[Bioc-devel] R long vectors not supported yet on R 3.3.2

[Kasper Daniel Hansen]

On Thu, Mar 9, 2017 at 2:44 AM, Sohaib Ghani <sohaibghani at hotmail.com>
wrote:

> I am trying to simulate hilbertcurve (of Bioconductor package) of level 16
> in R. It takes about 4^16=4 Billion points. I want to generate the hilbert
> curve of genome (size about 3 billion).
>
> But I am getting this error
>
> long vectors not supported yet: memory.c:1668
>
> I am using 64 bit version (R 3.3.2) so my guess is I can use vectors of
> length > 2^31. Also, my RAM is about 350GB
>

Your guess is wrong.

An R vector has a max length of 2^31-1 (or something like this).  Thats
what you run into.  To go beyond this you need something called "long
vectors" which can be much, much longer.  But it seems like HilbertCurve
(like many other instances) don't support long vectors yet.

Kasper




> The command I am using is
>
> itr=4^16
> hc = HilbertCurve(1, itr, 16, mode = "pixel", title = "pixel
> mode",start_from = "topleft")
>
> Even when I am reading the whole genome sometimes R is crashing in the
> process.
>
> I have read the other similar questions on this topic but could not find
> the solution. Please help me what should I use for this problem.
>
>
> Thanks
>
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