[R] Debugging Rmarkdown

[Thierry Onkelinx]

Dear Patrick,

This is not easy to debug without a reprex

I would check the content of zzz and wide.i in the loop

str(wide.i)
 zzz <- rbind(zzz, wide.i)
str(zzz)

Note that the Rmd always runs in a clean environment. This might explain
the difference

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
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Op do 18 apr. 2019 om 11:53 schreef Patrick Connolly <
p_connolly using slingshot.co.nz>:

> I have a function that works in ESS, but it fails if I include it in
> an .Rmd file that I tried to knit using Rstudio.  I found advice at:
>
> https://www.rstudio.com/products/rstudio/release-notes/debugging-with-rstudio/
>
> It seems to be not referring to markdown files.  Somewhere else
> suggested calling render() in the console pane.  I tried that.  The
> browser() function interrupts correctly, but I can't find out what the
> object zzz in the code below looks like.  Nothing prints the way it
> would in a "normal" R buffer.
>
> code outline:  making zzz out of two dataframes xx and yy
>
> ##
>     zzz <- NULL
>     for(i in xx$Sample){
>         raw.i <- <stuff>
>
>         etc. etc.
>
>         zzz <- rbind(zzz, wide.i)
> }
>    browser()
>
>     names(zzz) <- c("Cultivar", "Test", "Change")
> That line fails, with a complaint about zzz being NULL.
>
> It appears as though the rbind doesn't do anything, but I can't see
> what wide.i looks like to get an idea what could be the cause.
>
> Ideas what I should try are welcome.  I have no idea why the code
> works in an R environment but not an Rmd one.
>
>
> R-3.5.2,
> platform       x86_64-pc-linux-gnu
> arch           x86_64
> os             linux-gnu
> system         x86_64, linux-gnu
>
> Rstudio Version 1.1.383
>
>
>
> --
> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>    ___    Patrick Connolly
>  {~._.~}                   Great minds discuss ideas
>  _( Y )_                 Average minds discuss events
> (:_~*~_:)                  Small minds discuss people
>  (_)-(_)                              ..... Eleanor Roosevelt
>
> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>
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