[rkward-users] 'rk.show.question' is deprecated.

[Vojtěch Zeisek]

Hello,
thank You for super fast reaction. :-)

Dne neděle 23. ledna 2022 22:47:50 CET, Thomas Friedrichsmeier napsal(a):
> On Sun, 23 Jan 2022 12:02:35 +0100 Vojtěch Zeisek wrote:
> > And then regardless if clicking Yes or No I get in R console
> > Warning message:
> > 'rk.show.question' is deprecated.
> > Use 'rk.askYesNo' instead.
> > See help("Deprecated")
> 
> thanks for reporting. I addressed that in the development
> version, so if you are using the daily builds, this part
> of the problem should go away within 24 hours.

I use openSUSE Tumbleweed RPMs. I can grab the git snapshot, fork package and try myself.

> > I tried to play with limits for storing plots in history in RKWard
> > settings, but it didn't help. How to get rid of this? It's annoying...
> 
> I assume you're annoyed more by the pop than by the console warning
> message. I am somewhat surprised, you are seeing it this often. Could
> you, manually, run
>    object.size(recordPlot())
> for some of those plots, so I can get an idea, what size we are
> actually talking about? Possibly, the GUIs enforced maximum size
> is too strict, but I wonder by how much. BTW, setting
>    options("rk.graphics.hist.max.plotsize"=size_in_kb)
> will allow you to bypass the the GUI limit, for the active session.

The defaults are 20 items in history and maximal size of single figure 1024. If I enlarge to 10000 I get rid of most of warning, but not of all.
Full commands:
require("vcfR")
arabidopsis.vcf <- read.vcfR(file="https://soubory.trapa.cz/rcourse/arabidopsis.vcf.gz")
arabidopsis.vcf.dp <- extract.gt(x=arabidopsis.vcf, element="DP", as.numeric=TRUE)
arabidopsis.vcf.miss <- apply(X=arabidopsis.vcf.dp, MARGIN=2, FUN=function(x){sum(is.na(x))})
arabidopsis.vcf.miss <- arabidopsis.vcf.miss/nrow(arabidopsis.vcf)
barplot(height=arabidopsis.vcf.miss, ylab="Percentage of missing data", las=2)
object.size(recordPlot())
106864 bytes
I wouldn't say this is the most complex plot I have there...

> Of course the most definite solution to the problem will be
> to disable plot history, entirely, should nothing else help.

Yeah, I'd like to avoid that as I use to use it. It's nice feature. One more interesting problem of this sort is also, that after while after plotting plenty of images I get
WARNING! - RKWard
History limit reached, removing the first plot. Limits can be changed in Settings > RKWard > Output.
Do you want to be notified in future?
Yes / No
And even if I click No, I'm sometimes asked again with the same question... But this I'm unable to repeat every time... Surely it will be repeated next section latest, but that's probably intentional.
One more thing might be worth of change, but here I'm not sure where it comes from. Every time I start RKWard, the R console has soft line warp off, i.e. super long lines. And if I turn soft line wrap on in the View menu, it is not remembered for next startup.
One last thing, as I'm playing with it right now... I have RKWard 0.7.2, Plastma 5.23.5, Framework 5.90 and Qt 5.15.2 and if I in RKWard settings in Kate Plugins section activate "CLose Except/Like", it doesn't start at all and starting from terminal writes just one line about SIGSEGV...
Thank You for this nice tool. :-)
Sincerely,
V.

-- 
Vojtěch Zeisek
https://trapa.cz/

Komunita openSUSE GNU/Linuxu
Community of the openSUSE GNU/Linux
https://www.opensuse.org/
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