[Bioc-devel] Proposing patch to Bioconductor package

Duncan Murdoch murdoch@dunc@n @end|ng |rom gm@||@com
Sat Jan 14 16:41:23 CET 2023

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:


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.


> It really is up to the contributing developers to be aware of effects of 
> upstream changes,
> but this is an opportunity for us to be a little more proactive about 
> notifying contributors
> of events that could break packages in the release branch.
> We can communicate about the details off line and then get back to the 
> list about the
> basic process.  Or, if you want to handle the communications, go ahead 
> -- BiocPkgTools
> has some utilities that may be relevant.
> On Sat, Jan 14, 2023 at 5:33 AM Duncan Murdoch <murdoch.duncan using gmail.com 
> <mailto:murdoch.duncan using gmail.com>> wrote:
>     To BioC Devel:
>     I'm updating the rgl package.  I think about 30 Bioconductor packages
>     depend on it, and some of them are using obsolete functions which are
>     going to be deprecated in the next release.  I'd like to inform those
>     maintainers so their packages still work.
>     Are there specific BioC guidelines for how I should inform them, or is
>     it just like CRAN, do what the DESCRIPTION file says?
>     Duncan Murdoch
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