[Rd] Segfault in setMask in R 4.1

Mike Lee Williams m|ke @end|ng |rom m|ke@p|@ce
Tue Sep 21 23:08:56 CEST 2021 

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) 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/ 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://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
>
> 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>
>>  >
>>  > 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
>>  >
>>  > ______________________________________________
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> -- 
> 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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