From k@bem|@ @end|ng |rom northe@@tern@edu  Fri Aug 16 17:50:18 2019
From: k@bem|@ @end|ng |rom northe@@tern@edu (Bemis, Kylie)
Date: Fri, 16 Aug 2019 15:50:18 -0000
Subject: [Rd] Any plans for ALTREP lists (VECSXP)?
In-Reply-To: <CAD4oTHGaJFWCLtVRVQ3oG6ws2hj+Cuo1krw0-VBjNCuhKQYThg@mail.gmail.com>
References: <61E11B6B-E70C-4B92-9AC2-A3FA6678D626@northeastern.edu>
 <CAOQ5NyfEaZL+Uy_Ncw=Yy5sRcc4iuR1=3c1vMEB2xPSrHn6cvw@mail.gmail.com>
 <CAD4oTHGaJFWCLtVRVQ3oG6ws2hj+Cuo1krw0-VBjNCuhKQYThg@mail.gmail.com>
Message-ID: <68D37BB5-B8F4-4705-A43B-D990ABD9410F-4877@northeastern.edu>

Thanks for the suggestions, everyone.

Is it not a pressing issue requiring alternatives, since the ?matter_list? object already behaves like a list, and I am just looking for a way to present a native R list (VECSXP) when a regular list is required.

In this case (in my typical use case), the ?matter_list? is homogenous and I use it like a ragged array; however, in general each element could be a different atomic vector type (specifically raw, logical, integer, or double).

Here, as.altrep() is an S4 method for converting my custom ?matter?-class out-of-memory objects into their native R representations using ALTREP.

Seems to work well for the ?matter' vectors, matrices, and arrays, where it just .Call()s my C function for making the corresponding ALTREP object, but the lists were giving me trouble because there I use lapply() to extract and uncompress the ?matter_list? metadata for each list element into a separate S4 ?matter_vec? out-of-memory vector, each of which is then used to create an ALTREP object for the corresponding list element. So it gets costly...

The cost is mostly in re-creating all of the metadata as regular R objects that end up occupying the R_altrep_data1() spot for all of the individual list elements. If I could make an ALTREP list, I could leave the metadata as-is and avoid all of that.

Anyway, not a pressing issue for me either, just something I noticed where having an ALTREP list could be useful, so I was wondering if it was in the plans, which Luke answered.

Thanks,

-Kylie

On Jul 23, 2019, at 8:27 PM, Gabriel Becker <gabembecker at gmail.com<mailto:gabembecker at gmail.com>> wrote:

Hi Kylie,

Is it a list with only numerics in it? (I only see REALSXPs there, but obviously inspect isn't showing all of them). If so, you could load it up into one big vector and then also keep partitioning information around. Bioconductor does this (see ?IRanges::CompressedList ). The potential benefit here being that the underlying large vector could then be a big out-of-memory altrep. How helpful this would be depends somewhat on what you want to do with it, of course, but it is something that comes to mind.

Also, I would expect some overhead but that seems like a lot (without having done super much in the way of benchmarking). What exactly is as.altrep doing?

Best,
~G

On Tue, Jul 23, 2019 at 9:54 AM Michael Lawrence via R-devel <r-devel at r-project.org<mailto:r-devel at r-project.org>> wrote:
Hi Kylie,

As an alternative in the short term, you could consider deriving from
S4Vector's List class, implementing the getListElement() method to
lazily create the objects.

Michael

On Tue, Jul 23, 2019 at 9:09 AM Bemis, Kylie <k.bemis at northeastern.edu<mailto:k.bemis at northeastern.edu>> wrote:
>
> Hello,
>
> I was wondering if there were any plans for ALTREP lists (VECSXP)?
>
> It seems to me that they could be supported in a similar way to how ALTSTRING works, with Elt() and Set_elt() methods, or would there be some problems with that I?m not seeing due to lists not being atomic vectors?
>
> I was taking an approach of converting each list element (of a file-based list data structure) to an ALTREP representation to build up an ?ALTREP list?.
>
> This seems fine for shorter lists with large elements, but I noticed that for longer lists with smaller elements, this could be far more time-consuming than simply reading the entire list into memory and returning a non-ALTREP list:
>
> > x
> <34840 length> matter_list :: out-of-memory list
> (1.1 MB real | 543.3 MB virtual)
>
> > system.time(y <- as.list(x))
>    user  system elapsed
>   1.116   2.175   5.053
>
> > system.time(z <- as.altrep(x))
>    user  system elapsed
>  36.295   4.717  41.216
>
> > .Internal(inspect(y))
> @108255000 19 VECSXP g1c7 [MARK,NAM(7)] (len=34840, tl=0)
>   @7f9044d9fc00 14 REALSXP g1c7 [MARK] (len=1129, tl=0) 404.093,404.096,404.099,404.102,404.105,...
>   @7f9044d25e00 14 REALSXP g1c7 [MARK] (len=890, tl=0) 409.924,409.927,409.931,409.934,409.937,...
>   @7f9044da6000 14 REALSXP g1c7 [MARK] (len=1878, tl=0) 400.3,400.303,400.306,400.309,400.312,...
>   @7f9031a6b000 14 REALSXP g1c7 [MARK] (len=2266, tl=0) 402.179,402.182,402.185,402.188,402.191,...
>   @7f9031a77a00 14 REALSXP g1c7 [MARK] (len=1981, tl=0) 403.021,403.024,403.027,403.03,403.033,...
>   ...
>
> > .Internal(inspect(z))
> @108210000 19 VECSXP g1c7 [MARK,NAM(7)] (len=34840, tl=0)
>   @7f904eea7660 14 REALSXP g1c0 [MARK,NAM(7)] matter vector (mode=4, len=1129, mem=0)
>   @7f9050347498 14 REALSXP g1c0 [MARK,NAM(7)] matter vector (mode=4, len=890, mem=0)
>   @7f904d286b20 14 REALSXP g1c0 [MARK,NAM(7)] matter vector (mode=4, len=1878, mem=0)
>   @7f904fd38820 14 REALSXP g1c0 [MARK,NAM(7)] matter vector (mode=4, len=2266, mem=0)
>   @7f904c75ce90 14 REALSXP g1c0 [MARK,NAM(7)] matter vector (mode=4, len=1981, mem=0)
>   ...
>
> In this situation, it would be much faster and simpler for me to return a theoretical ALTREP list that serves SEXP elements on-demand, similar to how ALTSTRING seems to be implemented.
>
> I don?t know how many other people would get a use out of ALTREP lists, but I certainly would.
>
> Are there any plans for this?
>
> Thanks!
>
> ~~~
> Kylie Ariel Bemis
> Khoury College of Computer Sciences
> Northeastern University
> kuwisdelu.github.io<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fkuwisdelu.github.io&data=02%7C01%7Ck.bemis%40northeastern.edu%7C30d98923a37f405b4c9908d70f9b6875%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636995032467082904&sdata=QGe%2F4F1D%2B9Sz7LxkP9%2BsAXD2t5JDtLVkko450e5ecI4%3D&reserved=0><https://kuwisdelu.github.io<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fkuwisdelu.github.io&data=02%7C01%7Ck.bemis%40northeastern.edu%7C30d98923a37f405b4c9908d70f9b6875%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636995032467092912&sdata=PZKJtQ1wh%2FCyJn44DdGBQ7dLLI6eAYt00lK0uO%2BOrzA%3D&reserved=0>>
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--
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
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[Rd] Any plans for ALTREP lists (VECSXP)?
Bemis, Kylie