[adegenet-forum] Segmentation Fault

[Eric Crandall]

Hi Zhian and all,

	Thanks for your help - for the record, this suggestion worked. I thought it was unique to my computer but didn’t know where to take such an issue. I will refer technical issues such as this to the github issue system in the future.

-Eric


> On Apr 20, 2015, at 9:15 AM, Zhian Kamvar <zkamvar at gmail.com> wrote:
> 
> 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 <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 <mailto: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)

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20150420/d46c3a06/attachment-0002.html>