Hi Michael, On 03/29/2014 02:07 PM, Michael Lawrence wrote:
Just coerce the RleList to SimpleIntegerList.
Isn't what as(x, "IntegerList") should do when 'x' is a SimpleRleList? Thanks, H.
On Sat, Mar 29, 2014 at 1:10 PM, Gabe Becker <becker.g...@gene.com> wrote:Hi all, Apologies if this gets duplicated. I was not subscribed when I originally sent it. We have a very large RleList, such that the sum of the lengths is larger than INT.MAX, that we want to convert to an also very large IntegerList (whole genome coverages by chromosome I believe, though I'm not the author of the code that ran into this so I could be wrong about the details there). The IntegerList will fit in memory fine, but the coercion method is trying to collapse our RleList into a single Rle (in compress_listData() which is called from coerceToCompressedList() ) during the coercion step, which is too long and causes an integer overflow in the constructor. Specically the Rle_constructor C function is calling _sum_non_neg_ints C function, which throws an error. I can see that there is quite a bit of machinery trying to make these coercions go fast, but it seems they have introduced an unintended (?) limitation on the size of the *List objects involved. Is there a slower but more robust coercion machinery I don't know about, and if not could one be exposed? (Fast and more robust would also be acceptable ;-) ) Thanks, ~G [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel[[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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