Re: [R] plot.hclust point to older version
Hm -Original Message- From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us] Sent: Wednesday, November 26, 2014 8:09 PM To: PIKAL Petr; Martin Maechler Cc: R help Subject: Re: [R] plot.hclust point to older version Short answer to your question is R files and original data from external sources. I tend to keep my projects in separate directories. I make a core R I do the same. file that I can run from beginning to end using source() to generate my primary analysis objects. I then make another file to keep my source() function call in, as well as a few exploratory plot commands. Recently I have been also sourcing the analysis script in Rmd or Rnw files to knit my observations with the output. Some people complain that their analysis takes too long to be sourcing it all the time. When I have that problem I set up a variable outside my analysis script that I test in my analysis script. If the variable indicates it is time to recalculate, then I do all of that and then save the data in sn rds or rda file. If the variable indicates that I should reuse the cached data, then it skips the calculations and just loads the data. This way I always load the right libraries along with the data, and I don't accidentally save data that I changed outside the analysis script... keeping my results reproducible. (Rds files can be convenient if I have several different slow analyses to compare and I want to only work on one at a time. I set up one control variable for each analysis.) Some people (smarter than me?) like to build their analysis into an Sweave or knitr file. They can then strip out an analysis R file to use the way I have described if they choose to do so (literate programming) but I have not picked up that habit yet. The key is keeping a record of how every object that is in your save file was originally created. If you tolerate auto saving and loading of the environment then you lose that record, and pernicious errors can Not exactly. All commands are saved in .Rhistory, which from time to time I rename and keep for further use. And sometimes I also make a separate file with commands used, especially when I am at the end of my work on a project. creep into your environment from who knows where, and you might as well be using Excel if that is how you work. (Note that this means I hardly ever copy data straight from Excel via the clipboard as that is not reproducible. Usually this means Save As CSV in Excel to start my R analysis if that is the data source.) As I understand you do more sophisticated version what I am doing. The key is to keep projects in separate directories and do not polute them with unrelated objects. The problem in my way is when I accidentaly destroy an object and I need to restore it, which can sometimes be tedious work. OTOH it keeps me focused on what I am doing :-) Anyway, I shall consider save and saveRDS to keep copy of important objects outside .RData environment, if something went wrong. Thanks for idea. Best regards. Petr --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On November 26, 2014 2:05:54 AM PST, PIKAL Petr petr.pi...@precheza.cz wrote: 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 Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či
Re: [R] plot.hclust point to older version
PP == PIKAL Petr petr.pi...@precheza.cz
on Thu, 27 Nov 2014 13:40:36 + writes:
PP Hm
-Original Message-
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
Sent: Wednesday, November 26, 2014 8:09 PM
To: PIKAL Petr; Martin Maechler
Cc: R help
Subject: Re: [R] plot.hclust point to older version
Short answer to your question is R files and original data from
external sources.
I tend to keep my projects in separate directories. I make a core R
PP I do the same.
file that I can run from beginning to end using source() to generate my
primary analysis objects. I then make another file to keep my source()
function call in, as well as a few exploratory plot commands. Recently
I have been also sourcing the analysis script in Rmd or Rnw files to
knit my observations with the output.
Some people complain that their analysis takes too long to be sourcing
it all the time. When I have that problem I set up a variable outside
my analysis script that I test in my analysis script. If the variable
indicates it is time to recalculate, then I do all of that and then
save the data in sn rds or rda file. If the variable indicates that I
should reuse the cached data, then it skips the calculations and just
loads the data. This way I always load the right libraries along with
the data, and I don't accidentally save data that I changed outside the
analysis script... keeping my results reproducible. (Rds files can be
convenient if I have several different slow analyses to compare and I
want to only work on one at a time. I set up one control variable for
each analysis.)
Some people (smarter than me?) like to build their analysis into an
Sweave or knitr file. They can then strip out an analysis R file to use
the way I have described if they choose to do so (literate
programming) but I have not picked up that habit yet.
I do that occasionally, but in much less than in 50% of my R hacking
The key is keeping a record of how every object that is in your save
file was originally created. If you tolerate auto saving and loading of
the environment then you lose that record, and pernicious errors can
PP Not exactly. All commands are saved in .Rhistory, which from time to
time I rename and keep for further use. And sometimes I also make a separate
file with commands used, especially when I am at the end of my work on a
project.
Huaah Of course real useRs don't use .Rhistory either !
As Jeff says: Use name.R files - often more than one per
project.
And I did not say one should not use save() and load() or the
*.rds equivalent which is preferable but I still did not get
into the full habit of using... one reason is the mismatch of
saveRDS() and readRDS() {where as write - read; or save -
load are the natural word pairs for me}.
So, yes, Jeff indeed is one of the real useRs .. in my sense ;-)
creep into your environment from who knows where, and you might as well
be using Excel if that is how you work. (Note that this means I hardly
ever copy data straight from Excel via the clipboard as that is not
reproducible. Usually this means Save As CSV in Excel to start my R
analysis if that is the data source.)
PP As I understand you do more sophisticated version what I am doing. The
key is to keep projects in separate directories and do not polute them with
unrelated objects. The problem in my way is when I accidentaly destroy an
object and I need to restore it, which can sometimes be tedious work. OTOH it
keeps me focused on what I am doing :-)
PP Anyway, I shall consider save and saveRDS to keep copy of important
objects outside .RData environment, if something went wrong.
PP Thanks for idea.
Once you become careful about that and organizing your *.R files
which keep the project 100% reproducible you may start to
see that using .RData is just a hindrance for the discipline of
reproducible { research / data analysis / computational experiments }
using R...
Yes, I'm not sounding very nice, above... Sorry, please apologize.
Martin
PP Best regards.
PP Petr
---
Jeff NewmillerThe . . Go
Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live
Go...
Live: OO#.. Dead: OO#..
Playing
Research Engineer (Solar/BatteriesO.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#.
rocks...1k
---
Sent from my phone. Please excuse my brevity.
On November 26, 2014 2:05:54 AM PST, PIKAL Petr
petr.pi...@precheza.cz wrote:
Hi
You
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.comhttp://tibco.com
On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner
r.tur...@auckland.ac.nzmailto:r.tur...@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.tur...@auckland.ac.nzmailto:r.tur...@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@r-project.orgmailto:R-help@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.
--CONFIDENTIALITY NOTICE--: The information contained in this email is
intended for the exclusive use of the addressee and may contain confidential
information. If you are not the intended recipient, you are hereby notified
that any form of dissemination of this communication is strictly prohibited.
www.benaroyaresearch.org
[[alternative HTML version deleted]]
__
R-help@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.
__
R-help@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.
Re: [R] plot.hclust point to older version
into their ~/.emacs
{and I'd like to see a way to do this easily with RStudio...}
In RStudio:
Tools - Global Options - General - uncheck Restore .RData into
workspace at startup and choose Never for Save workspace to .RData
on exit
--
Pascal Oettli
Project Scientist
JAMSTEC
Yokohama, Japan
__
R-help@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.
Re: [R] plot.hclust point to older version
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-boun...@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.comhttp://tibco.com
On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner
r.tur...@auckland.ac.nzmailto:r.tur...@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.tur...@auckland.ac.nzmailto:r.tur...@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@r-project.orgmailto:R-help@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.
--CONFIDENTIALITY NOTICE--: The information contained in this email
is
intended for the exclusive use of the addressee and may contain
confidential information. If you
Re: [R] plot.hclust point to older version
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.)
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Wed, Nov 26, 2014 at 1:02 AM, Martin Maechler maech...@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.comhttp://tibco.com
On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner r.tur...@auckland.ac.nz
mailto:r.tur...@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.tur...@auckland.ac.nzmailto:
r.tur...@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@r-project.orgmailto:R-help@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.
--CONFIDENTIALITY NOTICE--: The information contained in this email is
intended for the exclusive use of the addressee and may contain
confidential information. If you are not the intended recipient, you are
hereby notified that any form of dissemination of this communication is
strictly prohibited. www.benaroyaresearch.org
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
Re: [R] plot.hclust point to older version
Short answer to your question is R files and original data from external sources. I tend to keep my projects in separate directories. I make a core R file that I can run from beginning to end using source() to generate my primary analysis objects. I then make another file to keep my source() function call in, as well as a few exploratory plot commands. Recently I have been also sourcing the analysis script in Rmd or Rnw files to knit my observations with the output. Some people complain that their analysis takes too long to be sourcing it all the time. When I have that problem I set up a variable outside my analysis script that I test in my analysis script. If the variable indicates it is time to recalculate, then I do all of that and then save the data in sn rds or rda file. If the variable indicates that I should reuse the cached data, then it skips the calculations and just loads the data. This way I always load the right libraries along with the data, and I don't accidentally save data that I changed outside the analysis script... keeping my results reproducible. (Rds files can be convenient if I have several different slow analyses to compare and I want to only work on one at a time. I set up one control variable for each analysis.) Some people (smarter than me?) like to build their analysis into an Sweave or knitr file. They can then strip out an analysis R file to use the way I have described if they choose to do so (literate programming) but I have not picked up that habit yet. The key is keeping a record of how every object that is in your save file was originally created. If you tolerate auto saving and loading of the environment then you lose that record, and pernicious errors can creep into your environment from who knows where, and you might as well be using Excel if that is how you work. (Note that this means I hardly ever copy data straight from Excel via the clipboard as that is not reproducible. Usually this means Save As CSV in Excel to start my R analysis if that is the data source.) --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On November 26, 2014 2:05:54 AM PST, PIKAL Petr petr.pi...@precheza.cz wrote: 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-boun...@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
Re: [R] plot.hclust point to older version
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 maech...@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.comhttp://tibco.com
On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner r.tur...@auckland.ac.nz
mailto:r.tur...@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.tur...@auckland.ac.nzmailto:
r.tur...@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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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [R] plot.hclust point to older version
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. -- Rolf Turner Technical Editor ANZJS __ R-help@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.
Re: [R] plot.hclust point to older version
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.tur...@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@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.
Re: [R] plot.hclust point to older version
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. Bill Dunlap TIBCO Software wdunlap tibco.com On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner r.tur...@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.tur...@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@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. [[alternative HTML version deleted]] __ R-help@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.
Re: [R] plot.hclust point to older version
Thanks! That worked From: William Dunlap wdun...@tibco.commailto:wdun...@tibco.com Date: Tuesday, November 25, 2014 12:53 PM To: Rolf Turner r.tur...@auckland.ac.nzmailto:r.tur...@auckland.ac.nz Cc: Michael Mason mma...@benaroyaresearch.orgmailto:mma...@benaroyaresearch.org, R help R-help@r-project.orgmailto:R-help@r-project.org Subject: Re: [R] plot.hclust point to older version 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. Bill Dunlap TIBCO Software wdunlap tibco.comhttp://tibco.com On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner r.tur...@auckland.ac.nzmailto:r.tur...@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.tur...@auckland.ac.nzmailto:r.tur...@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@r-project.orgmailto:R-help@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. --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org [[alternative HTML version deleted]] __ R-help@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.
