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.kalib...@gmail.com>
*Verzonden:* zondag 13 juni 2021 10:00:27
*Aan:* Voeten, C.C.; r-devel@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@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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Emeritus Professor of Applied Statistics, University of Oxford
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