Multiple platform build/check report for BioC 3.6 - CHECK report for debrowser on malbec1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings debrowser_1.6.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/debrowser.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.8’
* 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 ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc       6.2Mb
    extdata   2.1Mb
* 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 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
MAPlot: no visible global function definition for ‘:=’
MAPlot: no visible binding for global variable ‘size’
MAPlot: no visible binding for global variable ‘size.hover’
MAPlot: no visible binding for global variable ‘fillOpacity’
MAPlot: no visible binding for global variable ‘fillOpacity.hover’
MAPlot: no visible binding for global variable ‘fill.brush’
MAPlot: no visible binding for global variable ‘opacity’
MAPlot: no visible binding for global variable ‘key’
MAZoom: no visible global function definition for ‘:=’
MAZoom: no visible binding for global variable ‘size’
MAZoom: no visible binding for global variable ‘size.hover’
MAZoom: no visible binding for global variable ‘key’
bookmarkServer: no visible binding for global variable ‘NUL’
deServer: no visible binding for global variable ‘debrowser’
deServer: no visible global function definition for ‘renderImage’
getDensityPlot: no visible binding for global variable ‘samples’
getHoverPlots: no visible binding for global variable ‘conds’
getIQRPlot: no visible global function definition for ‘:=’
getIQRPlot: no visible binding for global variable ‘fill’
getKEGGModal: no visible global function definition for ‘div’
getKEGGModal: no visible global function definition for ‘imageOutput’
getSelectedDatasetInput: no visible binding for global variable
  ‘searched’
installpack: no visible global function definition for ‘biocLite’
load_data: no visible binding for global variable ‘demodata’
mainScatter: no visible global function definition for ‘:=’
mainScatter: no visible binding for global variable ‘size’
mainScatter: no visible binding for global variable ‘size.hover’
mainScatter: no visible binding for global variable ‘fillOpacity’
mainScatter: no visible binding for global variable ‘fillOpacity.hover’
mainScatter: no visible binding for global variable ‘fill.brush’
mainScatter: no visible binding for global variable ‘opacity’
mainScatter: no visible binding for global variable ‘key’
plot_pca: no visible global function definition for ‘:=’
plot_pca: no visible binding for global variable ‘key’
plot_pca: no visible binding for global variable ‘fontSize’
plot_pca: no visible binding for global variable ‘align’
plot_pca: no visible binding for global variable ‘baseline’
plot_pca: no visible binding for global variable ‘stroke’
runBayseq: no visible binding for global variable ‘fit’
scatterZoom: no visible global function definition for ‘:=’
scatterZoom: no visible binding for global variable ‘size’
scatterZoom: no visible binding for global variable ‘size.hover’
scatterZoom: no visible binding for global variable ‘key’
startDEBrowser: no visible binding for global variable
  ‘.startdebrowser.called’
volcanoPlot: no visible global function definition for ‘:=’
volcanoPlot: no visible binding for global variable ‘size’
volcanoPlot: no visible binding for global variable ‘size.hover’
volcanoPlot: no visible binding for global variable ‘fillOpacity’
volcanoPlot: no visible binding for global variable ‘fillOpacity.hover’
volcanoPlot: no visible binding for global variable ‘fill.brush’
volcanoPlot: no visible binding for global variable ‘opacity’
volcanoPlot: no visible binding for global variable ‘key’
volcanoZoom: no visible global function definition for ‘:=’
volcanoZoom: no visible binding for global variable ‘size’
volcanoZoom: no visible binding for global variable ‘size.hover’
volcanoZoom: no visible binding for global variable ‘key’
Undefined global functions or variables:
  .startdebrowser.called := NUL align baseline biocLite conds debrowser
  demodata div fill fill.brush fillOpacity fillOpacity.hover fit
  fontSize imageOutput key opacity renderImage samples searched size
  size.hover stroke
* 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 installed files from ‘inst/doc’ ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/debrowser.Rcheck/00check.log’
for details.

Installation output

* installing *source* package ‘debrowser’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (debrowser)

Tests output


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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)
Loading required package: ggvis
Loading required package: jsonlite

Attaching package: 'jsonlite'

The following object is masked from 'package:shiny':

    validate

Loading required package: shinyjs

Attaching package: 'shinyjs'

The following object is masked from 'package:shiny':

    runExample

The following objects are masked from 'package:methods':

    removeClass, show



##############################################################################
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).
##############################################################################


Attaching package: 'debrowser'

The following object is masked from 'package:shiny':

    actionButton

> 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, 3], 7.1)
+     expect_equal(demodata[29311, 6], 2)
+     expect_equal(demodata[29311, 7], 6)
+     expect_null(demodata[1, 8])
+ })
> 
> proc.time()
   user  system elapsed 
  9.168   0.180   9.348


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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)
Loading required package: shiny
Loading required package: ggvis
Loading required package: jsonlite

Attaching package: 'jsonlite'

The following object is masked from 'package:shiny':

    validate

Loading required package: shinyjs

Attaching package: 'shinyjs'

The following object is masked from 'package:shiny':

    runExample

The following objects are masked from 'package:methods':

    removeClass, show



##############################################################################
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).
##############################################################################


Attaching package: 'debrowser'

The following object is masked from 'package:shiny':

    actionButton

> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply

> library(edgeR)
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA

> library(testthat)
> 
> load(system.file("extdata", "demo", "demodata.Rda",
+     package = "debrowser"))
> 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])
> 
> test_that("Able to run DESeq2", {
+     deseqrun <- runDESeq(data, columns, conds)
+     expect_true(exists("deseqrun"))
+ })
> 
> test_that("Linked brush initialization", {
+     expect_silent( lb <- linked_brush())
+     expect_true(exists("lb"))
+ })
> 
> ##################################################
> deseqrun <- runDESeq(data, columns, conds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> lb <- linked_brush()
> 
> 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]
> ##################################################
> 
> test_that("Check the QC plots", {
+     expect_silent( all2all(data) )
+ 
+     heatmap <- runHeatmap(mtcars)
+     expect_false( is.null(heatmap) )
+     expect_silent( MAP <- MAPlot(dat, lb) )
+     expect_false( is.null(MAP) )
+ 
+     expect_silent( test_scat <- mainScatter(rdata, lb, 
+         x="Cond1", y="Cond2") )
+     expect_false(is.null(test_scat))
+     expect_silent( test_scat_zoom <- scatterZoom(rdata,
+         x="Cond1", y="Cond2") )
+     expect_false(is.null(test_scat_zoom))
+ 
+     expect_silent( test_volc <- volcanoPlot(rdata, lb) )
+     expect_false(is.null(test_volc))
+     expect_silent( test_volc_zoom <- volcanoZoom(rdata) )
+     expect_false(is.null(test_volc_zoom))
+ 
+     expect_silent( test_ma <- MAPlot(dat, lb) )
+     expect_false(is.null(test_ma))
+     expect_silent( test_ma_zoom <- MAZoom(dat) )
+     expect_false(is.null(test_ma_zoom))
+ })
> 
> 
> proc.time()
   user  system elapsed 
 29.508   0.256  29.788


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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)
Loading required package: ggvis
Loading required package: jsonlite

Attaching package: 'jsonlite'

The following object is masked from 'package:shiny':

    validate

Loading required package: shinyjs

Attaching package: 'shinyjs'

The following object is masked from 'package:shiny':

    runExample

The following objects are masked from 'package:methods':

    removeClass, show



##############################################################################
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).
##############################################################################


Attaching package: 'debrowser'

The following object is masked from 'package:shiny':

    actionButton

> library(testthat)
> 
> test_that("passing no data returns NULL", {
+     expect_null(getSampleNames(NULL))
+     expect_null(compareClust() )
+     expect_null(getGOPlots(NULL, NULL))
+     null_deseq <- runDESeq(NULL)
+     expect_null(null_deseq)
+     expect_null(mainScatter(NULL))
+     expect_null(scatterZoom(NULL))
+     expect_null(MAPlot(NULL))
+     expect_null(MAZoom(NULL))
+     expect_null(volcanoPlot(NULL))
+     expect_null(volcanoZoom(NULL))
+     expect_null(plot_pca(NULL))
+ })
> 
> proc.time()
   user  system elapsed 
  9.656   0.196   9.865


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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)
Loading required package: ggvis
Loading required package: jsonlite

Attaching package: 'jsonlite'

The following object is masked from 'package:shiny':

    validate

Loading required package: shinyjs

Attaching package: 'shinyjs'

The following object is masked from 'package:shiny':

    runExample

The following objects are masked from 'package:methods':

    removeClass, show



##############################################################################
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).
##############################################################################


Attaching package: 'debrowser'

The following object is masked from 'package:shiny':

    actionButton

> library(testthat)
> 
> test_that("able to create the basic UI", {
+     expect_silent( getDataPrep <- getDataPrepPanel(TRUE) )
+     expect_true(exists("getDataPrep"))
+     expect_equal(getDataPrep[[1]][[1]],"div")
+ })
> 
> 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(TRUE) )
+     expect_true(exists("downloads"))
+     expect_equal(downloads[[1]][[1]], "div")
+ 
+     expect_silent( getMain <- getMainPanel("randstr") )
+     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")
+ })
> 
> proc.time()
   user  system elapsed 
 10.448   0.196  10.649

Example timings

name	user	system	elapsed
MAPlot	0.000	0.000	0.001
MAZoom	0.000	0.000	0.001
actionButton	0.068	0.000	0.067
addDataCols	0.000	0.000	0.001
addID	0	0	0
add_title_pos	1.108	0.012	1.121
all2all	0.124	0.008	0.133
applyFilters	0.000	0.000	0.001
applyFiltersToMergedComparison	0.000	0.000	0.001
bookmarkServer	0	0	0
bookmarkUI	0.000	0.000	0.001
clusterData	0	0	0
compareClust	0	0	0
copy2newDirectory	0.000	0.000	0.001
correctBatchEffect	0.000	0.000	0.001
deServer	0.008	0.000	0.008
deUI	0.252	0.008	0.391
drawPCAExplained	0	0	0
getAfterLoadMsg	0	0	0
getColorShapeSelection	0.000	0.000	0.001
getColors	0.000	0.000	0.001
getCompSelection	0.024	0.000	0.027
getCondMsg	0	0	0
getConditionSelector	0	0	0
getConditionSelectorFromMeta	0.004	0.000	0.002
getCutOffSelection	0.076	0.000	0.079
getDataForTables	0	0	0
getDataPrepPanel	0	0	0
getDensityPlot	0.000	0.000	0.001
getDomains	0	0	0
getDown	0	0	0
getDownloadSection	0.004	0.000	0.000
getEnrichDO	0	0	0
getEnrichGO	0	0	0
getEnrichKEGG	0.004	0.000	0.000
getEntrezIds	0	0	0
getGOLeftMenu	0.084	0.000	0.083
getGOPlots	0	0	0
getGeneList	0.628	0.020	0.669
getGeneSetData	0.000	0.000	0.001
getGoPanel	0.040	0.000	0.038
getHelpButton	0	0	0
getHoverPlots	0	0	0
getIQRPlot	0.004	0.000	0.000
getInitialMenu	0.000	0.000	0.001
getIntHeatmap	0.000	0.000	0.001
getIntHeatmapVis	0.000	0.000	0.001
getJsonObj	0	0	0
getKEGGModal	0.028	0.000	0.027
getLeftMenu	0	0	0
getLegendSelect	0.004	0.000	0.003
getLoadingMsg	0.000	0.000	0.001
getLogo	0.000	0.000	0.001
getMainPanel	0	0	0
getMainPanelPlots	0.004	0.000	0.000
getMainPlotsLeftMenu	0.000	0.000	0.002
getMean	0.000	0.000	0.001
getMergedComparison	0	0	0
getMethodDetails	0	0	0
getMostVariedList	0	0	0
getNormalizedMatrix	0.044	0.000	0.044
getOrganism	0.000	0.000	0.001
getOrganismBox	0.004	0.000	0.003
getOrganismPathway	0	0	0
getPCAexplained	1.740	0.012	1.753
getPCselection	0.004	0.000	0.001
getProgramTitle	0	0	0
getQCLeftMenu	0	0	0
getQCPanel	0.032	0.000	0.054
getQCPlots	0.000	0.000	0.001
getQCReplot	0.000	0.000	0.001
getSampleNames	0.000	0.000	0.001
getSamples	0.000	0.000	0.001
getSearchData	0.000	0.000	0.001
getSelHeat	0.000	0.000	0.001
getSelectInputBox	0.000	0.000	0.001
getSelectedCols	0.000	0.000	0.001
getSelectedDatasetInput	0.000	0.000	0.001
getShapeColor	0.000	0.000	0.001
getStartPlotsMsg	0.004	0.000	0.004
getStartupMsg	0.004	0.000	0.004
getTableStyle	0.000	0.000	0.001
getTextOnOff	0.004	0.000	0.004
getToolTipPCA	0.000	0.000	0.001
getToolTipText	0.004	0.000	0.001
getUp	0.000	0.000	0.001
getUpDown	0.004	0.000	0.001
get_state_id	0.000	0.000	0.001
get_user_info	0.004	0.000	0.001
hideObj	0.000	0.000	0.001
installpack	0.000	0.000	0.001
link_brush	0.004	0.000	0.004
load_data	0	0	0
loadpack	0.028	0.008	0.038
logSliderJScode	0	0	0
mainScatter	0.000	0.000	0.001
panel.cor	0.000	0.000	0.001
panel.hist	0.004	0.000	0.001
plot_pca	1.160	0.012	1.172
prepAddQCPlots	0.000	0.000	0.001
prepDEOutput	0.004	0.000	0.000
prepDataContainer	0	0	0
prepDataForQC	0.000	0.000	0.001
push	0.004	0.000	0.001
readMetaData	0.000	0.000	0.001
removeBookmark	0.000	0.000	0.001
removeCols	0	0	0
round_vals	0	0	0
runBayseq	0.000	0.000	0.001
runDE	0.000	0.000	0.001
runDESeq	0.004	0.000	0.000
runDESeq2	0	0	0
runEdgeR	0	0	0
runHeatmap	0.300	0.000	0.298
runLimma	0	0	0
run_pca	0.932	0.008	0.938
saveQCPlot	0	0	0
scatterZoom	0	0	0
selectBatchEffect	0.000	0.000	0.001
selectConditions	0	0	0
selectedInput	0.000	0.000	0.001
setFilterParams	0.000	0.000	0.001
showObj	0	0	0
startDEBrowser	0	0	0
textareaInput	0.004	0.000	0.001
togglePanels	0.000	0.000	0.001
volcanoPlot	0	0	0
volcanoZoom	0.004	0.000	0.000
whitelist	0.000	0.000	0.001

CHECK report for debrowser on malbec1

Summary

Command output

Installation output

Tests output

Example timings