So far you haven't provided a reproducible example yet. I wonder what exactly the object `sample_analysis` is. Sounds like it is an environment. If that is the case, devtools::build_vignettes() will tangle (for the meaning of "tangle", see ?tools::buildVignette) your vignette into an invalid R script. Environments cannot be represented via dput(), so knitr's purl() (eventually called by the vignette engine) cannot really create a valid R script when your vignette contains `params` that uses environment values. Most other types of values should be fine.
Regards, Yihui -- https://yihui.name On Mon, Jul 9, 2018 at 10:37 AM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote: > On 09/07/2018 8:49 AM, Witold E Wolski wrote: >> >> Dear Duncan, >> >> Following your advice (Thank you for it) I did include into the vignettes >> params: >> configuration: !r get(data(sample_analysis)) >> data: !r get(data(skylineconfig)) >> >> And everything seemed (see below) to work fine. >> devtools::build_vignettes() builds the vignettes. >> >> Runs with NO error. By this the .Rmd file, html file and corresponding >> .R files is being placed into the inst/doc directory. >> >> However, when I did want to check the package by running >> devtools::check(build_args="--no-build-vignettes") >> >> The following warning is shown: >> >> Warning: parse error in file >> >> 'C:/Users/wolski/AppData/Local/Temp/Rtmp4QanHv/SRMService.Rcheck/SRMService/doc/tr_srm_summary.R': >> >> /Users/wolski/AppData/Local/Temp/Rtmp4QanHv/SRMService.Rcheck/SRMService/doc/tr_srm_summary.R:2:22: >> unexpected '<' >> 1: params <- >> 2: list(configuration = < >> >> This is how the start of the .R file produced from the vignette looks >> like. >> >> params <- >> list(configuration = <environment>, data = structure(list(protein_Id = >> c("CiRT standards", >> >> I am worried that this is the end of this road with parameterized >> vignettes then? What do you think? > > > Interesting. The issue is that the value being assigned to configuration is > an environment, and whatever code produces those lines in tr_srm_summary.R > isn't deparsing it into something parseable. (This isn't a big surprise: > dput and deparse both fail at that.) > > I'd guess a solution is not to save sample_analysis as an environment, but > maybe you didn't know you were doing that since some other structures are > implemented as environments. > > Perhaps you could use > > configuration: !r as.list(get(data(sample_analysis))) > > and then when you need to use it, convert it back to the original type? > > Duncan Murdoch >> >> >> regards >> Witek >> >> >> >> >> >> On 2 July 2018 at 18:21, Duncan Murdoch <murdoch.dun...@gmail.com> wrote: >>> >>> On 02/07/2018 11:22 AM, Witold E Wolski wrote: >>>> >>>> >>>> Hello, >>>> >>>> Thank you for the questions as well as remaining me of the default >>>> parameters in the yaml session. >>>> Indeed this seems to be the solution. >>>> >>>> >>>> But how would I assign package data as a default parameter? >>>> So originally I thought to render the markdown with : >>>> >>>> <code> >>>> data(sample_analysis) >>>> data(skylineconfig) >>>> x <- rmarkdown::render("report.Rmd", output_format = "html_document", >>>> params = list(data = sample_analysis, >>>> configuration = >>>> skylineconfig),envir = new.env()) >>>> <code> >>>> >>>> I do not think I can write: >>>> >>>> params: >>>> configuration: !r data(sample_analysis) >>>> data: !r data(skylineconfig) >>>> >>>> since data does not return the package just puts them in the env as a >>>> side effect. Is there a different base function to achieve it. >>> >>> >>> >>> I think you could use >>> >>> params: >>> configuration: !r get(data(sample_analysis)) >>> data: !r get(data(skylineconfig)) >>> >>> but if that doesn't work, a longer version is >>> >>> params: >>> configuration: !r {data(sample_analysis); sample_analysis} >>> data: !r {data(skylineconfig); skylineconfig} >>> >>> Duncan Murdoch >>> >>> >>>> >>>> >>>> Thank you >>>> Witek >>>> >>>> >>>> >>>> >>>> On 2 July 2018 at 16:56, Duncan Murdoch <murdoch.dun...@gmail.com> >>>> wrote: >>>>> >>>>> >>>>> On 02/07/2018 10:30 AM, Witold E Wolski wrote: >>>>>> >>>>>> >>>>>> >>>>>> Hello, >>>>>> >>>>>> I have a package which includes some parameterized r-markdown report >>>>>> which I would also like to build as package vignettes. >>>>>> >>>>>> Is there a way to run the parameterized vignette creation with the >>>>>> package build or package check? >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Doesn't the usual method work? You can specify defaults for parameters >>>>> in >>>>> the YAML header; I'd expect those to be the parameter values that get >>>>> used. >>>>> >>>>> You can give instructions to your users on how to rebuild the reports >>>>> with >>>>> different parameters. >>>>> >>>>> Duncan Murdoch >>>>> >>>>>> >>>>>> Thank you >>>>>> >>>>> >>>> >>>> >>>> >>> >> >> >> > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
