[R] plot.hclust point to older version

[Martin Maechler]

> Thanks! That worked

Of course: As in about 99.99% of all cases where Bill Dunlap  helps.


> You probably have a local copy of an old version of plot.hclust or plot.dendrogram in your global environmenet or another package that masks the one in package:stats.  E.g., I fired up R-2.14.2 and copied those 2 plot methods to .GlobalEnv and then saved by workspace when quitting R.  I then fired up R-3.1.1, which loads the workspace saved by the older version of R.  I get:

> > objects()
> [1] "plot.dendrogram" "plot.hclust"
> > plot(hclust(dist(c(2,3,5,7,11,13,17,19))))
> Error in .Internal(dend.window(n, merge, height, hang, labels, ...)) :
>   there is no .Internal function 'dend.window'
> > traceback()
> 2: plot.hclust(hclust(dist(c(2, 3, 5, 7, 11, 13, 17, 19))))
> 1: plot(hclust(dist(c(2, 3, 5, 7, 11, 13, 17, 19))))

> Note how calling traceback() after an error gives more information about the source of the error.

> To fix this, get rid of the .RData file that is being loaded when R starts.

In the spirit of the old -- now politically incorrect -- sayings
 `` Real men don't ..... '''
I'd like to emphasize my own view that
 "Real useRs don't use .RData"

in other words, experienced R users do not let their workspace
be saved automatically (to '.RData') and hence do not load any
.RData automatically at startup.

Consequently, use R with the '--no-save' command line argument
(maybe also with '--no-restore').

ESS (Emacs Speaks Statistics) users can put

(custom-set-variables
 '(inferior-R-args "--no-restore-history --no-save ")
)

into their ~/.emacs
{and I'd like to see a way to do this easily with RStudio...}

Martin Maechler,
ETH Zurich and R Core Team 

> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com<http://tibco.com>

> On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner <r.turner at auckland.ac.nz<mailto:r.turner at auckland.ac.nz>> wrote:
> On 26/11/14 08:53, Michael Mason wrote:
> Here you are. I expect most folks won't get the error.

> N   = 100; M = 1000
> mat = matrix(1:(N*M) + rnorm(N*M,0,.5),N,M)
> h   = hclust(as.dist(1-cor(mat)))
> plot(h)

> Error in .Internal(dend.window(n, merge, height2, hang, labels, ...)) :
>    there is no .Internal function 'dend.window'



> Thanks again


> On 11/25/14 11:29 AM, "Rolf Turner" <r.turner at auckland.ac.nz<mailto:r.turner at auckland.ac.nz>> wrote:



> Reproducible example???

> (I know from noddink about hclust, but I tried the example from the help
> page and it plotted without any problem.)

> cheers,

> Rolf Turner

> On 26/11/14 06:13, Michael Mason wrote:
> Hello fellow R users,

> I have recently updated to R 3.1.2. When trying to plot an hclust
> object to generate the dendrogram I get the following error:

> Error in .Internal(dend.window(n, merge, height2, hang, labels, ...)) :
>     there is no .Internal function 'dend.window'


> I am indeed using R3.1.2 but my understanding is that the .Internal API
> to the C code is no longer used. I have tried detaching the stats
> package and restarting R to no avail.
> I would love any help from any wiser guRus.

> Please keep communications on-list; there are others on the list far more likely to be able to help you than I.  I am cc-ing this reply to the list.

> For what it's worth, I can run your example without error.

> As to how to track down what is going wrong on your system, I'm afraid I have no idea.  Someone on the list may have some thoughts.

> cheers,

> Rolf Turner

> --
> Rolf Turner
> Technical Editor ANZJS

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