Re: [Bioc-devel] Error: node stack overflow

Great, thanks! I was curious and did: hpages@spectre:~/svn/R/R-3-5-branch$ svn diff -r 74669:74674 src/library/methods/R/methodsTable.R Index: src/library/methods/R/methodsTable.R === --- src/library/methods/R/methodsTable.R

Re: [Bioc-devel] Error: node stack overflow

I just pushed it to the 3.5 branch. On Mon, Apr 30, 2018 at 2:14 PM, Hervé Pagès wrote: > Excellent! Are you planning to commit this to the 3.5 branch too? > In that case we'll wait a couple more days before installing R 3.5 > patched on the build machines for the BioC 3.8

Re: [Bioc-devel] Error: node stack overflow

Excellent! Are you planning to commit this to the 3.5 branch too? In that case we'll wait a couple more days before installing R 3.5 patched on the build machines for the BioC 3.8 builds. Thanks, H. On 04/30/2018 01:43 PM, Michael Lawrence wrote: It's checked into devel now. Thanks for the

Re: [Bioc-devel] Error: node stack overflow

It's checked into devel now. Thanks for the well documented examples, Hervé. On Mon, Apr 30, 2018 at 10:26 AM, Michael Lawrence wrote: > I've fixed it and will push to R-devel as soon as it passes checks. > > Michael > > On Sun, Apr 29, 2018 at 9:04 PM, Michael Lawrence

Re: [Bioc-devel] Error: node stack overflow

I've fixed it and will push to R-devel as soon as it passes checks. Michael On Sun, Apr 29, 2018 at 9:04 PM, Michael Lawrence wrote: > Just noticed this thread. I will look into this and hopefully fix it. > > On Sun, Apr 29, 2018 at 6:12 PM, Hervé Pagès

Re: [Bioc-devel] Error: node stack overflow

Hi, I made progress on this. This has actually nothing to do with Java. You get the same thing with the flexmix package. What rJava and flexmix have in common is that they both define a method on the base::unique() implicit S4 generic. The issue actually originates in the methods package. In

Re: [Bioc-devel] Error: node stack overflow

Hi Zheng, I can totally reproduce this on my Ubuntu laptop: library(rJava) library(IRanges) unique(IRanges()) # Error in validObject(.Object) : # invalid class “MethodWithNext” object: Error : C stack usage 7969396 is too close to the limit See my seesionInfo() at the end of this

Re: [Bioc-devel] Error: node stack overflow

I get the following on MacOSX, after library(rJava); library(GenomicRanges) -- take rJava out of the mix and there is no error. I ran into this originally as an interaction between rJava and Gviz, and have reported to Florian. That seemed to be MacOSX-specific. > gr1 <-

Re: [Bioc-devel] Error: node stack overflow

Hi Zheng, Thanks for the report. I will look into this and will let you know. H. On 04/01/2018 02:38 AM, Zheng Wei wrote: Dear all, I find this error if calling library(rJava) before using BiocGenerics::unique The code is pasted below. Thanks, Zheng > library(rJava) >