Dear list members, I�m trying to install R Commander under Mac OSX Mountain Lion (10.8.2). After following all the steps described in the installation notes (I got this error message: Loading required package: tcltk Loading Tcl/Tk interface. Done Loading required package: car Loading required package: MASS Loading required package: nnet Error:.onLoad failed in loadNamespace for 'Rcmdr', details: call: structure(.External('dotTclObjv', objv, PACKAGE = 'tcltk'), class = 'tclObj') error: tcl invalid command name 'tkmessageBox'. In addition: Warning message: In fun(libname, pkgname): couldn't connect to display ':0' Error: package/namespace load failed for �Rcmdr� The strange thing is that I�ve installed Tcl/Tk and XQuark as recommended. I�ve also tried uninstalling R, reinstalling the latest version (2.15.1 signed) and all packages, and following the same official steps again. It didn�t work neither. Could you please help me?
R Commander always worked fine on my iMac, until I updated to Mountain Lion. Best regards, Marco. Prof.
![Mac Mac](/uploads/1/2/3/7/123763428/558652587.jpg)
Mello Universidade Federal de Minas Gerais ICB - Depto. Biologia Geral [email protected]. John Fox Dear Marco, To provide some background, you and I have corresponded about your problem, and now at least you appear to have the tcltk package installed. Did you reinstall R as I suggested? Have you checked that tcltk is working, following the instructions I sent you in an earlier email? I don't believe that the Rcmdr ever calls tkmessageBox directly, but there is a tkmessageBox function in tcltk, and you can check whether this is the source (or a symptom) of the problem by issuing the.
Dear Marco, To provide some background, you and I have corresponded about your problem, and now at least you appear to have the tcltk package installed. Did you reinstall R as I suggested? Have you checked that tcltk is working, following the instructions I sent you in an earlier email?
I don't believe that the Rcmdr ever calls tkmessageBox directly, but there is a tkmessageBox function in tcltk, and you can check whether this is the source (or a symptom) of the problem by issuing the following commands in a fresh R session: library(tcltk) tkmessageBox(message='test') That should, as the function name suggests, bring up a Tk message box. Also I'm not sure what's going on with 'couldn't connect to display ':0', which suggests an X-Windows issue.
![R commander for mac R commander for mac](/uploads/1/2/3/7/123763428/466310067.jpg)
Finally, I'm moving this discussion to r-sig-mac, where you're more likely to get knowledgeable assistance. Best, John - John Fox Senator McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada. Original Message- From: r-help-bounces at r-project.org mailto:r-help-bounces at r-project.org On Behalf Of Marco Mello Sent: Thursday, October 04, 2012 12:57 PM To: r-help at r-project.org Subject: R problem with the installation of r commander on a mac Dear list members, Im trying to install R Commander under Mac OSX Mountain Lion (10.8.2). After following all the steps described in the installation notes (notes.html), I got this error message: Loading required package: tcltk Loading Tcl/Tk interface. Done Loading required package: car Loading required package: MASS Loading required package: nnet Error:.onLoad failed in loadNamespace for 'Rcmdr', details: call: structure(.External('dotTclObjv', objv, PACKAGE = 'tcltk'), class = 'tclObj') error: tcl invalid command name 'tkmessageBox'. In addition: Warning message: In fun(libname, pkgname): couldn't connect to display ':0' Error: package/namespace load failed for Rcmdr The strange thing is that Ive installed Tcl/Tk and XQuark as recommended.
Ive also tried uninstalling R, reinstalling the latest version (2.15.1 signed) and all packages, and following the same official steps again. It didnt work neither. Could you please help me? R Commander always worked fine on my iMac, until I updated to Mountain Lion. Best regards, Marco.
Prof. Mello Universidade Federal de Minas Gerais ICB - Depto. Biologia Geral marmello at gmail.com. alternative HTML version deleted. Dear Marco, To provide some background, you and I have corresponded about your problem, and now at least you appear to have the tcltk package installed. Did you reinstall R as I suggested?
Have you checked that tcltk is working, following the instructions I sent you in an earlier email? I don't believe that the Rcmdr ever calls tkmessageBox directly, but there is a tkmessageBox function in tcltk, and you can check whether this is the source (or a symptom) of the problem by issuing the following commands in a fresh R session: library(tcltk) tkmessageBox(message='test') That should, as the function name suggests, bring up a Tk message box. Also I'm not sure what's going on with 'couldn't connect to display ':0', which suggests an X-Windows issue. Finally, I'm moving this discussion to r-sig-mac, where you're more likely to get knowledgeable assistance. Best, John - John Fox Senator McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada. Original Message- From: r-help-bounces at r-project.org mailto:r-help-bounces at r-project.org On Behalf Of Marco Mello Sent: Thursday, October 04, 2012 12:57 PM To: r-help at r-project.org Subject: R problem with the installation of r commander on a mac Dear list members, Im trying to install R Commander under Mac OSX Mountain Lion (10.8.2). After following all the steps described in the installation notes (notes.html), I got this error message: Loading required package: tcltk Loading Tcl/Tk interface.
Done Loading required package: car Loading required package: MASS Loading required package: nnet Error:.onLoad failed in loadNamespace for 'Rcmdr', details: call: structure(.External('dotTclObjv', objv, PACKAGE = 'tcltk'), class = 'tclObj') error: tcl invalid command name 'tkmessageBox'. In addition: Warning message: In fun(libname, pkgname): couldn't connect to display ':0' Error: package/namespace load failed for Rcmdr The strange thing is that Ive installed Tcl/Tk and XQuark as recommended. Ive also tried uninstalling R, reinstalling the latest version (2.15.1 signed) and all packages, and following the same official steps again. It didnt work neither. Could you please help me? R Commander always worked fine on my iMac, until I updated to Mountain Lion. Best regards, Marco.
Prof. Mello Universidade Federal de Minas Gerais ICB - Depto. Biologia Geral marmello at gmail.com. alternative HTML version deleted R-SIG-Mac mailing list R-SIG-Mac at r-project.org.
(Redirected from ) This file contains information on installing and using ( and ( on a computer running Mac OS X. Mac users in NATS 1500 and MATH 1532 (Winter 2010) encountered issues getting Rcmdr to work after following ( Edvin Vitaj in NATS 1500 prepared the following notes to help with the installation.
In contrast with the version of Rcmdr on the PC, the version on the Mac does not import Excel files. Course datasets need to be downloaded as comma-separated text files.
Instruction for downloading these files are given below. Table of contents. Installing R and Rcmdr. First download R-2.14.1.pkg (or the latest version) from. To install it just double click on the downloaded file and follow the usual steps as with any application. When the installation is finished, run the application (R64.app), select from the menu Packages & Data, then from the drop down menu select Package Installer. A new window will open, an image of the window is shown below.
In the right corner there is a box similar to the google search window in a web browser, type in there Rcmdr. On the left side, there is a button Get List, by clicking we select the Ontario, Canada and then click enter. A list will show up, select the first one, and before clicking Install Selected, the box under it Install dependencie should be checked. See the image which you can enlarge by clicking on it.
There is a red dot in the image for every point mentioned above. After clicking 'Install Selected', it will take more than 2 minutes with a fast internet connection to finish so you should wait until the ' sign is shown in the R Console. Then we type library(Rcmdr) command and the R Commander window should pop up. In the case that nothing happens, the R Commander window does not pop up, you should make sure that 'X11' application is running. You can run 'X11' before you run R, or you can run R first and then you will see in R Console the 'X11 button'. It is the fourth button, a white icon with an X in it.
Click that button and then issue library(Rcmdr) command. 'X11' will run in background, so you don't have to worry or do anything else with it. If 'X11' is not already installed in your machine, you can find it in the DVD installer disc that came with your computer, or you can download it from apple site. From the Mac OS X Tiger, 'X11' is included in the DVD installers disc.
For an older Mac OS X operating system, try this link which maybe will help you.
On May 9, 2017, at 3:08 PM, Jose G Conde Santiago via R-SIG-Mac wrote: HelloI recently upgraded to R 3.4.0, but now I get very poor fonts from Rcmdr 2.3-2 as shown below: I'm not an Rcmdr user but I tried bringing a current version up. (I included a request to install Rcmdr with all dependencies but X11 complained that aplpack was missing and that needed to be installed as well.) Seems you don't like teh proportionally space serif font you are seeing which was different than what I saw. Think you might want to show what this returns for you names(X11Fonts) 1 'serif' 'sans' 'mono' 'Times' 'Helvetica' 6 'CyrTimes' 'CyrHelvetica' 'Arial' 'Mincho' X11Fonts$serif 1 '-.-times-%s-%s-.-.-%d-.-.-.-.-.-.-.' I'm running R 3.4.0, El Cap, XQuartz 2.7.11 (xorg-server 1.18.4) and that won't change since my box is 'end of life' per Apple's inflexible OS support. I tried running your test code and it seemed to lock up my X11 session as well as my R console (Perhaps this is due to running Rcmder in the R.app GUI?) Best; David.
R-SIG-Mac mailing list David Winsemius Alameda, CA, USA R-SIG-Mac mailing list Fox, John 09.05.17 18:53. Dear David, Jose and I corresponded earlier today, and I can’t duplicate his problem on two MacBook Pros, both with apparently the same setup as Jose’s: macOS Sierra, R 3.4.0, Rcmdr 2.3-2, and XQuartz 2.7.11 (i.e., all current versions). If the problem were with availability of X11 fonts, why would the fonts appear properly for him with R 3.3.3 but not R 3.4.0? I thought that someone more familiar with Macs than I am might spot the cause of the problem from Jose’s screenshot, and so I suggested that he write to the R-SIG-Mac list.
Best, John - John Fox, Professor McMaster University Hamilton, Ontario, Canada Web: On 2017-05-09, 6:45 PM, 'R-SIG-Mac on behalf of David Winsemius' wrote: Simon Urbanek 12.05.17 11:26. In R versions before 3.4.0 we were shipping our own version of fontconfig which was using the following font directories -with-default-fonts=/usr/X11R6/lib/X11/fonts -with-add-fonts='/System/Library/Fonts,/Library/Fonts,/Library/Fonts' As of R 3.4.0 we are using fontconfig from XQuartz (since they started diverging from our version and thus causing issues) so it's now entirely up to the standard font configuration in XQuartz. So my guess would be that you may have some fonts in your private font library which is not configured - possibly in /Library/Fonts.
As far as I can tell XQuartz uses all of the above except for /Library/Fonts so you may need to either install the fonts your want at system level or change your fontconfig configuration to include your private font library. See fc-list to list all your fonts that fontconfig knows about. Cheers, Simon Jose G Conde Santiago via R-SIG-Mac 15.05.17 9:03. Dear Jose, It's a bit difficult to respond to your latest messages because you sent so many of them.
I'm not entirely sure what's producing your font problems - perhaps Simon will have some additional ideas - but you should be aware that you can't load the Rcmdr package - or, more generally, the tcltk package - without XQuartz (or another X11 system). Normally, XQuartz should start automatically when the Rcmdr (or tcltk) package is loaded.
That is, you should not have to start it separately. It may help to know that the Rcmdr package selects its default dialog font by querying the default Tk font, via the command tclvalue(.Tcl('font actual TkDefaultFont -family')) and sets the font for commands and output by querying the default Tk fixed-width font: tclvalue(.Tcl('font actual TkFixedFont -family')) On my Macs, these are respectively the helvetica and courier fonts.
In any event, I'm glad that you seem to have solved your problem. John peter dalgaard 16.05.17 4:28. It's a build issue relating to Tcl/Tk, not specifically Rcmdr (Rcmdr does something slightly weird. with the fonts too, but this seems to be orthogonal to the ugly-font issue).
To see the issue quickly, try library(tcltk).Tcl('::tk::pkgconfig get fontsystem') With CRAN 3.3.3, I get xft and likewise with a local nightly build of R-devel, but CRAN 3.4.0 says.Tcl('::tk::pkgconfig get fontsystem') Error in.Tcl('::tk::pkgconfig get fontsystem'): could not find function '.Tcl' as does a local build of R-patched (???!!!). This is pretty weird. I'll see if I can dig up some more about where the difference is.pd. Try library(tcltk); demo(tkfaq) then library(Rcmdr) and watch the font change in the tkfaq window. Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+1 Office: A 4.23 Email: Priv: R-SIG-Mac mailing list peter dalgaard 16.05.17 6:02. On May 16, 2017, at 12:20 PM, peter dalgaard wrote: Mystery solved after looking into the actual.pkg files.
They simply contain a full Tcl/Tk which installs into /usr/local, which obviously affects anything that links it dynamically. I somehow thought that they would install somewhere separate. (Stop grinning, Simon!) I'm not sure I understand the 'they' - is it us? The difference in R 3.4.0 is that we are using everything from the system (and XQuartz) whereas before we were building dependencies ourselves before. Anyways, the way forward must be to get Tcl/Tk compiled exactly as they were in 3.3.x.
R before 3.4.0 we used Tcl/Tk 8.6.0 for OS X Mavericks from 2013, for R 3.4.0 we are using Tcl/Tk 8.6.6 for El Capitan. FWIW the config flags were -disable-corefoundation -disable-framework -disable-aqua -enable-64bit -with-tcl=/usr/local/lib -with-x -x-includes=/opt/X11/include -x-libraries=/opt/X11/lib CC=clang CXX=clang I have no idea what you are talking about here so if anyone has suggestions to test, let me know.
Cheers, Simon Fox, John 16.05.17 10:58. On 16 May 2017, at 19:30, Simon Urbanek wrote: On May 16, 2017, at 12:20 PM, peter dalgaard wrote: Mystery solved after looking into the actual.pkg files. They simply contain a full Tcl/Tk which installs into /usr/local, which obviously affects anything that links it dynamically. I somehow thought that they would install somewhere separate. (Stop grinning, Simon!) I'm not sure I understand the 'they' - is it us? The files/libs.
The difference in R 3.4.0 is that we are using everything from the system (and XQuartz) whereas before we were building dependencies ourselves before. Anyways, the way forward must be to get Tcl/Tk compiled exactly as they were in 3.3.x. R before 3.4.0 we used Tcl/Tk 8.6.0 for OS X Mavericks from 2013, for R 3.4.0 we are using Tcl/Tk 8.6.6 for El Capitan. From where do we get those? FWIW the config flags were -disable-corefoundation -disable-framework -disable-aqua -enable-64bit -with-tcl=/usr/local/lib -with-x -x-includes=/opt/X11/include -x-libraries=/opt/X11/lib CC=clang CXX=clang I don't think the config flags for R matter in this regard.
The behaviour is completely paralleled by wish8.6: Peter-Dalgaards-MacBook-Air: pd$ /usr/local/bin/wish8.6% tk::pkgconfig get fontsystem invalid command name 'tk::pkgconfig' peter dalgaard 16.05.17 14:53. On 16 May 2017, at 21:03, peter dalgaard wrote: I don't think the config flags for R matter in this regard. The behaviour is completely paralleled by wish8.6: Hmmm, not sure the wish::tk::pkgconfig thing proves anything, after I tried some of the ActiveState installs and a source build. This stuff is making my head spin!
However, I discovered that it is possible to install R-3.4.0.pkg as usual, and then a customized install of (say) R-3.3-branch-mavericks.pkg, omitting everything except the Tcl/Tk stuff. That gives you R 3.4.0 and Rcmdr with antialiased fonts.
Peter Dalgaard 17.05.17 11:51. A few more data points: I tried building Tcl/Tk 8.6.6 from the sources from sourceforge.
Contrary to what it says on the package, it insists on building Tcl and Tk as frameworks, which in turn requires that R's configure needs special instructions. This works reasonably well for simple tcltk stuff (demos, the CRAN selection menu), but unfortunately, library(Rcmdr) causes an 'Abort trap: 6' almost immediately. (I get a sense of deja vu about this. Did Brian try something similar years ago?) It does actually seem to work to build R against the system-supplied v.8.5 frameworks. However, this is Aqua-based, and the fonts are a bit weird (smooth, but way too small) and the Rcmdr menus get moved to the top bar.
I am pretty sure by now that all this stuff is a generic tcltk build problem and way out of John's domain. (Thanks for posting the font code, John.
I hope I can get around to having a closer look at it at some point. Those.Tcl(paste) constructs make me cringe a bit, but not all are easily eliminated.) -pd peter dalgaard 17.05.17 12:22. Dear Peter, First, thank you very much for persisting with this.
I greatly appreciate it. -Original Message- From: Peter Dalgaard mailto: Sent: Wednesday, May 17, 2017 2:52 PM To: Simon Urbanek Cc: Fox, John; Subject: Re: R-SIG-Mac R commander fonts on R 3.4.0 A few more data points: I tried building Tcl/Tk 8.6.6 from the sources from sourceforge. Contrary to what it says on the package, it insists on building Tcl and Tk as frameworks, which in turn requires that R's configure needs special instructions. This works reasonably well for simple tcltk stuff (demos, the CRAN selection menu), but unfortunately, library(Rcmdr) causes an 'Abort trap: 6' almost immediately. (I get a sense of deja vu about this. Did Brian try something similar years ago?) I believe that Brian mentioned to me years ago that he was able to get R (and the Rcmdr package) to work fine with a native version of Tcl/Tk for Macs.
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Beyond that, I don't recall. It does actually seem to work to build R against the system-supplied v.8.5 frameworks. However, this is Aqua-based, and the fonts are a bit weird (smooth, but way too small) and the Rcmdr menus get moved to the top bar. Moving the menus to the top bar is desirable, in my opinion, because it's what Mac users expect. If the problem is simply with the font sizes, I should be able to adjust that automatically, as I do now. I am pretty sure by now that all this stuff is a generic tcltk build problem and way out of John's domain.
(Thanks for posting the font codeJohn. I hope I can get around to having a closer look at it at some point.
Those.Tcl(paste) constructs make me cringe a bit, but not all are easily eliminated.) If you see a better way to do this, of course I'd appreciate that. It took a fair amount of work to adjust the fonts so that they look right on Windows, macOS, and Linux systems. Best, John peter dalgaard 18.05.17 14:48. On 17 May 2017, at 21:28, Fox, John wrote: Dear Peter, First, thank you very much for persisting with this. I greatly appreciate it.Original Message- From: Peter Dalgaard Sent: Wednesday, May 17, 2017 2:52 PM To: Simon Urbanek Cc: Fox, John; Subject: Re: R-SIG-Mac R commander fonts on R 3.4.0 A few more data points: I tried building Tcl/Tk 8.6.6 from the sources from sourceforge. Contrary to what it says on the package, it insists on building Tcl and Tk as frameworks, which in turn requires that R's configure needs special instructions.
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This works reasonably well for simple tcltk stuff (demos, the CRAN selection menu), but unfortunately, library(Rcmdr) causes an 'Abort trap: 6' almost immediately. (I get a sense of deja vu about this. Did Brian try something similar years ago?) I believe that Brian mentioned to me years ago that he was able to get R (and the Rcmdr package) to work fine with a native version of Tcl/Tk for Macs. Beyond that, I don't recall.
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The thing I recall was something like 'We tried this approach but it crashed immediately so we gave up', but I may well be mistaken, or it was some other library,. It does actually seem to work to build R against the system-supplied v.8.5 frameworks.
However, this is Aqua-based, and the fonts are a bit weird (smooth, but way too small) and the Rcmdr menus get moved to the top bar. Moving the menus to the top bar is desirable, in my opinion, because it's what Mac users expect.
If the problem is simply with the font sizes, I should be able to adjust that automatically, as I do now. Incidentally, in the background, you see the regular XQuartz Rcmdr when using the TclTk from the R-3.3 packages (with the smooth fonts). I am pretty sure by now that all this stuff is a generic tcltk build problem and way out of John's domain.
(Thanks for posting the font code, John. I hope I can get around to having a closer look at it at some point.
Those.Tcl(paste) constructs make me cringe a bit, but not all are easily eliminated.) If you see a better way to do this, of course I'd appreciate that. It took a fair amount of work to adjust the fonts so that they look right on Windows, macOS, and Linux systems.
Running Fully updated: MACOSX 10.10.4, R 3.2.1 World Famous Astronaut, R commander 2.1.7, X11 2.7.7, Java 8, Biodiversity R 2.5.2 When i run script/data/commands that I know should work in Biodiversity R, I can run analysis, but when i try to create a plot the Quartz window crashes, beachball appears, and I can only escape by force quit. Two issues may or may not contribute to quartz crashing which i cannot resolve; When i first run R I randomly get this warning. By randomly I mean at anytime when working in r, not necessarily after I have run a command: WARNING: Method convertPointFromBase: in class NSView is deprecated on 10.7 and later.
It should not be used in new applications. When I run BiodiversityR, it launches fine, but I get this message: Attaching package: 'Rcmdr' The following objects are masked from 'package:tcltk': tclvalue, tkfocus I have uninstalled and reinstalled X11.
I can only find solutions so far that are relevant for older versions, so I am unsure of where my error is occurring. In my search a lot of people seem to be experiencing these errors and issues. Thank you to anyone who can help.