Alper Kucukural
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/debrowser |
| Branch: RELEASE_3_7 |
| Last Commit: 15dc641 |
| Last Changed Date: 2018-09-26 15:43:38 -0400 (Wed, 26 Sep 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:41:56 -0400 (Wed, 17 Oct 2018).
| Package 353/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| debrowser 1.8.5 Alper Kucukural
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: debrowser |
| Version: 1.8.5 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:debrowser.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings debrowser_1.8.5.tar.gz |
| StartedAt: 2018-10-17 01:29:00 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:38:42 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 581.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: debrowser.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:debrowser.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings debrowser_1.8.5.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/debrowser.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'debrowser/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'debrowser' version '1.8.5' * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE Namespace in Imports field not imported from: 'googleAuthR' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE deServer: no visible binding for global variable 'debrowser' deServer: no visible global function definition for 'getJsonObj' deServer: no visible global function definition for 'access_token' debrowserdataload: no visible binding for global variable 'demodata' getDensityPlot: no visible binding for global variable 'samples' getGeneList: no visible global function definition for 'showNotification' getMean: no visible binding for global variable 'norm_data' installpack: no visible global function definition for 'showNotification' 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: access_token debrowser demodata getJsonObj norm_data samples showNotification 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test-demo.R' Running 'test-deseq.R' Running 'test-null.R' Running 'test-ui.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.7-bioc/meat/debrowser.Rcheck/00check.log' for details.
debrowser.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/debrowser_1.8.5.tar.gz && rm -rf debrowser.buildbin-libdir && mkdir debrowser.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=debrowser.buildbin-libdir debrowser_1.8.5.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL debrowser_1.8.5.zip && rm debrowser_1.8.5.tar.gz debrowser_1.8.5.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2468k 100 2468k 0 0 25.7M 0 --:--:-- --:--:-- --:--:-- 27.7M
install for i386
* installing *source* package 'debrowser' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'debrowser'
finding HTML links ... done
BoxMainPlotControlsUI html
IQRPlotControlsUI html
actionButton html
addDataCols html
addID html
all2all html
all2allControlsUI html
applyFilters html
applyFiltersNew html
applyFiltersToMergedComparison html
barMainPlotControlsUI html
batchEffectUI html
batchMethod html
changeClusterOrder html
clustFunParamsUI html
clusterData html
compareClust html
condSelectUI html
correctCombat html
correctHarman html
customColorsUI html
cutOffSelectionUI html
dataLCFUI html
dataLoadUI html
deServer html
deUI html
debrowserIQRplot html
debrowserall2all html
debrowserbarmainplot html
debrowserbatcheffect html
debrowserboxmainplot html
debrowsercondselect html
debrowserdataload html
debrowserdeanalysis html
debrowserdensityplot html
debrowserheatmap html
debrowserhistogram html
debrowserlowcountfilter html
debrowsermainplot html
debrowserpcaplot html
dendControlsUI html
densityPlotControlsUI html
distFunParamsUI html
drawPCAExplained html
fileTypes html
fileUploadBox html
generateTestData html
getAfterLoadMsg html
getAll2AllPlotUI html
getBSTableUI html
getBarMainPlot html
getBarMainPlotUI html
getBoxMainPlot html
getBoxMainPlotUI html
getColorShapeSelection html
getColors html
getCompSelection html
getCondMsg html
getConditionSelector html
getConditionSelectorFromMeta html
getCutOffSelection html
getDEAnalysisText html
getDEResultsUI html
getDataAssesmentText html
getDataForTables html
getDataPreparationText html
getDensityPlot html
getDensityPlotUI html
getDomains html
getDown html
getDownloadSection html
getEnrichDO html
getEnrichGO html
getEnrichKEGG html
getEntrezIds html
getEntrezTable html
getGOLeftMenu html
getGOPlots html
getGeneList html
getGeneSetData html
getGoPanel html
getHeatmapUI html
getHelpButton html
getHideLegendOnOff html
getHistogramUI html
getIQRPlot html
getIQRPlotUI html
getIntroText html
getJSLine html
getKEGGModal html
getLeftMenu html
getLegendColors html
getLegendRadio html
getLegendSelect html
getLevelOrder html
getLoadingMsg html
getLogo html
getMainPanel html
getMainPlotUI html
getMainPlotsLeftMenu html
getMean html
getMergedComparison html
getMetaSelector html
getMethodDetails html
getMostVariedList html
getNormalizedMatrix html
getOrganism html
getOrganismBox html
getOrganismPathway html
getPCAPlotUI html
getPCAcontolUpdatesJS html
getPCAexplained html
getPCselection html
getPlotArea html
getProgramTitle html
getQAText html
getQCLeftMenu html
getQCPanel html
getSampleDetails html
getSampleNames html
getSamples html
getSearchData html
getSelHeat html
getSelectInputBox html
getSelectedCols html
getSelectedDatasetInput html
getShapeColor html
getStartPlotsMsg html
getStartupMsg html
getTabUpdateJS html
getTableDetails html
getTableModal html
getTableStyle html
getTextOnOff html
getUp html
getUpDown html
getVariationData html
get_conditions_given_selection html
heatmapControlsUI html
heatmapJScode html
heatmapServer html
heatmapUI html
hideObj html
histogramControlsUI html
installpack html
kmeansControlsUI html
lcfMetRadio html
loadpack html
mainPlotControlsUI html
mainScatterNew html
niceKmeans html
normalizationMethods html
palUI html
panel.cor html
panel.hist html
pcaPlotControlsUI html
plotData html
plotMarginsUI html
plotSizeMarginsUI html
plotSizeUI html
plot_pca html
prepDEOutput html
prepDataContainer html
prepGroup html
prepHeatData html
prepPCADat html
push html
removeCols html
round_vals html
runDE html
runDESeq2 html
runEdgeR html
runHeatmap html
runHeatmap2 html
runLimma html
run_pca html
selectConditions html
selectGroupInfo html
selectedInput html
sepRadio html
setBatch html
showObj html
startDEBrowser html
startHeatmap html
textareaInput html
togglePanels html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'debrowser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'debrowser' as debrowser_1.8.5.zip
* DONE (debrowser)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'debrowser' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
debrowser.Rcheck/tests_i386/test-demo.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 v1.8.5 For help: https://debrowser.readthedocs.org/
If you use DEBrowser in published research, please cite:
Alper Kucukural, Onur Yuksel, Deniz M. Ozata, Melissa J. Moore, Manuel Garber, DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data, Bioarxiv 2018, doi: 10.1101/399931
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, 2], 7.1)
+ expect_equal(demodata[29311, 5], 2)
+ expect_equal(demodata[29311, 6], 6)
+ expect_null(demodata[1, 7])
+ })
>
> proc.time()
user system elapsed
12.48 1.43 13.90
|
debrowser.Rcheck/tests_x64/test-demo.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 v1.8.5 For help: https://debrowser.readthedocs.org/
If you use DEBrowser in published research, please cite:
Alper Kucukural, Onur Yuksel, Deniz M. Ozata, Melissa J. Moore, Manuel Garber, DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data, Bioarxiv 2018, doi: 10.1101/399931
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, 2], 7.1)
+ expect_equal(demodata[29311, 5], 2)
+ expect_equal(demodata[29311, 6], 6)
+ expect_null(demodata[1, 7])
+ })
>
> proc.time()
user system elapsed
15.85 1.42 17.26
|
|
debrowser.Rcheck/tests_i386/test-deseq.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 v1.8.5 For help: https://debrowser.readthedocs.org/
If you use DEBrowser in published research, please cite:
Alper Kucukural, Onur Yuksel, Deniz M. Ozata, Melissa J. Moore, Manuel Garber, DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data, Bioarxiv 2018, doi: 10.1101/399931
Attaching package: 'debrowser'
The following object is masked _by_ 'package:shiny':
actionButton
> 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
29.84 2.09 31.92
|
debrowser.Rcheck/tests_x64/test-deseq.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 v1.8.5 For help: https://debrowser.readthedocs.org/
If you use DEBrowser in published research, please cite:
Alper Kucukural, Onur Yuksel, Deniz M. Ozata, Melissa J. Moore, Manuel Garber, DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data, Bioarxiv 2018, doi: 10.1101/399931
Attaching package: 'debrowser'
The following object is masked _by_ 'package:shiny':
actionButton
> 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
36.40 1.34 37.76
|
|
debrowser.Rcheck/tests_i386/test-null.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 v1.8.5 For help: https://debrowser.readthedocs.org/
If you use DEBrowser in published research, please cite:
Alper Kucukural, Onur Yuksel, Deniz M. Ozata, Melissa J. Moore, Manuel Garber, DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data, Bioarxiv 2018, doi: 10.1101/399931
Attaching package: 'debrowser'
The following object is masked from 'package:shiny':
actionButton
> 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
13.31 1.60 14.90
|
debrowser.Rcheck/tests_x64/test-null.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 v1.8.5 For help: https://debrowser.readthedocs.org/
If you use DEBrowser in published research, please cite:
Alper Kucukural, Onur Yuksel, Deniz M. Ozata, Melissa J. Moore, Manuel Garber, DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data, Bioarxiv 2018, doi: 10.1101/399931
Attaching package: 'debrowser'
The following object is masked from 'package:shiny':
actionButton
> 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
16.64 1.54 18.17
|
|
debrowser.Rcheck/tests_i386/test-ui.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 v1.8.5 For help: https://debrowser.readthedocs.org/
If you use DEBrowser in published research, please cite:
Alper Kucukural, Onur Yuksel, Deniz M. Ozata, Melissa J. Moore, Manuel Garber, DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data, Bioarxiv 2018, doi: 10.1101/399931
Attaching package: 'debrowser'
The following object is masked from 'package:shiny':
actionButton
> 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
13.01 1.54 14.56
|
debrowser.Rcheck/tests_x64/test-ui.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 v1.8.5 For help: https://debrowser.readthedocs.org/
If you use DEBrowser in published research, please cite:
Alper Kucukural, Onur Yuksel, Deniz M. Ozata, Melissa J. Moore, Manuel Garber, DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data, Bioarxiv 2018, doi: 10.1101/399931
Attaching package: 'debrowser'
The following object is masked from 'package:shiny':
actionButton
> 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
16.32 1.48 17.81
|
|
debrowser.Rcheck/examples_i386/debrowser-Ex.timings
|
debrowser.Rcheck/examples_x64/debrowser-Ex.timings
|