[Bioc-devel] Question about sumbition process and biocviews

[Martin Morgan]

On 11/06/2016 06:10 PM, Ioannis Vardaxis wrote:
> Hi,
>
> For the references I just used @references \insertRef{key}{pkg}, and
> although it shows up in the ??pkg::function help, I get an error in
> biocCheck

it's not enough to say that you got an error, because there are many 
possible errors. What error did you get?

>
> For the vignettes, my vignette is generated without any errors. What I get
> as en error in Rcheck is that: “From R version >=3.2 vignettes is required
> to be placed in /inst/doc”

If I build and then check the package here

   https://github.com/mtmorgan/PkgA/tree/no-vignette-engine

I see first of all during build that it does NOT say that it is loading 
the package to build the vignette

$ R CMD build PkgA
Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
* checking for file 'PkgA/DESCRIPTION' ... OK
* preparing 'PkgA':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'PkgA_0.0.1.tar.gz'

and then when I check the built package I see

$ R CMD check PkgA_0.0.1.tar.gz
...
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
   'vignette.Rmd'
Package has no Sweave vignette sources and no VignetteBuilder field.

The example package is missing the following lines in the vignette

---
vignette: >
     %\VignetteIndexEntry{Short title for my vignette}
     %\VignetteEngine{knitr::rmarkdown}
---

and the following field in the DESCRIPTION file

VignetteBuilder: knitr

If I add these, I see during package build that the vignette is being 
built 'creating vignettes ... OK'

$ R CMD build PkgA
Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
* checking for file 'PkgA/DESCRIPTION' ... OK
* preparing 'PkgA':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'PkgA_0.0.1.tar.gz'


and I do not see any vignette-related problems when I check the newly 
built vignette.

It is more helpful to cut and paste the message from R CMD check 
directly, perhaps with a translation, because the message often contains 
infromation that an approximate message does not convey, e.g., that my 
vignette uses R markdown. The solution to your problem might be slightly 
different if you are using an Rnw-based vignette.

> But if I do that the bioCheck gives an error, if I don’t then Rcheck gives
> an error. If I place vignettes in /inst/doc then Rcheck checks it without
> any error.
>
>


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