.004
correctCombat0.0010.0000.000
correctHarman0.0010.0000.000
customColorsUI0.0070.0000.006
cutOffSelectionUI0.0040.0000.003
dataLCFUI0.0170.0000.017
dataLoadUI0.0130.0000.013
deServer0.0020.0070.009
deUI0.1340.0050.137
debrowserIQRplot000
debrowserall2all000
debrowserbarmainplot000
debrowserbatcheffect0.0000.0010.000
debrowserboxmainplot000
debrowsercondselect0.0000.0010.000
debrowserdataload0.0000.0010.000
debrowserdeanalysis000
debrowserdensityplot0.0010.0010.000
debrowserheatmap0.0010.0000.000
debrowserhistogram0.0010.0000.000
debrowserlowcountfilter0.0010.0000.000
debrowsermainplot000
debrowserpcaplot000
dendControlsUI0.0040.0020.006
densityPlotControlsUI0.0010.0000.002
distFunParamsUI000
drawKEGG0.0010.0000.001
drawPCAExplained0.0010.0000.000
fileTypes000
fileUploadBox0.0020.0000.002
generateTestData0.0010.0000.000
getAfterLoadMsg0.0010.0000.000
getAll2AllPlotUI000
getBSTableUI000
getBarMainPlot000
getBarMainPlotUI0.0000.0000.001
getBoxMainPlot0.0000.0000.001
getBoxMainPlotUI0.0010.0000.001
getColorShapeSelection0.0010.0000.000
getColors0.0010.0000.000
getCompSelection0.0020.0000.002
getCondMsg0.0010.0000.001
getConditionSelector0.0010.0000.000
getConditionSelectorFromMeta0.0010.0000.000
getCovariateDetails000
getCutOffSelection0.0010.0000.001
getDEAnalysisText0.0010.0000.001
getDEResultsUI0.0010.0000.001
getDataAssesmentText0.0010.0000.002
getDataForTables0.0010.0000.001
getDataPreparationText0.0010.0000.001
getDensityPlot000
getDensityPlotUI000
getDomains0.0000.0000.001
getDown0.0010.0000.000
getDownloadSection0.0060.0000.006
getEnrichDO000
getEnrichGO0.0000.0010.000
getEnrichKEGG0.0000.0010.001
getEntrezIds0.0000.0000.001
getEntrezTable000
getGOLeftMenu0.0050.0030.008
getGOPlots0.0010.0000.001
getGSEA0.0000.0000.001
getGeneList0.3580.0760.433
getGeneSetData0.0000.0000.001
getGoPanel0.0170.0010.018
getGroupSelector0.0000.0000.001
getHeatmapUI0.0000.0000.001
getHelpButton0.0000.0000.001
getHideLegendOnOff0.0020.0000.002
getHistogramUI0.0000.0000.001
getIQRPlot0.0010.0000.001
getIQRPlotUI0.0000.0000.001
getIntroText0.0020.0000.001
getJSLine0.0020.0000.002
getKEGGModal0.0000.0020.003
getLeftMenu0.0000.0000.001
getLegendColors0.0000.0010.001
getLegendRadio0.0010.0010.002
getLegendSelect0.0020.0000.001
getLevelOrder0.0010.0010.000
getLoadingMsg0.0000.0010.001
getLogo0.0000.0010.001
getMainPanel0.0000.0010.001
getMainPlotUI000
getMainPlotsLeftMenu0.0590.0010.061
getMean0.0000.0000.001
getMergedComparison000
getMetaSelector000
getMethodDetails0.0010.0000.000
getMostVariedList000
getNormalizedMatrix0.0120.0030.015
getOrganism000
getOrganismBox0.0020.0000.002
getOrganismPathway000
getPCAPlotUI000
getPCAcontolUpdatesJS0.0000.0000.001
getPCAexplained2.7670.1112.881
getPCselection0.0010.0000.001
getPlotArea000
getProgramTitle0.0010.0000.001
getQAText0.0010.0000.001
getQCLeftMenu000
getQCPanel0.0020.0000.002
getSampleDetails000
getSampleNames000
getSamples000
getSearchData000
getSelHeat0.0010.0000.001
getSelectInputBox000
getSelectedCols000
getSelectedDatasetInput0.0000.0010.000
getShapeColor0.0000.0010.000
getStartPlotsMsg0.0000.0020.002
getStartupMsg0.0000.0020.002
getTabUpdateJS0.0000.0010.000
getTableDetails000
getTableModal0.0000.0060.007
getTableStyle000
getUp000
getUpDown0.0000.0000.001
getVariationData0.0010.0000.001
get_conditions_given_selection0.0000.0000.001
heatmapControlsUI0.030.000.03
heatmapJScode0.0000.0010.000
heatmapServer0.0000.0010.001
heatmapUI0.0570.0010.059
hideObj0.0000.0000.001
histogramControlsUI0.0010.0000.001
installpack0.0010.0000.001
kmeansControlsUI0.0010.0030.005
lcfMetRadio0.0020.0000.002
loadpack0.0050.0280.033
mainPlotControlsUI0.0010.0040.005
mainScatterNew0.0000.0010.000
niceKmeans0.0000.0000.001
normalizationMethods0.0000.0010.002
palUI0.0010.0000.001
panel.cor0.0010.0000.001
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0040.0000.004
plotData0.0010.0000.001
plotMarginsUI0.0040.0000.004
plotSizeMarginsUI0.0070.0000.007
plotSizeUI0.0020.0000.002
plotTypeUI0.0010.0000.001
plot_pca0.7550.0560.811
prepDEOutput000
prepDataContainer0.0010.0000.001
prepGroup0.0000.0000.001
prepHeatData000
prepPCADat0.0000.0010.000
push000
removeCols0.0000.0000.001
removeExtraCols0.0000.0010.001
round_vals0.0000.0010.000
runDE0.0000.0010.000
runDESeq20.0000.0010.000
runEdgeR0.0000.0010.000
runHeatmap0.0000.0010.000
runHeatmap20.0000.0010.000
runLimma0.0000.0010.000
run_pca0.6110.0040.616
selectConditions0.0010.0000.001
selectGroupInfo000
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