Dear all,

While trying to upgrade flowStats and flowMeans on an Ubuntu 16.04 LTS system I am experiencing segfaults and I don't know what is causing it or how to resolve the issues.

My sessionInfo() output is:

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.2

And I am using bioconductor 3.4.

The complete error traceback is the following (for flowStats, but looks comparable for flowMeans):

> biocLite("flowStats")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘flowStats’
trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/flowStats_3.32.0.tar.gz'
Content type 'application/x-gzip' length 4154422 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

* installing *source* package ‘flowStats’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

 *** caught segfault ***
address 0x20, cause 'memory not mapped'

Traceback:
 1: .Call(Module__functions_names, xp)
 2: Module(module, mustStart = TRUE, where = env)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(Module(module, mustStart = TRUE, where = env), error = function(e) e)
 7: loadModule(module = "Multicool", what = TRUE, env = ns, loadNow = TRUE)
 8: (function (ns) loadModule(module = "Multicool", what = TRUE, env = ns, loadNow = TRUE))(<environment>)
 9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch((function (ns) loadModule(module = "Multicool", what = TRUE, env = ns, loadNow = TRUE))(<environment>),     error = function(e) e)
13: eval(expr, envir, enclos)
14: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e),     list(FUN = f, WHERE = where)), where)
15: .doLoadActions(where, attach)
16: methods::cacheMetaData(ns, TRUE, ns)
17: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
18: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)
19: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
20: asNamespace(ns)
21: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,     .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
22: loadNamespace(package, lib.loc, keep.source, partial = TRUE)
23: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
24: suppressPackageStartupMessages(loadNamespace(package, lib.loc,     keep.source, partial = TRUE))
25: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source,     compress = compress)
26: makeLazyLoading(pkg_name, lib, keep.source = keep.source)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: 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))})
31: try({    suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE))    makeLazyLoading(pkg_name, lib, keep.source = keep.source)})
32: do_install_source(pkg_name, instdir, pkg, desc)
33: do_install(pkg)
34: tools:::.install_packages()
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)

The downloaded source packages are in
        ‘/tmp/RtmpGwm5X7/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘flowStats’ had non-zero exit status

The rgl is because I am running headless on an ubuntu server (but visualisation is done via rstudio server).

Thanks in advance for any suggestions