quartz hanging

Okay, it took me a while, but I now have a very small reprex for 
quartz (not xquartz) failing. I cannot repro this on linux with 
R-4.4.3 and the same package versions.

This is using emacs/ess, though it behaves the same on the console. I 
do not have RStudio installed.

|R.version # _ # platform aarch64-apple-darwin20 # arch aarch64 # os 
darwin20 # system aarch64, darwin20 # status # major 4 # minor 4.3 # 
year 2025 # month 02 # day 28 # svn rev 87843 # language R # 
version.string R version 4.4.3 (2025-02-28) # nickname Trophy Case 
Sys.info()[c("release","version")] # release # "24.5.0" # version # 
"Darwin Kernel Version 24.5.0: Tue Apr 22 19:53:27 PDT 2025; 
root:xnu-11417.121.6~2/RELEASE_ARM64_T6041" plot(1:10) |

(This can also be reproduced using |ggplot(mtcars, aes(mpg, disp)) + 
geom_point()|.)

At this point, change to the quartz window, it looks fine. Press 
|cmd-p| and a print dialog comes up, normal. Escape out. Press |cmd-p| 
again, and a bunch of rows dump all at once:

|2025-07-03 22:12:31.320 R[85631:98913917] The behavior of the 
UICollectionViewFlowLayout is not defined because: 2025-07-03 
22:12:31.320 R[85631:98913917] the item width must be less than the 
width of the UICollectionView minus the section insets left and right 
values, minus the content insets left and right values. 2025-07-03 
22:12:31.320 R[85631:98913917] The relevant UICollectionViewFlowLayout 
instance is <NSCollectionViewFlowLayout: 0x15b623740>, and it is 
attached to <NSCollectionView: 0x15b623000>. 2025-07-03 22:12:31.320 
R[85631:98913917] Make a symbolic breakpoint at 
UICollectionViewFlowLayoutBreakForInvalidSizes to catch this in the 
debugger. 2025-07-03 22:12:31.322 R[85631:98913917] The behavior of 
the UICollectionViewFlowLayout is not defined because: 2025-07-03 
22:12:31.322 R[85631:98913917] the item width must be less than the 
width of the UICollectionView minus the section insets left and right 
values, minus the content insets left and right values. 2025-07-03 
22:12:31.322 R[85631:98913917] The relevant UICollectionViewFlowLayout 
instance is <NSCollectionViewFlowLayout: 0x15b623740>, and it is 
attached to <NSCollectionView: 0x15b623000>. 2025-07-03 22:12:31.322 
R[85631:98913917] Make a symbolic breakpoint at 
UICollectionViewFlowLayoutBreakForInvalidSizes to catch this in the 
debugger. 2025-07-03 22:12:31.324 R[85631:98913917] The behavior of 
the UICollectionViewFlowLayout is not defined because: 2025-07-03 
22:12:31.324 R[85631:98913917] the item width must be less than the 
width of the UICollectionView minus the section insets left and right 
values, minus the content insets left and right values. 2025-07-03 
22:12:31.324 R[85631:98913917] The relevant UICollectionViewFlowLayout 
instance is <NSCollectionViewFlowLayout: 0x15b623740>, and it is 
attached to <NSCollectionView: 0x15b623000>. 2025-07-03 22:12:31.324 
R[85631:98913917] Make a symbolic breakpoint at 
UICollectionViewFlowLayoutBreakForInvalidSizes to catch this in the 
debugger. |

(Repeating the |cmd-p| for the above messages is not required, it?s 
just an oh-by-the-way. Not sure why it?s complaining, and I don?t 
entirely understand what the messages are really saying. But since 
it?s neither a warning nor a device-breaking error, I have been 
ignoring them.)

Now, load |kableExtra|. I haven?t tried many other packages, so far it 
is just this one package.

|library(kableExtra) |

That?s all, no more code/expressions/evaluation required. Back to the 
quartz window and press again |cmd-p|, and on the R console one of 
these errors appears. I say ?one of? because it varies slightly based 
on base graphics or ggplot2, or CRAN-vs-P3M ggplot2. Since the 
message-component is the same, I believe it to be the same underlying 
problem.

|### with base graphics alone, I see this: Error in 
getNamespace("grDevices") : Start tag expected, '<' not found [4] ### 
using ggplot2 from P3M, this is the only message I see Error in 
diff.default(xscale) : Start tag expected, '<' not found [4] ### using 
ggplot2 from CRAN, I see the p3m-error above or one of these two Error 
in length(x) : Start tag expected, '<' not found [4] Error in 
is.unit(y) : Start tag expected, '<' not found [4] |

The quartz window for that R process is now unresponsive, R will plot 
nothing more, and R will not open a new quartz window. I can 
|dev.off() ; dev.list()| and it suggests there are no windows, but the 
window is still present and unresponsive. |dev.new()| does nothing. 
Additional plot expressions (base or grid) do nothing, no error or 
warning, no rendering.

Interestingly, when I do this with base graphics, the print dialog 
remains up and is now unresponsive. (Does it matter that it says ?no 
printer found??) When I repro this using |ggplot2|, the print dialog 
does go away when the error hits, suggesting it is slightly later in 
code execution?

Variations attempted:

  * R is just the default R installer, I have not compiled it or any
    of its components manually;
  * base graphics vs |ggplot2| grid, barely-different behavior, same
    failure
  * |ggplot2_3.5.2| installed from CRAN (source) and from p3m.dev (mac
    binary), same behavior
  * |kableExtra_1.4.0| installed from p3m.dev, and
    |remotes::install_github("haozhu233/kableExtra")| installed
    |1.4.0.15|, same behavior
  * R from the shell and R from emacs/ess
  * I tried |library(kableExtra); detach("package:kableExtra",
    unload=TRUE)| (no attempt to print) and it still erred/broke
  * though I think it was a red-herring, I have uninstalled XQuartz,
    no change
  * this has been in multiple versions of R-4.4, not just 4.4.3, and
    not just one download/install; I have not yet tried R-4.5
  * XCode updated itself to 16.2 (I don?t recall upgrading it), though
    I would not expect this to be an issue if I compiled neither R nor
    the packages using its compilers; I?m happy to be wrong here!

I do not think that the two packages have any collisions, 
|intersect(ls(getNamespace("ggplot2")), 
ls(getNamespace("kableExtra")))| yields nothing in common. But since 
this repros with base graphics without |ggplot2| loaded, that?s a 
non-player anyway.

I?m hoping someone here can help with a couple requests/questions:

  * can anyone else repro this on their machine, or is it just me?
  * any ideas of what I might try to recompile, reinstall, or
    otherwise debug or deep-dive to see if there are any clear markers
    of what is causing the error?

Thanks!
Bill

On 6/2/25 17:28, Kasper Daniel Hansen wrote:

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 <bill+rsigmac at 8pawexpress.com 
<mailto:bill%2Brsigmac at 8pawexpress.com>> wrote:

    Thank you, Peter. I think that?s a misunderstanding of mine based on
    mis-reading mac.r-project.org <http://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,bill+rsigmac at 8pawexpress.com

    <mailto:bill%2Brsigmac at 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 <http://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+rsigmac at 8pawexpress.com

    <mailto:bill%2Brsigmac at 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 <http://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 at r-project.org
    >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

    >> ​
    >> [[alternative HTML version deleted]]
    >>
    >> _______________________________________________
    >> R-SIG-Mac mailing list
    >> R-SIG-Mac at r-project.org
    >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

    ​
    ? ? ? ? [[alternative HTML version deleted]]

​

setwd('/Users/rsparapa/')
library(ggplot2)
ggplot(mtcars, aes(mpg, disp)) + geom_point()
2025-07-05 15:53:31.754 R[72603:17617108] It's not legal to call -layoutSubtreeIfNeeded on a view which is already being laid out.  If you are implementing the view's -layout method, you can call -[super layout] instead. Break on void _NSDetectedLayoutRecursion(void) to debug.  This will be logged only once.  This may break in the future.

sessionInfo()

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 <bill+rsigmac at 8pawexpress.com
<mailto:bill%2Brsigmac at 8pawexpress.com>> wrote:

    Thank you, Peter. I think that?s a misunderstanding of mine based on
    mis-reading mac.r-project.org <https://urldefense.com/v3/__http://mac.r-project.org__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSBJ6fv7c$ > 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,bill+rsigmac at 8pawexpress.com

    <mailto:bill%2Brsigmac at 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 <https://urldefense.com/v3/__http://mac.r-project.org__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSBJ6fv7c$ >.

    >>

    >>> 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://urldefense.com/v3/__https://www.xquartz.org/FAQs.html__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuS4wUPUQ4$<https://urldefense.com/v3/__https:/www.xquartz.org/FAQs.html__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuS4wUPUQ4$>

    >> 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+rsigmac at 8pawexpress.com

    <mailto:bill%2Brsigmac at 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 <https://urldefense.com/v3/__http://dev.new__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSn5Yjmlc$ >() 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://urldefense.com/v3/__https://github.com/XQuartz/XQuartz/issues/431__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSR3JjMhM$<https://urldefense.com/v3/__https:/github.com/XQuartz/XQuartz/issues/431__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSR3JjMhM$> , 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://urldefense.com/v3/__https://github.com/XQuartz/XQuartz/issues/168__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSOLaWiU8$<https://urldefense.com/v3/__https:/github.com/XQuartz/XQuartz/issues/168__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSOLaWiU8$> , closed as ?not

    planned?,

    >>>> though this one is much older than the first (431) issue
    >>>>
    >>>> I?ve tried using something like |httpgd|
    >>>> <https://urldefense.com/v3/__https://github.com/nx10/httpgd/__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSEW4yGLE$ > 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://urldefense.com/v3/__https://github.com/nx10/httpgd/issues/215__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSCcqEGuU$ >). 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 at r-project.org
    >>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSPVCkDVU$<https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSPVCkDVU$>

    >> ​
    >> [[alternative HTML version deleted]]
    >>
    >> _______________________________________________
    >> R-SIG-Mac mailing list
    >> R-SIG-Mac at r-project.org
    >> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSPVCkDVU$<https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!H8mHWRdzp34!-YEpBLrLI6b_Mk0zf1f5h0O-bWSg2UBs07TqCgYQIYE-X-ULQQ1uoZD_NBd2nUVAzcNTm05C3SDAzebn0WuSPVCkDVU$>

    ​
            [[alternative HTML version deleted]]

Sorry, I can?t reproduce.? The second Cmd-P behaves as expected

with Apple M1 Max, emacs 29.4, ESS 24.01.1 and?

R Under development (unstable) (2024-11-10 r87316) -- "Unsuffered 
Consequences"

Copyright (C) 2024 The R Foundation for Statistical Computing

Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.

setwd('/Users/rsparapa/')

library(ggplot2)

ggplot(mtcars, aes(mpg, disp)) + geom_point()

2025-07-05 15:53:31.754 R[72603:17617108] It's not legal to call 

-layoutSubtreeIfNeeded on a view which is already being laid out.? If 
you are implementing the view's -layout method, you can call -[super 
layout] instead. Break on void _NSDetectedLayoutRecursion(void) to 
debug.? This will be logged only once.? This may break in the future.

sessionInfo()

R Under development (unstable) (2024-11-10 r87316)

Platform: aarch64-apple-darwin20

Running under: macOS Sonoma 14.7.2

Matrix products: default

BLAS: 
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 


LAPACK: 
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; 
LAPACK version 3.12.0

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago

tzcode source: internal

attached base packages:

[1] stats???? graphics? grDevices utils???? datasets methods?? base

other attached packages:

[1] ggplot2_3.5.1

loaded via a namespace (and not attached):

[1] labeling_0.4.3?? utf8_1.2.4?????? R6_2.5.1 tidyselect_1.2.1

[5] farver_2.1.2???? magrittr_2.0.3?? gtable_0.3.6 glue_1.8.0

?[9] tibble_3.2.1???? pkgconfig_2.0.3? generics_0.1.3 dplyr_1.1.4

[13] lifecycle_1.0.4? cli_3.6.3??????? fansi_1.0.6 scales_1.3.0

[17] grid_4.5.0?????? vctrs_0.6.5????? withr_3.0.2 compiler_4.5.0

[21] tools_4.5.0????? munsell_0.5.1??? pillar_1.9.0 colorspace_2.1-1

[25] rlang_1.1.4

-- 

Rodney Sparapani, Associate Professor of Biostatistics

President, Wisconsin Chapter of the American Statistical Association

Division of Biostatistics, Data Science Institute

Medical College of Wisconsin, Milwaukee Campus

*From: *R-SIG-Mac <r-sig-mac-bounces at r-project.org> on behalf of 
bill+rsigmac at 8pawexpress.com <bill+rsigmac at 8pawexpress.com>
*Date: *Friday, July 4, 2025 at 12:33?AM
*To: *r-mac <r-sig-mac at r-project.org>
*Subject: *Re: [R-SIG-Mac] quartz hanging

ATTENTION: This email originated from a sender outside of MCW. Use 
caution when clicking on links or opening attachments.

On 6 Jul 2025, at 01:54, bill+rsigmac at 8pawexpress.com wrote:

Thank you for trying it, but you did not execute the reprex completely: 
you never loaded |kableExtra|. The reprex in-short (I should have 
included it this way the first time):

|plot(1:2) # or ggplot(mtcars, aes(mpg, disp)) + geom_point() # with the 
quartz window active, press Cmd-P, no fail library(kableExtra) # with 
the quartz window active, press Cmd-P, fail |

I hope this is more readable as a regexp (for me your |-delimited blocks show up as a single line of text so it's very difficult to figure out which commands I'm supposed to execute).

plot(1:2)
# press Cmd-P in quartz window ? works
library(kableExtra)
# press Cmd-P in quartz window ? error, hangs, options(error=browser) doesn't help

The first lines were just intended to show that kableExtra is actually the culprit ? which is not quite true. The real cause of the error seems to be the xml2 package imported by kableExtra.  I get the same problem with this sequence

library(xml2)
plot(1:2)
# press Cmd-P in quartz window ? error, hangs, options(error=browser) doesn't help

I have reproduced this on MacBook M1Max, macOS Sonoma 14.7.6, R 4.5.1 RC (2025-06-05 r88292) in a command-line session, so no Emacs/ESS involved.

Best,
Stephanie

On 6 Jul 2025, at 01:54, bill+rsigmac at 8pawexpress.com wrote:

Thank you for trying it, but you did not execute the reprex completely: 
you never loaded |kableExtra|. The reprex in-short (I should have 
included it this way the first time):

|plot(1:2) # or ggplot(mtcars, aes(mpg, disp)) + geom_point() # with the 
quartz window active, press Cmd-P, no fail library(kableExtra) # with 
the quartz window active, press Cmd-P, fail |

[[alternative HTML version deleted]]

I hope this is more readable as a regexp (for me your |-delimited 
blocks show up as a single line of text so it's very difficult to 
figure out which commands I'm supposed to execute).

plot(1:2)
# press Cmd-P in quartz window ? works
library(kableExtra)
# press Cmd-P in quartz window ? error, hangs, options(error=browser) 
doesn't help

The first lines were just intended to show that kableExtra is actually 
the culprit ? which is not quite true. The real cause of the error 
seems to be the xml2 package imported by kableExtra. ?I get the same 
problem with this sequence

library(xml2)
plot(1:2)
# press Cmd-P in quartz window ? error, hangs, options(error=browser) 
doesn't help

The mailing lists strip html formatting... what you see is not what we see unless you set your email client program to compose and send plain text.

I have reproduced this on MacBook M1Max, macOS Sonoma 14.7.6, R 
4.5.1?RC (2025-06-05 r88292) in a command-line session, so no 
Emacs/ESS involved.

Best,
Stephanie

On 6 Jul 2025, at 01:54, bill+rsigmac at 8pawexpress.com wrote:

Thank you for trying it, but you did not execute the reprex completely:
you never loaded |kableExtra|. The reprex in-short (I should have
included it this way the first time):

|plot(1:2) # or ggplot(mtcars, aes(mpg, disp)) + geom_point() # with the
quartz window active, press Cmd-P, no fail library(kableExtra) # with
the quartz window active, press Cmd-P, fail |

I hope this is more readable as a regexp (for me your |-delimited 
blocks show up as a single line of text so it's very difficult to 
figure out which commands I'm supposed to execute).

plot(1:2)
# press Cmd-P in quartz window ? works
library(kableExtra)
# press Cmd-P in quartz window ? error, hangs, options(error=browser) 
doesn't help

The first lines were just intended to show that kableExtra is actually 
the culprit ? which is not quite true. The real cause of the error 
seems to be the xml2 package imported by kableExtra. ?I get the same 
problem with this sequence

library(xml2)
plot(1:2)
# press Cmd-P in quartz window ? error, hangs, options(error=browser) 
doesn't help
I have reproduced this on MacBook M1Max, macOS Sonoma 14.7.6, R 
4.5.1?RC (2025-06-05 r88292) in a command-line session, so no 
Emacs/ESS involved.

On 7/6/25 11:21, Stephanie Evert wrote:

I hope this is more readable as a regexp (for me your |-delimited 
blocks show up as a single line of text so it's very difficult to 
figure out which commands I'm supposed to execute).

plot(1:2)
# press Cmd-P in quartz window ? works
library(kableExtra)
# press Cmd-P in quartz window ? error, hangs, options(error=browser) 
doesn't help

The first lines were just intended to show that kableExtra is 
actually the culprit ? which is not quite true. The real cause of the 
error seems to be the xml2 package imported by kableExtra. ?I get the 
same problem with this sequence

library(xml2)
plot(1:2)
# press Cmd-P in quartz window ? error, hangs, options(error=browser) 
doesn't help

Thank you for verifying and digging deeper! I was making no assumption 
(yet) that kableExtra was the clear problem; while it does import 
grDevices and graphics, I wouldn?t expect a simple import to do it. 
Having said that, xml2 imports neither package directly. In fact, 
loading each of xml2?s imports does not trigger the error, so that 
suggests it?s either in xml2?s ?./src/*? files or linking against 
libxml2.

I apologize for the formatting issue. I use Markdown Here Revival for 
Thunderbird/Betterbird so that I can type in markdown and have it 
rendered into HTML. It surprises me only a little that the 
stripped-out html leaves a bit to be desired.

On 7/6/25 11:44, Jeff Newmiller via R-SIG-Mac wrote:

The mailing lists strip html formatting... what you see is not what we see unless you set your email client program to compose and send plain text.

That makes sense, I?d forgotten about that.

Bill

I have reproduced this on MacBook M1Max, macOS Sonoma 14.7.6, R 
4.5.1?RC (2025-06-05 r88292) in a command-line session, so no 
Emacs/ESS involved.

Best,
Stephanie

On 6 Jul 2025, at 01:54, bill+rsigmac at 8pawexpress.com wrote:

Thank you for trying it, but you did not execute the reprex completely:
you never loaded |kableExtra|. The reprex in-short (I should have
included it this way the first time):

|plot(1:2) # or ggplot(mtcars, aes(mpg, disp)) + geom_point() # with the
quartz window active, press Cmd-P, no fail library(kableExtra) # with
the quartz window active, press Cmd-P, fail |

​