[Rd] Bracketed paste issues on Linux
Voeten, C.C.
c@c@voeten @end|ng |rom hum@|e|denun|v@n|
Tue Jun 15 11:17:29 CEST 2021
Thanks to both for these suggested workarounds! I had indeed modified my .inputrc to disable bracketed paste; thanks for also making me aware of the existence of source("clipboard").
Of course, it would be nice if there still was a way for bracketed paste to work even with large amounts of text, but I understand that this may be technically infeasible (and/or, quite simply, unimportant!).
Cesko
> -----Original Message-----
> From: Tomas Kalibera <tomas.kalibera using gmail.com>
> Sent: Tuesday, June 15, 2021 11:11 AM
> To: Prof Brian Ripley <ripley using stats.ox.ac.uk>; Voeten, C.C.
> <c.c.voeten using hum.leidenuniv.nl>; r-devel using r-project.org
> Subject: Re: [Rd] Bracketed paste issues on Linux
>
> One can also disable bracketed paste for R in .inputrc:
>
> $if R
> set enable-bracketed-paste off
> $endif
>
> Tomas
>
> On 6/15/21 11:09 AM, Prof Brian Ripley wrote:
> > 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>
> >> ______________________________________________
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> >
> >
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