similar to: Questions regarding ALTREP_SET_ELT APIs

On Tue, 30 Jul 2019, Wang Jiefei wrote: > Hi all, > > I'm wondering if there is any way to define a `SET_ELT` function for an > ALTREP class? I see there are ` ALTINTEGER_SET_ELT` etc. functions exported > in Rinternal.h, but there is no corresponding ALTREP APIs to define them. > The only way to set the value of an ALTREP is through a pointer, which will > require that

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

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

I can work on this. Thanks Luke. ~G On Wed, Jul 24, 2019 at 8:25 AM Tierney, Luke <luke-tierney at 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

Hi all, I am not able to export an ALTREP object when `gctorture` is on in the worker. The package simplemmap can be used to reproduce the problem. See the example below ``` ## Create a temporary file filePath <- tempfile() con <- file(filePath, "wrb") writeBin(rep(0.0,10),con) close(con) library(simplemmap) library(parallel) cl <- makeCluster(1) x <- mmap(filePath,

Hello, I have encountered two bugs when using ALTREP APIs. 1. STDVEC_DATAPTR >From RInternal.h file it has a comment: /* ALTREP support */ > void *(STDVEC_DATAPTR)(SEXP x); However, this comment might not be true, the easiest way to verify it is to define a C++ function: void C_testFunc(SEXP a) > { > STDVEC_DATAPTR(a); > } and call it in R via > a=1:10 > >

This Index: src/main/altrep.c =================================================================== --- src/main/altrep.c (revision 79385) +++ src/main/altrep.c (working copy) @@ -275,10 +275,11 @@ SEXP psym = ALTREP_SERIALIZED_CLASS_PKGSYM(info); SEXP class = LookupClass(csym, psym); if (class == NULL) { - SEXP pname = ScalarString(PRINTNAME(psym)); + SEXP pname =

Hi devel team, I'm working on C/C++ level ALTREP compatibility for a package. The package previously used pointers to access the data of a SEXP, so it would not work for some ALTREP objects which do not have a pointer. I plan to rewrite the code and use functions like get_elt, get_region, and get_subset to access the values of a vector, so I have a few questions for ALTREP: 1. Since an

Thank Denes for the clarification, glad to see my package got one citation from my own question:) Also, thank Benjamin for sending many useful documents. Actually, the question is related to the SharedObject package that Benjamin has pointed to. I wanna avoid sharing an object that has already been shared, so I need to check whether an object is an ALTREP that is defined in my package. Since the

Benjamin, You happened to send a link which points to the OP's own package :) I think Jiefei would like to know how one can "officially" determine if an arbitrary ALTERP object belongs to a class that he owns. Regards, Denes On 10/19/20 10:22 AM, Benjamin Christoffersen wrote: > It seems as if you can you use the ALTREP macro as done in this > package:

Sorry for post a lot of things, for the first part of code, I copied my C++ iter macro by mistake(and you can see an explicit type casting). Here is the macro definition from R_exts/Itermacros.h #define ITERATE_BY_REGION_PARTIAL(sx, px, idx, nb, etype, vtype, \ strt, nfull, expr) do { \ * const** etype *px = DATAPTR_OR_NULL(sx); *

Hi all, I would like to determine if an ALTREP object is from my package, I see there is a function `ALTREP_CLASS` defined in RInternal.h but its return value is neither a `R_altrep_class_t` object nor an STRSXP representing a class name. I do not know how to correctly use it. Any suggestions? Thanks, Jiefei [[alternative HTML version deleted]]

Hello Luke and Gabriel, Thank you very much for your quick responses. The explanation of STDVEC is very helpful and I appreciate it! For the wrapper, I have a few new questions. 1. Like Luke said a mutable object is not possible. However, I noticed that there is one extra argument *deep* in the function duplicate. I've googled all the available documentation for ALTREP but I did not find

Hi Bob, Thanks for sending around the link to that. It looks mostly right and looks like a useful onramp. There are a few things to watch out for though (I've cc'ed Romain so he's aware of these comments). @romain I hope you taake the following comments as they are intended, as help rather than attacks. The largest issue I see is that the contract for Get_region is that it *populates

A useful extension of ALTREP is having two new string methods which return the number of characters of a given string element and to return a substring of an element. Having these methods would allow retrieving these values without needing to create a CHARSXP for the full element data, which could potentially be costly for long elements. For example say you have an ALTREP altstring vector where

Hi all, The coercion function defined for the ALTREP object will not be called by R when an assignment operation implicitly introduces coercion for a large ALTREP object. For example, If I create a vector of length 10, the ALTREP coercion function seems to work fine. ``` > x <- 1:10 > y <- wrap_altrep(x) > .Internal(inspect(y)) @0x000000001f9271c0 13 INTSXP g0c0 [REF(2)] I am

Hi Gabriel, here is a simple package for reproducing the problem. https://github.com/Jiefei-Wang/testPkg Best, Jiefei On Thu, Oct 8, 2020 at 5:04 AM Gabriel Becker <gabembecker at gmail.com> wrote: > Jiefei, > > Where does the code for your altrep class live? > > Thanks, > ~G > > On Wed, Oct 7, 2020 at 4:25 AM Jiefei Wang <szwjf08 at gmail.com> wrote: >

Hi Gabriel, Thanks for your explanation, I totally understand that it is almost impossible to change the data structure of STRSXP. However, what I'm proposing is not about changing the internal representation, but rather about how we design and use the ALTREP API. I might do not state the workarounds clearly as English is not my first language. Please let me explain them again in detail.

Hello, I have two related ALTREP questions. It seems like there is no way to assign attributes to an ALTREP vector without using C++ code. To be more specifically, I want to make an ALTREP matrix, I have tried the following R code but none of them work. ``` .Internal(inspect(1:6)) .Internal(inspect(matrix(1:6, 2,3))) .Internal(inspect(as.matrix(1:6))) .Internal(inspect(structure(1:6, dim =

Hello from Bioconductor, I'm developing a package to share R objects across clusters using boost library. The concept is similar to mmap package: https://cran.r-project.org/web/packages/mmap/index.html . However, I have a problem when I was trying to write Dataptr_method for the alternative string. Based on my understanding, the return value of the Dataptr_method function should be a vector