runApp() crashes R session on OS X Mavericks with R version 3.1.1

[Hunt Sparra]

I am trying to use runApp() to run a Shiny app locally from RSudio but R crashes with the message: 

"R Session Aborted. 

R encountered a fatal error.

The session was terminated" 

runExample("01_hello") also results in the crash. R is version 3.1.1 and RStudio is version 0.98.1028. 

[Hunt Sparra]

I updated all my packages and the problem persists. I also tried removing and re-installing the "Rcpp", "httpuv", and the "shiny" packages but R still crashes.

[Hunt Sparra]

I have narrowed the problem down to a single line in a renderPlot() function in the server.R file:

ggplot(data2, aes_string(x=input$x, y=input$y)) + geom_point()

library(ggplot2) is called at the top of the file along with library(shiny). x and y are both from two selectInput() functions in the ui.R and have default values and their values are both columns in the data frame, data2. Running the code outside shiny works as expected. 

On Tuesday, August 19, 2014 3:30:25 PM UTC-4, Hunt Sparra wrote:

[Fereshteh Karimeddini]

Hunt,

Can you please provide output of sessionInfo() command?

We will look into this, but for future you might want to post Shiny-specific questions/issues to this forum:

https://groups.google.com/forum/#!forum/shiny-discuss

You probably get more responses from the community of Shiny users on that forum.

Best,

Fereshteh

[Hunt Sparra]

Here is the output from sessionInfo() just before running the app with runApp().

R version 3.1.1 (2014-07-10)

Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

[1] shiny_0.10.1

loaded via a namespace (and not attached):

[1] bitops_1.0-6    caTools_1.17    digest_0.6.4    htmltools_0.2.4 httpuv_1.3.0    Rcpp_0.11.2     RJSONIO_1.3-0   tools_3.1.1     xtable_1.7-3  

Thank you for the pointer to the other group.

[Hunt Sparra]

In case this helps you here is what is output when run from R.app:

Listening on http://127.0.0.1:4627

Warning: Removed 4 rows containing missing values (geom_point).

 *** caught segfault ***

address 0x0, cause 'memory not mapped'

Traceback:

 1: .Call("bitShiftR", a, b, PACKAGE = "bitops")

 2: bitShiftR(x[1, ], 2)

 3: base64encode(fileData)

 4: shinysession$fileUrl(name, outfile, contentType = "image/png")

 5: orig(name = name, shinysession = .self)

 6: func()

 7: withCallingHandlers(expr, error = function(e) {    handle <- getOption("shiny.error")    if (is.function(handle))         handle()})

 8: shinyCallingHandlers(func())

 9: doTryCatch(return(expr), name, parentenv, handler)

10: tryCatchOne(expr, names, parentenv, handlers[[1L]])

11: tryCatchList(expr, classes, parentenv, handlers)

12: tryCatch(shinyCallingHandlers(func()), shiny.silent.error = function(cond) {    structure(NULL, class = "try-error", condition = cond)})

13: doTryCatch(return(expr), name, parentenv, handler)

14: tryCatchOne(expr, names, parentenv, handlers[[1L]])

15: tryCatchList(expr, classes, parentenv, handlers)

16: 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 = stderr())        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})

17: try({    tryCatch(shinyCallingHandlers(func()), shiny.silent.error = function(cond) {        structure(NULL, class = "try-error", condition = cond)    })}, silent = FALSE)

18: func()

19: withCallingHandlers(expr, error = function(e) {    handle <- getOption("shiny.error")    if (is.function(handle))         handle()})

20: shinyCallingHandlers(func())

21: env$runWith(.self, func)

22: tryCatchList(expr, classes, parentenv, handlers)

23: tryCatch(env$runWith(.self, func), finally = .graphExitContext(id))

24: withReactiveDomain(.domain, {    env <- .getReactiveEnvironment()    .graphEnterContext(id)    tryCatch(env$runWith(.self, func), finally = .graphExitContext(id))})

25: ctx$run(.func)

26: run()

27: func()

28: withCallingHandlers({    func()}, warning = function(e) {}, error = function(e) {})

29: FUN(X[[1L]], ...)

30: lapply(.flushCallbacks, function(func) {    withCallingHandlers({        func()    }, warning = function(e) {    }, error = function(e) {    })})

31: ctx$executeFlushCallbacks()

32: .getReactiveEnvironment()$flush()

33: flushReact()

34: handler(binary, message)

35: doTryCatch(return(expr), name, parentenv, handler)

36: tryCatchOne(expr, names, parentenv, handlers[[1L]])

37: tryCatchList(expr, classes, parentenv, handlers)

38: 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 = stderr())        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})

39: try(handler(binary, message))

40: (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()        }    }})("106652629379264", FALSE, "{\"method\":\"init\",\"data\":{\"names\":false,\"recent\":false,\"y\":\"range\",\"x\":\"lbs\",\"color\":\"year\",\".clientdata_output_plot1_width\":1784,\".clientdata_output_plot1_height\":400,\".clientdata_output_plot1_hidden\":false,\".clientdata_pixelratio\":1,\".clientdata_url_protocol\":\"http:\",\".clientdata_url_hostname\":\"127.0.0.1\",\".clientdata_url_port\":\"4627\",\".clientdata_url_pathname\":\"/\",\".clientdata_url_search\":\"\",\".clientdata_url_hash_initial\":\"\",\".clientdata_singletons\":\"\",\".clientdata_allowDataUriScheme\":true}}")

41: eval(substitute(expr), envir, enclos)

42: 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()        }    }})("106652629379264", FALSE, "{\"method\":\"init\",\"data\":{\"names\":false,\"recent\":false,\"y\":\"range\",\"x\":\"lbs\",\"color\":\"year\",\".clientdata_output_plot1_width\":1784,\".clientdata_output_plot1_height\":400,\".clientdata_output_plot1_hidden\":false,\".clientdata_pixelratio\":1,\".clientdata_url_protocol\":\"http:\",\".clientdata_url_hostname\":\"127.0.0.1\",\".clientdata_url_port\":\"4627\",\".clientdata_url_pathname\":\"/\",\".clientdata_url_search\":\"\",\".clientdata_url_hash_initial\":\"\",\".clientdata_singletons\":\"\",\".clientdata_allowDataUriScheme\":true}}"),     <environment>)

43: doTryCatch(return(expr), name, parentenv, handler)

44: tryCatchOne(expr, names, parentenv, handlers[[1L]])

45: tryCatchList(expr, classes, parentenv, handlers)

46: 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()        }    }})("106652629379264", FALSE, "{\"method\":\"init\",\"data\":{\"names\":false,\"recent\":false,\"y\":\"range\",\"x\":\"lbs\",\"color\":\"year\",\".clientdata_output_plot1_width\":1784,\".clientdata_output_plot1_height\":400,\".clientdata_output_plot1_hidden\":false,\".clientdata_pixelratio\":1,\".clientdata_url_protocol\":\"http:\",\".clientdata_url_hostname\":\"127.0.0.1\",\".clientdata_url_port\":\"4627\",\".clientdata_url_pathname\":\"/\",\".clientdata_url_search\":\"\",\".clientdata_url_hash_initial\":\"\",\".clientdata_singletons\":\"\",\".clientdata_allowDataUriScheme\":true}}"),     <environment>), error = .rcpp_error_recorder)

47: .Call("httpuv_run", PACKAGE = "httpuv", timeoutMillis)

48: run(timeoutMs)

49: service(timeout)

50: serviceApp()

51: withCallingHandlers(expr, error = function(e) {    handle <- getOption("shiny.error")    if (is.function(handle))         handle()})

52: shinyCallingHandlers(while (!.globals$stopped) {    serviceApp()    Sys.sleep(0.001)})

53: runApp()

Possible actions:

1: abort (with core dump, if enabled)

2: normal R exit

3: exit R without saving workspace

4: exit R saving workspace

I reinstalled the base64enc package and now RStudio does not crash, however, R.app stiller returns the same message.

On Tuesday, August 19, 2014 5:50:23 PM UTC-4, Fereshteh Karimeddini wrote:

[Yihui Xie]

Interesting. The issue should be irrelevant to the base64enc package,
since shiny does not use it. Instead, caTools::base64encode() is used.
If you need to reinstall anything, you should reinstall bitops
package. Or just reinstall everything:

install.packages(rownames(installed.packages(priority = 'NA')))

Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
Web: http://yihui.name

[Hunt Sparra]

Reinstalling all packages eliminated the issue.