[Rd] Segfault in setMask in R 4.1
Paul Murrell
p@u| @end|ng |rom @t@t@@uck|@nd@@c@nz
Tue Sep 21 23:24:39 CEST 2021
Hi
The Cairo_1.5-12.2.tar.gz sources on CRAN contain the changes. It looks
like they have still not been merged back into the main package sources
on R Forge (cc'ing the package maintainer as a gentle reminder).
I think the Cairo package NEWS file should say 4.1.0 rather than 4.0.0
Paul
On 9/22/2021 9:08 AM, Mike Lee Williams wrote:
> Thanks! AFAICT I am already using the latest version of Cairo, but these
> links gives me a ton of leads to follow up.
>
> One question (which may be better directed at the maintainer of Cairo):
> exactly which version (or commit) of Cairo implements support for the
> new setMask API?
>
> CRAN still points to 1.5-12.2. The NEWS file
> (https://www.rforge.net/Cairo/news.html
> <https://www.rforge.net/Cairo/news.html>)
> refers to changes implemented to support R 4.0.0 in Cairo 1.5-12, but my
> understanding is that setMask was added in R 4.1.0.
>
> I see no mention of changes to support setMask or R 4.1.x in Cairo
> 1.5-13 (not on CRAN yet, but the only release since 1.5-12 according to
> the NEWS file). The 1.5-13 tarball at
> https://www.rforge.net/Cairo/files/
> <https://www.rforge.net/Cairo/files>
> contains no mention of strings like "setMask", "releasePattern" or
> "setPattern", which seem like they should be in there if that version
> has implemented support for the new API.
>
> Mike
>
> On Tue, Sep 21, 2021, at 1:41 PM, Paul Murrell wrote:
> > Hi
> >
> > dev->setMask() was introduced in R 4.1.0 ...
> >
> >
> https://developer.r-project.org/Blog/public/2020/07/15/new-features-in-the-r-graphics-engine/
> <https://developer.r-project.org/Blog/public/2020/07/15/new-features-in-the-r-graphics-engine>
> >
> >
> https://www.stat.auckland.ac.nz/~paul/Reports/GraphicsEngine/definitions/definitions.html
> <https://www.stat.auckland.ac.nz/~paul/Reports/GraphicsEngine/definitions/definitions.html>
> >
> > If your application is using its own custom graphics device, it will
> > need updating, see ...
> >
> >
> https://www.stat.auckland.ac.nz/~paul/Reports/GraphicsEngine/definitions/definitions.html#devices
> <https://www.stat.auckland.ac.nz/~paul/Reports/GraphicsEngine/definitions/definitions.html#devices>
> >
> > But it looks like you may just be using the graphics device provided by
> > the 'Cairo' package, which has already been updated. If that is the
> > case, your problem may be solved simply be reinstalling the 'Cairo'
> package.
> >
> > Paul
> >
> > p.s. the reason why it only happens for 'ggplot2' plots is that only
> > 'grid' (which underlies 'ggplot2') attempts to set masks (the 'graphics'
> > package does not).
> >
> > On 9/22/2021 4:52 AM, Mike Lee Williams wrote:
> >> Thank you! Here is the output of option("devices"), which I think means
> >> we're using Cairo:
> >>
> >> $device
> >> function (width = 1280, height = 960, pointsize = 24, units = "px",
> >> bg = "white", dpi = 160, ...)
> >> {
> >> devSym <- basename(tempfile(pattern = "SensePlot", tmpdir = ""))
> >> newDev <- Cairo(width = width, height = height, pointsize = pointsize,
> >> bg = bg, units = units, dpi = dpi, type = "raster", ...)
> >> attr(newDev, "units") <- units
> >> attr(newDev, "dpi") <- dpi
> >> assign(devSym, newDev, SenseDevices)
> >> invisible(newDev)
> >> }
> >> <bytecode: 0x55b08ba031c0>
> >> <environment: namespace:Cairo>
> >>
> >> "Sense" is the internal name of our application. I'm not sure what
> >> "devSym" and "newDev" are, but If there are no known issues with Cairo
> >> itself then our own code is presumably part of the problem.
> >>
> >> I would like to confirm that by failing to reproduce the bug in
> >> "vanilla" R 4.1 with a Cairo device. If anyone has any tips for how to
> >> do that (on Linux) or any other comments I would be very grateful.
> >>
> >> If our code is the problem then I'm still confused why a regular plot()
> >> works, but a ggplot2 qplot() segfaults. Maybe this is a clue!
> >>
> >> I will post again if I figure anything out!
> >>
> >> Mike
> >>
> >> On Tue, Sep 21, 2021, at 3:37 AM, GILLIBERT, Andre wrote:
> >> > Hello,
> >> >
> >> > Which graphic device (backend) do you use?
> >> > The setMask() function calls the internal setMask function associated
> >> > to the graphic device.
> >> > If the Web application uses one of the standard graphic backend, the
> >> > bug may come from the R core. If it uses a custom graphic backend, the
> >> > bug may be in the backend.
> >> >
> >> > --
> >> > Sincerely
> >> > André GILLIBERT
> >> >
> >> > ATTENTION: Cet e-mail provient d’une adresse mail extérieure au CHU de
> >> > Rouen. Ne cliquez pas sur les liens ou n'ouvrez pas les pièces jointes
> >> > à moins de connaître l'expéditeur et de savoir que le contenu est sûr.
> >> > En cas de doute, transférer le mail à « DSI, Sécurité » pour analyse.
> >> > Merci de votre vigilance
> >> >
> >> >
> >> > I have inherited a build of R. We compile R from source and then use
> >> a custom
> >> > web application to allow users to enter R statements and render the
> >> output (it's
> >> > kind of like RStudio although the UX is quite different).
> >> >
> >> > Things were going fine until I tried to upgrade to R 4.1.x. The build
> >> succeeds,
> >> > but I get the following segfault when I make qplot (ggplot2) calls:
> >> >
> >> > *** caught segfault ***
> >> > address (nil), cause 'memory not mapped'
> >> >
> >> > Traceback:
> >> > 1: .setMask(NULL, NULL)
> >> > 2: resolveMask.NULL(NULL)
> >> > 3: (function (path) { UseMethod("resolveMask")})(NULL)
> >> > 4: grid.newpage()
> >> > 5: print.ggplot(x)
> >> > 6: (function (x, ...) UseMethod("print"))(x)
> >> >
> >> > I am not an R developer, so I don't really know how to read this. I
> >> am wondering
> >> > if this is a known issue or if anyone has any suggestions. Here's
> >> some things
> >> > I've tested:
> >> >
> >> > - I get the same segfault in R 4.1.0 and R 4.1.1. I do not get this
> >> error in R
> >> > 4.0.4 or R 4.0.5.
> >> >
> >> > - The problem appears to be specific to the (graphics?) features of R
> >> that
> >> > ggplot2 uses. I do not get a segfault if I do a generic
> `plot(c(1,2,3))`.
> >> >
> >> > - I have tried versions of ggplot2 3.3.3 and 3.3.5.
> >> >
> >> > - The traceback points to files that were introduced in this commit
> >> >
> >> >
> >>
> https://github.com/wch/r-source/commit/16755bcddffe0cb4238d8a4979387d92b93a8324#diff-5c63f74229830cdde7886a50bf06dafcdf1d5b3d42cfa06b26814876e58c5ab0
> <https://github.com/wch/r-source/commit/16755bcddffe0cb4238d8a4979387d92b93a8324#diff-5c63f74229830cdde7886a50bf06dafcdf1d5b3d42cfa06b26814876e58c5ab0>
>
> >>
> <https://github.com/wch/r-source/commit/16755bcddffe0cb4238d8a4979387d92b93a8324#diff-5c63f74229830cdde7886a50bf06dafcdf1d5b3d42cfa06b26814876e58c5ab0
> <https://github.com/wch/r-source/commit/16755bcddffe0cb4238d8a4979387d92b93a8324#diff-5c63f74229830cdde7886a50bf06dafcdf1d5b3d42cfa06b26814876e58c5ab0>>
> >> >
> >> > I am not an R user or R developer so I'm a bit stuck here. I would be
> >> happy to
> >> > give the output of any commands. If anyone has any suggestions then
> >> please let
> >> > me know!
> >> >
> >> > Thanks!
> >> > Mike Lee Williams
> >> >
> >> > ______________________________________________
> >> > R-devel using r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/r-devel
> <https://stat.ethz.ch/mailman/listinfo/r-devel>
>
> >> <https://stat.ethz.ch/mailman/listinfo/r-devel
> <https://stat.ethz.ch/mailman/listinfo/r-devel>>
> >>
> >> ______________________________________________
> >> R-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> <https://stat.ethz.ch/mailman/listinfo/r-devel>
>
> >> <https://stat.ethz.ch/mailman/listinfo/r-devel
> <https://stat.ethz.ch/mailman/listinfo/r-devel>>
> >
> > --
> > Dr Paul Murrell
> > Department of Statistics
> > The University of Auckland
> > Private Bag 92019
> > Auckland
> > New Zealand
> > 64 9 3737599 x85392
> > paul using stat.auckland.ac.nz
> > http://www.stat.auckland.ac.nz/~paul/
> <http://www.stat.auckland.ac.nz/~paul>
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul using stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
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