[Bioc-devel] Proposing patch to Bioconductor package

[Duncan Murdoch]

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