[adegenet-forum] Segmentation Fault

[Zhian Kamvar]

I have experience this error before and I was lucky enough to have a segfault at address 0x18, because that's the result that produces the most helpful answers. 

It is not an issue with adegenet, but rather something corrupted in your library. The recommendation is to reinstall all of your packages as suggested here: http://stackoverflow.com/a/25833832/2752888

Since this is not an adegenet issue and I have had experience with this, you may respond to me (not to the list) if you have any more inquiries.

Cheers,
Zhian

> On Apr 20, 2015, at 02:22 , adegenet-forum-request at lists.r-forge.r-project.org wrote:
> 
> Dear Thibault or whom it may concern,
> 
> 	Adegenet has recently started causing R to crash with a segmentation fault upon loading the library. I have tried re-installing the package from binary and from source, as well as re-installing R - all to no avail. Below is a traceback of the error from the R-console. Below that, I have posted an error message that is given when I try to install the package from source. I don?t encounter this error with any other R package that I have used recently. I am running R on a 2014 Macbook with OS X 10.10.3.
> 
> Many thanks for your help and let me know if I can provide additional information.
> 
> Sincerely,
> 
> Eric Crandall
> Assistant Researcher
> University of Hawaii
> 
> 
>> R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
>> Copyright (C) 2015 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> 
>> 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.
>> 
>> Natural language support but running in an English locale
>> 
>> 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.
>> 
>> [R.app GUI 1.65 (6913) x86_64-apple-darwin13.4.0]
>> 
>> [Workspace restored from /Users/eric/.RData]
>> [History restored from /Users/eric/.Rapp.history]
>> 
>>> library(adegenet)
>> Loading required package: ade4
>> 
>> *** caught segfault ***
>> address 0x0, cause 'memory not mapped'
>> 
>> Traceback:
>> 1: doTryCatch(return(expr), name, parentenv, handler)
>> 2: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> 3: tryCatchList(expr, classes, parentenv, handlers)
>> 4: tryCatch(fun(libname, pkgname), error = identity)
>> 5: runHook(".onLoad", env, package.lib, package)
>> 6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
>> 7: asNamespace(ns)
>> 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,     .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
>> 9: loadNamespace(package, c(which.lib.loc, lib.loc))
>> 10: doTryCatch(return(expr), name, parentenv, handler)
>> 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> 12: tryCatchList(expr, classes, parentenv, handlers)
>> 13: 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))})
>> 14: try({    ns <- loadNamespace(package, c(which.lib.loc, lib.loc))    env <- attachNamespace(ns, pos = pos, deps)})
>> 15: library(adegenet)
>