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 them have \Sexpr{} in the man. (only rowwise from dplyr, for which I deleted the \Sexpr{} from the header). Best wishes. *Stefano * Stefano Mangiola | Postdoctoral fellow Papenfuss Laboratory The Walter Eliza Hall Institute of Medical Research +61 (0)466452544 Il giorno gio 4 giu 2020 alle ore 16:09 Henrik Bengtsson < henrik.bengts...@gmail.com> ha scritto: > On Wed, Jun 3, 2020 at 10:40 PM Vincent Carey > <st...@channing.harvard.edu> wrote: > > > > On Wed, Jun 3, 2020 at 11:48 PM stefano <mangiolastef...@gmail.com> > 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’ ... OK > > > > * preparing ‘tidybulk’: > > > > * checking DESCRIPTION meta-information ... OK > > > > * installing the package to process help pages > > > > * building the PDF package manual > > > > Hmm ... looks like a package > > > > Converting Rd files to LaTeX ................. > > > > Creating pdf output from LaTeX ... > > > > > > which produces a 147 page manual, and as you note many > > > > non-user-visible symbols are documented in manual. I've > > > > never seen the "process help pages" phase in any > >) > > of my packages, and I don't know why. > > This step happens iff you have \Sexpr{} macros in your man/*.Rd files > (see > https://github.com/wch/r-source/blob/5bd6e3ce1430374105ebf02101f9d55173496cfe/src/library/tools/R/build.R#L582-L586 > ) > > /Henrik > > > > > > > I don't have experience with the RdMacros setting in > > > > DESCRIPTION, and the way S3 methods are being handled > > > > in the package leads, I think, to an excess of Rd > > > > files relative to what you have as visible symbols > > > > in the package namespace. > > > > > > Perhaps some tidyverse experts can comment. > > > > > > > ``` > > > #' Get differential transcription information to a tibble using edgeR. > > > #' > > > #' @import dplyr > > > #' @import tidyr > > > #' @import tibble > > > #' @importFrom magrittr set_colnames > > > #' @importFrom stats model.matrix > > > #' @importFrom utils installed.packages > > > #' @importFrom utils install.packages > > > #' @importFrom purrr when > > > #' > > > #' > > > #' @param .data A tibble > > > #' @param .formula a formula with no response variable, referring only > to > > > numeric variables > > > #' @param .sample The name of the sample column > > > #' @param .transcript The name of the transcript/gene column > > > #' @param .abundance The name of the transcript/gene abundance column > > > #' @param .contrasts A character vector. See edgeR makeContrasts > > > specification for the parameter `contrasts`. If contrasts are not > present > > > the first covariate is the one the model is tested against (e.g., ~ > > > factor_of_interest) > > > #' @param method A string character. Either "edgeR_quasi_likelihood" > (i.e., > > > QLF), "edgeR_likelihood_ratio" (i.e., LRT) > > > #' @param significance_threshold A real between 0 and 1 > > > #' @param minimum_counts A positive integer. Minimum counts required > for at > > > least some samples. > > > #' @param minimum_proportion A real positive number between 0 and 1. > It is > > > the threshold of proportion of samples for each transcripts/genes that > have > > > to be characterised by a cmp bigger than the threshold to be included > for > > > scaling procedure. > > > #' @param fill_missing_values A boolean. Whether to fill missing > > > sample/transcript values with the median of the transcript. This is > rarely > > > needed. > > > #' @param scaling_method A character string. The scaling method passed > to > > > the backend function (i.e., edgeR::calcNormFactors; > > > "TMM","TMMwsp","RLE","upperquartile") > > > #' @param omit_contrast_in_colnames If just one contrast is specified > you > > > can choose to omit the contrast label in the colnames. > > > #' > > > #' @return A tibble with edgeR results > > > #' > > > get_differential_transcript_abundance_bulk <- function > > > [...] > > > ``` > > > > > > However this leads to 2 problems > > > > > > 1) The PDF manual includes many function that are not accessible to the > > > user. How can I hide documented non-exported function from the manual > > > 2) I receive the Biocheck note. "You have <TO_MANY> initialised > objects". > > > Again how can I document an object without initialising it? > > > > > > Thanks a lot. > > > > > > Best wishes. > > > > > > *Stefano * > > > > > > > > > > > > Stefano Mangiola | Postdoctoral fellow > > > > > > Papenfuss Laboratory > > > > > > The Walter Eliza Hall Institute of Medical Research > > > > > > +61 (0)466452544 > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > -- > > The information in this e-mail is intended only for the ...{{dropped:18}} > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel