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 <wdun...@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 <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. >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> ______________________________________________ >>>>> R-help@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] >>> >>> bayesianlogi...@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@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@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-tier...@uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu ______________________________________________ R-help@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.