From bmbroom at gmail.com  Mon Mar  6 13:55:35 2017
From: bmbroom at gmail.com (Bradley Broom)
Date: Mon, 6 Mar 2017 06:55:35 -0600
Subject: [Rd] Please add me to bugzilla
In-Reply-To: <22717.12500.568807.583249@stat.math.ethz.ch>
References: <CACCRr6GzeBhOQMNKwNRMwkirP3BH2SXnrim=fRM6Ydryds=Ang@mail.gmail.com>
	<22717.12500.568807.583249@stat.math.ethz.ch>
Message-ID: <CACCRr6HKe-Niv6v_DqFmGvwj5DDQY+sYXQM=BMYRMRtNwbNnzQ@mail.gmail.com>

Apologies, I thought I was following exactly that sentence and trying to
make a minimal post that would waste as little developer bandwidth as
possible given the lack of a better system.

Anyway, I have been using R for like forever (20 years).

In my current project, I have run into problems with stack overflows in R's
dendrogram code when trying to use either str() or as.hclust() on very deep
dendrograms.

To duplicate, use this function from tests/reg-tests-1c.R in the R source
code:
mkDend <- function(n, lab, method = "complete",
                   ## gives *ties* often:
                   rGen = function(n) 1+round(16*abs(rnorm(n)))) {
    stopifnot(is.numeric(n), length(n) == 1, n >= 1, is.character(lab))
    a <- matrix(rGen(n*n), n, n)
    colnames(a) <- rownames(a) <- paste0(lab, 1:n)
    .HC. <<- hclust(as.dist(a + t(a)), method=method)
    as.dendrogram(.HC.)
}

Get a nasty dendrogram:

de <- mkDend(2000, 'x', 'single')

1st bug:
sink('somefile.txt'); str(de); sink();

What happens:
Error in getOption("OutDec") : node stack overflow

Also, the last call to sink() isn't executed because of the error, so
you'll need to call sink() after the error to clear the diversion.

What should happen:
Function completes without a stack overflow.

2nd bug:
hh <- as.hclust(de)

What happens:
Error: C stack usage  7971248 is too close to the limit

What should happen:
Function completes without a stack overflow.

A knowledgeable user might be able to increase R's limits to avoid these
errors on this particular dendrogram, but a) my users aren't that
knowledgeable about R and this is expected to be a common problem, and b)
there will be bigger dendrograms (up to at least 25000 leaves).

Please see attached patch for non-recursive implementations.

Regards,
Bradley



On Mon, Mar 6, 2017 at 3:50 AM, Martin Maechler <maechler at stat.math.ethz.ch>
wrote:

> >>>>> Bradley Broom <bmbroom at gmail.com>
> >>>>>     on Sun, 5 Mar 2017 16:03:30 -0600 writes:
>
>     > Please add me to R bugzilla.  Thanks, Bradley
>
> Well, I will not do it just like that (mean "after such a
> minimal message").
>
> I don't see any evidence as to your credentials, knowledge of R,
> etc, as part of this request.  We are all professionals,
> devoting part of our (work and free) time to the R project
> (rather than employees of the company you paid to serve you ...)
>
> It may be that you have read   https://www.r-project.org/bugs.html
>
> Notably this part
>
> --> NOTE: due to abuse by spammers, since 2016-07-09 only users who have
> previously submitted bugs can submit new ones on R?s Bugzilla. We?re
> working on a better system? In the mean time, post (e-mail) to R-devel or
> ask an R Core member to add you manually to R?s Bugzilla members.
>
> The last sentence was *meant* to say you should post (possibly
> parts, ideally a minimal reproducible example of) your bug
> report to R-devel so others could comment on it, agree or
> disagree with your assessment etc,
> __or__ ask an R-core member to add you to bugzilla (if you really read the
> other parts of the 'R bugs' web page above).
>
> Posting to all 1000 R-devel readers with no content about what
> you consider a bug  is a waste of bandwidth for at least 99% of
> these readers.
>
> [Yes, I'm also using their time ... in the hope to *improve* the
>  quality of future such postings].
>
> Martin Maechler
> ETH Zurich
>
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[Rd] Please add me to bugzilla
Bradley Broom