[Bioc-devel] help with package dependencies on packages in remote repositories

Joern Toedling toedling at ebi.ac.uk
Fri Sep 15 13:37:15 CEST 2006

Hi all,

I would very much appreciate if anyone of you could help me to get rid
of two totally unnecessary warning messages regarding dependencies on
remote data packages.

The situations is as follows:

In its vignette, my package "macat" requires a large data package,
called "stjudem", that I keep in a local repository. I wrote a small
function that checks if that data package is installed, if not it
retrieves it from the repository, and then loads the data package. This
function is only used in the package's vignette, but seems to work
nicely. However, I get the following two warnings:

* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:

"mydatapkg" is actually the name of the argument in that small function
that I use to retrieve and/or to load the data package. There is no
package named "mydatapkg".

* checking package vignettes in 'inst/doc' ... WARNING
* Installing *source* package 'stjudem' ...

So the function recognized that the data package was not installed,
retrieved and installed it as I intended it to do. Unfortunately, it
still feels the need to report this as a warning message.

I believe both of these warning message are totally unnecessary. Listing
the data package "stjudem" under Suggests does not work, since it is
kept in local repository and therefore not found, resulting in a check
error. Using "suppressWarnings" when using the retrieval function does
also not do the trick.

I could easily get rid of these two messages by not using the data
package and the installation function in the vignette, but I feel that
would be a suboptimal solution.

Any thoughts and suggestions on this subject are welcome.

Thank you and best regards,

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