[R] R 3.6.1 and apcluster package

[William Dunlap]

If you use version=3, ascii=TRUE and look at the file made up to the point
of the error, you can see a quasi-infinite repeat of a block of 165 numbers
(after a deferred string called "base"?).  Looks like inappropriate
recursion.

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Thu, Jul 18, 2019 at 7:38 AM William Dunlap <wdunlap using tibco.com> 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 <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
>> http://667-per-cm.net
>>
>> member,
>>
>> ... American Statistical Association
>> ... International Society for Bayesian Analysis
>> ... Ecological Society of America
>> ... International Association of Survey Statisticians
>> ... American Association for the Advancement of Science
>> ... TeX Users Group
>>
>> (pronouns: *he, him, his*)
>>
>> *Keep your energy local*. --John Farrell, *ILSR <http://ilsr.org/>*
>>
>>
>>         [[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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