[Bioc-devel] segfault when using RleList in DataFrames

[Leonard Goldstein]

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: