I have been using quartz from inside Emacs for a long time and I basically never (or at least very rarely) have any issues. I rarely use XQuartz and never with R installed on my local machine (mostly to start X windows from a remote server). There is a way to configure the default device in R, so I would try to start the quartz device manually with R> quartz() R> plot(1:10) and check that is the same as R> plot(1:10) to rule out any configuration issues and make sure we're talking about the same device.
Are you compiling R from source or are you using the CRAN binaries? That might have an impact. Best, Kasper On Sun, Jun 1, 2025 at 8:26 AM <[email protected]> wrote: > Thank you, Peter. I think that’s a misunderstanding of mine based on > mis-reading mac.r-project.org and incomplete research. I have since > uninstalled XQuartz and indeed |quartz()| still works, so my bug-report > has been a misdirection. With this, I’ve changed the here from “xquartz > hanging” to “quartz hanging”. > > I’m still working on a reprex, haven’t found the culprit yet. (I haven’t > had a repeat since I uninstalled and reinstalled then uninstalled XQuartz.) > > Thank you again, > Bill > > On 6/1/25 07:24, peter dalgaard wrote: > > > I'm puzzled why you need XQuartz in the first place. R in a terminal > usually fires up the quartz() graphics device and that has nothing to do > with XQuartz (which is X on top of Quartz, not the other way around). > > > > We do have an annoyance with XQuartz though: When install.packages() > goes looking for a CRAN mirror (*), it fires up a Tk selector and that will > require XQuartz to fire up. Every now and again that hangs for me too, but > as it is usually the first thing I do in an R session, I can ctr-Z and kill > the process and start over. But it really could do with a looking into. (I > do miss strace/truss from days of yore, where you could just probe into a > running process and see what it is up to.) > > > > -pd > > > > (*) Yeah, I know, it should be in a configuration file ... somewhere. > > > >> On 1 Jun 2025, at 00.08,[email protected] wrote: > >> > >> Thanks for the feedback, Marc! Very interesting. > >> > >> On 5/31/25 13:04, Marc Schwartz wrote: > >> > >>> Hi, > >>> > >>> I am currently running R 4.5.0 on macOS 15.5 (Sequoia), and I also use > emacs (30.1) and ess (25.1.0), the latter from elpa, along with other emacs > packages. > >> It seems we (emacs/ess users) are a diminishing crowd :-( > >>> I do not have the issue that you are referring to below, and did not > under prior versions to the best of my recollection. > >> Then there’s hope :-) > >>> I do tend to stay up to date on the versions of all of the above and > do clean installs of R and packages with each new version, fully removing > the older version file tree first (/Library/Frameworks/R.framework). > >>> > >>> Thus, you might consider updating both macOS and R to current versions. > >> I had already planned to upgrade to macos-15.5. I’m not able to > >> upgrade (fully) to R-4.5 in the immediate future … worse, I need > >> to have multiple R versions on-hand for some backwards-compatibility > >> testing (work apps/apis). > >> > >> I do subscribe occasionally to the “three-finger salute” way of > >> fixing some OS or program issues, but I really dislike the fact that > >> it works much more frequently than I think it should. > >> > >>> I don't use ggplot*, so cannot comment if there may be something > specific to that package causing any issues, > >> |ggplot2| does tend to be more complex and test the graphics device > >> more than typical base graphics; I recall an issue with ggplot on > >> windows several years ago that caused the window to dump, > >> occasionally causing R to dump and crash as well, triggered by a > >> mouse-wheel action on a ggplot graphics pane. This is not the same > >> issue, certainly, but speaks to the difference with base graphics. > >> > >> For the record, while I use it much much less frequently, I have yet > >> to see the issue appear when a base-graphics plot is displayed. This > >> is not conclusive. > >> > >>> One thing that you should do, if you have not, is to be sure to > re-install XQuartz after upgrading R versions, and this is referenced on > the R macOS CRAN page. > >> The only mentions I can find of XQuartz on the R-Mac pages are: > >> > >> * Big Sur and newer require XQuartz 2.8.5 (I’m good, installed 2.8.5 > >> from the start) > >> * “Always re-install XQuartz when upgrading your macOS to a new > >> major version”: not applicable, I’ve been on 15.3 or newer on this > >> laptop (unless … is 15.4 a “major version” over 15.3?) > >> > >> Regardless of that, I don’t understand how an xorg-server would be > >> at all tied to (needing to be reinstalled/relinked after) changes in > >> a client library (R plotting services). Can you provide more > >> information (a link) where they say XQuartz needs to be reinstalled > >> with each R upgrade? I apologize if I’m missing it on mac.r-project.org > . > >> > >>> See if re-installing XQuartz has any impact on the issues that you are > observing. > >> Regardless of “why” it may work, I think I’m going to uninstall and > >> reinstall XQuartz when I do the macos upgrade. “It can’t hurt”, > >> famous last words. > >>> You might also want to fully uninstall XQuartz first, before > re-installing it, and the instructions for that are available on their FAQ > page: > >>> > >>> https://www.xquartz.org/FAQs.html > >> Sage advice, I appreciate it. > >>> One additional thing to consider is to try to replicate the behavior > that you are observing by running R in Terminal and/or via R.app, to try to > exclude the possibility that there is something going on with your > emacs/ess installation. > >> That’s been on my list, but since I still don’t know exactly what > >> causes it to hang, I have not spent the time trying to repeat it > >> from outside of my normal R use. > >> > >> Once thing I find interesting is that it is particular to one R > >> process, but not to XQuartz. That is, when one R process’ graphics > >> device is hung, I can open a new R process and plotting works > >> without issue. I can close the first process, eventually its hung > >> window closes, and other processes continue to plot without issue. I > >> don’t know if this narrows it down at all, since a bug in either R > >> or XQuartz could show that specificity. (The major pain is that > >> often I’m working with many GBs of data, and reloading and > >> reprocessing is a not-free chore. Usually not impossible, just many > >> many minutes and reacquiring my mental focus.) > >> > >> Thanks again for your experience, Marc! > >> > >>> If you can replicate the issues in Terminal and/or R.app, that would > help to exclude emacs/ess from involvement at least. If you cannot, then > you might be sure that you are running the latest versions of emacs and ess > to see if that helps, in case they are adding a source of conflict. > >>> > >>> Regards, > >>> > >>> Marc Schwartz > >>> > >>> > >>>> On May 31, 2025, at 10:35 AM,[email protected] wrote: > >>>> > >>>> Are there easy fixes or alternatives to using XQuartz for R plots? > >>>> > >>>> I’m running R-4.4.3 (emacs/ess) on macos 15.4.1 and have xquartz-2.8.5 > >>>> installed. Most of the time plotting in R works well enough (I tend to > >>>> use ggplot2, I don’t know if it happens as often with base plots). > >>>> Occasionally (several times a week), “something” happens with the plot > >>>> window, and from then on that R process can no longer plot anything > >>>> more. The “something” is not well defined for me yet, I think it’s a > >>>> mouse-wheel or mouse-click or similar; the snark in me says “well > don’t > >>>> do that”, but I cannot nail down exactly how/when it breaks, it just > does. > >>>> > >>>> When it happens, the current device window is still open, but it has a > >>>> mac spinning-colorwheel, no new plotting commands work, and I cannot > >>>> close the window myself. I cannot dev.off() it, nor does dev.new() > give > >>>> me a new plotting window. When this happens for a particular R > process, > >>>> my only options for plotting are either (a) close the R process and > >>>> start over, or (b) manually plot to a PDF or similar one-shot graphics > >>>> device, viewing in a different app. > >>>> > >>>> There are several related issues I can find: > >>>> > >>>> https://github.com/XQuartz/XQuartz/issues/431, specific to macos > 15.4 or > >>>> newer I think; some mention of “minimizing windows” but I don’t > minimize > >>>> my plot windows, so perhaps not that > >>>> https://github.com/XQuartz/XQuartz/issues/168, closed as “not > planned”, > >>>> though this one is much older than the first (431) issue > >>>> > >>>> I’ve tried using something like |httpgd| > >>>> <https://github.com/nx10/httpgd/> since it can (mostly) provide an > >>>> “always updating graphics device” for example without xquartz. > >>>> Unfortunately, with some other packages (namely plumber that I use > >>>> frequently-enough) it can put the R’s REPL into an unbreakable state > >>>> (#215<https://github.com/nx10/httpgd/issues/215>). If that were fixed > >>>> I’d be a lot more comfortable using that as my workaround. > >>>> > >>>> My research has not shown any other options for fixing or replacing > >>>> xquartz with a more stable solution. Are there good ways to > troubleshoot > >>>> and try to fix the xquartz issue? Does anybody else have a workaround > or > >>>> alternative that is less unwieldy than pdf(..); plot(..); dev.off()? > >>>> > >>>> Thanks, > >>>> Bill > >>>> > >>>> ​ > >>>> ​ > >>>> [[alternative HTML version deleted]] > >>>> > >>>> _______________________________________________ > >>>> R-SIG-Mac mailing list > >>>> [email protected] > >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >> ​ > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> R-SIG-Mac mailing list > >> [email protected] > >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ​ > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
