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_conno...@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_conno...@slingshot.co.nz <mailto:p_conno...@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.onkel...@inbo.be <mailto:thierry.onkel...@inbo.be> >> <mailto:thierry.onkel...@inbo.be ><mailto:thierry.onkel...@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_conno...@slingshot.co.nz <mailto:p_conno...@slingshot.co.nz> >> <mailto:p_conno...@slingshot.co.nz >> <mailto:p_conno...@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@r-project.org <mailto:R-help@r-project.org> >> <mailto:R-help@r-project.org <mailto:R-help@r-project.org>> >> mailing list -- >> > To UNSUBSCRIBE and more, see >> > https://stat.ethz.ch/mailman/listinfo/r-help >> > PLEASE do read the posting guide >> > http://www.R-project.org/posting-guide.html >> > and provide commented, minimal, self-contained, >reproducible >> code. >> > >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org <mailto:R-help@r-project.org> mailing list >-- >> To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible >code. >> > > [[alternative HTML version deleted]] > >______________________________________________ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. -- Sent from my phone. Please excuse my brevity. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.