[Bioc-devel] Important Bioconductor Release Deadlines

[Henrik Bengtsson]

> ... I'm on Mac OS 12.5.

I've heard good things about 'rig' (The R Installation Manager;
https://github.com/r-lib/rig). It can install multiple R versions in
parallel on macOS, Windows, and Linux, without the different versions
conflicting with each other.  I recommend trying it out, because being
able to run different versions of R is always useful, even if you're
not a package maintainer.

/Henrik

On Thu, Apr 4, 2024 at 8:08 PM Anatoly Sorokin <lptolik using gmail.com> wrote:
>
> Hi Henrik,
>
> thank you for the prompt reply. I'm on Mac OS 12.5.
>
> And regarding the linking version of Bioconductor and R my major complaint is the timing, if R 4.4 hasn't been released yet, why not postpone this dependency to the October release of Bioconductor?
>
> And it is also true that we have a lot of complaints from people working on centrally maintained machines or HPC clusters, that they have no access to the latest R versions. So sometimes even for demonstration purposes, we had to install the package from the GitHub source, rather than from BiocManager.
>
> Cheers,
> Anatoly
>
> On Fri, Apr 5, 2024 at 11:57 AM Henrik Bengtsson <henrik.bengtsson using gmail.com> wrote:
>>
>> Hello,
>>
>> these days, it's quite straight forward to have multiple versions of R
>> installed in parallel without them conflicting with each other. I know
>> it works out of the box on MS Windows (just install all versions you'd
>> like), and I know there are various tools to achieve the same on
>> macOS.  I'm on Linux, and I build R from source, so that solves it for
>> me.  What's platform are you working on?  If you share that, I think
>> you'll get 1-2-3 instructions for how to install R 4.4 pre-release
>> from users on that operating system.
>>
>> Regarding Bioc versions being tied to specific R versions: That is a
>> design decision that goes back to day one of the Bioconductor project.
>> It's a rather big thing to change.  That said, I've always been in the
>> camp that thinks we should move away from that model for many reasons;
>> one is the friction added to developers, another is the friction added
>> to end-users, and some people may be stuck with older versions of R
>> and in no control of updating.
>>
>> Hope this helps,
>>
>> Henrik
>>
>> On Thu, Apr 4, 2024 at 7:29 PM Anatoly Sorokin <lptolik using gmail.com> wrote:
>> >
>> > Hi all,
>> >
>> > I'm sorry for the complaint, but do you really think it is wise to make the
>> > new release dependent on the R version which has not released yet?
>> >
>> > I have a lot of R-related projects going on apart from maintaining the
>> > Bioconductor package and I'm not comfortable installing the unreleased
>> > version of R on my machine and spending time debugging it in the case of
>> > possible problems.
>> >
>> > At the same time, I have an error, possibly caused by a new version of
>> > GO.db package, which BioNAR is dependent upon and I can not fix it
>> > until the R 4.4 release on the 24th of April when I would have less than a
>> > day to fix the possible problem and fit into R CMD build and R CMD check by
>> > the Friday April 26th. Don't you think this is a rather tight time frame?
>> >
>> >
>> > Sorry once again, for the complaint.
>> >
>> > Cheers,
>> > Anatoly
>> >
>> > On Tue, Mar 26, 2024 at 11:06 PM Kern, Lori via Bioc-devel <
>> > bioc-devel using r-project.org> wrote:
>> >
>> > > Import update:  The Bioconductor Release will be May 1 following the
>> > > release of R 4.4 on April 24.
>> > >
>> > > The Bioconductor 3.18 branch will be frozen Monday April 15th. After that
>> > > date, no changes will be permitted ever on that branch.
>> > >
>> > > The deadline for devel Bioconductor 3.19 for packages to pass R CMD build
>> > > and R CMD check is Friday April 26th. While you will still be able to make
>> > > commits past this date, This ensures any changes pushed to
>> > > git.bioconductor.org are reflected in at least one build report before
>> > > the devel branch will be copied to a release 3.19 branch.
>> > >
>> > > Cheers,
>> > >
>> > >
>> > >
>> > > Lori Shepherd - Kern
>> > >
>> > > Bioconductor Core Team
>> > >
>> > > Roswell Park Comprehensive Cancer Center
>> > >
>> > > Department of Biostatistics & Bioinformatics
>> > >
>> > > Elm & Carlton Streets
>> > >
>> > > Buffalo, New York 14263
>> > >
>> > >
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