Quantiles from Rle's with long lengths

The goal is to calculate quantiles on aggregated long Rle's. The information is split by chr, and combining it naively fails.

suppressMessages(library("IRanges"))

## Create dummy data
lengths <- c(249250621, 243199373, 198022430, 191154276, 180915260, 171115067,
    159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878,
    107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520,
    48129895, 51304566, 155270560, 59373566)
chrdata <- lapply(lengths, function(x) {
    Rle(rep(0, x))
})

## Just to see visualize explore it (doesn't matter if the type is
## numeric-Rle or integer-Rle)
head(chrdata)

## [[1]]
## numeric-Rle of length 249250621 with 1 run
##   Lengths: 249250621
##   Values :         0
## 
## [[2]]
## numeric-Rle of length 243199373 with 1 run
##   Lengths: 243199373
##   Values :         0
## 
## [[3]]
## numeric-Rle of length 198022430 with 1 run
##   Lengths: 198022430
##   Values :         0
## 
## [[4]]
## numeric-Rle of length 191154276 with 1 run
##   Lengths: 191154276
##   Values :         0
## 
## [[5]]
## numeric-Rle of length 180915260 with 1 run
##   Lengths: 180915260
##   Values :         0
## 
## [[6]]
## numeric-Rle of length 171115067 with 1 run
##   Lengths: 171115067
##   Values :         0

## Trying to combine
unlist(RleList(chrdata), use.names = FALSE)

## Error: error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "IRanges") : 
##   integer overflow while summing elements in 'lengths'
## Calls: RleList ...  -> Rle -> Rle -> .local -> .Call2 -> .Call

traceback()

## No traceback available

## Works manually up to the first 12
tmp <- c(chrdata[[1]], chrdata[[2]], chrdata[[3]], chrdata[[4]], chrdata[[5]],
    chrdata[[6]], chrdata[[7]], chrdata[[8]], chrdata[[9]], chrdata[[10]], chrdata[[11]],
    chrdata[[12]])

## For the first 13 it breaks
tmp <- c(chrdata[[1]], chrdata[[2]], chrdata[[3]], chrdata[[4]], chrdata[[5]],
    chrdata[[6]], chrdata[[7]], chrdata[[8]], chrdata[[9]], chrdata[[10]], chrdata[[11]],
    chrdata[[12]], chrdata[[13]])

## Error: integer overflow while summing elements in 'lengths'

traceback()

## No traceback available

## Note the main issue is related to the 2^31 ceiling
plot(cumsum(lengths), main = "Length of Rle exceeding 2^31")
abline(v = 13, col = "red")
abline(h = 2^31, col = "orange")

plot of chunk unnamed-chunk-2

One idea: leave the Rle-world and use some kind of weighted quantile.

## Manually combine in two parts
part1 <- unlist(RleList(chrdata[1:12]), use.names = FALSE)
part2 <- unlist(RleList(chrdata[13:length(chrdata)]), use.names = FALSE)
parts <- list(part1, part2)

## Reduce number of runs in the Rle's by sorting (kind of doing table())
sortedParts <- lapply(parts, function(x) sort(x))

## Leave Rle-world
info <- lapply(sortedParts, function(y) {
    data.frame(value = runValue(y), length = runLength(y))
})
info <- do.call(rbind, info)

## Format
info$length <- as.numeric(info$length)

## Collapse
collapsed <- tapply(info$length, info$value, sum)
weights <- as.integer(names(collapsed))

## Calculate weighted quantile of interest
library("Hmisc")

## Loading required package: survival
## Loading required package: splines
## Loading required package: Formula
## Hmisc library by Frank E Harrell Jr
## 
## Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview')
## to see overall documentation.
## 
## 
## Attaching package: 'Hmisc'
## 
## The following object is masked from 'package:survival':
## 
##     untangle.specials
## 
## The following object is masked from 'package:BiocGenerics':
## 
##     combine
## 
## The following objects are masked from 'package:base':
## 
##     format.pval, round.POSIXt, trunc.POSIXt, units

wtd.quantile(collapsed, weights = weights, probs = 0.5)

##       50% 
## 3.096e+09

Is there a way to calculate the quantiles of the aggregated Rle's without all this machinery? Are there other possibly more efficients ways to do so?

## Reproducibility
sessionInfo()

## R version 3.0.2 (2013-09-25)
## Platform: x86_64-apple-darwin10.8.0 (64-bit)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] splines   parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
## [1] Hmisc_3.12-2       Formula_1.1-1      survival_2.37-4   
## [4] IRanges_1.20.4     BiocGenerics_0.8.0 knitr_1.5         
## 
## loaded via a namespace (and not attached):
##  [1] cluster_1.14.4  evaluate_0.5.1  formatR_0.10    grid_3.0.2     
##  [5] highr_0.3       lattice_0.20-24 rpart_4.1-3     stats4_3.0.2   
##  [9] stringr_0.6.2   tools_3.0.2