Hi,
Ran into an intermittent bug in findOverlaps when using select="arbitrary" -
I managed to narrow it down the problem to the C call
> library(IRanges)
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin,
pmin.int, rbind, rep.int, table
> temp <- IRanges(sample(10000000, 100000), width=10000)
> for (i in 1:1000000) xx <- findOverlaps(temp, IntervalTree(temp),
select="arbitrary")
Error in .IntervalTreeCall(subject, fun, query, query_ord) :
INTEGER() can only be applied to a 'integer', not a 'character'
> i
[1] 7
> traceback()
5: .Call(fun, obj...@ptr, ..., PACKAGE = "IRanges")
4: .IntervalTreeCall(subject, fun, query, query_ord)
3: .local(query, subject, maxgap, minoverlap, type, select, ...)
2: findOverlaps(temp, IntervalTree(temp), select = "arbitrary")
1: findOverlaps(temp, IntervalTree(temp), select = "arbitrary")
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-07-06 r52460)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] IRanges_1.7.32
Thanks,
Aaron
--
Aaron Statham
Postgraduate Scholar, Cancer Epigenetics
Garvan Institute of Medical Research Tel: (02) 9295 8393
384 Victoria St Darlinghurst 2010 Fax: (02) 9295 8316
NSW Australia email: [email protected]
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