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 > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
