[Bioc-devel] Important Bioconductor Release Deadlines

[Anatoly Sorokin]

Dear Henrik,

thank you very much for pointing me to the rig project. It works fine and I
have two independent R versions on my machine at the moment.

Thank you,
Anatoly

On Tue, Apr 9, 2024 at 4:19 AM Henrik Bengtsson <henrik.bengtsson using gmail.com>
wrote:

> > ... 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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