R kernel unable to start in jupyter notebook when use anaconda

[Divya Gehlot]

Hi ,

Environment - RHEL 7.3

Anaconda version - https://repo.continuum.io/archive/Anaconda2-5.2.0-Linux-x86_64.sh

I have followed below steps to install the Jupyter notebook through Anaconda 

1. wget https://repo.continuum.io/archive/Anaconda2-5.2.0-Linux-x86_64.sh

2. bash Anaconda2-5.2.0-Linux-x86_64.sh

3. conda install  -c r r-essentials 

4 . jupyter notebook --ip=* --no-browser 

after starting Jupyter note book I keep getting below messages in the terminal :

 *** caught segfault ***

address 0x38, cause 'memory not mapped'

Traceback:

 1: dyn.load(libPath)

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

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

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

 5: 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))})

 6: try(dyn.load(libPath), silent = TRUE)

 7: tryLoadMKL(full_path, mklSymbol)

 8: fun(libname, pkgname)

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

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

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

12: tryCatch(fun(libname, pkgname), error = identity)

13: runHook(".onLoad", env, package.lib, package)

14: loadNamespace(package, lib.loc)

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

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

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

18: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})

19: library("RevoUtilsMath")

20: do.call("library", list(package))

21: load_if_installed("RevoUtilsMath")

In UI it says Kernel died and it generates R core files too 

Why its happening 

Appreciate the advise !!

Thanks ,

Divya 

[Roland Weber]

Have you activated the conda environment before starting Jupyter?

If not, library paths are probably not set correctly.

I'm not using the full-blown installer myself, but I think this does the trick:

   source activate base

[Jaipreet Singh]

Getting the same error. Were you able to find a work around?

Thanks,

Jaipreet