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List:       r-devel
Subject:    Re: [Rd]  [External]  Something is wrong with the unserialize function
From:       luke-tierney () uiowa ! edu
Date:       2020-10-29 17:42:50
Message-ID: alpine.DEB.2.21.2010291233301.3311 () luke-Latitude-7480
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I found that also; fixed in r79386 in the trunk. Will port to R-patched
shortly.

Best,

luke

On Thu, 29 Oct 2020, Martin Morgan wrote:

> 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 = PROTECT(ScalarString(PRINTNAME(psym)));
> 	    R_tryCatchError(find_namespace, pname,
> 			    handle_namespace_error, NULL);
> 	    class = LookupClass(csym, psym);
> +	    UNPROTECT(1);
> 	}
> 	return class;
> }
> 
> seems to remove the warning; I'm guessing that the other SEXP already exist so \
> don't need protecting? 
> Martin Morgan
> 
> 
> On 10/29/20, 12:47 PM, "R-devel on behalf of luke-tierney@uiowa.edu" \
> <r-devel-bounces@r-project.org on behalf of luke-tierney@uiowa.edu> wrote: 
> Thanks for the report. Will look into it when I get a chance unless
> someone else gets there first.
> 
> A simpler reprex:
> 
> ## create and serialize a memmory-mapped file object
> filePath <- "x.dat"
> con <- file(filePath, "wrb")
> writeBin(rep(0.0,10),con)
> close(con)
> 
> library(simplemmap)
> x <- mmap(filePath, "double")
> saveRDS(x, file = "x.Rds")
> 
> ## in a separate R process:
> gctorture()
> readRDS("x.Rds")
> 
> Looks like a missing PROTECT somewhere.
> 
> Best,
> 
> luke
> 
> On Thu, 29 Oct 2020, Jiefei Wang wrote:
> 
> > 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, "double")
> > ## Turn gctorture on
> > clusterEvalQ(cl, gctorture())
> > clusterExport(cl, "x")
> > ## x is an 0-length vector on the worker
> > clusterEvalQ(cl, x)
> > stopCluster(cl)
> > ```
> > 
> > you can find more info on the problem if you manually build a connection
> > between two R processes and export the ALTREP object. See output below
> > ```
> > > con <- socketConnection(port = 1234,server = FALSE)
> > > gctorture()
> > > x <- unserialize(con)
> > Warning message:
> > In unserialize(con) :
> > cannot unserialize ALTVEC object of class 'mmap_real' from package
> > 'simplemmap'; returning length zero vector
> > ```
> > It seems like  simplemmap did not get loaded correctly on the worker. If
> > you run `library( simplemmap)` before unserializing the ALTREP, there will
> > be no problem. But I suppose we should be able to unserialize objects
> > without preloading the library?
> > 
> > This issue can be reproduced on Ubuntu with R version 4.0.2 (2020-06-22)
> > and Windows with R Under development (unstable) (2020-09-03 r79126).
> > 
> > Here is the link to simplemmap:
> > https://github.com/ALTREP-examples/Rpkg-simplemmap
> > 
> > Best,
> > Jiefei
> > 
> > 	[[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-tierney@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
> 

-- 
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-tierney@uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
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