[R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

? Mon, 20 Mar 2023 08:38:41 +0000
"Ruff, Sergej" <Sergej.Ruff at tiho-hannover.de> ?????:

When Limma is ?re-installed, I get the following Note:


"Package suggested but not available for checking: 'limma'".


Seems like the functions isnt installing limma.

Is there something I am missing?

No, this is exactly how it's supposed to behave under R CMD check. The
CRAN policy forbids packages to install other packages ("Packages
should not write in the user?s home filespace <...> nor anywhere else
on the file system") except when the user gives permission to do so
("Limited exceptions may be allowed in interactive sessions if the
package obtains confirmation from the user").

Under R CMD check, interactive() is FALSE because there is no user to
ask permission from, so the function correctly decides not to install
the package. The resulting NOTE is the expected result here. The
important part is that your example doesn't crash because it's unable
to load the limma namespace.

Best regards,
Ivan