Fair enough, though an indication of the length limit in the documentation at ?IntegerList or a more informative error message would be nice.
Apologies for the noise. ~G On Sat, Mar 29, 2014 at 2:07 PM, Michael Lawrence <lawrence.mich...@gene.com > wrote: > Just coerce the RleList to SimpleIntegerList. > > > 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
