search for: protein_ids

...ppose to look like that: I have: FBpp0070086;FBpp0099643;FBpp0112915 I would like to have: "FBpp0070086","FBpp0099643","FBpp0112915" I tried with various numbers of backslashes, but noe have worked. for example: gsub(";", "\\\",\"", data$protein_ids) gsub(";", "\\",\"", data$protein_ids) gsub(";", "\",\"", data$protein_ids) gsub(";", "\\',\\'", data$protein_ids) gsub(";", '"',data$protein_ids) What do I miss? Thanks Assa [[alterna...

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

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

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

Dear Yihui, Thank you for the valuable questions. sample_analysis is a "tibble" while configuration is an "R6" class. But I also have parametrized reports where I pass R reference classes as arguments. This is the Rmd yaml params part corresponding to the error message. params: configuration: !r get(data(skylineconfig)) data: !r get(data(sample_analysis)) Might the R6

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 =