Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 515/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
debrowser 1.34.0 (landing page) Alper Kucukural
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the debrowser package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/debrowser.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: debrowser |
Version: 1.34.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:debrowser.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings debrowser_1.34.0.tar.gz |
StartedAt: 2024-12-20 00:41:14 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:49:17 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 483.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: debrowser.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:debrowser.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings debrowser_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/debrowser.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'debrowser/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'debrowser' version '1.34.0' * 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 code 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE checkCountData : <anonymous>: no visible binding for global variable 'err' debrowserdataload: no visible binding for global variable 'demodata' debrowserhistogram: no visible global function definition for 'config' generateTestData: no visible binding for global variable 'metadata' getBarMainPlot: no visible global function definition for 'config' getBoxMainPlot: no visible global function definition for 'config' getDensityPlot: no visible binding for global variable 'samples' getDensityPlot: no visible global function definition for 'config' getGOPlots: no visible global function definition for 'facet_grid' getGSEA: no visible global function definition for 'is' getIQRPlot: no visible global function definition for 'config' mainScatterNew: no visible global function definition for 'config' plot_pca: no visible binding for global variable 'x' plot_pca: no visible binding for global variable 'y' plot_pca: no visible binding for global variable 'textName' plot_pca: no visible global function definition for 'config' runHeatmap: no visible global function definition for 'config' Undefined global functions or variables: config demodata err facet_grid is metadata samples textName x y Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 ... 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 'F:/biocbuild/bbs-3.20-bioc/meat/debrowser.Rcheck/00check.log' for details.
debrowser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL debrowser ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'debrowser' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (debrowser)
debrowser.Rcheck/tests/test-demo.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 v1.34.0 For help: https://debrowser.readthedocs.org/ If you use DEBrowser in published research, please cite: Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data BMC Genomics 2019 20:6 doi:0.1186/s12864-018-5362-x > library(testthat) > > test_that("demo data can be loaded", { + load(system.file("extdata", "demo", "demodata.Rda", + package = "debrowser")) + expect_true(is.data.frame(demodata)) + expect_equal(demodata[29311, 2], 2) + expect_equal(demodata[29311, 5], 7.1) + expect_equal(demodata[29311, 6], 6) + expect_null(demodata[1, 7]) + }) Test passed 🥇 > > proc.time() user system elapsed 16.10 1.48 17.71
debrowser.Rcheck/tests/test-deseq.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 v1.34.0 For help: https://debrowser.readthedocs.org/ If you use DEBrowser in published research, please cite: Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data BMC Genomics 2019 20:6 doi:0.1186/s12864-018-5362-x > library(testthat) > > load(system.file("extdata", "demo", "demodata.Rda", + package = "debrowser")) > metadata <- metadatatable > columns <- c("exper_rep1", "exper_rep2", "exper_rep3", + "control_rep1", "control_rep2", "control_rep3") > conds <- factor( c("Control", "Control", "Control", + "Treat", "Treat", "Treat") ) > data <- data.frame(demodata[, columns]) > > #Run DESeq2 with the following parameters > params <- c("DESeq2", "NoCovariate", "parametric", F, "Wald", "None") > non_expressed_cutoff <- 10 > data <- subset(data, rowSums(data) > 10) > test_that("Able to run DESeq2", { + deseqrun <- runDE(data, metadata, columns, conds, params) + expect_true(exists("deseqrun")) + }) Test passed 😀 > > ################################################## > deseqrun <- runDE(data, metadata, columns, conds, params) estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing > > de_res <- data.frame(deseqrun) > norm_data <- getNormalizedMatrix(data[, columns]) > rdata <- cbind(rownames(de_res), norm_data[rownames(de_res), columns], + log10(rowMeans(norm_data[rownames(de_res), + paste(c("exper_rep1", "exper_rep2", "exper_rep3"))]) + + 0.1), log10( rowMeans( norm_data[ rownames( de_res ), + paste(c("control_rep1", "control_rep2", "control_rep3"))]) + + 0.1), de_res[rownames(de_res), + c("padj", "log2FoldChange")], 2 ^ de_res[rownames(de_res), + "log2FoldChange"], -1 * + log10(de_res[rownames(de_res), "padj"])) > colnames(rdata) <- c("ID", columns, "Cond1", "Cond2", "padj", + "log2FoldChange", "foldChange", "log10padj") > rdata <- as.data.frame(rdata) > rdata$padj[is.na(rdata$padj)] <- 1 > > padj_cutoff <- 0.01 > foldChange_cutoff <- 2 > > rdata$Legend <- character(nrow(rdata)) > rdata$Legend[rdata$log2FoldChange > log2(foldChange_cutoff) & + rdata$padj < padj_cutoff] <- "Up" > rdata$Legend[rdata$log2FoldChange < log2(1 / foldChange_cutoff) & + rdata$padj < padj_cutoff] <- "Down" > rdata$Legend[abs(rdata$log2FoldChange) <= + log2(foldChange_cutoff)] <- "NS" > rdata$Legend[is.null(rdata$log10padj)] <- "NA" > rdata$Size <- character(nrow(rdata)) > rdata[, "Size"] <- "40" > > dat <- rdata > dat$M <- rdata$Cond1 - rdata$Cond2 > dat$A <- (rdata$Cond1 + rdata$Cond2) / 2 > > updown <- rdata[rdata$Legend=="Up" | rdata$Legend=="Down",columns] > ################################################## > > > > proc.time() user system elapsed 38.59 1.75 40.32
debrowser.Rcheck/tests/test-null.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 v1.34.0 For help: https://debrowser.readthedocs.org/ If you use DEBrowser in published research, please cite: Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data BMC Genomics 2019 20:6 doi:0.1186/s12864-018-5362-x > library(testthat) > > test_that("passing no data returns NULL", { + expect_null(compareClust() ) + expect_null(getGOPlots(NULL, NULL)) + null_deseq <- runDE(NULL) + expect_null(null_deseq) + expect_null(plot_pca(NULL)) + }) Test passed 🌈 > > proc.time() user system elapsed 16.84 1.34 18.17
debrowser.Rcheck/tests/test-ui.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 v1.34.0 For help: https://debrowser.readthedocs.org/ If you use DEBrowser in published research, please cite: Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data BMC Genomics 2019 20:6 doi:0.1186/s12864-018-5362-x > library(testthat) > > test_that("able to create panel UI", { + expect_silent( QCPanel <- getQCPanel() ) + expect_true(exists("QCPanel")) + expect_equal(QCPanel[[1]][[1]], "div") + + expect_silent( downloads <- getDownloadSection() ) + expect_true(exists("downloads")) + expect_equal(downloads[[1]][[1]], "div") + + expect_silent( getMain <- getMainPanel() ) + expect_true(exists("getMain")) + expect_equal(getMain[[1]][[1]], "div") + + expect_silent( getStart <- getStartupMsg() ) + expect_true(exists("getStart")) + expect_equal(getStart[[1]][[1]], "div") + + expect_silent( getAfter <- getAfterLoadMsg() ) + expect_true(exists("getAfter")) + expect_equal(getAfter[[1]][[1]], "div") + + expect_silent(getGO <- getGoPanel() ) + expect_true(exists("getGO")) + expect_equal(getGO[[1]][[1]], "div") + }) Test passed 🎊 > > proc.time() user system elapsed 16.40 1.62 18.03
debrowser.Rcheck/debrowser-Ex.timings
name | user | system | elapsed | |
BoxMainPlotControlsUI | 0.03 | 0.00 | 0.92 | |
IQRPlotControlsUI | 0.02 | 0.00 | 0.01 | |
actionButtonDE | 0.00 | 0.02 | 0.02 | |
addDataCols | 0 | 0 | 0 | |
addID | 0 | 0 | 0 | |
all2all | 0.16 | 0.01 | 0.26 | |
all2allControlsUI | 0.03 | 0.00 | 0.85 | |
applyFilters | 0 | 0 | 0 | |
applyFiltersNew | 0 | 0 | 0 | |
applyFiltersToMergedComparison | 0 | 0 | 0 | |
barMainPlotControlsUI | 0 | 0 | 0 | |
batchEffectUI | 0.08 | 0.00 | 0.15 | |
batchMethod | 0.00 | 0.02 | 0.02 | |
changeClusterOrder | 0 | 0 | 0 | |
checkCountData | 0.95 | 0.00 | 0.95 | |
checkMetaData | 0 | 0 | 0 | |
clustFunParamsUI | 0 | 0 | 0 | |
clusterData | 0 | 0 | 0 | |
compareClust | 0 | 0 | 0 | |
condSelectUI | 0 | 0 | 0 | |
correctCombat | 0 | 0 | 0 | |
correctHarman | 0 | 0 | 0 | |
customColorsUI | 0.02 | 0.00 | 0.01 | |
cutOffSelectionUI | 0 | 0 | 0 | |
dataLCFUI | 0.02 | 0.00 | 0.02 | |
dataLoadUI | 0.01 | 0.00 | 0.02 | |
deServer | 0 | 0 | 0 | |
deUI | 0.11 | 0.00 | 0.11 | |
debrowserIQRplot | 0 | 0 | 0 | |
debrowserall2all | 0 | 0 | 0 | |
debrowserbarmainplot | 0 | 0 | 0 | |
debrowserbatcheffect | 0 | 0 | 0 | |
debrowserboxmainplot | 0 | 0 | 0 | |
debrowsercondselect | 0 | 0 | 0 | |
debrowserdataload | 0 | 0 | 0 | |
debrowserdeanalysis | 0 | 0 | 0 | |
debrowserdensityplot | 0 | 0 | 0 | |
debrowserheatmap | 0 | 0 | 0 | |
debrowserhistogram | 0 | 0 | 0 | |
debrowserlowcountfilter | 0 | 0 | 0 | |
debrowsermainplot | 0 | 0 | 0 | |
debrowserpcaplot | 0 | 0 | 0 | |
dendControlsUI | 0.01 | 0.00 | 0.01 | |
densityPlotControlsUI | 0 | 0 | 0 | |
distFunParamsUI | 0 | 0 | 0 | |
drawKEGG | 0 | 0 | 0 | |
drawPCAExplained | 0 | 0 | 0 | |
fileTypes | 0 | 0 | 0 | |
fileUploadBox | 0 | 0 | 0 | |
generateTestData | 0.02 | 0.00 | 0.02 | |
getAfterLoadMsg | 0 | 0 | 0 | |
getAll2AllPlotUI | 0 | 0 | 0 | |
getBSTableUI | 0 | 0 | 0 | |
getBarMainPlot | 0 | 0 | 0 | |
getBarMainPlotUI | 0 | 0 | 0 | |
getBoxMainPlot | 0 | 0 | 0 | |
getBoxMainPlotUI | 0 | 0 | 0 | |
getColorShapeSelection | 0 | 0 | 0 | |
getColors | 0 | 0 | 0 | |
getCompSelection | 0.01 | 0.00 | 0.01 | |
getCondMsg | 0 | 0 | 0 | |
getConditionSelector | 0 | 0 | 0 | |
getConditionSelectorFromMeta | 0 | 0 | 0 | |
getCovariateDetails | 0 | 0 | 0 | |
getCutOffSelection | 0 | 0 | 0 | |
getDEAnalysisText | 0 | 0 | 0 | |
getDEResultsUI | 0.02 | 0.00 | 0.02 | |
getDataAssesmentText | 0 | 0 | 0 | |
getDataForTables | 0 | 0 | 0 | |
getDataPreparationText | 0 | 0 | 0 | |
getDensityPlot | 0 | 0 | 0 | |
getDensityPlotUI | 0 | 0 | 0 | |
getDomains | 0 | 0 | 0 | |
getDown | 0 | 0 | 0 | |
getDownloadSection | 0.01 | 0.00 | 0.01 | |
getEnrichDO | 0 | 0 | 0 | |
getEnrichGO | 0 | 0 | 0 | |
getEnrichKEGG | 0 | 0 | 0 | |
getEntrezIds | 0 | 0 | 0 | |
getEntrezTable | 0.00 | 0.01 | 0.02 | |
getGOLeftMenu | 0 | 0 | 0 | |
getGOPlots | 0 | 0 | 0 | |
getGSEA | 0 | 0 | 0 | |
getGeneList | 0.97 | 0.31 | 1.29 | |
getGeneSetData | 0 | 0 | 0 | |
getGoPanel | 0.01 | 0.00 | 0.01 | |
getGroupSelector | 0 | 0 | 0 | |
getHeatmapUI | 0 | 0 | 0 | |
getHelpButton | 0 | 0 | 0 | |
getHideLegendOnOff | 0 | 0 | 0 | |
getHistogramUI | 0 | 0 | 0 | |
getIQRPlot | 0 | 0 | 0 | |
getIQRPlotUI | 0 | 0 | 0 | |
getIntroText | 0 | 0 | 0 | |
getJSLine | 0.02 | 0.00 | 0.02 | |
getKEGGModal | 0 | 0 | 0 | |
getLeftMenu | 0 | 0 | 0 | |
getLegendColors | 0 | 0 | 0 | |
getLegendRadio | 0 | 0 | 0 | |
getLegendSelect | 0 | 0 | 0 | |
getLevelOrder | 0 | 0 | 0 | |
getLoadingMsg | 0.00 | 0.02 | 0.01 | |
getLogo | 0 | 0 | 0 | |
getMainPanel | 0 | 0 | 0 | |
getMainPlotUI | 0 | 0 | 0 | |
getMainPlotsLeftMenu | 0.08 | 0.00 | 0.08 | |
getMean | 0 | 0 | 0 | |
getMergedComparison | 0 | 0 | 0 | |
getMetaSelector | 0 | 0 | 0 | |
getMethodDetails | 0 | 0 | 0 | |
getMostVariedList | 0 | 0 | 0 | |
getNormalizedMatrix | 0.01 | 0.00 | 0.01 | |
getOrganism | 0 | 0 | 0 | |
getOrganismBox | 0 | 0 | 0 | |
getOrganismPathway | 0 | 0 | 0 | |
getPCAPlotUI | 0 | 0 | 0 | |
getPCAcontolUpdatesJS | 0 | 0 | 0 | |
getPCAexplained | 2.39 | 0.08 | 2.48 | |
getPCselection | 0 | 0 | 0 | |
getPlotArea | 0 | 0 | 0 | |
getProgramTitle | 0 | 0 | 0 | |
getQAText | 0.02 | 0.00 | 0.02 | |
getQCLeftMenu | 0 | 0 | 0 | |
getQCPanel | 0 | 0 | 0 | |
getSampleDetails | 0 | 0 | 0 | |
getSampleNames | 0 | 0 | 0 | |
getSearchData | 0 | 0 | 0 | |
getSelHeat | 0 | 0 | 0 | |
getSelectInputBox | 0.01 | 0.00 | 0.02 | |
getSelectedCols | 0 | 0 | 0 | |
getSelectedDatasetInput | 0 | 0 | 0 | |
getShapeColor | 0 | 0 | 0 | |
getStartPlotsMsg | 0 | 0 | 0 | |
getStartupMsg | 0 | 0 | 0 | |
getTabUpdateJS | 0 | 0 | 0 | |
getTableDetails | 0 | 0 | 0 | |
getTableModal | 0 | 0 | 0 | |
getTableStyle | 0 | 0 | 0 | |
getUp | 0 | 0 | 0 | |
getUpDown | 0 | 0 | 0 | |
getVariationData | 0 | 0 | 0 | |
get_conditions_given_selection | 0 | 0 | 0 | |
heatmapControlsUI | 0.06 | 0.00 | 0.06 | |
heatmapJScode | 0 | 0 | 0 | |
heatmapServer | 0 | 0 | 0 | |
heatmapUI | 0.08 | 0.03 | 0.11 | |
hideObj | 0 | 0 | 0 | |
histogramControlsUI | 0 | 0 | 0 | |
installpack | 0 | 0 | 0 | |
kmeansControlsUI | 0.02 | 0.00 | 0.02 | |
lcfMetRadio | 0 | 0 | 0 | |
loadpack | 0.06 | 0.20 | 0.26 | |
mainPlotControlsUI | 0.02 | 0.00 | 0.02 | |
mainScatterNew | 0 | 0 | 0 | |
niceKmeans | 0 | 0 | 0 | |
normalizationMethods | 0 | 0 | 0 | |
palUI | 0 | 0 | 0 | |
panel.cor | 0 | 0 | 0 | |
panel.hist | 0 | 0 | 0 | |
pcaPlotControlsUI | 0 | 0 | 0 | |
plotData | 0 | 0 | 0 | |
plotMarginsUI | 0.01 | 0.00 | 0.01 | |
plotSizeMarginsUI | 0.02 | 0.00 | 0.02 | |
plotSizeUI | 0 | 0 | 0 | |
plotTypeUI | 0 | 0 | 0 | |
plot_pca | 1.00 | 0.03 | 1.03 | |
prepDataContainer | 0 | 0 | 0 | |
prepGroup | 0 | 0 | 0 | |
prepHeatData | 0 | 0 | 0 | |
prepPCADat | 0 | 0 | 0 | |
push | 0 | 0 | 0 | |
removeCols | 0 | 0 | 0 | |
removeExtraCols | 0 | 0 | 0 | |
round_vals | 0 | 0 | 0 | |
runDE | 0 | 0 | 0 | |
runDESeq2 | 0 | 0 | 0 | |
runEdgeR | 0 | 0 | 0 | |
runHeatmap | 0 | 0 | 0 | |
runHeatmap2 | 0 | 0 | 0 | |
runLimma | 0.00 | 0.02 | 0.02 | |
run_pca | 0.92 | 0.00 | 0.92 | |
selectConditions | 0 | 0 | 0 | |
selectGroupInfo | 0 | 0 | 0 | |
selectedInput | 0 | 0 | 0 | |
sepRadio | 0 | 0 | 0 | |
setBatch | 0 | 0 | 0 | |
showObj | 0 | 0 | 0 | |
startDEBrowser | 0 | 0 | 0 | |
startHeatmap | 0 | 0 | 0 | |
textareaInput | 0 | 0 | 0 | |
togglePanels | 0 | 0 | 0 | |