[Bioc-devel] IntAE buffers needs to be freed or not??

Hervé Pagès hpages at fhcrc.org
Sat Jul 20 02:05:30 CEST 2013

Hi Ge,

No you don't. At least not currently, because those buffers use
transient memory which will be freed automatically when .Call()
returns. However, I might change the implementation of the IntAE
buffers to use user-controlled memory at some point (malloc() is
so much faster than R_alloc(), about 10x-20x for me), so when this
happens you will need to do something like

   .Call("AEbufs_free", PACKAGE="IRanges")

unless you call your .Call entry point with .Call2 (defined in the
IRanges package), which will take care of doing that for you. I highly
recommend you do that if you use the IntAE buffers in your C code or
if you call C functions that use the IntAE buffers (and a lot of C
functions in IRanges and Biostrings use them).


On 07/19/2013 03:35 AM, Ge Tan wrote:
> Hi all,
> I am using the IntAE buffers (taken from IRanges packages) in my .Call() code.
> Sample code in C:
> IntAE width_buf;
> width_buf = new_IntAE(0, 0, 0);
> for(…){
>      IntAE_insert_at(&width_buf, IntAE_get_nelt(&width_buf), width);
> }
> PROTECT(width = new_INTEGER_from_IntAE(&width_buf));
> return(width);
> So after using .Call(), do I need to run something like ".Call("AEbufs_free", PACKAGE="IRanges")" in R?
> I got this from the IRanges/src/AEbufs.c.
> Thanks!
> Ge 		 	   		
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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