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.
