[R] R 3.6.1 and apcluster package

[Jan Galkowski]

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 <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.
>>  [snip]

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