[adegenet-forum] Segmentation Fault

[Federico Calboli]

> On 20 Apr 2015, at 01:54, Eric Crandall <eric.d.crandall at gmail.com> 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 cannot reproduce it (i.e. the library loads fine):

library(adegenet)
Loading required package: ade4
   ==========================
    adegenet 1.4-2 is loaded
   ==========================

 - to start, type '?adegenet'
 - to browse adegenet website, type 'adegenetWeb()'
 - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org

…

R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

Mac OS 10.10.3

BW

F






> 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)
> 
> 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
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