[R] Debugging Rmarkdown
Jeff Newmiller
jdnewm|| @end|ng |rom dcn@d@v|@@c@@u@
Sat Apr 20 00:39:28 CEST 2019
Chunks are not isolated... they are executed in sequence in the same environment, starting with a fresh environment unrelated to whatever is present when you invoke render().
On April 19, 2019 3:00:33 PM PDT, Patrick Connolly <p_connolly using slingshot.co.nz> wrote:
>There are options to set echo and messages but AFAIK, the text appears
>in the resultant file, but if the script fails, there's no file to
>inspect.
>
>On 20/04/19 9:50 AM, Bert Gunter wrote:
>> 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 <mailto: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
>> > INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR
>> NATURE
>> > AND FOREST
>> > Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality
>> Assurance
>> > thierry.onkelinx using inbo.be <mailto:thierry.onkelinx using inbo.be>
>> <mailto:thierry.onkelinx using inbo.be
><mailto:thierry.onkelinx using inbo.be>>
>> > Havenlaan 88 bus 73, 1000 Brussel
>> > www.inbo.be <http://www.inbo.be> <http://www.inbo.be>
>> >
>> >
>>
>///////////////////////////////////////////////////////////////////////////////////////////
>> > To call in the statistician after the experiment is done may be
>no
>> > more than asking him to perform a post-mortem examination: he
>> may be
>> > able to say what the experiment died of. ~ Sir Ronald Aylmer
>Fisher
>> > The plural of anecdote is not data. ~ Roger Brinner
>> > The combination of some data and an aching desire for an answer
>> does
>> > not ensure that a reasonable answer can be extracted from a
>> given body
>> > of data. ~ John Tukey
>> >
>>
>///////////////////////////////////////////////////////////////////////////////////////////
>> >
>> > <https://www.inbo.be>
>> >
>> >
>> > Op do 18 apr. 2019 om 11:53 schreef Patrick Connolly
>> > <p_connolly using slingshot.co.nz <mailto:p_connolly using slingshot.co.nz>
>> <mailto: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
>> >
>> >
>>
> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>> >
>> > ______________________________________________
>> > R-help using r-project.org <mailto:R-help using r-project.org>
>> <mailto:R-help using r-project.org <mailto:R-help using r-project.org>>
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>> > and provide commented, minimal, self-contained,
>reproducible
>> code.
>> >
>>
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>>
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>> PLEASE do read the posting guide
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>> and provide commented, minimal, self-contained, reproducible
>code.
>>
>
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>
>______________________________________________
>R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
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>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
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