[R] Debugging segfault in foreach

[Steve Lianoglou]

Hi,

I'm using R-2.12 on a linux 64bit machine.

When I run a chunk of code inside a foreach() %do% { ...} or %dopar%
{...} (with doMC backend) I keep getting a segfault. Running the
*same* code within lapply(something, function(x) ... ) doesn't result
in any segfaults. I'll paste the output below, but I'm not sure it
would be helpful.

I'm more curious how to go about smoking out what's causing this, as
getting back "into" the code block that is crashing is tricky inside
the code block executed by foreach().

If anybody has any suggestions on how they debug with foreach, I'd be
happy to hear them. Setting .veborse=TRUE isn't providing anything
informative.

Anyway, I'll paste the segfault bomb below, followed by sessionInfo()

======== Segfault dump ==========

result of evaluating expression:

 *** caught segfault ***
address 0x30, cause 'memory not mapped'

Traceback:
 1: format(x[[i]], ..., justify = justify)
 2: format.data.frame(x, digits = digits, na.encode = FALSE)
 3: as.matrix(format.data.frame(x, digits = digits, na.encode = FALSE))
 4: print.data.frame(r)
 5: print(r)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch({    repeat {        args <- nextElem(it)        if
(obj$verbose) {            cat(sprintf("evaluation # %d:\n", i))
     print(args)        }        for (a in names(args)) assign(a\
, args[[a]], pos = envir,             inherits = FALSE)        r <-
tryCatch(eval(expr, envir = envir), error = function(e) e)        if
(obj$verbose) {            cat("result of evaluating expression\
:\n")            print(r)        }
tryCatch(accumulator(list(r), i), error = function(e) {
cat("error calling combine function:\n")            print(e)
 NULL        })     \
   i <- i + 1    }}, error = function(e) {    if
(!identical(conditionMessage(e), "StopIteration"))
stop(simpleError(conditionMessage(e), expr))})
10: doSEQ(obj, substitute(ex), parent.frame())
11: foreach(chr = chrs, .packages = "GenomicFeaturesX", .verbose =
TRUE) %do%     {        .gc <- duplicate(gcache, pre.load = NULL)
  on.exit(dispose(.gc))        cat("===", chr, "===\n")       \
 apaSummary(expt, .gc, chr, pvd.policy, utr.index, polya.variants,
        gene.collapse)    }
12: apaSummaryCrank(bpm[[1]], gcr, chrs[21:22], gene.collapse = "longest")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

============= sessionInfo ==============

R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

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=C              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] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] reshape2_1.0          ShortRead_1.8.0       lattice_0.19-13
 [4] ggplot2_0.8.8         proto_0.3-8           reshape_0.8.3
 [7] doMC_1.2.1            multicore_0.1-3       foreach_1.3.0
[10] codetools_0.2-2       iterators_1.0.3       data.table_1.5.1
[13] plyr_1.2.1            GenomeGraphs_1.10.0   biomaRt_2.6.0
[16] bitops_1.0-4.1        Rsamtools_1.2.0       RSQLite_0.9-2
[19] DBI_0.2-5             Biostrings_2.18.0     GenomicFeaturesX_0.2
[22] GenomicFeatures_1.2.0 GenomicRanges_1.2.1   IRanges_1.8.2

loaded via a namespace (and not attached):
 [1] annotate_1.28.0      AnnotationDbi_1.12.0 Biobase_2.10.0
 [4] BSgenome_1.18.0      hwriter_1.2          RCurl_1.4-3
 [7] rtracklayer_1.10.2   stringr_0.4          XML_3.2-0
[10] xtable_1.5-6

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact