R SIG Debian - Apr 2020 - problem with `viridis` on Ubuntu 20.04

Il 30/04/20 01:39, Dirk Eddelbuettel ha scritto:
> 
> On 30 April 2020 at 01:24, Samuele Carcagno wrote:
> | I've hit a bug on Ubuntu 20.04. The issue occurred both with the R
> | version that shipped with Ubuntu last week, and it is occurring now with
> | the CRAN packages from one of the mirros (deb
> | http://cran.mirror.garr.it/mirrors/CRAN/bin/linux/ubuntu/
> | focal-cran40/). The issue occurs whether I use the deb package for
> | viridis in the Ubuntu repos, or I install it with `install.packages()` in
R.
> |
> | The issue is that when I call a function from the 'viridis'
package
> | (e.g. running the first example in the `viridis` vignette:
> |
https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html)
> | R gets stuck indefinitely; the system monitor shows the R process using
> | CPU resources but nothing happens at the terminal and I'm also unable
to
> | stop the function with Ctrl-C.
> |
> | I did a little digging and simply calling the function `viridis` from
> | the `viridisLite` package causes the same problem, execution gets stuck
> | at the line:
> |
> |      cols <- fn_cols(seq(begin, end, length.out = n)) / 255
> |
> | which is line 177 here:
> | https://github.com/sjmgarnier/viridisLite/blob/master/R/viridis.R#L177
> |
> | I'm dual booting Debian Buster on the same machine and no such issue
> | occurs with R 4.0.0 and the same versions of the `viridis` and
> | `viridisLite` packages. Also no such issue occurs on Windows 10 or on a
> | Mac both with R 4.0.0 and the latest versions of `viridis` and
> | `viridisLite`.
> |
> | I was not sure where should I report the bug, so I thought of asking for
> | advice here first.
> 
> Can we make it reproducible, please?  Can you provide a minimal script with
> values for begin, end, n, ... etc pp or a concrete call?
> 
> I got lost in your description above between what version of R from where
you
> ran with which package or function.
> 
> Keep. It. Simple. And. Concise.
> 
> And reproducible.
I've attached a script that triggers the bug on my system. It's just two
lines, one to load `viridisLite`, and one to call the `viridis` 
function. I've also attached the output of `sessionInfo`.

To sum up all the additional info in my previous e-mail: the bug occurs 
on Ubuntu 20.04 with R 4.0.0, but does not occur on Debian, Windows, or 
Mac using the same version of R (R 4.0.0), and the same version of 
viridisLite.

Best,

Sam
> 
> For what it is worth, it _works for me with R 4.0.0 on Ubuntu 19.10_ with
the
> binary .deb from my PPA (as blogged about, but should be identical to what
> Michael built and ships via CRAN).  Log of a fresh Emacs session below. I
> double Ubuntu 20.04 is different but "one never knows".
> 
> Thank you!
> 
> Dirk
> 
> Log below
> 
> R version 4.0.0 (2020-04-24) -- "Arbor Day"
> Copyright (C) 2020 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>    Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
> 
> There's an informal tradition that those announcements [about R
releases] contain at least one mistake, but apparently I forgot this time, so
users have to make up their own....
>     -- Peter Dalgaard (about an apparent non-bug report in his former
R-announce message)
>        R-help (December 2009)
> 
> R> setwd('/home/edd/')
> R>
> R> library(viridisLite)
> R> example(viridis)
> 
> viridsR> library(ggplot2)
> 
> viridsR> library(hexbin)
> 
> viridsR> dat <- data.frame(x = rnorm(10000), y = rnorm(10000))
> 
> viridsR> ggplot(dat, aes(x = x, y = y)) +
> virids+   geom_hex() + coord_fixed() +
> virids+   scale_fill_gradientn(colours = viridis(256, option =
"D"))
> Hit <Return> to see next plot:
> 
> viridsR> # using code from RColorBrewer to demo the palette
> viridsR> n = 200
> 
> viridsR> image(
> virids+   1:n, 1, as.matrix(1:n),
> virids+   col = viridis(n, option = "D"),
> virids+   xlab = "viridis n", ylab = "", xaxt =
"n", yaxt = "n", bty = "n"
> virids+ )
> Hit <Return> to see next plot:
> R>
> 
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On 30 April 2020 at 03:05, Samuele Carcagno wrote:
| Il 30/04/20 01:39, Dirk Eddelbuettel ha scritto:
| > Keep. It. Simple. And. Concise.
| > 
| > And reproducible.
| 
| I've attached a script that triggers the bug on my system. It's just
two
| lines, one to load `viridisLite`, and one to call the `viridis` 
| function. I've also attached the output of `sessionInfo`.
| 
| To sum up all the additional info in my previous e-mail: the bug occurs 
| on Ubuntu 20.04 with R 4.0.0, but does not occur on Debian, Windows, or 
| Mac using the same version of R (R 4.0.0), and the same version of 
| viridisLite.

Can you decompose it to see if the data generation is the problem (likely R)
or the drawing (maybe a change in graphics ?)

What does capabilities() say? Anything missing?  On 19.10 I have

R> capabilities()
       jpeg         png        tiff       tcltk         X11 
       TRUE        TRUE        TRUE        TRUE        TRUE 
       aqua    http/ftp     sockets      libxml        fifo 
      FALSE        TRUE        TRUE        TRUE        TRUE 
     cledit       iconv         NLS     profmem       cairo 
      FALSE        TRUE        TRUE        TRUE        TRUE 
        ICU long.double     libcurl 
       TRUE        TRUE        TRUE 
R> 

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

Il 30/04/20 03:14, Dirk Eddelbuettel ha scritto:
> 
> On 30 April 2020 at 03:05, Samuele Carcagno wrote:
> | Il 30/04/20 01:39, Dirk Eddelbuettel ha scritto:
> | > Keep. It. Simple. And. Concise.
> | >
> | > And reproducible.
> |
> | I've attached a script that triggers the bug on my system. It's
just two
> | lines, one to load `viridisLite`, and one to call the `viridis`
> | function. I've also attached the output of `sessionInfo`.
> |
> | To sum up all the additional info in my previous e-mail: the bug occurs
> | on Ubuntu 20.04 with R 4.0.0, but does not occur on Debian, Windows, or
> | Mac using the same version of R (R 4.0.0), and the same version of
> | viridisLite.
> 
> Can you decompose it to see if the data generation is the problem (likely
R)
> or the drawing (maybe a change in graphics ?)
I'm not familiar with the internals of `viridisLite`, so I'm not sure 
I'd be able to help there. I could open a bug report on the 
`viridisLite` repo and see if the author has suggestions on how to 
narrow down the issue.
> 
> What does capabilities() say? Anything missing?  On 19.10 I have
below is the output of `capabilities()` from my system:

 > capabilities()
        jpeg         png        tiff       tcltk         X11        aqua
        TRUE        TRUE        TRUE        TRUE        TRUE       FALSE
    http/ftp     sockets      libxml        fifo      cledit       iconv
        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE
         NLS     profmem       cairo         ICU long.double     libcurl
        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE

> 
> R> capabilities()
>         jpeg         png        tiff       tcltk         X11
>         TRUE        TRUE        TRUE        TRUE        TRUE
>         aqua    http/ftp     sockets      libxml        fifo
>        FALSE        TRUE        TRUE        TRUE        TRUE
>       cledit       iconv         NLS     profmem       cairo
>        FALSE        TRUE        TRUE        TRUE        TRUE
>          ICU long.double     libcurl
>         TRUE        TRUE        TRUE
> R>
> 
> Dirk
>