Alper Kucukural
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/debrowser |
| Branch: RELEASE_3_6 |
| Last Commit: b90f280 |
| Last Changed Date: 2017-12-04 11:24:56 -0400 (Mon, 04 Dec 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:27:44 -0400 (Thu, 12 Apr 2018).
| Package 338/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| debrowser 1.6.8 Alper Kucukural
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: debrowser |
| Version: 1.6.8 |
| Command: rm -rf debrowser.buildbin-libdir debrowser.Rcheck && mkdir debrowser.buildbin-libdir debrowser.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=debrowser.buildbin-libdir debrowser_1.6.8.tar.gz >debrowser.Rcheck\00install.out 2>&1 && cp debrowser.Rcheck\00install.out debrowser-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=debrowser.buildbin-libdir --install="check:debrowser-install.out" --force-multiarch --no-vignettes --timings debrowser_1.6.8.tar.gz |
| StartedAt: 2018-04-11 23:22:52 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:32:07 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 554.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: debrowser.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf debrowser.buildbin-libdir debrowser.Rcheck && mkdir debrowser.buildbin-libdir debrowser.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=debrowser.buildbin-libdir debrowser_1.6.8.tar.gz >debrowser.Rcheck\00install.out 2>&1 && cp debrowser.Rcheck\00install.out debrowser-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=debrowser.buildbin-libdir --install="check:debrowser-install.out" --force-multiarch --no-vignettes --timings debrowser_1.6.8.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/debrowser.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.6.8'
* 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 whether package 'debrowser' can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.3Mb
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
* 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
** checking loading without being on the library search path ... 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 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 ...
** 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-3.6-bioc/meat/debrowser.Rcheck/00check.log'
for details.
debrowser.Rcheck/00install.out
install for i386
* installing *source* package 'debrowser' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'debrowser'
finding HTML links ... done
MAPlot html
MAZoom html
actionButton html
addDataCols html
addID html
add_title_pos html
all2all html
applyFilters html
applyFiltersToMergedComparison html
bookmarkServer html
bookmarkUI html
clusterData html
compareClust html
copy2newDirectory html
correctBatchEffect html
deServer html
deUI html
drawPCAExplained html
getAfterLoadMsg html
getColorShapeSelection html
getColors html
getCompSelection html
getCondMsg html
getConditionSelector html
getConditionSelectorFromMeta html
getCutOffSelection html
getDataForTables html
getDataPrepPanel html
getDensityPlot html
getDomains html
getDown html
getDownloadSection html
getEnrichDO html
getEnrichGO html
getEnrichKEGG html
getEntrezIds html
getGOLeftMenu html
getGOPlots html
getGeneList html
getGeneSetData html
getGoPanel html
getHelpButton html
getHoverPlots html
getIQRPlot html
getInitialMenu html
getIntHeatmap html
getIntHeatmapVis html
getJsonObj html
getKEGGModal html
getLeftMenu html
getLegendSelect html
getLoadingMsg html
getLogo html
getMainPanel html
getMainPanelPlots html
getMainPlotsLeftMenu html
getMean html
getMergedComparison html
getMethodDetails html
getMostVariedList html
getNormalizedMatrix html
getOrganism html
getOrganismBox html
getOrganismPathway html
getPCAexplained html
getPCselection html
getProgramTitle html
getQCLeftMenu html
getQCPanel html
getQCPlots html
getQCReplot html
getSampleNames html
getSamples html
getSearchData html
getSelHeat html
getSelectInputBox html
getSelectedCols html
getSelectedDatasetInput html
getShapeColor html
getStartPlotsMsg html
getStartupMsg html
getTableStyle html
getTextOnOff html
getToolTipPCA html
getToolTipText html
getUp html
getUpDown html
get_state_id html
get_user_info html
hideObj html
installpack html
link_brush html
load_data html
loadpack html
logSliderJScode html
mainScatter html
panel.cor html
panel.hist html
plot_pca html
prepAddQCPlots html
prepDEOutput html
prepDataContainer html
prepDataForQC html
push html
readMetaData html
removeBookmark html
removeCols html
round_vals html
runBayseq html
runDE html
runDESeq html
runDESeq2 html
runEdgeR html
runHeatmap html
runLimma html
run_pca html
saveQCPlot html
scatterZoom html
selectBatchEffect html
selectConditions html
selectedInput html
setFilterParams html
showObj html
startDEBrowser html
textareaInput html
togglePanels html
volcanoPlot html
volcanoZoom html
whitelist 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_1.6.8.zip
* DONE (debrowser)
In R CMD INSTALL
In R CMD INSTALL
|
debrowser.Rcheck/tests_i386/test-demo.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
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
9.59 0.56 10.14
|
debrowser.Rcheck/tests_x64/test-demo.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
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
10.85 0.62 11.46
|
|
debrowser.Rcheck/tests_i386/test-deseq.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
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
31.03 0.92 31.93
|
debrowser.Rcheck/tests_x64/test-deseq.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
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
32.82 0.65 33.48
|
|
debrowser.Rcheck/tests_i386/test-null.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
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
8.76 0.65 9.40
|
debrowser.Rcheck/tests_x64/test-null.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
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
13.93 0.59 14.53
|
|
debrowser.Rcheck/tests_i386/test-ui.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
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
9.04 0.73 9.76
|
debrowser.Rcheck/tests_x64/test-ui.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
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
13.21 0.82 14.03
|
|
debrowser.Rcheck/examples_i386/debrowser-Ex.timings
|
debrowser.Rcheck/examples_x64/debrowser-Ex.timings
|