[R] plot.hclust point to older version

PIKAL Petr
2014-11-26T10:05:54Z

Hi

You say

> 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.

I save/load .RData for years without any issues (except of not installed
packages when working on different PCs).I usually keep each project in separated
.RData (and separated folder, together with all stuff belonging to that
project), which prevent to mess things together.

There is no such warning as "do not use .RData" in books I have
available.

I wonder how experienced useR keep track of several projects without using
startup loading .RData?
What would you recommend for keeping track of commands and created objects
instead of .RData?

Petr


> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Martin
> Maechler
> Sent: Wednesday, November 26, 2014 10:03 AM
> To: Michael Mason
> Cc: R help
> Subject: Re: [R] plot.hclust point to older version
>
>
> > 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
>
> > ______________________________________________
> > R-help at r-project.org<mailto:R-help at r-project.org> mailing
list
> > 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.
>
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> ______________________________________________
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