On 14/01/2023 10:41 a.m., Duncan Murdoch wrote:
On 14/01/2023 9:50 a.m., Vincent Carey wrote:
Thanks for checking in Duncan. I don't believe we have a guideline on this.
We have code.bioconductor.org <http://code.bioconductor.org> that
facilitates search of the entire codebase. If
you provide a list of the functions that should not be used, I will see
about making
a focused message to the developers who need to change their code.
Thanks Vince.
I have sent individual email messages to the BioC packages that look
problematic: BioNet, destiny, MAIT, SpacePAC, triplex, and xcms, so I
don't think you need to do so. But I may have missed some.
The list of functions to be deprecated is fairly long. It's in the
first news item here:
https://dmurdoch.github.io/rgl/dev/news/index.html
This isn't released yet; I'll probably be sending it to CRAN in a week
or two.
I'll email all reverse dependency maintainers, whether I have spotted
issues or not, to warn them to watch out.
I think I probably won't do that. There are too many of them. I was
expecting a lot of repetition, but in fact most maintainers of rgl
reverse dependency packages only maintain one.
Duncan Murdoch
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