CRAN Warnings for Package with Bioconductor Dependencies

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

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


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.

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


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?

This topic was automatically closed after 45 days. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.