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Jiefei Wang

2020-Oct-29 13:53 UTC

[Rd] Something is wrong with the unserialize function

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]]

iuke-tier@ey m@iii@g oii uiow@@edu

2020-Oct-29 16:46 UTC

head link

[Rd] [External] Something is wrong with the unserialize function

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 at 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 at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

Martin Morgan

2020-Oct-29 17:10 UTC

head link

[Rd] [External] Something is wrong with the unserialize function

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 at
uiowa.edu" <r-devel-bounces at r-project.org on behalf of luke-tierney
at 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 at 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 at uiowa.edu
    Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

    ______________________________________________
    R-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-devel

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