install only from BiocManager, update vignette

[lwaldron]

No description provided.

[lwaldron]

Do you know why no automatic checks were performed on this pull request?

[seandavi]

Probably need to think a bit more about this one. The GH actions stuff is performed with the current checkout. That may not correspond to the master branch of the repository. Is there a way to have BiocManager::install use the local (checked out) package as the install source?

[lwaldron]

I don't think BiocManager can do that. @LiNk-NY can you comment on how we should install the local package in this situation?

[csoneson]

Might combining it with something like this work, to just install (outdated) dependencies with BiocManager? https://github.com/csoneson/ExploreModelMatrix/actions/runs/166602031/workflow#L84-L90

[LiNk-NY]

Hi all, @seandavi @lwaldron @csoneson
I don't think that BiocManager has to do the install.
It can just do the installation / updating of the dependencies as Charlotte said.
The package is installed further down the line in the Check step by rcmdcheck(".").

Edit: I forgot about the Dockerfile which does the installation. I need to investigate more to see how that comes into play and if it needs to.