Entering edit mode
Julian Gehring
★
1.3k
@julian-gehring-5818
Last seen 5.8 years ago
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
