R Shiny Server Segmentation Fault

Question

I have been getting the following a Segmentation Fault on my Shiny Server running on a Linux machine:

-bash: line 1: 29254 Segmentation fault      R --no-save --slave -f \/opt\/shiny-server\/R\/SockJSAdapter\.R
"

It started three days ago on an application that was previously working fine. The application does not give an error on my Windows machine. I have renewed all the packages and RStudio on the machine. I have tried to find an answer, but there is very little info about Segfaults.

I have tried to reproduce the error and stripped the code to bare minimum. I discovered that rendering text and tables (base and DataTables) is OK, but rendering any plot (base, ggplot, plotly) produces the segmentation error. The code that gives an error and the error messege from JavaScript console is below.

I also tried starting the code through a web browser from the RStudio on the Linux machine to see if I can get more info, but it just crached giving me the following error message: Rstudio browser error message

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0

ui.R

library(shinydashboard)

dashboardPage(

  dashboardHeader(),


  dashboardSidebar(),


  dashboardBody(
    h4('Text'),
    textOutput('TextT'),
    dataTableOutput('Tabel'),
    plotOutput('Plot')

  )

)

server.R

server <- function(input, output, session) { 

  output$TextT = renderText('text text')

  output$Tabel = renderDataTable(data.frame(A = 1))

  output$Plot = renderPlot(plot(data.frame(x = c(1:10), y = c(11:20))))

}

JavaScript error console:

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()        }    }})("60893360", FALSE, "{\"method\":\"init\",\"data\":{\"sidebarItemExpanded\":null,\"sidebarCollapsed\":false,\".clientdata_output_Plot_width\":1190,\".clientdata_output_Plot_height\":400,\".clientdata_output_TextT_hidden\":false,\".clientdata_output_Tabel_hidden\":false,\".clientdata_output_Plot_hidden\":false,\".clientdata_pixelratio\":0.8695651888847351,\".clientdata_url_protocol\":\"http:\",\".clientdata_url_hostname\":\"apps.teed.ee\",\".clientdata_url_port\":\"\",\".clientdata_url_pathname\":\"/VisualiseerimineVer2/\",\".clientdata_url_search\":\"\",\".clientdata_url_hash_initial\":\"\",\".clientdata_url_hash\":\"\",\".clientdata_singletons\":\"\",\".clientdata_allowDataUriScheme\":true}}")
80: 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()        }    }})("60893360", FALSE, "{\"method\":\"init\",\"data\":{\"sidebarItemExpanded\":null,\"sidebarCollapsed\":false,\".clientdata_output_Plot_width\":1190,\".clientdata_output_Plot_height\":400,\".clientdata_output_TextT_hidden\":false,\".clientdata_output_Tabel_hidden\":false,\".clientdata_output_Plot_hidden\":false,\".clientdata_pixelratio\":0.8695651888847351,\".clientdata_url_protocol\":\"http:\",\".clientdata_url_hostname\":\"apps.teed.ee\",\".clientdata_url_port\":\"\",\".clientdata_url_pathname\":\"/VisualiseerimineVer2/\",\".clientdata_url_search\":\"\",\".clientdata_url_hash_initial\":\"\",\".clientdata_url_hash\":\"\",\".clientdata_singletons\":\"\",\".clientdata_allowDataUriScheme\":true}}"),     <environment>)
81: 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()        }    }})("60893360", FALSE, "{\"method\":\"init\",\"data\":{\"sidebarItemExpanded\":null,\"sidebarCollapsed\":false,\".clientdata_output_Plot_width\":1190,\".clientdata_output_Plot_height\":400,\".clientdata_output_TextT_hidden\":false,\".clientdata_output_Tabel_hidden\":false,\".clientdata_output_Plot_hidden\":false,\".clientdata_pixelratio\":0.8695651888847351,\".clientdata_url_protocol\":\"http:\",\".clientdata_url_hostname\":\"apps.teed.ee\",\".clientdata_url_port\":\"\",\".clientdata_url_pathname\":\"/VisualiseerimineVer2/\",\".clientdata_url_search\":\"\",\".clientdata_url_hash_initial\":\"\",\".clientdata_url_hash\":\"\",\".clientdata_singletons\":\"\",\".clientdata_allowDataUriScheme\":true}}"),     <environment>)
82: doTryCatch(return(expr), name, parentenv, handler)
83: tryCatchOne(expr, names, parentenv, handlers[[1L]])
84: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
85: doTryCatch(return(expr), name, parentenv, handler)
86: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
87: tryCatchList(expr, classes, parentenv, handlers)
88: 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()        }    }})("60893360", FALSE, "{\"method\":\"init\",\"data\":{\"sidebarItemExpanded\":null,\"sidebarCollapsed\":false,\".clientdata_output_Plot_width\":1190,\".clientdata_output_Plot_height\":400,\".clientdata_output_TextT_hidden\":false,\".clientdata_output_Tabel_hidden\":false,\".clientdata_output_Plot_hidden\":false,\".clientdata_pixelratio\":0.8695651888847351,\".clientdata_url_protocol\":\"http:\",\".clientdata_url_hostname\":\"apps.teed.ee\",\".clientdata_url_port\":\"\",\".clientdata_url_pathname\":\"/VisualiseerimineVer2/\",\".clientdata_url_search\":\"\",\".clientdata_url_hash_initial\":\"\",\".clientdata_url_hash\":\"\",\".clientdata_singletons\":\"\",\".clientdata_allowDataUriScheme\":true}}"),     <environment>), error = function (x) x, interrupt = function (x) x)
89: .Call("httpuv_run", PACKAGE = "httpuv", timeoutMillis)
90: run(timeoutMs)
91: service(timeout)
92: serviceApp()
93: withCallingHandlers(expr, error = function(e) {    if (is.null(attr(e, "stack.trace", exact = TRUE))) {        calls <- sys.calls()        attr(e, "stack.trace") <- calls        stop(e)    }})
94: captureStackTraces({    scheduleFlush()    while (!.globals$stopped) {        serviceApp()        Sys.sleep(0.001)    }})
95: ..stacktraceoff..(captureStackTraces({    scheduleFlush()    while (!.globals$stopped) {        serviceApp()        Sys.sleep(0.001)    }}))
96: runApp(Sys.getenv("SHINY_APP"), port = port, launch.browser = FALSE)
An irrecoverable exception occurred. R is aborting now ...
-bash: line 1:  3049 Segmentation fault      R --no-save --slave -f \/opt\/shiny-server\/R\/SockJSAdapter\.

Do you have any idea what might be behind it or how to fix it?

Thank you in advance.

PS: I am using Shiny Dashboard, but I get the same message, when I run it as a regular Shiny app

No. It is a server (dell R620 with an Intel processor and graphics card) — Karmen Kütt
Did you find the problem and solution for it? I have the same problem and was wondering. — Fisseha Berhane
Hey everyone who is experiencing this: See this Github issue (especially the comment here -- TLDR version: add options(java.parameters = "-Xss2560k") at the top of your app). If this answers the problem, either me or someone else can write up an answer for future users struggling with the same thing. If not, also do let me know! — Bárbara Borges

冷雨夜客冷雨夜客 · Accepted Answer · 2020-09-25T06:28:35

0

votes

Update rJava to the latest version resolved my problem.

R Shiny Server Segmentation Fault

2 Answers