I just run each chunk in sequence starting from an fresh restart of R by copying code to the R console. However you can use knitr::purl to extract all of the code into a regular R script to do whatever debugging you are most familiar with.
On April 19, 2019 2:03:00 PM PDT, Patrick Connolly <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> >> Havenlaan 88 bus 73, 1000 Brussel >> 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>>: >> >> 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> 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.
