[BioC] VariantFiltering: Installation segfault

Thu Jun 12 14:43:02 CEST 2014

hi again,

i found the problem, it wasn't a memory leak but something more subtle 
(i'll write about it in the devel list). this is now fixed in 
VariantFiltering release version 1.0.2 which should become available via 
biocLite() in the next day or two.

thanks again for reporting the problem,

robert.

On 06/12/2014 06:17 AM, Julian Gehring wrote:
> 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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-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550