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

Wolfgang Huber huber at ebi.ac.uk
Fri Sep 15 14:44:30 CEST 2006

Hi Joern,

re 1., replace "library" by "require" in your code in loaddatapkg.R.
This is recommended by the man page of the 'library' and 'require'

re 2., I am also not sure why there needs to be a warning.

  Best wishes

Joern Toedling wrote:
> 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:
> 1.)
> * checking package dependencies ... WARNING
> 'library' or 'require' calls not declared from:
>   mydatapkg
> "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".
> 2.)
> * 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,
> Joern
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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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