plot.hclust point to older version

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plot.hclust point to older version

Michael Mason
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.
Thanks in advance,
Mike
________________________________
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Re: plot.hclust point to older version

Rolf Turner


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

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, reproducible code.
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Re: plot.hclust point to older version

Rolf Turner
In reply to this post by Michael Mason
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" <[hidden email]> 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

______________________________________________
[hidden email] 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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Re: plot.hclust point to older version

William Dunlap
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 <[hidden email]>
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" <[hidden email]> 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
>
> ______________________________________________
> [hidden email] 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]]

______________________________________________
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Re: plot.hclust point to older version

Michael Mason
Thanks! That worked

From: William Dunlap <[hidden email]<mailto:[hidden email]>>
Date: Tuesday, November 25, 2014 12:53 PM
To: Rolf Turner <[hidden email]<mailto:[hidden email]>>
Cc: Michael Mason <[hidden email]<mailto:[hidden email]>>, R help <[hidden email]<mailto:[hidden email]>>
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.com<http://tibco.com>

On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner <[hidden email]<mailto:[hidden email]>> 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" <[hidden email]<mailto:[hidden email]>> 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

______________________________________________
[hidden email]<mailto:[hidden email]> 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]]

______________________________________________
[hidden email] 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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Re: 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 <[hidden email]<mailto:[hidden email]>> 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" <[hidden email]<mailto:[hidden email]>> 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

> ______________________________________________
> [hidden email]<mailto:[hidden email]> 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]]

> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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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Re: plot.hclust point to older version

Pascal Oettli-2
> 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

______________________________________________
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https://stat.ethz.ch/mailman/listinfo/r-help
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Re: plot.hclust point to older version

PIKAL Petr
In reply to this post by Martin Maechler
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:[hidden email]] 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
> <[hidden email]<mailto:[hidden email]>> 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"
> <[hidden email]<mailto:[hidden email]>> 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
>
> > ______________________________________________
> > [hidden email]<mailto:[hidden email]> 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]]
>
> > ______________________________________________
> > [hidden email] 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.
>
> ______________________________________________
> [hidden email] 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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- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá.

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Re: plot.hclust point to older version

William Dunlap
In reply to this post by Martin Maechler
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 <[hidden email]
> 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 <[hidden email]
> <mailto:[hidden email]>> 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" <[hidden email]<mailto:
> [hidden email]>> 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
>
> > ______________________________________________
> > [hidden email]<mailto:[hidden email]> 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]]
>
> > ______________________________________________
> > [hidden email] 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]]

______________________________________________
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Re: plot.hclust point to older version

Jeff Newmiller
In reply to this post by PIKAL Petr
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 Newmiller                        The     .....       .....  Go Live...
DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
                                      Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/Batteries            O.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 <[hidden email]> 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:[hidden email]] 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
>> <[hidden email]<mailto:[hidden email]>> 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"
>> <[hidden email]<mailto:[hidden email]>> 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
>>
>> > ______________________________________________
>> > [hidden email]<mailto:[hidden email]> 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]]
>>
>> > ______________________________________________
>> > [hidden email] 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.
>>
>> ______________________________________________
>> [hidden email] 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.
>
>________________________________
>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 zpožděním přenosu e-mailu.
>
>V případě, že je tento e-mail součástí obchodního jednání:
>- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření
>smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu.
>- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně
>přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky
>ze strany příjemce s dodatkem či odchylkou.
>- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve
>výslovným dosažením shody na všech jejích náležitostech.
>- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za
>společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně
>zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly
>adresátovi tohoto emailu případně osobě, kterou adresát zastupuje,
>předloženy nebo jejich existence je adresátovi či osobě jím zastoupené
>známá.
>
>This e-mail and any documents attached to it may be confidential and
>are intended only for its intended recipients.
>If you received this e-mail by mistake, please immediately inform its
>sender. Delete the contents of this e-mail with all attachments and its
>copies from your system.
>If you are not the intended recipient of this e-mail, you are not
>authorized to use, disseminate, copy or disclose this e-mail in any
>manner.
>The sender of this e-mail shall not be liable for any possible damage
>caused by modifications of the e-mail or by delay with transfer of the
>email.
>
>In case that this e-mail forms part of business dealings:
>- the sender reserves the right to end negotiations about entering into
>a contract in any time, for any reason, and without stating any
>reasoning.
>- if the e-mail contains an offer, the recipient is entitled to
>immediately accept such offer; The sender of this e-mail (offer)
>excludes any acceptance of the offer on the part of the recipient
>containing any amendment or variation.
>- the sender insists on that the respective contract is concluded only
>upon an express mutual agreement on all its aspects.
>- the sender of this e-mail informs that he/she is not authorized to
>enter into any contracts on behalf of the company except for cases in
>which he/she is expressly authorized to do so in writing, and such
>authorization or power of attorney is submitted to the recipient or the
>person represented by the recipient, or the existence of such
>authorization is known to the recipient of the person represented by
>the recipient.
>______________________________________________
>[hidden email] 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.

______________________________________________
[hidden email] 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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Re: plot.hclust point to older version

David Winsemius
In reply to this post by William Dunlap

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 <[hidden email]
>> 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 <[hidden email]
>> <mailto:[hidden email]>> 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" <[hidden email]<mailto:
>> [hidden email]>> 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
>>
>>> ______________________________________________
>>> [hidden email]<mailto:[hidden email]> 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]]
>>
>>> ______________________________________________
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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.
>>
>
> [[alternative HTML version deleted]]
>
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> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

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Re: plot.hclust point to older version

PIKAL Petr
In reply to this post by Jeff Newmiller
Hm

> -----Original Message-----
> From: Jeff Newmiller [mailto:[hidden email]]
> 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 Newmiller                        The     .....       .....  Go
> Live...
> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live
> Go...
>                                       Live:   OO#.. Dead: OO#..
> Playing
> Research Engineer (Solar/Batteries            O.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
> <[hidden email]> 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


________________________________
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This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients.
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The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email.

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Re: plot.hclust point to older version

Martin Maechler
>>>>> "PP" == PIKAL Petr <[hidden email]>
>>>>>     on Thu, 27 Nov 2014 13:40:36 +0000 writes:

    PP> Hm
    >> -----Original Message-----
    >> From: Jeff Newmiller [mailto:[hidden email]]
    >> 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 Newmiller                        The     .....       .....  Go
    >> Live...
    >> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live
    >> Go...
    >> Live:   OO#.. Dead: OO#..
    >> Playing
    >> Research Engineer (Solar/Batteries            O.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
    >> <[hidden email]> 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


    PP> ________________________________
    PP> Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům.
    PP> 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.
    PP> Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
    PP> Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu.

    PP> V případě, že je tento e-mail součástí obchodního jednání:
    PP> - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu.
    PP> - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou.
    PP> - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech.
    PP> - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá.

    PP> This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients.
    PP> If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system.
    PP> If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner.
    PP> The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email.

    PP> In case that this e-mail forms part of business dealings:
    PP> - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning.
    PP> - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation.
    PP> - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects.
    PP> - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient.
    PP> ______________________________________________
    PP> [hidden email] mailing list
    PP> https://stat.ethz.ch/mailman/listinfo/r-help
    PP> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    PP> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
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