If one of you wanted to try to create a patch to support ALTREP generic vectors here are some notes:
The main challenge I am aware of (there might be others): Allowing DATAPTR to return a writable pointer would be too dangerous because the GC write barrier needs to see all mutations. So it would be best if Dataptr and Dataptr_or_null methods were not allowed to be defined. The default methods in altrep.c should do the right think. A reasonable name for the abstract class would be 'altlist'. 'altrep' methods that a class can provide: Unserialize or UnserializeEX Serialized_state Duplicate or DuplicateEx Coerce Inspect Length 'altvec' methods a class should provide: Extract_subset not Dataptr not Dataptr_or_null 'altlist' specific methods: Elt Set_elt Best, luke On Tue, 23 Jul 2019, Gabriel Becker 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@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.be...@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://kuwisdelu.github.io> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> >> >> -- >> Michael Lawrence >> Scientist, Bioinformatics and Computational Biology >> Genentech, A Member of the Roche Group >> Office +1 (650) 225-7760 >> micha...@gene.com >> >> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube >> >> ______________________________________________ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Luke Tierney Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics and Fax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke-tier...@uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
