[R] [External] Re: R 3.6.1 and apcluster package

Thu Jul 18 17:36:18 CEST 2019

Something about the deferred string conversion object in

a <- names(attributes(apresX)[[4]][[1]][[1]])

is malformed; .Internal(inspect(a)) also infinite loops.
Will try to narrow this down.

Best,

luke

On Thu, 18 Jul 2019, William Dunlap via R-help wrote:

> 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.
>>>
>>
>
> 	[[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.
>

-- 
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 using uiowa.edu
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