[Bioc-devel] segfault when using RleList in DataFrames

Hi Leonard,

Thanks for the report. This segfault was due to a long-standing bug
in the "window" method for Rle objects when the object has length 0:

  > window(Rle(), 1, 0)  # you might need to try many times before

                         # you get the segfault
   *** caught segfault ***
  address 0x12f69d74, cause 'memory not mapped'

  Traceback:
   1: .Call(.NAME, ..., PACKAGE = PACKAGE)
   2: .Call2("Rle_getStartEndRunAndOffset", x, start, end, PACKAGE =
"IRanges")
   3: getStartEndRunAndOffset(x, start(solved_SEW), end(solved_SEW))
   4: .local(x, ...)
   5: window(Rle(), 1, 0)
   6: window(Rle(), 1, 0)

  Possible actions:
  1: abort (with core dump, if enabled)
  2: normal R exit
  3: exit R without saving workspace
  4: exit R saving workspace
  Selection: 2
  Save workspace image? [y/n/c]:

It is now fixed in release (S4Vectors 0.8.4 and IRanges 2.4.5) and
devel (S4Vectors 0.9.12 and IRanges 2.5.10).

Cheers,
H.



On 12/05/2015 03:29 PM, Leonard Goldstein wrote:

Hi all,

I ran into problems when using an RleList as column in a DataFrame
object (see example below).

Many thanks in advance for your help.

Leonard

sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

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=en_US.UTF-8    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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] IRanges_2.4.4       S4Vectors_0.8.3     BiocGenerics_0.16.1

df <- DataFrame(ID = 1:3)
x <- RleList(IntegerList(vector("list", 3)))
df$rle <- x
df

DataFrame with 3 rows and 2 columns

  *** caught segfault ***
address 0x9b00364, cause 'memory not mapped'

Traceback:
  1: .Call(.NAME, ..., PACKAGE = PACKAGE)
  2: .Call2("Rle_getStartEndRunAndOffset", x, start, end, PACKAGE =
"S4Vectors")
  3: S4Vectors:::getStartEndRunAndOffset(x, start(solved_SEW),
end(solved_SEW))
  4: .local(x, ...)
  5: window(x, start = 1L, width = n)
  6: window(x, start = 1L, width = n)
  7: .local(x, ...)
  8: head(x, 3)
  9: head(x, 3)

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

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
Seattle, WA 98109-1024

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