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Bioconductor / basilisk

Clone of the Bioconductor repository for the basilisk package.
https://bioconductor.org/packages/devel/bioc/html/basilisk.html
GNU General Public License v3.0
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Commented on the licensing problems with the defaults channel. #38

Closed LTLA closed 4 months ago

LTLA commented 4 months ago

The defaults packages haven't been free to use for a long time, which makes it difficult to use any default-dependent Bioconductor packages in commercial settings. Perhaps a more general notification to affected packages (e.g., FLAMES) would also be helpful if they can be persuaded to drop defaults.

vjcitn commented 4 months ago

I merged it but I want to discuss the version bump with build group. I have been holding back my changes to consolidate the external package references because a bump to basilisk requires that all client packages get a new miniconda download. I am going to hold those changes anyway until next devel is started but these comments may need to go in now.

LTLA commented 4 months ago

Sure, no rush on getting this in, the advice will probably only be read by developers of new packages anyway. For a more direct solution, we should just explicitly notify maintainers of the relevant packages to see if they are willing to drop defaults. FLAMES is one, pareg is another.

Is there a problem with a full wipe-and-reinstall in devel? It's usually better to be safe than sorry when dealing with potentially stale caches. If the burden on the build system is too much, I suppose we could change the "package version" in basilisk.utils::getExternalDir() to something more manual.

vjcitn commented 4 months ago

I don't think it is a problem, but on the cusp of a release I want to check with those who are making it all work. We seem to be in a pretty good place right now so maybe it can just go in.