CRAN Warnings for Package with Bioconductor Dependencies

[js87]

Hi all,

we have a package, called GiANT, in CRAN. This package recently throws Errors when checking the examples. We have three packages from bio conductor in "Suggests" and the check reports these packages are not available for checking :
Packages suggested but not available for checking:
'GlobalAncova', 'globaltest', 'DESeq2'

Reverse search showed, that all packages suggesting bioconductor packages such as "DESeq2" show similar errors.

Are their any changes in how to deal with dependencies from the bioconductor repository?
Did anyone have similar problems and knows a solution for that?

Best regards, Julian

[jimhester]

In examples where you use Suggested packages you need to condition on the presence of the package, e.g.

\examples{

if (requireNamespace("DESeq2")) {
  # my example function or code that uses DESeq2
}
}

This allows the examples to execute without errors even if the packages in Suggests are not installed.

[js87]

Thank you for this reply.
However, we then still receive notes (leading to a decline by CRAN) that the packages are not available for testing:

Version: 1.3.1
Flags: --no-vignettes
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'DESeq2'
Flavor: r-devel-linux-x86_64-debian-clang

(See https://cran-archive.r-project.org/web/checks/2021/2021-03-24_check_results_GiANT.html)

As I get this, there is currently a problem with bioconductor dependencies in CRAN packages in general. Is this correct? Are there ideas how to fix this?