[Bioc-devel] How I hide non-exported function from the manual
Martin Morgan
mtmorg@n@b|oc @end|ng |rom gm@||@com
Thu Jun 4 13:30:25 CEST 2020
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 <TO_MANY> initialised objects"
so you must tell us exactly what you are doing to produce this.
Martin
On 6/4/20, 4:04 AM, "Bioc-devel on behalf of stefano" <bioc-devel-bounces using r-project.org on behalf of mangiolastefano using gmail.com> wrote:
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.bengtsson using gmail.com> ha scritto:
> On Wed, Jun 3, 2020 at 10:40 PM Vincent Carey
> <stvjc using channing.harvard.edu> wrote:
> >
> > On Wed, Jun 3, 2020 at 11:48 PM stefano <mangiolastefano using 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 using 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}}
> >
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