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Tim Rayner
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270
@tim-rayner-2913
Last seen 9.6 years ago
Hi,
I'm trying to run the bayespeak function on some BED files published
by Araki et al. (PMID 19523850, GEO accession GSE12616), and I'm
having segfault problems which seem to relate to memory usage. I
originally tried running the function on the whole BED files but that
ran into problems very quickly, so I've split the BED files up by
chromosome. Many of these files have now been processed without
problems, but some give an error message similar to that given below,
for no immediately obvious reason (i.e., typically it is *not* the
largest files which yield this error):
----------------------------------------------------------------------
----------------------------------------------------------------------
---------------------------------------------------
[0% done] Starting chr13:17927925-114127244:.............
*** caught segfault ***
address 0x110660000, cause 'memory not mapped'
Traceback:
1: .Call("bayespeak", as.integer(tr$"+"$norm[659981:720020]),
as.integer(tr$"-"$norm[659981:720020]),
as.integer(w$norm[659981:720020]), as.double(w$norm[659981:720020]),
as.integer(max(w$norm[659981:720020])), as.integer(60000),
as.character(ch), start = as.integer(83925925), end =
as.integer(89929925), as.integer(bin.size),
as.integer(iterations), para = as.double(para.list),
as.double(prior))
2: eval(expr, envir, enclos)
3: eval(parse(text = x))
4: eval(parse(text = x))
5: FUN(X[[2L]], ...)
6: lapply(S, FUN, ...)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: 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 <- paste(prefix, "\n ", sep =
"") } else prefix <- "Error : " msg <- paste(prefix,
conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1L])) if (!silent &&
identical(getOption("show.error.messages"), TRUE)) {
cat(msg, file = stderr()) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error"))})
11: try(lapply(S, FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(S, FUN, ...), silent = TRUE))
13: FUN(1:6[[6L]], ...)
14: lapply(1:cores, inner.do)
15: multicore::mclapply(jobs, function(x) { eval(parse(text = x))},
mc.cores = mc.cores)
16: bayespeak(bedfiles[n], use.multicore = TRUE, mc.cores = 6)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 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 <- paste(prefix, "\n ", sep =
"") } else prefix <- "Error : " msg <- paste(prefix,
conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1L])) if (!silent &&
identical(getOption("show.error.messages"), TRUE)) {
cat(msg, file = stderr()) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error"))})
21: try(x <- bayespeak(bedfiles[n], use.multicore = TRUE, mc.cores =
6))
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
----------------------------------------------------------------------
----------------------------------------------------------------------
---------------------------------------------------
I've tried switching off the multicore option, but that doesn't seem
to help. I'm running this using 64-bit R on MacOSX 10.5.8. Has anybody
else experienced this problem? I'm going to try and break this down to
a small test case, but given that the problem apparently occurs in the
C call I'm not tremendously optimistic. I've included my sessionInfo()
at the end of this email.
Best regards,
Tim Rayner
--
Bioinformatician
Smith Lab, CIMR
University of Cambridge
> sessionInfo()
R version 2.11.0 Patched (2010-04-30 r51866)
x86_64-apple-darwin9.8.0
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] multicore_0.1-3 BayesPeak_1.0.0 IRanges_1.6.0
