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CHECK report for debrowser on malbec1

This page was generated on 2019-04-16 11:51:56 -0400 (Tue, 16 Apr 2019).

Package 376/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.10.9
Alper Kucukural
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/debrowser
Branch: RELEASE_3_8
Last Commit: 02d3a86
Last Changed Date: 2019-02-02 22:04:17 -0400 (Sat, 02 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: debrowser
Version: 1.10.9
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings debrowser_1.10.9.tar.gz
StartedAt: 2019-04-15 23:20:19 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:27:28 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 428.5 seconds
RetCode: 0
Status:  OK 
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings debrowser_1.10.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/debrowser.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.10.9’
* 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’
getDensityPlot: no visible binding for global variable ‘samples’
getMean: no visible binding for global variable ‘norm_data’
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 ‘samples’
Undefined global functions or variables:
  demodata err norm_data samples 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-3.8-bioc/meat/debrowser.Rcheck/00check.log’
for details.



Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL debrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘debrowser’ ...
** 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
* DONE (debrowser)

Tests output

debrowser.Rcheck/tests/test-demo.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 v1.10.9  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])
+ })
> 
> proc.time()
   user  system elapsed 
 14.984   0.464  15.491 

debrowser.Rcheck/tests/test-deseq.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 v1.10.9  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"))
> 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])
> params <-
+         #Run DESeq2 with the following parameters
+         c("DESeq2", "parametric", F, "Wald") 
> non_expressed_cutoff <- 10
> data <- subset(data, rowSums(data) > 10)
> test_that("Able to run DESeq2", {
+     deseqrun <- runDE(data, columns, conds, params)
+     expect_true(exists("deseqrun"))
+ })
> 
> ##################################################
> deseqrun <- runDE(data, 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]
> ##################################################
> 
> test_that("Check the QC plots", {
+     expect_silent( all2all(data) )
+ })
> 
> 
> proc.time()
   user  system elapsed 
 46.620   0.708  47.483 

debrowser.Rcheck/tests/test-null.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 v1.10.9  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))
+ })
> 
> proc.time()
   user  system elapsed 
 15.024   0.500  15.668 

debrowser.Rcheck/tests/test-ui.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 v1.10.9  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")
+ })
> 
> proc.time()
   user  system elapsed 
 16.344   0.640  17.053 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0080.0000.006
IQRPlotControlsUI0.0040.0000.001
actionButtonDE0.0040.0000.005
addDataCols000
addID0.0040.0000.000
all2all0.2360.0040.240
all2allControlsUI0.0040.0000.004
applyFilters000
applyFiltersNew000
applyFiltersToMergedComparison000
barMainPlotControlsUI0.0000.0000.001
batchEffectUI0.0800.0040.083
batchMethod0.0040.0000.004
changeClusterOrder0.0040.0000.001
checkCountData000
checkMetaData000
clustFunParamsUI000
clusterData000
compareClust000
condSelectUI0.0080.0000.007
correctCombat0.0000.0000.001
correctHarman0.0040.0000.001
customColorsUI0.0080.0000.030
cutOffSelectionUI0.0040.0000.005
dataLCFUI0.0320.0000.071
dataLoadUI0.0240.0040.049
deServer0.0160.0000.028
deUI0.2000.0240.449
debrowserIQRplot0.0000.0000.001
debrowserall2all0.0040.0000.001
debrowserbarmainplot000
debrowserbatcheffect000
debrowserboxmainplot000
debrowsercondselect0.0000.0000.001
debrowserdataload0.0000.0000.001
debrowserdeanalysis000
debrowserdensityplot000
debrowserheatmap0.0000.0000.001
debrowserhistogram0.0000.0000.001
debrowserlowcountfilter000
debrowsermainplot0.0000.0040.001
debrowserpcaplot000
dendControlsUI0.0080.0000.009
densityPlotControlsUI0.0000.0000.001
distFunParamsUI000
drawKEGG000
drawPCAExplained0.0000.0000.001
fileTypes000
fileUploadBox0.0040.0000.005
generateTestData000
getAfterLoadMsg0.0000.0000.001
getAll2AllPlotUI0.0000.0000.001
getBSTableUI0.0000.0040.001
getBarMainPlot0.0000.0000.001
getBarMainPlotUI000
getBoxMainPlot000
getBoxMainPlotUI000
getColorShapeSelection000
getColors000
getCompSelection0.0000.0000.003
getCondMsg0.0000.0000.001
getConditionSelector0.0000.0000.001
getConditionSelectorFromMeta0.0040.0000.004
getCutOffSelection0.0040.0000.002
getDEAnalysisText0.0000.0000.002
getDEResultsUI0.0000.0000.002
getDataAssesmentText0.0040.0000.002
getDataForTables0.0000.0000.001
getDataPreparationText0.0000.0000.001
getDensityPlot0.0000.0040.001
getDensityPlotUI0.0000.0000.001
getDomains0.0000.0000.001
getDown0.0000.0000.001
getDownloadSection0.0080.0000.012
getEnrichDO000
getEnrichGO000
getEnrichKEGG000
getEntrezIds0.0040.0000.001
getEntrezTable0.0000.0000.001
getGOLeftMenu0.0160.0000.014
getGOPlots0.0000.0000.001
getGeneList0.9400.0280.972
getGeneSetData000
getGoPanel0.0280.0000.027
getHeatmapUI000
getHelpButton000
getHideLegendOnOff0.0040.0000.003
getHistogramUI000
getIQRPlot0.0000.0000.001
getIQRPlotUI000
getIntroText0.0000.0000.001
getJSLine0.0200.0000.018
getKEGGModal0.0000.0000.002
getLeftMenu0.0000.0000.001
getLegendColors0.0000.0000.001
getLegendRadio0.0000.0000.002
getLegendSelect0.0000.0000.003
getLevelOrder000
getLoadingMsg0.0000.0000.002
getLogo0.0000.0000.002
getMainPanel0.0040.0000.001
getMainPlotUI000
getMainPlotsLeftMenu0.0560.0040.059
getMean0.0000.0000.001
getMergedComparison0.0000.0000.001
getMetaSelector0.0000.0000.001
getMethodDetails0.0000.0000.001
getMostVariedList000
getNormalizedMatrix0.0160.0000.018
getOrganism000
getOrganismBox0.0040.0000.003
getOrganismPathway0.0000.0000.001
getPCAPlotUI0.0000.0000.001
getPCAcontolUpdatesJS000
getPCAexplained4.7000.0804.798
getPCselection0.0040.0000.002
getPlotArea0.0000.0000.001
getProgramTitle0.0000.0000.001
getQAText0.0040.0000.002
getQCLeftMenu0.0000.0000.001
getQCPanel0.0040.0000.004
getSampleDetails0.0000.0000.001
getSampleNames000
getSamples000
getSearchData0.0000.0000.001
getSelHeat0.0000.0000.001
getSelectInputBox0.0000.0000.001
getSelectedCols0.0000.0000.001
getSelectedDatasetInput0.0000.0000.001
getShapeColor0.0000.0000.001
getStartPlotsMsg0.0000.0000.003
getStartupMsg0.0040.0000.003
getTabUpdateJS0.0040.0000.000
getTableDetails0.0000.0000.001
getTableModal0.0120.0000.012
getTableStyle0.0000.0000.001
getTextOnOff0.0000.0000.003
getUp000
getUpDown000
getVariationData000
get_conditions_given_selection000
heatmapControlsUI0.0440.0000.048
heatmapJScode000
heatmapServer0.0000.0000.001
heatmapUI0.1040.0080.112
hideObj0.0040.0000.000
histogramControlsUI000
installpack000
kmeansControlsUI0.0040.0040.006
lcfMetRadio0.0040.0000.003
loadpack0.0240.0120.034
mainPlotControlsUI0.0040.0000.006
mainScatterNew0.0040.0000.000
niceKmeans000
normalizationMethods0.0040.0000.004
palUI0.0040.0000.004
panel.cor0.0000.0000.001
panel.hist0.0000.0000.001
pcaPlotControlsUI0.0080.0000.010
plotData0.0000.0000.001
plotMarginsUI0.0040.0000.003
plotSizeMarginsUI0.0040.0000.006
plotSizeUI0.0000.0000.002
plot_pca2.7120.0202.764
prepDEOutput000
prepDataContainer0.0040.0000.000
prepGroup000
prepHeatData0.0000.0000.001
prepPCADat000
push0.0000.0000.001
removeCols000
removeExtraCols0.0000.0040.001
round_vals000
runDE000
runDESeq2000
runEdgeR0.0000.0000.001
runHeatmap0.0000.0000.001
runHeatmap2000
runLimma000
run_pca1.2400.0001.241
selectConditions0.0040.0000.002
selectGroupInfo000
selectedInput000
sepRadio0.0040.0000.002
setBatch000
showObj000
startDEBrowser000
startHeatmap0.0000.0000.001
textareaInput000
togglePanels0.0000.0040.000