Re: [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  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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Re: [Bioc-devel] Proposing patch to Bioconductor package

[Duncan Murdoch]

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  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.


Duncan



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 > 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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Re: [Bioc-devel] Proposing patch to Bioconductor package

[Vincent Carey]

Thanks for checking in Duncan.  I don't believe we have a guideline on this.

We have 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.

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 
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
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
The information in this e-mail is intended only for the ...{{dropped:18}}

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[Bioc-devel] Proposing patch to Bioconductor package

[Duncan Murdoch]

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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