[adegenet-forum] Segmentation Fault

[Eric Crandall]

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"
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> [R.app GUI 1.65 (6913) x86_64-apple-darwin13.4.0]
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> [Workspace restored from /Users/eric/.RData]
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> 
>> 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)

Installing the package from source:

> > install.packages("/Users/eric/Downloads/adegenet_1.4-2.tar", repos = NULL, type="source")
> Installing package into ‘/Users/eric/Rlibs’
> (as ‘lib’ is unspecified)
> * installing *source* package ‘adegenet’ ...
> ** package ‘adegenet’ successfully unpacked and MD5 sums checked
> ** libs
> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c GLfunctions.c -o GLfunctions.o
> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c adesub.c -o adesub.o
> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c monmonier-utils.c -o monmonier-utils.o
> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sharedAll.c -o sharedAll.o
> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c snpbin.c -o snpbin.o
> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o adegenet.so GLfunctions.o adesub.o monmonier-utils.o sharedAll.o snpbin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
> installing to /Users/eric/Rlibs/adegenet/libs
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> 
>  *** 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, lib.loc, keep.source, partial = TRUE)
> 10: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
> 11: suppressPackageStartupMessages(loadNamespace(package, lib.loc,     keep.source, partial = TRUE))
> 12: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source,     compress = compress)
> 13: makeLazyLoading(pkg_name, lib, keep.source = keep.source)
> 14: doTryCatch(return(expr), name, parentenv, handler)
> 15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 16: tryCatchList(expr, classes, parentenv, handlers)
> 17: 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))})
> 18: try({    suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE))    makeLazyLoading(pkg_name, lib, keep.source = keep.source)})
> 19: do_install_source(pkg_name, instdir, pkg, desc)
> 20: do_install(pkg)
> 21: tools:::.install_packages()
> aborting ...
> /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 12376 Done                    echo 'tools:::.install_packages()'
>      12377 Segmentation fault: 11  | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
> Warning in install.packages :
>   installation of package ‘/Users/eric/Downloads/adegenet_1.4-2.tar’ had non-zero exit status