Re: [Rd] Parametrized Vignettest in R packages

2018-07-09 Thread Yihui Xie
I wonder if get(data(foo, package="myPackage")) could be rewritten as myPackage::foo. The latter will be a little more rigorous, because data(foo) simply returns a character string "foo", so you are essentially calling get ("foo"), and the default get(, inherits = FALSE) may cause you trouble somet

Re: [Rd] Parametrized Vignettest in R packages

2018-07-09 Thread Witold E Wolski
Dear Duncan, Was close to giving up to use the parameterized rmarkown as vignettes. But your suggestions to use quote and eval, as well as to use the package parameter in data made it work, with all devtools::install,check,build and build_vignettes as well as with R CMD ... etc. But most importan

Re: [Rd] Parametrized Vignettest in R packages

2018-07-09 Thread Duncan Murdoch
On 09/07/2018 3:24 PM, Witold E Wolski wrote: 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

Re: [Rd] Parametrized Vignettest in R packages

2018-07-09 Thread Witold E Wolski
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:

Re: [Rd] Parametrized Vignettest in R packages

2018-07-09 Thread Duncan Murdoch
On 09/07/2018 12:24 PM, Yihui Xie wrote: 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::buildVig

Re: [Rd] Parametrized Vignettest in R packages

2018-07-09 Thread Yihui Xie
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 scri

Re: [Rd] Parametrized Vignettest in R packages

2018-07-09 Thread Duncan Murdoch
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_vigne

Re: [Rd] Parametrized Vignettest in R packages

2018-07-09 Thread Witold E Wolski
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.

Re: [Rd] Parametrized Vignettest in R packages

2018-07-02 Thread Duncan Murdoch
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 markd

Re: [Rd] Parametrized Vignettest in R packages

2018-07-02 Thread Duncan Murdoch
On 02/07/2018 10:34 AM, Gabe Becker wrote: Witold, Vignettes, in the package sense, are and must be entirely self-contained as far as I know. They are run automatically in completely clean R sessions. I'm not sure a parameterized vignette makes a ton of sense within that context. The defaults

Re: [Rd] Parametrized Vignettest in R packages

2018-07-02 Thread Witold E Wolski
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 : data(sample_analysis) data(skylineco

Re: [Rd] Parametrized Vignettest in R packages

2018-07-02 Thread Duncan Murdoch
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 usu

Re: [Rd] Parametrized Vignettest in R packages

2018-07-02 Thread Gabe Becker
Witold, Vignettes, in the package sense, are and must be entirely self-contained as far as I know. They are run automatically in completely clean R sessions. I'm not sure a parameterized vignette makes a ton of sense within that context. Can you explain what you would want to have happen when the