I have confirmed that a complete workaround to these problems is available if,
as Bill Dunlap suggested, "version=2" is used in all *save* incantations.
Thanks Bill!
- Jan
On Thu, Jul 18, 2019, at 10:39, William Dunlap wrote:
> Note that you can reproduce this in R-3.5.1 if you specify serialization
> version 3 (which became the default in 3.6.0).
>
> > save(apresX, file="351-2.RData", version=2)
> > save(apresX, file="351-2.RData", version=3)
> Error: C stack usage 7969184 is too close to the limit
> > version$version.string
> [1] "R version 3.5.1 (2018-07-02)"
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Thu, Jul 18, 2019 at 12:46 AM Jan Galkowski <bayesianlogi...@gmail.com>
> wrote:
>> > # Test for saving. Jan Galkowski, 17th July 2019.
>> > # produceProtectionFault.R
>> >
>> > library(apcluster)
>> > cl1 <- cbind(rnorm(100, 0.2, 0.05), rnorm(100, 0.8, 0.06))
>> > cl2 <- cbind(rnorm(50, 0.7, 0.08), rnorm(50, 0.3, 0.05))
>> > x <- rbind(cl1, cl2)
>> >
>> > ## compute similarity matrix and run affinity propagation
>> > ## (p defaults to median of similarity)
>> > simil<- negDistMat(x, r=2)
>> > apres <- apcluster(s=simil, details=TRUE)
>> > apresX<- aggExCluster(s=simil, x=apres)
>> >
>> > show(apres)
>> > show(apresX)
>> >
>> > saveRDS(object=apresX, file="foo.rds", compress=TRUE)
>> >
>> > #save(apresX, file="bar.data", compress=TRUE)
>> >
>> > #save.image("crazy.RData")
>>
>> The example is from the apcluster documentation. Leaving any one of the
>> "save"s uncommented produces said fault.
>>
>> - Jan
>>
>> On Wed, Jul 17, 2019, at 08:18, Jeff Newmiller wrote:
>> > It would never make sense for such messages to reflect normal and
>> expected operation, so hypothesizing about intentionally changing stack
>> behavior doesn't make sense.
>> >
>> > The default format for saveRDS changed in 3.6.0. There may be bugs
>> associated with that, but rolling back to 3.6.0 would just trade bugs.
>> >
>> > https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
>> >
>> > On July 16, 2019 8:56:28 PM CDT, Jan Galkowski
>> <bayesianlogi...@gmail.com> wrote:
>> > >Did something seriously change in R 3.6.1 at least for Windows in terms
>> > >of stack impacts?
>> > >
>> > >I'm encountering many problems with the 00UNLOCK, needing to disable
>> > >locking during installations.
>> > >
>> > >And I'm encountering
>> > >
>> > >> Error: C stack usage 63737888 is too close to the limit
>> > >
>> > >for cases I did not before, even when all I'm doing is serializing an
>> > >object to be saved with *saveRDS* or even *save.image(.)*.
>> > >
>> > >Yes, I know, I did not append a minimally complete example. Just wanted
>> > >to see if it was just me, or if anyone else was seeing this.
>> > >
>> > >It's on Windows 7 HE and I've run *R* here for years.
>> > >
>> > >My inclination is to drop back to 3.6.0 if it is just me or if no one
>> > >knows about this problem.
>> > >
>> > >Thanks,
>> > >
>> > > - Jan Galkowski.
>> [snip]
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