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

[Ge Tan]

Hi Hervé,

Thank you very much!
So how about Calloc? Does it run much slower than the direct malloc() too?

Best,
Ge

----------------------------------------
> Date: Fri, 19 Jul 2013 17:05:30 -0700
> From: hpages at fhcrc.org
> To: ge_tan at live.com
> CC: bioc-devel at r-project.org
> Subject: Re: [Bioc-devel] IntAE buffers needs to be freed or not??
>
> 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).
>
> Cheers,
> H.
>
> 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));
>> UNPROTECT(1);
>> 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
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
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