Re: [Bioc-devel] How I hide non-exported function from the manual

2020-06-04 Thread Martin Morgan
None of the items below are \Sexp{}. Only \Sexp{} are \Sexp{}. I built your package from github git clone https://github.com/stemangiola/tidybulk R CMD build tidybulk R CMD BiocCheck tidybulk and saw many (easily fixable) problems, but I did not see a line You have initialised objec

Re: [Bioc-devel] How I hide non-exported function from the manual

2020-06-04 Thread Lluís Revilla
Hi Stefano, About 1) you can document internal functions but remove them from the index if you use #' @keywords internal tag. See the vignette of roxygen2 https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html under Other tags. About 2) perhaps you have too many/long examples? Hope th

Re: [Bioc-devel] How I hide non-exported function from the manual

2020-06-04 Thread stefano
Thanks to Both, since I cannot find any exhaustive documentation about \Sexpr{} I will ask here. - is \examples{} an \Sexpr{} - is \value{} an \Sexpr{} - is \arguments{} an \Sexpr{} - is \item{} an \Sexpr{} Because although all my functions in the manual have, for example \value{}, non of t

Re: [Bioc-devel] How I hide non-exported function from the manual

2020-06-03 Thread Henrik Bengtsson
On Wed, Jun 3, 2020 at 10:40 PM Vincent Carey wrote: > > On Wed, Jun 3, 2020 at 11:48 PM stefano wrote: > > > Hello Community, > > > > I am used to document function although hey are not exported > > > > > I suppose you are talking about tidybulk? I am somewhat mystified by the > behavior > of >

Re: [Bioc-devel] How I hide non-exported function from the manual

2020-06-03 Thread Vincent Carey
On Wed, Jun 3, 2020 at 11:48 PM stefano wrote: > Hello Community, > > I am used to document function although hey are not exported > > I suppose you are talking about tidybulk? I am somewhat mystified by the behavior of %vjcair> R CMD build tidybulk * checking for file ‘tidybulk/DESCRIPTION’ .

Re: [Bioc-devel] How I hide non-exported function from the manual

2020-06-03 Thread Vincent Carey
hi stefano what package are you talking about, what is the exact error message you are concerned about (please transcribe or copy exactly) and what version of R are you working with? thank you On Wed, Jun 3, 2020 at 11:48 PM stefano wrote: > Hello Community, > > I am used to document function

[Bioc-devel] How I hide non-exported function from the manual

2020-06-03 Thread stefano
Hello Community, I am used to document function although hey are not exported ``` #' Get differential transcription information to a tibble using edgeR. #' #' @import dplyr #' @import tidyr #' @import tibble #' @importFrom magrittr set_colnames #' @importFrom stats model.matrix #' @importFrom uti