likelet / idea Goto Github PK

when i try to start IDEA it gives the following error
ERROR: could not find function "bsProgressBar"
was working fine till last week, Is there any dependency im missing?

Warning: Error in tag: could not find function "bsProgressBar"
Stack trace (innermost first):
    60: tag
    59: tags$div
    58: div
    57: tag
    56: tags$div
    55: div
    54: tag
    53: tags$div
    52: div
    51: tag
    50: tags$div
    49: div
    48: tag
    47: tags$div
    46: div
    45: tagList
    44: attachDependencies
    43: bootstrapPage
    42: shinyUI
     2: shiny::runApp
     1: runIDEA
Error : could not find function "bsProgressBar"

Thank you

hi,
When I try to run idea, it starts but when I upload a file or use example data, it stuck in loading in progress screen and don't proceed further, the following is the message displayed in the terminal.

library(IDEA)
runIDEA()
Loading required package: shiny

Listening on http://127.0.0.1:3759
Loading required package: RJSONIO
Loading required package: plyr

Attaching package: ‘shinysky’

The following object is masked from ‘package:shiny’:

actionButton

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, xtabs

The following objects are masked from ‘package:base’:

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

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:plyr’:

rename

The following objects are masked from ‘package:base’:

colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:plyr’:

desc

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")'.

Warning in is.na(x[[i]]) :
is.na() applied to non-(list or vector) of type 'environment'
'BiocParallel' did not register default BiocParallelParams:
invalid class “MulticoreParam” object: 1: ‘cluster’, ‘.clusterargs’, ‘.uid’, ‘RNGseed’ must be length 1
invalid class “MulticoreParam” object: 2: ‘.clusterargs’, ‘.controlled’, ‘logdir’, ‘resultdir’ must be length 1
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

Attaching package: ‘gplots’

The following object is masked from ‘package:IRanges’:

space

The following object is masked from ‘package:S4Vectors’:

space

The following object is masked from ‘package:stats’:

lowess

Loading required package: combinat

Attaching package: ‘combinat’

The following object is masked from ‘package:utils’:

combn

Loading required package: splines
Loading required package: impute
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following object is masked from ‘package:SummarizedExperiment’:

rowRanges

The following objects are masked from ‘package:Biobase’:

anyMissing, rowMedians

The following object is masked from ‘package:plyr’:

count

Loading required package: Matrix

Attaching package: ‘Matrix’

The following object is masked from ‘package:S4Vectors’:

expand

Attaching package: ‘NOISeq’

The following object is masked from ‘package:edgeR’:

rpkm

Loading required package: grid
Loading required package: futile.logger

Attaching package: ‘RobustRankAggreg’

The following object is masked from ‘package:Matrix’:

rankMatrix

converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[1] "condition"
Warning: Error in checkContrast: 'contrast', as a character vector of length 3, should have the form:
contrast = c('factorName','numeratorLevel','denominatorLevel'),
see the manual page of ?results for more information
Stack trace (innermost first):
97: checkContrast
96: results
95: DEseqGetNBDEdata [/usr/local/lib/R/site-library/IDEA/IDEA/server.R#1061]
94: reactive:getDEseqResultTable [/usr/local/lib/R/site-library/IDEA/IDEA/server.R#1024]
83: getDEseqResultTable
82: renderDataTable [/usr/local/lib/R/site-library/IDEA/IDEA/server.R#1032]
81: func
80: origRenderFunc
79: output$DEseqTable
2: shiny::runApp
1: runIDEA

*** caught segfault ***
address 0xb7, cause 'memory not mapped'

Traceback:
1: .External("cairo_create_new_device", as.character(ctype), file, width, height, pointsize, bg, canvas, umpl, dpi, ..., PACKAGE = "Cairo")
2: Cairo(width, height, type = "png", file = filename, pointsize = pointsize, bg = bg, res = res, ...)
3: pngfun(filename = filename, width = width, height = height, res = res, ...)
4: (function (func, filename = tempfile(fileext = ".png"), width = 400, height = 400, res = 72, ...) { if (capabilities("aqua")) { pngfun <- grDevices::png } else if ((getOption("shiny.usecairo") %OR% TRUE) && nchar(system.file(package = "Cairo"))) { pngfun <- Cairo::CairoPNG } else { pngfun <- grDevices::png } pngfun(filename = filename, width = width, height = height, res = res, ...) op <- graphics::par(mar = rep(0, 4)) tryCatch(graphics::plot.new(), finally = graphics::par(op)) dv <- grDevices::dev.cur() on.exit(grDevices::dev.off(dv), add = TRUE) func() filename})(function () { success <- FALSE tryCatch({ grDevices::dev.control(displaylist = "enable") result <- withVisible(func()) success <- TRUE }, finally = { if (!success) { getDims() } }) if (result$visible) { utils::capture.output({ plotResult <<- ..stacktraceon..(print(result$value)) }) } recordedPlot <<- grDevices::recordPlot() if (inherits(plotResult, "ggplot_build_gtable")) { coordmap <<- getGgplotCoordmap(plotResult, pixelratio, res) } else { coordmap <<- getPrevPlotCoordmap(dims$width, dims$height) }}, width = 629.999983310699, height = 629.999983310699, res = 64.7999982833862)
5: do.call(plotPNG, c(plotFunc, width = dims$width * pixelratio, height = dims$height * pixelratio, res = res * pixelratio, args))
6: ..stacktraceoff..(do.call(plotPNG, c(plotFunc, width = dims$width * pixelratio, height = dims$height * pixelratio, res = res * pixelratio, args)))
7: <reactive:plotObj>(...)
8: ..stacktraceon..(<reactive:plotObj>(...))
9: .func()
10: withVisible(.func())
11: withCallingHandlers({ .error <<- FALSE withVisible(.func())}, error = function(cond) { .value <<- cond .error <<- TRUE .visible <<- FALSE})
12: contextFunc()
13: env$runWith(self, func)
14: withReactiveDomain(.domain, { env <- .getReactiveEnvironment() .graphEnterContext(id) on.exit(.graphExitContext(id), add = TRUE) env$runWith(self, func)})
15: ctx$run(function() { result <- withCallingHandlers({ .error <<- FALSE withVisible(.func()) }, error = function(cond) { .value <<- cond .error <<- TRUE .visible <<- FALSE }) .value <<- result$value .visible <<- result$visible})
16: self$.updateValue()
17: ..stacktraceoff..(self$.updateValue())
18: plotObj()
19: origRenderFunc(...)
20: output$DEseqDispersionsPlot(...)
21: ..stacktraceon..(output$DEseqDispersionsPlot(...))
22: orig(name = name, shinysession = self)
23: func()
24: withCallingHandlers(expr, error = function(e) { if (is.null(attr(e, "stack.trace", exact = TRUE))) { calls <- sys.calls() attr(e, "stack.trace") <- calls stop(e) }})
25: captureStackTraces(expr)
26: withCallingHandlers(captureStackTraces(expr), error = function(e) { if (inherits(e, "shiny.silent.error")) return() handle <- getOption("shiny.error") if (is.function(handle)) handle()})
27: shinyCallingHandlers(func())
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
33: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
36: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch(shinyCallingHandlers(func()), shiny.custom.error = function(cond) { if (isTRUE(getOption("show.error.messages"))) printError(cond) structure(list(), class = "try-error", condition = cond)}, shiny.output.cancel = function(cond) { structure(list(), class = "cancel-output")}, shiny.silent.error = function(cond) { structure(list(), class = "try-error", condition = cond)}, error = function(cond) { if (isTRUE(getOption("show.error.messages"))) printError(cond) if (getOption("shiny.sanitize.errors", FALSE)) { cond <- simpleError(paste("An error has occurred. Check your", "logs or contact the app author for", "clarification.")) } invisible(structure(list(), class = "try-error", condition = cond))}, finally = { private$sendMessage(recalculating = list(name = name, status = "recalculated"))})
41: observerFunc()
42: doTryCatch(return(expr), name, parentenv, handler)
43: tryCatchOne(expr, names, parentenv, handlers[[1L]])
44: tryCatchList(expr, classes, parentenv, handlers)
45: tryCatch(if (..stacktraceon) ..stacktraceon..(observerFunc()) else observerFunc(), shiny.silent.error = function(e) NULL)
46: contextFunc()
47: env$runWith(self, func)
48: withReactiveDomain(.domain, { env <- .getReactiveEnvironment() .graphEnterContext(id) on.exit(.graphExitContext(id), add = TRUE) env$runWith(self, func)})
49: ctx$run(.func)
50: run()
51: withCallingHandlers(expr, error = function(e) { if (is.null(attr(e, "stack.trace", exact = TRUE))) { calls <- sys.calls() attr(e, "stack.trace") <- calls stop(e) }})
52: captureStackTraces(expr)
53: withCallingHandlers(captureStackTraces(expr), error = function(e) { if (inherits(e, "shiny.silent.error")) return() handle <- getOption("shiny.error") if (is.function(handle)) handle()})
54: shinyCallingHandlers(run())
55: doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchOne(expr, names, parentenv, handlers[[1L]])
57: tryCatchList(expr, classes, parentenv, handlers)
58: tryCatch({ if (!.destroyed) shinyCallingHandlers(run())}, error = function(e) { printError(e) if (!is.null(.domain)) { .domain$unhandledError(e) }})
59: flushCallback()
60: FUN(X[[i]], ...)
61: lapply(.flushCallbacks, function(flushCallback) { flushCallback()})
62: ctx$executeFlushCallbacks()
63: .getReactiveEnvironment()$flush()
64: flushReact()
65: force(expr)
66: withRestoreContext(shinysession$restoreContext, { msg$data <- applyInputHandlers(msg$data) switch(msg$method, init = { serverFunc <- withReactiveDomain(NULL, serverFuncSource()) if (!identicalFunctionBodies(serverFunc, appvars$server)) { appvars$server <- serverFunc if (!is.null(appvars$server)) { attr(appvars$server, "shinyServerFunction") <- TRUE registerDebugHook("server", appvars, "Server Function") } } if (.globals$showcaseOverride && exists(".clientdata_url_search", where = msg$data)) { mode <- showcaseModeOfQuerystring(msg$data$.clientdata_url_search) if (!is.null(mode)) shinysession$setShowcase(mode) } shinysession$manageInputs(msg$data) if (!is.null(msg$data$.clientdata_singletons)) { shinysession$singletons <- strsplit(msg$data$.clientdata_singletons, ",")[[1]] } local({ args <- argsForServerFunc(serverFunc, shinysession) withReactiveDomain(shinysession, { do.call(wrapFunctionLabel(appvars$server, "server", ..stacktraceon = TRUE), args) }) }) }, update = { shinysession$manageInputs(msg$data) }, shinysession$dispatch(msg)) shinysession$manageHiddenOutputs() if (exists(".shiny__stdout", globalenv()) && exists("HTTP_GUID", ws$request)) { shiny_stdout <- get(".shiny__stdout", globalenv()) writeLines(paste("_n_flushReact ", get("HTTP_GUID", ws$request), " @ ", sprintf("%.3f", as.numeric(Sys.time())), sep = ""), con = shiny_stdout) flush(shiny_stdout) flushReact() writeLines(paste("_x_flushReact ", get("HTTP_GUID", ws$request), " @ ", sprintf("%.3f", as.numeric(Sys.time())), sep = ""), con = shiny_stdout) flush(shiny_stdout) } else { flushReact() } flushAllSessions()})
67: withReactiveDomain(shinysession, { if (is.character(msg)) msg <- charToRaw(msg) traceOption <- getOption("shiny.trace", FALSE) if (isTRUE(traceOption) || traceOption == "recv") { if (binary) message("RECV ", "$$binary data$$") else message("RECV ", rawToChar(msg)) } if (identical(charToRaw("\003\xe9"), msg)) return() msg <- decodeMessage(msg) if (is.null(shinysession$restoreContext)) { bookmarkStore <- getShinyOption("bookmarkStore", default = "disable") if (bookmarkStore == "disable") { shinysession$restoreContext <- RestoreContext$new() } else { shinysession$restoreContext <- RestoreContext$new(msg$data$.clientdata_url_search) } } withRestoreContext(shinysession$restoreContext, { msg$data <- applyInputHandlers(msg$data) switch(msg$method, init = { serverFunc <- withReactiveDomain(NULL, serverFuncSource()) if (!identicalFunctionBodies(serverFunc, appvars$server)) { appvars$server <- serverFunc if (!is.null(appvars$server)) { attr(appvars$server, "shinyServerFunction") <- TRUE registerDebugHook("server", appvars, "Server Function") } } if (.globals$showcaseOverride && exists(".clientdata_url_search", where = msg$data)) { mode <- showcaseModeOfQuerystring(msg$data$.clientdata_url_search) if (!is.null(mode)) shinysession$setShowcase(mode) } shinysession$manageInputs(msg$data) if (!is.null(msg$data$.clientdata_singletons)) { shinysession$singletons <- strsplit(msg$data$.clientdata_singletons, ",")[[1]] } local({ args <- argsForServerFunc(serverFunc, shinysession) withReactiveDomain(shinysession, { do.call(wrapFunctionLabel(appvars$server, "server", ..stacktraceon = TRUE), args) }) }) }, update = { shinysession$manageInputs(msg$data) }, shinysession$dispatch(msg)) shinysession$manageHiddenOutputs() if (exists(".shiny__stdout", globalenv()) && exists("HTTP_GUID", ws$request)) { shiny_stdout <- get(".shiny__stdout", globalenv()) writeLines(paste("_n_flushReact ", get("HTTP_GUID", ws$request), " @ ", sprintf("%.3f", as.numeric(Sys.time())), sep = ""), con = shiny_stdout) flush(shiny_stdout) flushReact() writeLines(paste("_x_flushReact ", get("HTTP_GUID", ws$request), " @ ", sprintf("%.3f", as.numeric(Sys.time())), sep = ""), con = shiny_stdout) flush(shiny_stdout) } else { flushReact() } flushAllSessions() })})
68: messageHandler(binary, msg)
69: withCallingHandlers(expr, error = function(e) { if (is.null(attr(e, "stack.trace", exact = TRUE))) { calls <- sys.calls() attr(e, "stack.trace") <- calls stop(e) }})
70: captureStackTraces(expr)
71: withCallingHandlers(captureStackTraces(expr), error = function(cond) { if (inherits(cond, "shiny.silent.error")) return() if (isTRUE(getOption("show.error.messages"))) { printError(cond, full = full, offset = offset) }})
72: withLogErrors(messageHandler(binary, msg))
73: handler(binary, message)
74: doTryCatch(return(expr), name, parentenv, handler)
75: tryCatchOne(expr, names, parentenv, handlers[[1L]])
76: tryCatchList(expr, classes, parentenv, handlers)
77: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
78: try(handler(binary, message))
79: (function (handle, binary, message) { for (handler in .wsconns[[as.character(handle)]]$.messageCallbacks) { result <- try(handler(binary, message)) if (inherits(result, "try-error")) { .wsconns[[as.character(handle)]]$close() return() } }})("44250960", FALSE, "{"method":"update","data":{".clientdata_output_DEseqDispersionsPlot_width":800,".clientdata_output_DEseqDispersionsPlot_height":0,".clientdata_output_DEseqMAplot_width":1097,".clientdata_output_DEseqMAplot_height":0,".clientdata_output_DESeqVolcanoPlotRender_width":1097,".clientdata_output_DESeqVolcanoPlotRender_height":0,".clientdata_output_DESeqheatmapRender_width":1097,".clientdata_output_DESeqheatmapRender_height":0,".clientdata_output_DESeqPvalueDistributionplotRender_width":1097,".clientdata_output_DESeqPvalueDistributionplotRender_height":0,".clientdata_output_DataInputswitchUI_hidden":true,".clientdata_output_designSwitchUI_hidden":true,".clientdata_output_interestvariablesUI_hidden":true,".clientdata_output_ConditionSelectionUI_hidden":true,".clientdata_output_DEseqTable_hidden":false,".clientdata_output_DESeqDisperplotDownload_hidden":false,".clientdata_output_DEseqDispersionsPlot_hidden":false,".clientdata_output_DEseqMAplotDownload_hidden":false,".clientdata_output_DEseqMAplot_hidden":false,".clientdata_output_normalizeFactor_hidden":false,".clientdata_output_DEseqVolcanoPlotDownload_hidden":false,".clientdata_output_DESeqVolcanoPlotRender_hidden":false,".clientdata_output_DESeqHeatmapDownload_hidden":false,".clientdata_output_DESeqheatmapRender_hidden":false,".clientdata_output_DESeqPvalueDistributionplotDownload_hidden":false,".clientdata_output_DESeqPvalueDistributionplotRender_hidden":false,".clientdata_output_comparisonSampleTextRenderUI2_hidden":false,".clientdata_output_DEseqdownloadDEtable_hidden":false,".clientdata_output_DownloadDESeqReport_hidden":false}}")
80: eval(substitute(expr), envir, enclos)
81: eval(substitute(expr), envir, enclos)
82: eval(substitute(expr), envir, enclos)
83: evalq((function (handle, binary, message) { for (handler in .wsconns[[as.character(handle)]]$.messageCallbacks) { result <- try(handler(binary, message)) if (inherits(result, "try-error")) { .wsconns[[as.character(handle)]]$close() return() } }})("44250960", FALSE, "{"method":"update","data":{".clientdata_output_DEseqDispersionsPlot_width":800,".clientdata_output_DEseqDispersionsPlot_height":0,".clientdata_output_DEseqMAplot_width":1097,".clientdata_output_DEseqMAplot_height":0,".clientdata_output_DESeqVolcanoPlotRender_width":1097,".clientdata_output_DESeqVolcanoPlotRender_height":0,".clientdata_output_DESeqheatmapRender_width":1097,".clientdata_output_DESeqheatmapRender_height":0,".clientdata_output_DESeqPvalueDistributionplotRender_width":1097,".clientdata_output_DESeqPvalueDistributionplotRender_height":0,".clientdata_output_DataInputswitchUI_hidden":true,".clientdata_output_designSwitchUI_hidden":true,".clientdata_output_interestvariablesUI_hidden":true,".clientdata_output_ConditionSelectionUI_hidden":true,".clientdata_output_DEseqTable_hidden":false,".clientdata_output_DESeqDisperplotDownload_hidden":false,".clientdata_output_DEseqDispersionsPlot_hidden":false,".clientdata_output_DEseqMAplotDownload_hidden":false,".clientdata_output_DEseqMAplot_hidden":false,".clientdata_output_normalizeFactor_hidden":false,".clientdata_output_DEseqVolcanoPlotDownload_hidden":false,".clientdata_output_DESeqVolcanoPlotRender_hidden":false,".clientdata_output_DESeqHeatmapDownload_hidden":false,".clientdata_output_DESeqheatmapRender_hidden":false,".clientdata_output_DESeqPvalueDistributionplotDownload_hidden":false,".clientdata_output_DESeqPvalueDistributionplotRender_hidden":false,".clientdata_output_comparisonSampleTextRenderUI2_hidden":false,".clientdata_output_DEseqdownloadDEtable_hidden":false,".clientdata_output_DownloadDESeqReport_hidden":false}}"), )
84: doTryCatch(return(expr), name, parentenv, handler)
85: tryCatchOne(expr, names, parentenv, handlers[[1L]])
86: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
87: doTryCatch(return(expr), name, parentenv, handler)
88: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
89: tryCatchList(expr, classes, parentenv, handlers)
90: tryCatch(evalq((function (handle, binary, message) { for (handler in .wsconns[[as.character(handle)]]$.messageCallbacks) { result <- try(handler(binary, message)) if (inherits(result, "try-error")) { .wsconns[[as.character(handle)]]$close() return() } }})("44250960", FALSE, "{"method":"update","data":{".clientdata_output_DEseqDispersionsPlot_width":800,".clientdata_output_DEseqDispersionsPlot_height":0,".clientdata_output_DEseqMAplot_width":1097,".clientdata_output_DEseqMAplot_height":0,".clientdata_output_DESeqVolcanoPlotRender_width":1097,".clientdata_output_DESeqVolcanoPlotRender_height":0,".clientdata_output_DESeqheatmapRender_width":1097,".clientdata_output_DESeqheatmapRender_height":0,".clientdata_output_DESeqPvalueDistributionplotRender_width":1097,".clientdata_output_DESeqPvalueDistributionplotRender_height":0,".clientdata_output_DataInputswitchUI_hidden":true,".clientdata_output_designSwitchUI_hidden":true,".clientdata_output_interestvariablesUI_hidden":true,".clientdata_output_ConditionSelectionUI_hidden":true,".clientdata_output_DEseqTable_hidden":false,".clientdata_output_DESeqDisperplotDownload_hidden":false,".clientdata_output_DEseqDispersionsPlot_hidden":false,".clientdata_output_DEseqMAplotDownload_hidden":false,".clientdata_output_DEseqMAplot_hidden":false,".clientdata_output_normalizeFactor_hidden":false,".clientdata_output_DEseqVolcanoPlotDownload_hidden":false,".clientdata_output_DESeqVolcanoPlotRender_hidden":false,".clientdata_output_DESeqHeatmapDownload_hidden":false,".clientdata_output_DESeqheatmapRender_hidden":false,".clientdata_output_DESeqPvalueDistributionplotDownload_hidden":false,".clientdata_output_DESeqPvalueDistributionplotRender_hidden":false,".clientdata_output_comparisonSampleTextRenderUI2_hidden":false,".clientdata_output_DEseqdownloadDEtable_hidden":false,".clientdata_output_DownloadDESeqReport_hidden":false}}"), ), error = function (x) x, interrupt = function (x) x)
91: .Call("httpuv_run", PACKAGE = "httpuv", timeoutMillis)
92: run(timeoutMs)
93: service(timeout)
94: serviceApp()
95: withCallingHandlers(expr, error = function(e) { if (is.null(attr(e, "stack.trace", exact = TRUE))) { calls <- sys.calls() attr(e, "stack.trace") <- calls stop(e) }})
96: captureStackTraces({ scheduleFlush() while (!.globals$stopped) { serviceApp() Sys.sleep(0.001) }})
97: ..stacktraceoff..(captureStackTraces({ scheduleFlush() while (!.globals$stopped) { serviceApp() Sys.sleep(0.001) }}))
98: shiny::runApp(system.file("IDEA", package = "IDEA"))
99: runIDEA()

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

I tried running the example, but it didn't work for me.

See below for the steps I tried to follow.

Hi there,
I have a data with 4 conditions and have the matrix of experimental design, when I run DESeq2 to compare condition1 to condition4 and condition 2 to condtion4 both shows the same result, while edgeR gives different results for same analysis, I think DESeq2 script has some problem, can you please rectify it?
Thanks
Pradyumna

hello,
I would like to suggest that it would be helpful if the output file names are saved in the name of condition instead of time and date. like currently output name for deseq analysis is like DEseqDEresult2017-03-07 22-09-12.csv instead if it is like DEseqDEresultCondition1vsCondition2.csv it will be easy to differentiate the files.

When I change the Ensembl id to gene names in my input data the analysis stops giving following error
Error:non-numeric argument to mathematical function
Is there any way to overcome this? providing facility to use gene names would be more helpful.
Thank you
Pradyumna