[R] Debugging Rmarkdown

[Patrick Connolly]

On 19/04/19 12:13 AM, Thierry Onkelinx wrote:
> 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)
>
That's just what I'm trying to achieve but the debugging doesn't work 
how it does with regular R code.

> Note that the Rmd always runs in a clean environment. This might 
> explain the difference
>
The data frames xx and yy are defined in earlier code chunks. Maybe I 
need to define them again.


I'll look closer at it after Easter.


Thanks for the suggestion.

> Best regards,
>
> ir. Thierry Onkelinx
> Statisticus / Statistician
>
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>
> Op do 18 apr. 2019 om 11:53 schreef Patrick Connolly 
> <p_connolly using slingshot.co.nz <mailto: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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