[Rd] Bracketed paste issues on Linux
Prof Brian Ripley
r|p|ey @end|ng |rom @t@t@@ox@@c@uk
Tue Jun 15 11:09:15 CEST 2021
I would have used source("clipboard") on systems which support it (Tomas
has confirmed it works on Linux). See ?file.
The macOS equivalent source(pipe("pbpaste")) also works.
On 14/06/2021 11:06, Cesko Voeten wrote:
> Making it 1024 times larger gives:
>
> installing 'sysdata.rda'
> Error: segfault from C stack overflow
>
> Making it only 4 times larger provides a usable R. In my test case of
> copying&pasting mgcv::gam, I observe the same visual corruption at the
> prompt as before, but when pressing return it has actually been received
> correctly. My real-world problem involved a file 33KiB in size, which -
> as expected, since 16KiB < 33KiB - still has the same problem as before.
>
> I know nothing about readline, but I presume that there is no way for
> this buffer size to be dynamically resized at run time. In that case,
> maybe R should simply force-disable readline's bracketed paste? By the
> way, according to readline's changelog, this does indeed seem to be a
> feature that changed (viz. was enabled in more places) from readline-8.0
> to readline-8.1.
>
> Finally, please disregard my earlier comment about vim and nano working
> just fine. They do, but they don't actually use readline (according to
> ldd), so don't provide a valid comparison.
>
> Thanks for your efforts!
> Cesko
>
> On 14-06-2021 at 08:33, Tomas Kalibera wrote:
>> Thanks, Cesko, for more debugging. As you are already compiling the
>> code, could you please try increasing CONSOLE_BUFFER_SIZE in
>> ./include/Defn.h from 4096 to some very large value (e.g. 1024 times),
>> rebuild R and check if the problems (not all bytes received correctly,
>> visual corruption) go away for texts of the size you looked at before?
>>
>>
>> Thanks,
>> Tomas
>>
>>
>>
>> On 6/13/21 10:59 AM, Voeten, C.C. wrote:
>>>
>>> Thanks for looking into this! I've just compiled today's R-devel
>>> snapshot, and it shows the same issue. extSoftVersion() from that build:
>>>
>>> zlib
>>> "1.2.11"
>>> bzlib
>>> "1.0.8, 13-Jul-2019"
>>> xz
>>> "5.2.5"
>>> PCRE
>>> "10.37 2021-05-26"
>>> ICU
>>> "69.1"
>>> TRE
>>> "TRE 0.8.0 R_fixes (BSD)"
>>> iconv
>>> "glibc 2.33"
>>> readline
>>> "8.1"
>>> BLAS
>>> "/home/cesko/r-devel/usr/lib64/R/lib/libRblas.so"
>>>
>>> Thanks for your observation that it works on your system - that
>>> implicates my readline-8.1 as being the culprit. Unfortunately, I
>>> don't dare attempt to downgrade it on my system to test, and
>>> regardless we still don't know why other readline-using programs can
>>> paste in the same text with no issues.
>>>
>>>
>>> I've made some further progress on debugging: I noticed that text
>>> <4096 bytes in size arrives fine (although sometimes with visual
>>> corruption), but text >4096 bytes doesn't. Pasting in the result of
>>> perl -e 'print ("if(T)cat(\"a\")\n"x292)' works as expected, changing
>>> the 292 to 293 causes R to print a bunch of a's followed by the
>>> source code of the cat function.
>>>
>>>
>>> To still answer your question: with mgcv::gam, pasting in the first
>>> 94 lines (as printed by R with options(width=80)) produces a visual
>>> corruption of the prompt (it reads "G$family <-
>>> familyar.summaryintercept = drop.intercept)) control$scalePenalty,")
>>> but if I press return and type the closing "}" the code has actually
>>> arrived just fine. The text up to and including that line is 4023
>>> bytes in size; when trying to add in more, it fails again.
>>>
>>>
>>> Cesko
>>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>
>>> *Van:* Tomas Kalibera <tomas.kalibera using gmail.com>
>>> *Verzonden:* zondag 13 juni 2021 10:00:27
>>> *Aan:* Voeten, C.C.; r-devel using r-project.org
>>> *Onderwerp:* Re: [Rd] Bracketed paste issues on Linux
>>> Thanks for the report. Could you please also post output from
>>> extSoftVersion() ?
>>>
>>> What happens if you paste just a smaller part of the code before the
>>> long line? Is the output still corrupted? If so, is it corrupted the
>>> same way, at the same places?
>>>
>>> (It seems to be working on my Ubuntu 20.04, readline 8.0, R-devel)
>>>
>>> Thanks
>>> Tomas
>>>
>>> On 6/12/21 3:44 PM, Cesko Voeten wrote:
>>> > I am on an up-to-date Arch Linux system, using the GNOME desktop
>>> environment. By default, this turns on bracketed paste in terminal
>>> emulators; for those not familiar with this concept: it makes it so
>>> that if you paste in multiple lines of code, they are received in a
>>> single chunk. This works just fine with R, up to a certain amount of
>>> text: for chunks past a certain length, some amount of text in the
>>> middle of the chunk goes missing. For example, if I print the source
>>> of mgcv::gam into my R session and then attempt to copy and paste it
>>> back in, what I end up with is:
>>> >
>>> > <snip 53 perfectly good lines>
>>> > pmf$formula <- gp$pf
>>> > pmf <- eval(pmf, parent.frame())
>>> > } objectvironment(attr(object$pred.formula, "full")) <-
>>> .GlobalEnv<- environment(object$terms) <- environment(object$pterms)
>>> <- .GlobalEnv
>>> >
>>> > So:
>>> > - the first 55 lines in this example arrive perfectly fine
>>> > - then a bunch go completely missing
>>> > - then various parts of the last few lines are jumbled together
>>> into one line
>>> >
>>> > For reference on the third point, the actual last 10 lines of my
>>> version of mgcv::gam are:
>>> > if (is.null(object$deviance))
>>> > object$deviance <- sum(residuals(object, "deviance")^2)
>>> > names(object$gcv.ubre) <- method
>>> > environment(object$formula) <-
>>> environment(object$pred.formula) <- environment(object$terms) <-
>>> environment(object$pterms) <- .GlobalEnv
>>> > if (!is.null(object$model))
>>> > environment(attr(object$model, "terms")) <- .GlobalEnv
>>> > if (!is.null(attr(object$pred.formula, "full")))
>>> > environment(attr(object$pred.formula, "full")) <- .GlobalEnv
>>> > object
>>> > }
>>> >
>>> > parts of which can be recognized in the last line of what was pasted.
>>> > Naturally, the pasted function is not parsed properly: if I press
>>> return I get the expected "+" signaling that the REPL is expecting
>>> more input. So it is not merely a visual issue.
>>> >
>>> > I can reproduce this both in GNOME Terminal and in xterm, so it is
>>> not a bug specific to my terminal emulator. In addition, pasting the
>>> exact same code into either vim or nano running within the same
>>> terminal works fine. So I believe that this may be a bug in R itself.
>>> It's easy to work around by disabling bracketed paste in the
>>> terminal, but it would be great if this could actually be made to
>>> work, especially given that bracketed paste is the default on my
>>> desktop environment.
>>> >
>>> > If given an account, I would be happy to file this as a bug; let me
>>> know if that is desired. In the meantime, have others run into this
>>> and perhaps identified the root cause and/or a different workaround?
>>> >
>>> > Thanks,
>>> > Cesko
>>> >
>>> > sessionInfo():
>>> >
>>> > R version 4.1.0 (2021-05-18)
>>> > Platform: x86_64-pc-linux-gnu (64-bit)
>>> > Running under: Arch Linux
>>> >
>>> > Matrix products: default
>>> > BLAS/LAPACK: /opt/intel/mkl/lib/intel64/libmkl_gf_lp64.so
>>> >
>>> > locale:
>>> > [1] LC_CTYPE=nl_NL.UTF-8 LC_NUMERIC=C
>>> > [3] LC_TIME=nl_NL.UTF-8 LC_COLLATE=nl_NL.UTF-8
>>> > [5] LC_MONETARY=nl_NL.UTF-8 LC_MESSAGES=nl_NL.UTF-8
>>> > [7] LC_PAPER=nl_NL.UTF-8 LC_NAME=C
>>> > [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> > [11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C
>>> >
>>> > attached base packages:
>>> > [1] stats graphics grDevices utils datasets methods base
>>> >
>>> > loaded via a namespace (and not attached):
>>> > [1] compiler_4.1.0 Matrix_1.3-4 mgcv_1.8-36 splines_4.1.0
>>> > [5] nlme_3.1-152 grid_4.1.0 lattice_0.20-44
>>> >
>>> > ______________________________________________
>>> > R-devel using r-project.org mailing list
>>> > 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
--
Brian D. Ripley, ripley using stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
More information about the R-devel
mailing list