[R] pvclust crashing R on Ubuntu 10.10

[Ista Zahn]

I confirm this bug exists and is 100% replicable on

R version 2.12.2 (2011-02-25)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] pvclust_1.2-1

loaded via a namespace (and not attached):
[1] tools_2.12.2


interestingly, plot(x$hclust) works fine, which is strange because
this is the main function called by plot.pvclust (everything else just
looks like setting up labels and such).

HTH,
Ista








On Sat, Mar 5, 2011 at 4:15 AM, Stefan Th. Gries <stgries at gmail.com> wrote:
> Hi all
>
> I am writing to you with a question regarding the pvclust package. And
> yes, before the usual people produce their usual
> contact-the-package-maintainers line, ye, I tried that but the emails
> one can find on the web either bounce or are not responded to. Also,
> yes, this error has already been reported as a bug but been shot down
> as not reproducible
> (<http://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14430>). Thus,
> here's now the version that I can reproduce. When I run this:
>
> ###
> library(pvclust); data(iris)
> x <- pvclust(iris[,1:4], method.dist="canberra", method.hclust="ward",
> nboot=100)
> plot(x)
> ###
>
> I get this:
>
> ###
> address 0x7fffa22b5000, cause 'memory not mapped'
> ###
>
> Here is some info that might help:
>
> ###
> Ubuntu 10.10
> Linux kernel: 2.6.35-27 generic
>
>> R.version
> platform x86_64-pc-linux-gnu
> arch x86_64
> os linux-gnu
> system x86_64, linux-gnu
> status
> major 2
> minor 12.2
> year 2011
> month 02
> day 25
> svn rev 54585
> language R
> version.string R version 2.12.2 (2011-02-25)
> ###
>
> Paradoxically enough, R for Windows installed on this machine (running
> with Wine) causes no problems, but on Linux ... Any ideas what that
> could be?
>
> Thanks a lot,
> STG
> --
> Stefan Th. Gries
> -----------------------------------------------
> University of California, Santa Barbara
> http://www.linguistics.ucsb.edu/faculty/stgries
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org