[R] Debugging Rmarkdown

[Bert Gunter]

This might be offbase, but do you need to set options to cache the results
in the original code chunks to reuse in later chunks? (I haven't worked
with knitr lately, so this may be nonsense).

Cheers,
Bert

On Fri, Apr 19, 2019 at 2:03 PM Patrick Connolly <p_connolly using slingshot.co.nz>
wrote:

>
> 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
> >
> > Vlaamse Overheid / Government of Flanders
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> >
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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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>
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>
> ______________________________________________
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