Skip to content

avoid importing BiocGenerics::data - #35

Open
Artur-man wants to merge 2 commits into
yguitton:develfrom
Artur-man:devel
Open

avoid importing BiocGenerics::data#35
Artur-man wants to merge 2 commits into
yguitton:develfrom
Artur-man:devel

Conversation

@Artur-man

Copy link
Copy Markdown

Recently BiocGenerics::data has been added as a new generic:
Bioconductor/BiocGenerics@93a0f55

This PR fixes the following warning by avoid importing data from BiocGenerics:

> devtools::load_all(".")
ℹ Loading metaMS
Warning message:
replacing previous importBiocGenerics::databyutils::datawhen loadingmetaMS

CC @hpages

@hpages

hpages commented May 27, 2026

Copy link
Copy Markdown
Contributor

Thanks @Artur-man.

A few comments:

  1. The new warning can be seen on the Bioconductor daily report for BioC 3.24:

  2. Artür's PR still imports BiocGenerics::data via the import(BiocGenerics, except=relist) line in NAMESPACE, so the title of the PR is a little bit misleading. What this PR does is that it no longer imports the full utils namespace because that is not needed. And that's because the NAMESPACE file already has an importFrom() directive that selectively imports what the metaMS package needs. Maybe you can update the title @Artur-man? (I don't know if that's possible.)

  3. @yguitton The devel branch of the metaMS repo here on GitHub seems to be lagging significantly behind the devel branch of the metaMS repo on git.bioconductor.org. I'd recommend that you resync the two repos before you merge this PR. This might introduce some conflicts with the current PR that will need to be resolved. The other way to go would be to resync the two repos after merging the PR. If there are conflicts they will appear one way or another but maybe the first approach will make it easier to deal with them. See https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories for how to sync a GitHub repo with a repo on git.bioconductor.org.

BTW @yguitton, I see that you are in Nantes. Moi je suis Vendéen expatrié à Seattle. Did you know that Nantes and Seattle are sister cities? 😉

@yguitton yguitton self-assigned this May 27, 2026
@yguitton

Copy link
Copy Markdown
Owner

Many thanks for the @Artur-man for the PR, I will look at it and do as recommended by @hpages.

To be honnest metaMS is one of my favorite R package but I'm not at all an expert in git so I may need a bit of time to go through the whole rsync process

I'll do my best

Bonne journée from Nantes

@hpages j'ai profité dans ma jeunesse d'un échange avec Seattle une super expérience. :)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants