Thanks! That worked From: William Dunlap <wdunlap at tibco.com<mailto:wdunlap at tibco.com>> Date: Tuesday, November 25, 2014 12:53 PM To: Rolf Turner <r.turner at auckland.ac.nz<mailto:r.turner at auckland.ac.nz>> Cc: Michael Mason <mmason at benaroyaresearch.org<mailto:mmason at benaroyaresearch.org>>, R help <R-help at r-project.org<mailto:R-help at 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.com<http://tibco.com> On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner <r.turner at auckland.ac.nz<mailto:r.turner at auckland.ac.nz>> wrote: On 26/11/14 08:53, Michael Mason wrote: Here you are. I expect most folks won't get the error. N = 100; M = 1000 mat = matrix(1:(N*M) + rnorm(N*M,0,.5),N,M) h = hclust(as.dist(1-cor(mat))) plot(h) Error in .Internal(dend.window(n, merge, height2, hang, labels, ...)) : there is no .Internal function 'dend.window' Thanks again On 11/25/14 11:29 AM, "Rolf Turner" <r.turner at auckland.ac.nz<mailto:r.turner at auckland.ac.nz>> wrote: Reproducible example??? (I know from noddink about hclust, but I tried the example from the help page and it plotted without any problem.) cheers, Rolf Turner On 26/11/14 06:13, Michael Mason wrote: Hello fellow R users, I have recently updated to R 3.1.2. When trying to plot an hclust object to generate the dendrogram I get the following error: Error in .Internal(dend.window(n, merge, height2, hang, labels, ...)) : there is no .Internal function 'dend.window' I am indeed using R3.1.2 but my understanding is that the .Internal API to the C code is no longer used. I have tried detaching the stats package and restarting R to no avail. I would love any help from any wiser guRus. Please keep communications on-list; there are others on the list far more likely to be able to help you than I. I am cc-ing this reply to the list. For what it's worth, I can run your example without error. As to how to track down what is going wrong on your system, I'm afraid I have no idea. Someone on the list may have some thoughts. cheers, Rolf Turner -- Rolf Turner Technical Editor ANZJS ______________________________________________ R-help at r-project.org<mailto:R-help at r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ________________________________ --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]]
> Thanks! That workedOf course: As in about 99.99% of all cases where Bill Dunlap helps.> You probably have a local copy of an old version of plot.hclust or plot.dendrogram in your global environmenet or another package that masks the one in package:stats. E.g., I fired up R-2.14.2 and copied those 2 plot methods to .GlobalEnv and then saved by workspace when quitting R. I then fired up R-3.1.1, which loads the workspace saved by the older version of R. I get:> > objects() > [1] "plot.dendrogram" "plot.hclust" > > plot(hclust(dist(c(2,3,5,7,11,13,17,19)))) > Error in .Internal(dend.window(n, merge, height, hang, labels, ...)) : > there is no .Internal function 'dend.window' > > traceback() > 2: plot.hclust(hclust(dist(c(2, 3, 5, 7, 11, 13, 17, 19)))) > 1: plot(hclust(dist(c(2, 3, 5, 7, 11, 13, 17, 19))))> Note how calling traceback() after an error gives more information about the source of the error.> To fix this, get rid of the .RData file that is being loaded when R starts.In the spirit of the old -- now politically incorrect -- sayings `` Real men don't ..... ''' I'd like to emphasize my own view that "Real useRs don't use .RData" in other words, experienced R users do not let their workspace be saved automatically (to '.RData') and hence do not load any .RData automatically at startup. Consequently, use R with the '--no-save' command line argument (maybe also with '--no-restore'). ESS (Emacs Speaks Statistics) users can put (custom-set-variables '(inferior-R-args "--no-restore-history --no-save ") ) into their ~/.emacs {and I'd like to see a way to do this easily with RStudio...} Martin Maechler, ETH Zurich and R Core Team> Bill Dunlap > TIBCO Software > wdunlap tibco.com<http://tibco.com>> On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner <r.turner at auckland.ac.nz<mailto:r.turner at auckland.ac.nz>> wrote: > On 26/11/14 08:53, Michael Mason wrote: > Here you are. I expect most folks won't get the error.> N = 100; M = 1000 > mat = matrix(1:(N*M) + rnorm(N*M,0,.5),N,M) > h = hclust(as.dist(1-cor(mat))) > plot(h)> Error in .Internal(dend.window(n, merge, height2, hang, labels, ...)) : > there is no .Internal function 'dend.window'> Thanks again> On 11/25/14 11:29 AM, "Rolf Turner" <r.turner at auckland.ac.nz<mailto:r.turner at auckland.ac.nz>> wrote:> Reproducible example???> (I know from noddink about hclust, but I tried the example from the help > page and it plotted without any problem.)> cheers,> Rolf Turner> On 26/11/14 06:13, Michael Mason wrote: > Hello fellow R users,> I have recently updated to R 3.1.2. When trying to plot an hclust > object to generate the dendrogram I get the following error:> Error in .Internal(dend.window(n, merge, height2, hang, labels, ...)) : > there is no .Internal function 'dend.window'> I am indeed using R3.1.2 but my understanding is that the .Internal API > to the C code is no longer used. I have tried detaching the stats > package and restarting R to no avail. > I would love any help from any wiser guRus.> Please keep communications on-list; there are others on the list far more likely to be able to help you than I. I am cc-ing this reply to the list.> For what it's worth, I can run your example without error.> As to how to track down what is going wrong on your system, I'm afraid I have no idea. Someone on the list may have some thoughts.> cheers,> Rolf Turner> -- > Rolf Turner > Technical Editor ANZJS> ______________________________________________ > R-help at r-project.org<mailto:R-help at r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.> ________________________________ > --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 at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
> 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
Hi You say> in other words, experienced R users do not let their workspace be saved > automatically (to '.RData') and hence do not load any .RData > automatically at startup.I save/load .RData for years without any issues (except of not installed packages when working on different PCs).I usually keep each project in separated .RData (and separated folder, together with all stuff belonging to that project), which prevent to mess things together. There is no such warning as "do not use .RData" in books I have available. I wonder how experienced useR keep track of several projects without using startup loading .RData? What would you recommend for keeping track of commands and created objects instead of .RData? Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Martin > Maechler > Sent: Wednesday, November 26, 2014 10:03 AM > To: Michael Mason > Cc: R help > Subject: Re: [R] plot.hclust point to older version > > > > Thanks! That worked > > Of course: As in about 99.99% of all cases where Bill Dunlap helps. > > > > You probably have a local copy of an old version of plot.hclust or > plot.dendrogram in your global environmenet or another package that > masks the one in package:stats. E.g., I fired up R-2.14.2 and copied > those 2 plot methods to .GlobalEnv and then saved by workspace when > quitting R. I then fired up R-3.1.1, which loads the workspace saved > by the older version of R. I get: > > > > objects() > > [1] "plot.dendrogram" "plot.hclust" > > > plot(hclust(dist(c(2,3,5,7,11,13,17,19)))) > > Error in .Internal(dend.window(n, merge, height, hang, labels, ...)) > : > > there is no .Internal function 'dend.window' > > > traceback() > > 2: plot.hclust(hclust(dist(c(2, 3, 5, 7, 11, 13, 17, 19)))) > > 1: plot(hclust(dist(c(2, 3, 5, 7, 11, 13, 17, 19)))) > > > Note how calling traceback() after an error gives more information > about the source of the error. > > > To fix this, get rid of the .RData file that is being loaded when R > starts. > > In the spirit of the old -- now politically incorrect -- sayings `` > Real men don't ..... ''' > I'd like to emphasize my own view that > "Real useRs don't use .RData" > > in other words, experienced R users do not let their workspace be saved > automatically (to '.RData') and hence do not load any .RData > automatically at startup. > > Consequently, use R with the '--no-save' command line argument (maybe > also with '--no-restore'). > > ESS (Emacs Speaks Statistics) users can put > > (custom-set-variables > '(inferior-R-args "--no-restore-history --no-save ") > ) > > into their ~/.emacs > {and I'd like to see a way to do this easily with RStudio...} > > Martin Maechler, > ETH Zurich and R Core Team > > > Bill Dunlap > > TIBCO Software > > wdunlap tibco.com<http://tibco.com> > > > On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner > <r.turner at auckland.ac.nz<mailto:r.turner at auckland.ac.nz>> wrote: > > On 26/11/14 08:53, Michael Mason wrote: > > Here you are. I expect most folks won't get the error. > > > N = 100; M = 1000 > > mat = matrix(1:(N*M) + rnorm(N*M,0,.5),N,M) > > h = hclust(as.dist(1-cor(mat))) > > plot(h) > > > Error in .Internal(dend.window(n, merge, height2, hang, labels, ...)) > : > > there is no .Internal function 'dend.window' > > > > > Thanks again > > > > On 11/25/14 11:29 AM, "Rolf Turner" > <r.turner at auckland.ac.nz<mailto:r.turner at auckland.ac.nz>> wrote: > > > > > Reproducible example??? > > > (I know from noddink about hclust, but I tried the example from the > > help page and it plotted without any problem.) > > > cheers, > > > Rolf Turner > > > On 26/11/14 06:13, Michael Mason wrote: > > Hello fellow R users, > > > I have recently updated to R 3.1.2. When trying to plot an hclust > > object to generate the dendrogram I get the following error: > > > Error in .Internal(dend.window(n, merge, height2, hang, labels, ...)) > : > > there is no .Internal function 'dend.window' > > > > I am indeed using R3.1.2 but my understanding is that the .Internal > > API to the C code is no longer used. I have tried detaching the stats > > package and restarting R to no avail. > > I would love any help from any wiser guRus. > > > Please keep communications on-list; there are others on the list far > more likely to be able to help you than I. I am cc-ing this reply to > the list. > > > For what it's worth, I can run your example without error. > > > As to how to track down what is going wrong on your system, I'm > afraid I have no idea. Someone on the list may have some thoughts. > > > cheers, > > > Rolf Turner > > > -- > > Rolf Turner > > Technical Editor ANZJS > > > ______________________________________________ > > R-help at r-project.org<mailto:R-help at r-project.org> mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > ________________________________ > > --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 at r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code.________________________________ Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. 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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 <maechler at stat.math.ethz.ch> wrote:> > > Thanks! That worked > > Of course: As in about 99.99% of all cases where Bill Dunlap helps. > > > > You probably have a local copy of an old version of plot.hclust or > plot.dendrogram in your global environmenet or another package that masks > the one in package:stats. E.g., I fired up R-2.14.2 and copied those 2 > plot methods to .GlobalEnv and then saved by workspace when quitting R. I > then fired up R-3.1.1, which loads the workspace saved by the older version > of R. I get: > > > > objects() > > [1] "plot.dendrogram" "plot.hclust" > > > plot(hclust(dist(c(2,3,5,7,11,13,17,19)))) > > Error in .Internal(dend.window(n, merge, height, hang, labels, ...)) : > > there is no .Internal function 'dend.window' > > > traceback() > > 2: plot.hclust(hclust(dist(c(2, 3, 5, 7, 11, 13, 17, 19)))) > > 1: plot(hclust(dist(c(2, 3, 5, 7, 11, 13, 17, 19)))) > > > Note how calling traceback() after an error gives more information about > the source of the error. > > > To fix this, get rid of the .RData file that is being loaded when R > starts. > > In the spirit of the old -- now politically incorrect -- sayings > `` Real men don't ..... ''' > I'd like to emphasize my own view that > "Real useRs don't use .RData" > > in other words, experienced R users do not let their workspace > be saved automatically (to '.RData') and hence do not load any > .RData automatically at startup. > > Consequently, use R with the '--no-save' command line argument > (maybe also with '--no-restore'). > > ESS (Emacs Speaks Statistics) users can put > > (custom-set-variables > '(inferior-R-args "--no-restore-history --no-save ") > ) > > into their ~/.emacs > {and I'd like to see a way to do this easily with RStudio...} > > Martin Maechler, > ETH Zurich and R Core Team > > > Bill Dunlap > > TIBCO Software > > wdunlap tibco.com<http://tibco.com> > > > On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner <r.turner at auckland.ac.nz > <mailto:r.turner at auckland.ac.nz>> wrote: > > On 26/11/14 08:53, Michael Mason wrote: > > Here you are. I expect most folks won't get the error. > > > N = 100; M = 1000 > > mat = matrix(1:(N*M) + rnorm(N*M,0,.5),N,M) > > h = hclust(as.dist(1-cor(mat))) > > plot(h) > > > Error in .Internal(dend.window(n, merge, height2, hang, labels, ...)) : > > there is no .Internal function 'dend.window' > > > > > Thanks again > > > > On 11/25/14 11:29 AM, "Rolf Turner" <r.turner at auckland.ac.nz<mailto: > r.turner at auckland.ac.nz>> wrote: > > > > > Reproducible example??? > > > (I know from noddink about hclust, but I tried the example from the help > > page and it plotted without any problem.) > > > cheers, > > > Rolf Turner > > > On 26/11/14 06:13, Michael Mason wrote: > > Hello fellow R users, > > > I have recently updated to R 3.1.2. When trying to plot an hclust > > object to generate the dendrogram I get the following error: > > > Error in .Internal(dend.window(n, merge, height2, hang, labels, ...)) : > > there is no .Internal function 'dend.window' > > > > I am indeed using R3.1.2 but my understanding is that the .Internal API > > to the C code is no longer used. I have tried detaching the stats > > package and restarting R to no avail. > > I would love any help from any wiser guRus. > > > Please keep communications on-list; there are others on the list far > more likely to be able to help you than I. I am cc-ing this reply to the > list. > > > For what it's worth, I can run your example without error. > > > As to how to track down what is going wrong on your system, I'm afraid I > have no idea. Someone on the list may have some thoughts. > > > cheers, > > > Rolf Turner > > > -- > > Rolf Turner > > Technical Editor ANZJS > > > ______________________________________________ > > R-help at r-project.org<mailto:R-help at r-project.org> mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > ________________________________ > > --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 at r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]