[R] R 3.6.1 and apcluster package

[William Dunlap]

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 <bayesianlogic.1 using 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 <
> bayesianlogic.1 using 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.
> > >
> > >
> > > [[alternative HTML version deleted]]
> > >
> > >______________________________________________
> > >R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > >https://stat.ethz.ch/mailman/listinfo/r-help
> > >PLEASE do read the posting guide
> > >http://www.R-project.org/posting-guide.html
> > >and provide commented, minimal, self-contained, reproducible code.
> >
> > --
> > Sent from my phone. Please excuse my brevity.
> >
>
> --
> Jan Galkowski (o°)
>
> 607.239.1834 [mobile]
> 607.239.1834 [home]
>
> bayesianlogic.1 using gmail.com
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>
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>
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>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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