[Bioc-devel] Question about sumbition process and biocviews

[Martin Morgan]

On 11/08/2016 08:26 AM, Ioannis Vardaxis wrote:
>
> Create a folder \inst and place the REFERENCES.bib in it. (see attached)
> Then in the R function add: #’ @references \insertRef{ENCODE_1}{PkgA}.
> You have to have the Rdpack installed.

when I do that (see 
https://github.com/mtmorgan/PkgA/tree/parse-Rd-insertRef) and run R CMD 
build I see

$ R CMD build PkgA
* checking for file 'PkgA/DESCRIPTION' ... OK
* preparing 'PkgA':
* checking DESCRIPTION meta-information ... OK
Warning: /tmp/RtmpFDYMzj/Rbuild2deb22881ea6/PkgA/man/fun.Rd:13: unknown 
macro '\insertRef'
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'PkgA_0.0.1.tar.gz'

so the problem reported by BiocCheck is already visible in R CMD build.

Consulting the vignette for Rdpack

https://cran.r-project.org/web/packages/Rdpack/vignettes/Inserting_bibtex_references.pdf

I see that the solution is to add the line

RdMacros: Rdpack

to the DESCRIPTION file. I disagree with the package author that the 
Rdpack package does not need to be in the Suggests: field; if it were 
not there then how would something like the Bioconductor build system 
know that it needed to have the Rdpack available when the package is built?

I updated the github repo with correct package.

Martin


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