I can work on this. Thanks Luke. ~G
On Wed, Jul 24, 2019 at 8:25 AM Tierney, Luke <luke-tier...@uiowa.edu> wrote: > 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 [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
