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:
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
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