[BioC] VariantFiltering: Installation segfault

Julian Gehring julian.gehring at embl.de
Thu Jun 12 06:17:07 CEST 2014 

Hi,

On one of my machines, the installation the 'VariantFiltering' package 
fails on both the latest bioc-stable and bioc-devel with a segfault (see 
below for the output).  Since the installation works fine on other 
machines, does anyone have an idea what is causing this?

Best wishes
Julian


------------------
   biocLite("VariantFiltering")

[...]
Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help
* installing *source* package ‘VariantFiltering’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG 
-I"/home/foo/.R/library/x86_64-pc-linux-gnu/3.1/IRanges/include" 
-I"/home/foo/.R/library/x86_64-pc-linux-gnu/3.1/XVector/include" 
-I"/home/foo/.R/library/x86_64-pc-linux-gnu/3.1/Biostrings/include" 
-fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Biostrings_stubs.c -o 
Biostrings_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG 
-I"/home/foo/.R/library/x86_64-pc-linux-gnu/3.1/IRanges/include" 
-I"/home/foo/.R/library/x86_64-pc-linux-gnu/3.1/XVector/include" 
-I"/home/foo/.R/library/x86_64-pc-linux-gnu/3.1/Biostrings/include" 
-fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c 
R_init_VariantFiltering.c -o R_init_VariantFiltering.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG 
-I"/home/foo/.R/library/x86_64-pc-linux-gnu/3.1/IRanges/include" 
-I"/home/foo/.R/library/x86_64-pc-linux-gnu/3.1/XVector/include" 
-I"/home/foo/.R/library/x86_64-pc-linux-gnu/3.1/Biostrings/include" 
-fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c 
methods-WeightMatrix.c -o methods-WeightMatrix.o
gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o 
VariantFiltering.so Biostrings_stubs.o R_init_VariantFiltering.o 
methods-WeightMatrix.o -L/usr/lib/R/lib -lR
installing to 
/home/foo/.R/library/x86_64-pc-linux-gnu/3.1/VariantFiltering/libs
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems 
equivalent to one from package ‘BiocGenerics’: not turning on duplicate 
class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems 
equivalent to one from package ‘BiocGenerics’: not turning on duplicate 
class definitions for this class.

  *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
  1: .Call("scoss_read_wm", fname)
  2: initialize(value, ...)
  3: initialize(value, ...)
  4: new("WeightMatrix", wm = .Call("scoss_read_wm", fname))
  5: readWm(file.path(data_dir, "hsap.donors.hcmc10_15_1.ibn"))
  6: fun(libname, pkgname)
  7: doTryCatch(return(expr), name, parentenv, handler)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(fun(libname, pkgname), error = identity)
11: runHook(".onLoad", env, package.lib, package)
12: loadNamespace(package, c(which.lib.loc, lib.loc))
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, classes, parentenv, handlers)
16: 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))})
17: try({    ns <- loadNamespace(package, c(which.lib.loc, lib.loc)) 
env <- attachNamespace(ns, pos = pos, deps)})
18: library(pkg_name, lib.loc = lib, character.only = TRUE, 
logical.return = TRUE)
19: withCallingHandlers(expr, packageStartupMessage = function(c) 
invokeRestart("muffleMessage"))
20: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, 
character.only = TRUE, logical.return = TRUE))
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: 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))})
25: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, 
     character.only = TRUE, logical.return = TRUE)))
26: tools:::.test_load_package("VariantFiltering", 
"/home/foo/.R/library/x86_64-pc-linux-gnu/3.1")
aborting ...
Segmentation fault
ERROR: loading failed


------------------
   sessionInfo()

R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] BiocInstaller_1.14.2

loaded via a namespace (and not attached):
[1] tools_3.1.0

------------------
   gcc --version

gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2

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