R devel - Jun 2014 - Should a package that indirectly Suggests: a vignette engine pass R CMD check?

A package uses VignetteEngine: knitr; the package itself does not Suggests: 
knitr, but it Suggests: BiocStyle which in turn Suggests: knitr. Nonetheless, R 
CMD check fails indicating that a package required for checking is not declared.
Is it really the intention that the original package duplicate Suggests: knitr?

This is only with a recent R. In detail, with

$ Rdev --version|head -3
R Under development (unstable) (2014-06-14 r65947) -- "Unsuffered
Consequences"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

trying to  check the Bioconductor genefilter package leads to

$ Rdev --vanilla CMD check genefilter_1.47.5.tar.gz
* using log directory ?/home/mtmorgan/b/Rpacks/genefilter.Rcheck?
* using R Under development (unstable) (2014-06-13 r65941)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ?genefilter/DESCRIPTION? ... OK
* this is package ?genefilter? version ?1.47.5?
* checking package namespace information ... OK
* checking package dependencies ... ERROR
VignetteBuilder package not declared: ?knitr?

See the information on DESCRIPTION files in the chapter ?Creating R
packages? of the ?Writing R Extensions? manual.

I interpret this to mean that knitr should be mentioned in Suggests: or other 
dependency field. The package does not Suggests: knitr, but it does Suggests: 
BiocStyle, which itself Suggests: knitr. The author knows that they are using 
the BiocStyle package for their vignette, and the BiocStyle package suggests the
appropriate builder.

Martin Morgan
-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

On 14/06/2014, 7:48 AM, Martin Morgan wrote:
> A package uses VignetteEngine: knitr; the package itself does not Suggests:
> knitr, but it Suggests: BiocStyle which in turn Suggests: knitr.
Nonetheless, R
> CMD check fails indicating that a package required for checking is not
declared.
> Is it really the intention that the original package duplicate Suggests:
knitr?
Yes.  The VignetteEngine setting requires that knitr be available for
building and checking, but it doesn't imply how.  You need to also
declare knitr in one of the other ways (Depends, Suggests, etc.).

It would be possible to change the checks so that a dependency of a
dependency was sufficient, but a suggestion of a suggestion would not
be. You can pass a check without having the Suggests of BiocStyle
present, because checking your package doesn't require doing anything
with BiocStyle that would need its suggestions.  However, I don't think
it's worth complicating the check code to support this.  If you need
knitr to be present to build your vignettes, why not just declare it
explicitly?

Duncan Murdoch
> 
> This is only with a recent R. In detail, with
> 
> $ Rdev --version|head -3
> R Under development (unstable) (2014-06-14 r65947) -- "Unsuffered
Consequences"
> Copyright (C) 2014 The R Foundation for Statistical Computing
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> trying to  check the Bioconductor genefilter package leads to
> 
> $ Rdev --vanilla CMD check genefilter_1.47.5.tar.gz
> * using log directory ?/home/mtmorgan/b/Rpacks/genefilter.Rcheck?
> * using R Under development (unstable) (2014-06-13 r65941)
> * using platform: x86_64-unknown-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file ?genefilter/DESCRIPTION? ... OK
> * this is package ?genefilter? version ?1.47.5?
> * checking package namespace information ... OK
> * checking package dependencies ... ERROR
> VignetteBuilder package not declared: ?knitr?
> 
> See the information on DESCRIPTION files in the chapter ?Creating R
> packages? of the ?Writing R Extensions? manual.
> 
> I interpret this to mean that knitr should be mentioned in Suggests: or
other
> dependency field. The package does not Suggests: knitr, but it does
Suggests:
> BiocStyle, which itself Suggests: knitr. The author knows that they are
using
> the BiocStyle package for their vignette, and the BiocStyle package
suggests the
> appropriate builder.
> 
> Martin Morgan
>