[R] plot.hclust point to older version

Wed Nov 26 20:26:19 CET 2014

On Nov 26, 2014, at 9:49 AM, William Dunlap wrote:

> How disruptive would it be if R were changed so the startup line
>   [Previously saved workspace restored]
> were changed to show the complete name, from normalizePath(), of the
> saved workspace file?  E.g.,
>   [Previously saved workspace restored from 'C:\Program Files\R\.RData']
> 
> (It is bad enough that the file name starts with a dot so it is hidden from
> 'ls',
> but on Windows lots of people don't know what directory R is starting in.
> On
> my Windows PC R-3.1.2 starts in C:/Program Files/R, the parent of its RHOME
> directory.)

On the Mac Gui that happens with no effort as well as a message saying where the GUI history file resides. I just checked my .Rprofile file to make sure it wasn't doing that. I also have a line that prints the data and time:

utils:::timestamp(stamp = Sys.Date() )

Couldn't you just create a template .Rprofile with the appropriate message printed to console?

-- 
david.
> 
> 
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
> 
> On Wed, Nov 26, 2014 at 1:02 AM, Martin Maechler <maechler at stat.math.ethz.ch
>> wrote:
> 
>> 
>>> 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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> ______________________________________________
> 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.

David Winsemius
Alameda, CA, USA