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, bill+rsig...@8pawexpress.com 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,bill+rsig...@8pawexpress.com 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 >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ​ > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business SchoolSolbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd....@cbs.dk Priv: pda...@gmail.com _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
